Update drop version for /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo to version 1.2.4 WARNING: Less than 30 IDs in DROP_GROUP outrider WARNING: Less than 30 IDs in DROP_GROUP outrider_external WARNING: Less than 30 IDs in DROP_GROUP fraser WARNING: Less than 30 IDs in DROP_GROUP fraser_external check for missing R packages Structuring dependencies... Dependencies file generated at: /tmp/tmph81md22x Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Job stats: job count min threads max threads --------------------------------------------------------------------------- ------- ------------- ------------- AberrantExpression_Overview_R 1 1 1 AberrantExpression_pipeline_Counting_Datasets_R 1 1 1 AberrantExpression_pipeline_Counting_Summary_R 2 1 1 AberrantExpression_pipeline_Counting_countReads_R 10 1 1 AberrantExpression_pipeline_Counting_filterCounts_R 2 1 1 AberrantExpression_pipeline_Counting_mergeCounts_R 2 1 1 AberrantExpression_pipeline_OUTRIDER_Datasets_R 1 1 1 AberrantExpression_pipeline_OUTRIDER_Summary_R 2 1 1 AberrantExpression_pipeline_OUTRIDER_results_R 2 1 1 AberrantExpression_pipeline_OUTRIDER_runOutrider_R 2 1 1 AberrantExpression_pipeline_aberrant_expression_readme_md 1 1 1 AberrantSplicing_Overview_R 1 1 1 AberrantSplicing_pipeline_Counting_00_define_datasets_from_anno_R 2 1 1 AberrantSplicing_pipeline_Counting_01_0_countRNA_init_R 2 1 1 AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R 18 1 1 AberrantSplicing_pipeline_Counting_01_2_countRNA_splitReads_merge_R 2 1 1 AberrantSplicing_pipeline_Counting_01_3_countRNA_nonSplitReads_samplewise_R 18 1 1 AberrantSplicing_pipeline_Counting_01_4_countRNA_nonSplitReads_merge_R 2 1 1 AberrantSplicing_pipeline_Counting_01_5_countRNA_collect_R 2 1 1 AberrantSplicing_pipeline_Counting_02_psi_value_calculation_FraseR_R 2 1 1 AberrantSplicing_pipeline_Counting_03_filter_expression_FraseR_R 2 1 1 AberrantSplicing_pipeline_Counting_DatasetsF_R 1 1 1 AberrantSplicing_pipeline_Counting_Summary_R 2 1 1 AberrantSplicing_pipeline_FRASER_04_fit_hyperparameters_FraseR_R 2 1 1 AberrantSplicing_pipeline_FRASER_05_fit_autoencoder_FraseR_R 2 1 1 AberrantSplicing_pipeline_FRASER_06_calculation_stats_AE_FraseR_R 2 1 1 AberrantSplicing_pipeline_FRASER_07_extract_results_FraseR_R 2 1 1 AberrantSplicing_pipeline_FRASER_Datasets_R 1 1 1 AberrantSplicing_pipeline_FRASER_Summary_R 2 1 1 AberrantSplicing_pipeline_aberrant_splicing_readme_md 1 1 1 Index 1 1 1 MonoallelicExpression_Overview_R 1 1 1 MonoallelicExpression_pipeline_MAE_Datasets_R 1 1 1 MonoallelicExpression_pipeline_MAE_Results_R 1 1 1 MonoallelicExpression_pipeline_MAE_deseq_mae_R 3 1 1 MonoallelicExpression_pipeline_MAE_gene_name_mapping_R 1 1 1 MonoallelicExpression_pipeline_QC_DNA_RNA_matrix_plot_R 1 1 1 MonoallelicExpression_pipeline_QC_Datasets_R 1 1 1 MonoallelicExpression_pipeline_QC_create_matrix_dna_rna_cor_R 1 1 1 MonoallelicExpression_pipeline_QC_deseq_qc_R 3 1 1 MonoallelicExpression_pipeline_mae_readme_md 1 1 1 Pipeline_SampleAnnotation_R 1 1 1 Pipeline_preprocessGeneAnnotation_R 1 1 1 aberrantExpression 1 1 1 aberrantExpression_bamStats 10 1 1 aberrantExpression_dependency 1 1 1 aberrantExpression_mergeBamStats 2 1 1 aberrantSplicing 1 1 1 aberrantSplicing_dependency 1 1 1 all 1 1 1 allVariants 2 1 1 applyBQSR 3 1 1 bqsr 3 1 1 changeHeader 3 1 1 combineGVCFs 2 1 1 create_dict 1 1 1 dependencyGraph 1 1 1 filterVCF 2 1 1 genotypeGVCFs 2 1 1 haplotypeCaller 3 1 1 leftNormalVCF 2 1 1 mae 1 1 1 mae_allelicCounts 6 1 1 mae_createSNVs 6 1 1 mae_dependency 1 1 1 markDuplicates 3 1 1 maskMultiVCF 2 1 1 readme_md 1 1 1 reorderBAM 3 1 1 rnaVariantCalling 1 1 1 rnaVariantCalling_Overview_R 1 1 1 rnaVariantCalling_dependency 1 1 1 rnaVariantCalling_pipeline_countVariants_Datasets_R 1 1 1 rnaVariantCalling_pipeline_countVariants_Results_R 2 1 1 rnaVariantCalling_pipeline_countVariants_batch_data_table_R 2 1 1 rnaVariantCalling_pipeline_rvc_readme_md 1 1 1 simpleAnnotateVCF 2 1 1 sortBam 3 1 1 sortIndexRepeatMask 1 1 1 splitNcigar 3 1 1 split_multiVCF 3 1 1 total 194 1 1 Select jobs to execute... [Mon Jan 30 11:59:27 2023] rule mae_createSNVs: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/Pipeline/chr_NCBI_UCSC.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/Pipeline/chr_UCSC_NCBI.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/dna_vcf/demo_chr21.vcf.gz, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00106.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/MonoallelicExpression/pipeline/MAE/filterSNVs.sh, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/params/snvs/HG00106_snvParams.csv output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/snvs/HG00106--HG00106.vcf.gz, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/snvs/HG00106--HG00106.vcf.gz.tbi jobid: 120 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/snvs/HG00106--HG00106.vcf.gz wildcards: vcf=HG00106, rna=HG00106 resources: tmpdir=/tmp Filter SNVs Lines total/split/realigned/skipped: 6023/0/0/0 Lines total/split/realigned/skipped: 6023/0/0/0 Using GATK jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar SelectVariants -V /tmp/tmp.cHSUhURjQN -sn HG00106 -select vc.getGenotype('HG00106').isHet() -O /tmp/tmp.td5Lzay1LP 11:59:32.652 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 11:59:32.866 INFO SelectVariants - ------------------------------------------------------------ 11:59:32.867 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.3.0.0 11:59:32.867 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/ 11:59:32.867 INFO SelectVariants - Executing as plassard@flash-node10 on Linux v4.19.0-18-amd64 amd64 11:59:32.867 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v11.0.1-internal+0-adhoc..src 11:59:32.868 INFO SelectVariants - Start Date/Time: 30 janvier 2023 à 11:59:32 CET 11:59:32.868 INFO SelectVariants - ------------------------------------------------------------ 11:59:32.868 INFO SelectVariants - ------------------------------------------------------------ 11:59:32.869 INFO SelectVariants - HTSJDK Version: 3.0.1 11:59:32.869 INFO SelectVariants - Picard Version: 2.27.5 11:59:32.870 INFO SelectVariants - Built for Spark Version: 2.4.5 11:59:32.870 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2 11:59:32.870 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 11:59:32.870 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 11:59:32.870 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 11:59:32.871 INFO SelectVariants - Deflater: IntelDeflater 11:59:32.871 INFO SelectVariants - Inflater: IntelInflater 11:59:32.871 INFO SelectVariants - GCS max retries/reopens: 20 11:59:32.871 INFO SelectVariants - Requester pays: disabled 11:59:32.871 INFO SelectVariants - Initializing engine 11:59:33.074 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/tmp.cHSUhURjQN 11:59:33.125 INFO SelectVariants - Done initializing engine 11:59:33.239 INFO SelectVariants - Including sample 'HG00106' 11:59:33.244 WARN GATKVariantContextUtils - Can't determine output variant file format from output file extension "td5Lzay1LP". Defaulting to VCF. 11:59:33.288 INFO ProgressMeter - Starting traversal 11:59:33.288 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute 11:59:33.745 INFO ProgressMeter - 21:47408915 0.0 5538 728684.2 11:59:33.745 INFO ProgressMeter - Traversal complete. Processed 5538 total variants in 0.0 minutes. 11:59:33.792 INFO SelectVariants - Shutting down engine [30 janvier 2023 à 11:59:33 CET] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=2113929216 Using GATK jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar SelectVariants --restrict-alleles-to BIALLELIC -V /tmp/tmp.td5Lzay1LP -O /tmp/tmp.cHSUhURjQN 11:59:37.583 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 11:59:37.797 INFO SelectVariants - ------------------------------------------------------------ 11:59:37.798 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.3.0.0 11:59:37.798 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/ 11:59:37.798 INFO SelectVariants - Executing as plassard@flash-node10 on Linux v4.19.0-18-amd64 amd64 11:59:37.798 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v11.0.1-internal+0-adhoc..src 11:59:37.799 INFO SelectVariants - Start Date/Time: 30 janvier 2023 à 11:59:37 CET 11:59:37.799 INFO SelectVariants - ------------------------------------------------------------ 11:59:37.799 INFO SelectVariants - ------------------------------------------------------------ 11:59:37.800 INFO SelectVariants - HTSJDK Version: 3.0.1 11:59:37.800 INFO SelectVariants - Picard Version: 2.27.5 11:59:37.800 INFO SelectVariants - Built for Spark Version: 2.4.5 11:59:37.801 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2 11:59:37.801 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 11:59:37.801 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 11:59:37.801 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 11:59:37.801 INFO SelectVariants - Deflater: IntelDeflater 11:59:37.801 INFO SelectVariants - Inflater: IntelInflater 11:59:37.802 INFO SelectVariants - GCS max retries/reopens: 20 11:59:37.802 INFO SelectVariants - Requester pays: disabled 11:59:37.802 INFO SelectVariants - Initializing engine 11:59:37.998 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/tmp.td5Lzay1LP 11:59:38.056 INFO SelectVariants - Done initializing engine 11:59:38.142 WARN GATKVariantContextUtils - Can't determine output variant file format from output file extension "cHSUhURjQN". Defaulting to VCF. 11:59:38.201 INFO ProgressMeter - Starting traversal 11:59:38.201 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute 11:59:38.337 INFO ProgressMeter - unmapped 0.0 558 248000.0 11:59:38.337 INFO ProgressMeter - Traversal complete. Processed 558 total variants in 0.0 minutes. 11:59:38.385 INFO SelectVariants - Shutting down engine [30 janvier 2023 à 11:59:38 CET] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=2113929216 converting from NCBI to UCSC format [Mon Jan 30 11:59:38 2023] Finished job 120. 1 of 194 steps (1%) done Select jobs to execute... [Mon Jan 30 11:59:38 2023] rule aberrantExpression_bamStats: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00126.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/Pipeline/chr_UCSC_NCBI.txt output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00126.txt jobid: 20 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00126.txt wildcards: sampleID=HG00126 resources: tmpdir=/tmp [Mon Jan 30 11:59:38 2023] Finished job 20. 2 of 194 steps (1%) done Select jobs to execute... [Mon Jan 30 11:59:38 2023] rule aberrantExpression_bamStats: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00132.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/Pipeline/chr_UCSC_NCBI.txt output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00132.txt jobid: 27 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00132.txt wildcards: sampleID=HG00132 resources: tmpdir=/tmp [Mon Jan 30 11:59:38 2023] Finished job 27. 3 of 194 steps (2%) done Select jobs to execute... [Mon Jan 30 11:59:39 2023] rule rnaVariantCalling_dependency: output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/html/rvc-pipeline_dep.svg jobid: 182 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/html/rvc-pipeline_dep.svg resources: tmpdir=/tmp WARNING: Less than 30 IDs in DROP_GROUP outrider WARNING: Less than 30 IDs in DROP_GROUP outrider_external WARNING: Less than 30 IDs in DROP_GROUP fraser WARNING: Less than 30 IDs in DROP_GROUP fraser_external check for missing R packages Structuring dependencies... Dependencies file generated at: /tmp/tmp48u55tos Building DAG of jobs... Error: Directory cannot be locked. This usually means that another Snakemake instance is running on this directory. Another possibility is that a previous run exited unexpectedly. [Mon Jan 30 11:59:44 2023] Finished job 182. 4 of 194 steps (2%) done Select jobs to execute... [Mon Jan 30 11:59:44 2023] rule AberrantSplicing_pipeline_aberrant_splicing_readme_md: input: Scripts/AberrantSplicing/pipeline/aberrant_splicing_readme.md output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/html/Scripts_AberrantSplicing_pipeline_aberrant_splicing_readme.html jobid: 95 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/html/Scripts_AberrantSplicing_pipeline_aberrant_splicing_readme.html resources: tmpdir=/tmp [WARNING] Deprecated: --self-contained. use --embed-resources --standalone [Mon Jan 30 11:59:44 2023] Finished job 95. 5 of 194 steps (3%) done Select jobs to execute... [Mon Jan 30 11:59:44 2023] rule changeHeader: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00096_ncbi.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00096_ncbi.bam.bai, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/rnaVariantCalling/pipeline/GATK_BASH/changeHeader.sh output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_dropHeader.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_dropHeader.bam.bai, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_newDropHeader.txt log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/logs/changeHeader/HG00096.log jobid: 152 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_dropHeader.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_dropHeader.bam.bai wildcards: sample=HG00096 resources: tmpdir=/tmp WARNING Internal Header is designated: 0 SampleID is HG00096 Forcing 0 to match HG00096 new header can be found here:/shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_newDropHeader.txt [Mon Jan 30 11:59:44 2023] Finished job 152. 6 of 194 steps (3%) done Select jobs to execute... [Mon Jan 30 11:59:44 2023] rule sortBam: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_dropHeader.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_dropHeader.bam.bai output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.out.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.out.bam.bai log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/logs/sortBam/HG00096.log jobid: 151 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.out.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.out.bam.bai; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_dropHeader.bam.bai, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_dropHeader.bam wildcards: sample=HG00096 resources: tmpdir=/tmp [Mon Jan 30 11:59:45 2023] Finished job 151. 7 of 194 steps (4%) done Removing temporary output /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_dropHeader.bam. Removing temporary output /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_dropHeader.bam.bai. Select jobs to execute... [Mon Jan 30 11:59:45 2023] rule markDuplicates: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.out.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.out.bam.bai output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.dupMarked.out.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.dupMarked.out.bai log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/logs/markDuplicates/HG00096.log jobid: 150 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.dupMarked.out.bam; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.out.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.out.bam.bai wildcards: sample=HG00096 resources: tmpdir=/tmp Tool returned: 0 [Mon Jan 30 11:59:54 2023] Finished job 150. 8 of 194 steps (4%) done Removing temporary output /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.out.bam. Removing temporary output /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.out.bam.bai. Removing temporary output /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.dupMarked.out.bai. Select jobs to execute... [Mon Jan 30 11:59:54 2023] rule mae_createSNVs: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/Pipeline/chr_NCBI_UCSC.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/Pipeline/chr_UCSC_NCBI.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/dna_vcf/demo_chr21_ncbi.vcf.gz, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00096_ncbi.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/MonoallelicExpression/pipeline/MAE/filterSNVs.sh, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/params/snvs/HG00096_snvParams.csv output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/snvs/HG00096--HG00096.vcf.gz, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/snvs/HG00096--HG00096.vcf.gz.tbi jobid: 113 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/snvs/HG00096--HG00096.vcf.gz wildcards: vcf=HG00096, rna=HG00096 resources: tmpdir=/tmp Filter SNVs Lines total/split/realigned/skipped: 6023/0/0/0 Lines total/split/realigned/skipped: 6023/0/0/0 Using GATK jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar SelectVariants -V /tmp/tmp.MKTC7WYt5l -sn HG00096 -select vc.getGenotype('HG00096').isHet() -O /tmp/tmp.msB6AYQaF5 11:59:58.618 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 11:59:58.811 INFO SelectVariants - ------------------------------------------------------------ 11:59:58.812 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.3.0.0 11:59:58.812 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/ 11:59:58.812 INFO SelectVariants - Executing as plassard@flash-node10 on Linux v4.19.0-18-amd64 amd64 11:59:58.812 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v11.0.1-internal+0-adhoc..src 11:59:58.813 INFO SelectVariants - Start Date/Time: 30 janvier 2023 à 11:59:58 CET 11:59:58.813 INFO SelectVariants - ------------------------------------------------------------ 11:59:58.813 INFO SelectVariants - ------------------------------------------------------------ 11:59:58.814 INFO SelectVariants - HTSJDK Version: 3.0.1 11:59:58.814 INFO SelectVariants - Picard Version: 2.27.5 11:59:58.814 INFO SelectVariants - Built for Spark Version: 2.4.5 11:59:58.814 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2 11:59:58.814 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 11:59:58.815 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 11:59:58.815 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 11:59:58.815 INFO SelectVariants - Deflater: IntelDeflater 11:59:58.815 INFO SelectVariants - Inflater: IntelInflater 11:59:58.815 INFO SelectVariants - GCS max retries/reopens: 20 11:59:58.815 INFO SelectVariants - Requester pays: disabled 11:59:58.815 INFO SelectVariants - Initializing engine 11:59:59.005 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/tmp.MKTC7WYt5l 11:59:59.047 INFO SelectVariants - Done initializing engine 11:59:59.156 INFO SelectVariants - Including sample 'HG00096' 11:59:59.161 WARN GATKVariantContextUtils - Can't determine output variant file format from output file extension "msB6AYQaF5". Defaulting to VCF. 11:59:59.204 INFO ProgressMeter - Starting traversal 11:59:59.205 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute 11:59:59.678 INFO ProgressMeter - 21:47408915 0.0 5538 702494.7 11:59:59.678 INFO ProgressMeter - Traversal complete. Processed 5538 total variants in 0.0 minutes. 11:59:59.725 INFO SelectVariants - Shutting down engine [30 janvier 2023 à 11:59:59 CET] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=2113929216 Using GATK jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar SelectVariants --restrict-alleles-to BIALLELIC -V /tmp/tmp.msB6AYQaF5 -O /tmp/tmp.MKTC7WYt5l 12:00:03.614 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 12:00:03.823 INFO SelectVariants - ------------------------------------------------------------ 12:00:03.824 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.3.0.0 12:00:03.824 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/ 12:00:03.824 INFO SelectVariants - Executing as plassard@flash-node10 on Linux v4.19.0-18-amd64 amd64 12:00:03.824 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v11.0.1-internal+0-adhoc..src 12:00:03.825 INFO SelectVariants - Start Date/Time: 30 janvier 2023 à 12:00:03 CET 12:00:03.825 INFO SelectVariants - ------------------------------------------------------------ 12:00:03.825 INFO SelectVariants - ------------------------------------------------------------ 12:00:03.826 INFO SelectVariants - HTSJDK Version: 3.0.1 12:00:03.826 INFO SelectVariants - Picard Version: 2.27.5 12:00:03.826 INFO SelectVariants - Built for Spark Version: 2.4.5 12:00:03.827 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2 12:00:03.827 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 12:00:03.827 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 12:00:03.827 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 12:00:03.827 INFO SelectVariants - Deflater: IntelDeflater 12:00:03.827 INFO SelectVariants - Inflater: IntelInflater 12:00:03.828 INFO SelectVariants - GCS max retries/reopens: 20 12:00:03.828 INFO SelectVariants - Requester pays: disabled 12:00:03.828 INFO SelectVariants - Initializing engine 12:00:04.020 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/tmp.msB6AYQaF5 12:00:04.080 INFO SelectVariants - Done initializing engine 12:00:04.156 WARN GATKVariantContextUtils - Can't determine output variant file format from output file extension "MKTC7WYt5l". Defaulting to VCF. 12:00:04.203 INFO ProgressMeter - Starting traversal 12:00:04.204 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute 12:00:04.335 INFO ProgressMeter - unmapped 0.0 545 251538.5 12:00:04.335 INFO ProgressMeter - Traversal complete. Processed 545 total variants in 0.0 minutes. 12:00:04.381 INFO SelectVariants - Shutting down engine [30 janvier 2023 à 12:00:04 CET] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=2113929216 [Mon Jan 30 12:00:04 2023] Finished job 113. 9 of 194 steps (5%) done Select jobs to execute... [Mon Jan 30 12:00:04 2023] rule Pipeline_SampleAnnotation_R: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/sample_annotation.tsv, Scripts/Pipeline/SampleAnnotation.R output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/sample_anno/genes_overlapping_HPO_terms.tsv, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/html/Scripts_Pipeline_SampleAnnotation.html log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/.drop/tmp/SampleAnnotation.Rds jobid: 193 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/html/Scripts_Pipeline_SampleAnnotation.html resources: tmpdir=/tmp Le chargement a nécessité le package : knitr Le chargement a nécessité le package : rmarkdown [1] TRUE processing file: /tmp/Rtmpv0RLm3/filea2278a5cf83/SampleAnnotation.spin.Rmd | | | 0% | |..... | 6% | |.......... | 11% (unnamed-chunk-1) | |............... | 17% | |.................... | 22% (unnamed-chunk-2) | |.......................... | 28% | |............................... | 33% (unnamed-chunk-3) | |.................................... | 39% | |......................................... | 44% (unnamed-chunk-4) | |.............................................. | 50% | |................................................... | 56% (unnamed-chunk-5) | |........................................................ | 61% | |............................................................. | 67% (unnamed-chunk-6) | |.................................................................. | 72% | |........................................................................ | 78% (unnamed-chunk-7) | |............................................................................. | 83% | |.................................................................................. | 89% (unnamed-chunk-8) | |....................................................................................... | 94% (unnamed-chunk-9) | |............................................................................................| 100% output file: /tmp/Rtmpv0RLm3/filea2278a5cf83/SampleAnnotation.knit.md /shared/ifs/home/plassard/Conda/envs_conda_flash/drop_env/bin/pandoc +RTS -K512m -RTS /tmp/Rtmpv0RLm3/filea2278a5cf83/SampleAnnotation.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/Rtmpv0RLm3/filea2273272ee22/Scripts_Pipeline_SampleAnnotation.html --lua-filter /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/lib/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/lib/R/library/rmarkdown/rmarkdown/lua/latex-div.lua --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/lib/R/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --css lib/add_content_table.css --css lib/leo_style.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/Rtmpv0RLm3/rmarkdown-stra227d78e767.html --variable code_folding=hide --variable source_embed=SampleAnnotation.R --include-after-body /tmp/Rtmpv0RLm3/filea22760f1e73f.html --variable code_menu=1 Output created: /tmp/Rtmpv0RLm3/filea2273272ee22/Scripts_Pipeline_SampleAnnotation.html [1] TRUE TRUE TRUE TRUE Touching output file /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/sample_anno/genes_overlapping_HPO_terms.tsv. [Mon Jan 30 12:00:11 2023] Finished job 193. 10 of 194 steps (5%) done Select jobs to execute... [Mon Jan 30 12:00:11 2023] rule AberrantSplicing_pipeline_Counting_00_define_datasets_from_anno_R: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/sample_annotation.tsv, Scripts/AberrantSplicing/pipeline/Counting/00_define_datasets_from_anno.R output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/annotations/fraser.tsv, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/html/AberrantSplicing/annotations/fraser.html log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/.drop/tmp/AS/fraser/00_defineDataset.Rds jobid: 52 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/annotations/fraser.tsv wildcards: dataset=fraser resources: tmpdir=/tmp Le chargement a nécessité le package : knitr Le chargement a nécessité le package : rmarkdown [1] TRUE processing file: /tmp/RtmpBBzkvb/filea28b3750addd/00_define_datasets_from_anno.spin.Rmd | | | 0% | |.......... | 11% | |.................... | 22% (unnamed-chunk-1) | |............................... | 33% (input) | |......................................... | 44% (dataset name) | |................................................... | 56% | |............................................................. | 67% (unnamed-chunk-2) | |........................................................................ | 78% | |.................................................................................. | 89% (savetable) | |............................................................................................| 100% output file: /tmp/RtmpBBzkvb/filea28b3750addd/00_define_datasets_from_anno.knit.md /shared/ifs/home/plassard/Conda/envs_conda_flash/drop_env/bin/pandoc +RTS -K512m -RTS /tmp/RtmpBBzkvb/filea28b3750addd/00_define_datasets_from_anno.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpBBzkvb/filea28b52e762d7/fraser.html --lua-filter /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/lib/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/lib/R/library/rmarkdown/rmarkdown/lua/latex-div.lua --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/lib/R/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --css lib/add_content_table.css --css lib/leo_style.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpBBzkvb/rmarkdown-stra28b7084f66.html --variable code_folding=hide --variable source_embed=00_define_datasets_from_anno.R --include-after-body /tmp/RtmpBBzkvb/filea28b4f9f4808.html --variable code_menu=1 Output created: /tmp/RtmpBBzkvb/filea28b52e762d7/fraser.html [1] TRUE TRUE TRUE [Mon Jan 30 12:00:46 2023] Finished job 52. 11 of 194 steps (6%) done Select jobs to execute... [Mon Jan 30 12:00:46 2023] rule readme_md: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/readme.md output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/html/readme.html jobid: 190 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/html/readme.html resources: tmpdir=/tmp [WARNING] Deprecated: --self-contained. use --embed-resources --standalone [Mon Jan 30 12:00:46 2023] Finished job 190. 12 of 194 steps (6%) done Select jobs to execute... [Mon Jan 30 12:00:46 2023] rule Pipeline_preprocessGeneAnnotation_R: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/gencode_annotation_trunc.gtf, Scripts/Pipeline/preprocessGeneAnnotation.R output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/preprocess/v29/txdb.db, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/preprocess/v29/gene_name_mapping_v29.tsv, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/count_ranges.Rds log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/.drop/tmp/AE/v29/preprocess.Rds jobid: 7 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/preprocess/v29/gene_name_mapping_v29.tsv, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/preprocess/v29/txdb.db, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/count_ranges.Rds wildcards: annotation=v29 resources: tmpdir=/tmp Import genomic features from the file as a GRanges object ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... OK Message d'avis : Dans .get_cds_IDX(mcols0$type, mcols0$phase) : The "phase" metadata column contains non-NA values for features of type stop_codon. This information was ignored. TxDb object: # Db type: TxDb # Supporting package: GenomicFeatures # Data source: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/gencode_annotation_trunc.gtf # Organism: NA # Taxonomy ID: NA # miRBase build ID: NA # Genome: NA # Nb of transcripts: 2378 # Db created by: GenomicFeatures package from Bioconductor # Creation time: 2023-01-30 12:01:12 +0100 (Mon, 30 Jan 2023) # GenomicFeatures version at creation time: 1.50.2 # RSQLite version at creation time: 2.2.20 # DBSCHEMAVERSION: 1.2 [1] TRUE [Mon Jan 30 12:01:14 2023] Finished job 7. 13 of 194 steps (7%) done Select jobs to execute... [Mon Jan 30 12:01:14 2023] rule AberrantExpression_pipeline_Counting_countReads_R: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00176.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/count_ranges.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/params/counts/HG00176_countParams.csv, Scripts/AberrantExpression/pipeline/Counting/countReads.R output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00176.Rds log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/.drop/tmp/AE/v29/counts/HG00176.Rds jobid: 10 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00176.Rds; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/count_ranges.Rds wildcards: annotation=v29, sampleID=HG00176 resources: tmpdir=/tmp input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00176.bam output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00176.Rds count mode: IntersectionStrict paired end: TRUE inter.feature: FALSE strand: no strand specific: FALSE chr21 counting done [1] "2.465215 secs" [1] 37036 [Mon Jan 30 12:01:30 2023] Finished job 10. 14 of 194 steps (7%) done Select jobs to execute... [Mon Jan 30 12:01:31 2023] rule AberrantExpression_pipeline_Counting_countReads_R: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00116.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/count_ranges.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/params/counts/HG00116_countParams.csv, Scripts/AberrantExpression/pipeline/Counting/countReads.R output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00116.Rds log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/.drop/tmp/AE/v29/counts/HG00116.Rds jobid: 14 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00116.Rds; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/count_ranges.Rds wildcards: annotation=v29, sampleID=HG00116 resources: tmpdir=/tmp input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00116.bam output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00116.Rds count mode: IntersectionStrict paired end: TRUE inter.feature: FALSE strand: no strand specific: FALSE chr21 counting done [1] "2.173668 secs" [1] 38422 [Mon Jan 30 12:01:47 2023] Finished job 14. 15 of 194 steps (8%) done Select jobs to execute... [Mon Jan 30 12:01:47 2023] rule MonoallelicExpression_pipeline_MAE_gene_name_mapping_R: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/gencode_annotation_trunc.gtf, Scripts/MonoallelicExpression/pipeline/MAE/gene_name_mapping.R output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/gene_name_mapping_v29.tsv log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/.drop/tmp/MAE/v29.Rds jobid: 121 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/gene_name_mapping_v29.tsv wildcards: annotation=v29 resources: tmpdir=/tmp [Mon Jan 30 12:02:05 2023] Finished job 121. 16 of 194 steps (8%) done Select jobs to execute... [Mon Jan 30 12:02:05 2023] rule aberrantExpression_bamStats: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00111.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/Pipeline/chr_UCSC_NCBI.txt output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00111.txt jobid: 18 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00111.txt wildcards: sampleID=HG00111 resources: tmpdir=/tmp [Mon Jan 30 12:02:06 2023] Finished job 18. 17 of 194 steps (9%) done Select jobs to execute... [Mon Jan 30 12:02:06 2023] rule aberrantExpression_bamStats: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00096_ncbi.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/Pipeline/chr_UCSC_NCBI.txt output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00096.txt jobid: 24 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00096.txt wildcards: sampleID=HG00096 resources: tmpdir=/tmp [Mon Jan 30 12:02:06 2023] Finished job 24. 18 of 194 steps (9%) done Select jobs to execute... [Mon Jan 30 12:02:06 2023] rule AberrantExpression_pipeline_Counting_countReads_R: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00132.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/count_ranges.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/params/counts/HG00132_countParams.csv, Scripts/AberrantExpression/pipeline/Counting/countReads.R output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00132.Rds log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/.drop/tmp/AE/v29/counts/HG00132.Rds jobid: 16 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00132.Rds; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/count_ranges.Rds wildcards: annotation=v29, sampleID=HG00132 resources: tmpdir=/tmp input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00132.bam output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00132.Rds count mode: IntersectionStrict paired end: TRUE inter.feature: FALSE strand: no strand specific: FALSE chr21 counting done [1] "2.78172 secs" [1] 49977 [Mon Jan 30 12:02:22 2023] Finished job 16. 19 of 194 steps (10%) done Select jobs to execute... [Mon Jan 30 12:02:23 2023] rule aberrantExpression_bamStats: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00149.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/Pipeline/chr_UCSC_NCBI.txt output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00149.txt jobid: 19 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00149.txt wildcards: sampleID=HG00149 resources: tmpdir=/tmp [Mon Jan 30 12:02:23 2023] Finished job 19. 20 of 194 steps (10%) done Select jobs to execute... [Mon Jan 30 12:02:23 2023] rule mae_createSNVs: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/Pipeline/chr_NCBI_UCSC.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/Pipeline/chr_UCSC_NCBI.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/qc_vcf_1000G.vcf.gz, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00096_ncbi.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/MonoallelicExpression/pipeline/MAE/filterSNVs.sh, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/params/snvs/HG00096_snvParams.csv output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/snvs/QC--HG00096.vcf.gz, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/snvs/QC--HG00096.vcf.gz.tbi jobid: 134 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/snvs/QC--HG00096.vcf.gz wildcards: vcf=QC, rna=HG00096 resources: tmpdir=/tmp Filter SNVs Lines total/split/realigned/skipped: 26402/0/0/0 Lines total/split/realigned/skipped: 26402/0/0/0 Using GATK jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar SelectVariants -V /tmp/tmp.wjHdq77P01 -O /tmp/tmp.oHoeHNFCKH 12:02:28.242 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 12:02:28.464 INFO SelectVariants - ------------------------------------------------------------ 12:02:28.464 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.3.0.0 12:02:28.465 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/ 12:02:28.465 INFO SelectVariants - Executing as plassard@flash-node10 on Linux v4.19.0-18-amd64 amd64 12:02:28.465 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v11.0.1-internal+0-adhoc..src 12:02:28.465 INFO SelectVariants - Start Date/Time: 30 janvier 2023 à 12:02:28 CET 12:02:28.466 INFO SelectVariants - ------------------------------------------------------------ 12:02:28.466 INFO SelectVariants - ------------------------------------------------------------ 12:02:28.467 INFO SelectVariants - HTSJDK Version: 3.0.1 12:02:28.467 INFO SelectVariants - Picard Version: 2.27.5 12:02:28.467 INFO SelectVariants - Built for Spark Version: 2.4.5 12:02:28.467 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2 12:02:28.467 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 12:02:28.468 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 12:02:28.468 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 12:02:28.468 INFO SelectVariants - Deflater: IntelDeflater 12:02:28.468 INFO SelectVariants - Inflater: IntelInflater 12:02:28.468 INFO SelectVariants - GCS max retries/reopens: 20 12:02:28.469 INFO SelectVariants - Requester pays: disabled 12:02:28.469 INFO SelectVariants - Initializing engine 12:02:28.664 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/tmp.wjHdq77P01 12:02:28.691 INFO SelectVariants - Done initializing engine 12:02:28.709 WARN GATKVariantContextUtils - Can't determine output variant file format from output file extension "oHoeHNFCKH". Defaulting to VCF. 12:02:28.726 INFO ProgressMeter - Starting traversal 12:02:28.726 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute 12:02:29.679 INFO ProgressMeter - chr22:30163526 0.0 26402 1663991.6 12:02:29.679 INFO ProgressMeter - Traversal complete. Processed 26402 total variants in 0.0 minutes. 12:02:29.900 INFO SelectVariants - Shutting down engine [30 janvier 2023 à 12:02:29 CET] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.03 minutes. Runtime.totalMemory()=2629828608 Using GATK jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar SelectVariants --restrict-alleles-to BIALLELIC -V /tmp/tmp.oHoeHNFCKH -O /tmp/tmp.wjHdq77P01 12:02:33.636 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 12:02:33.829 INFO SelectVariants - ------------------------------------------------------------ 12:02:33.830 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.3.0.0 12:02:33.830 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/ 12:02:33.831 INFO SelectVariants - Executing as plassard@flash-node10 on Linux v4.19.0-18-amd64 amd64 12:02:33.831 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v11.0.1-internal+0-adhoc..src 12:02:33.831 INFO SelectVariants - Start Date/Time: 30 janvier 2023 à 12:02:33 CET 12:02:33.831 INFO SelectVariants - ------------------------------------------------------------ 12:02:33.831 INFO SelectVariants - ------------------------------------------------------------ 12:02:33.832 INFO SelectVariants - HTSJDK Version: 3.0.1 12:02:33.832 INFO SelectVariants - Picard Version: 2.27.5 12:02:33.833 INFO SelectVariants - Built for Spark Version: 2.4.5 12:02:33.833 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2 12:02:33.833 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 12:02:33.833 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 12:02:33.833 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 12:02:33.833 INFO SelectVariants - Deflater: IntelDeflater 12:02:33.834 INFO SelectVariants - Inflater: IntelInflater 12:02:33.834 INFO SelectVariants - GCS max retries/reopens: 20 12:02:33.834 INFO SelectVariants - Requester pays: disabled 12:02:33.834 INFO SelectVariants - Initializing engine 12:02:34.030 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/tmp.oHoeHNFCKH 12:02:34.068 INFO SelectVariants - Done initializing engine 12:02:34.084 WARN GATKVariantContextUtils - Can't determine output variant file format from output file extension "wjHdq77P01". Defaulting to VCF. 12:02:34.096 INFO ProgressMeter - Starting traversal 12:02:34.096 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute 12:02:34.975 INFO ProgressMeter - chr22:30163526 0.0 26402 1804236.9 12:02:34.975 INFO ProgressMeter - Traversal complete. Processed 26402 total variants in 0.0 minutes. 12:02:35.157 INFO SelectVariants - Shutting down engine [30 janvier 2023 à 12:02:35 CET] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.03 minutes. Runtime.totalMemory()=2113929216 converting from UCSC to NCBI format [Mon Jan 30 12:02:35 2023] Finished job 134. 21 of 194 steps (11%) done Select jobs to execute... [Mon Jan 30 12:02:35 2023] rule mae_dependency: output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/html/mae-pipeline_dep.svg jobid: 135 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/html/mae-pipeline_dep.svg resources: tmpdir=/tmp WARNING: Less than 30 IDs in DROP_GROUP outrider WARNING: Less than 30 IDs in DROP_GROUP outrider_external WARNING: Less than 30 IDs in DROP_GROUP fraser WARNING: Less than 30 IDs in DROP_GROUP fraser_external check for missing R packages Structuring dependencies... Dependencies file generated at: /tmp/tmpbyqq3xby Building DAG of jobs... Error: Directory cannot be locked. This usually means that another Snakemake instance is running on this directory. Another possibility is that a previous run exited unexpectedly. [Mon Jan 30 12:02:41 2023] Finished job 135. 22 of 194 steps (11%) done Select jobs to execute... [Mon Jan 30 12:02:41 2023] rule create_dict: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21_ncbi.fa, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21.fa output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21_ncbi.dict, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21.dict jobid: 114 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21.dict, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21_ncbi.dict resources: tmpdir=/tmp Using GATK jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar CreateSequenceDictionary --REFERENCE /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21_ncbi.fa INFO 2023-01-30 12:02:45 CreateSequenceDictionary Output dictionary will be written in /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21_ncbi.dict 12:02:45.230 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so [Mon Jan 30 12:02:45 CET 2023] CreateSequenceDictionary --REFERENCE /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21_ncbi.fa --TRUNCATE_NAMES_AT_WHITESPACE true --NUM_SEQUENCES 2147483647 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Mon Jan 30 12:02:45 CET 2023] Executing as plassard@flash-node10 on Linux 4.19.0-18-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.1-internal+0-adhoc..src; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.3.0.0 [Mon Jan 30 12:02:45 CET 2023] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=2113929216 Tool returned: 0 Using GATK jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar CreateSequenceDictionary --REFERENCE /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21.fa INFO 2023-01-30 12:02:49 CreateSequenceDictionary Output dictionary will be written in /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21.dict 12:02:49.346 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so [Mon Jan 30 12:02:49 CET 2023] CreateSequenceDictionary --REFERENCE /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21.fa --TRUNCATE_NAMES_AT_WHITESPACE true --NUM_SEQUENCES 2147483647 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Mon Jan 30 12:02:49 CET 2023] Executing as plassard@flash-node10 on Linux 4.19.0-18-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.1-internal+0-adhoc..src; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.3.0.0 [Mon Jan 30 12:02:49 CET 2023] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=2113929216 Tool returned: 0 [Mon Jan 30 12:02:50 2023] Finished job 114. 23 of 194 steps (12%) done Select jobs to execute... [Mon Jan 30 12:02:50 2023] rule reorderBAM: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.dupMarked.out.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21_ncbi.dict output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.dupMarked.FAorder.out.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.dupMarked.FAorder.out.bai jobid: 149 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.dupMarked.FAorder.out.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.dupMarked.FAorder.out.bai; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.dupMarked.out.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21_ncbi.dict wildcards: sample=HG00096 resources: tmpdir=/tmp ReorderSam Using GATK jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Djava.io.tmpdir=/tmp -jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar ReorderSam -I /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.dupMarked.out.bam -O /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.dupMarked.FAorder.out.bam --SEQUENCE_DICTIONARY /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21_ncbi.dict -S true --CREATE_INDEX true 12:02:53.495 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so [Mon Jan 30 12:02:53 CET 2023] ReorderSam --INPUT /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.dupMarked.out.bam --OUTPUT /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.dupMarked.FAorder.out.bam --SEQUENCE_DICTIONARY /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21_ncbi.dict --ALLOW_INCOMPLETE_DICT_CONCORDANCE true --CREATE_INDEX true --ALLOW_CONTIG_LENGTH_DISCORDANCE false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Mon Jan 30 12:02:53 CET 2023] Executing as plassard@flash-node10 on Linux 4.19.0-18-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.1-internal+0-adhoc..src; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.3.0.0 INFO 2023-01-30 12:02:53 ReorderSam SAM/BAM/CRAM file INFO 2023-01-30 12:02:53 ReorderSam SN=1 LN=249250621 INFO 2023-01-30 12:02:53 ReorderSam SN=10 LN=135534747 INFO 2023-01-30 12:02:53 ReorderSam SN=11 LN=135006516 INFO 2023-01-30 12:02:53 ReorderSam SN=12 LN=133851895 INFO 2023-01-30 12:02:53 ReorderSam SN=13 LN=115169878 INFO 2023-01-30 12:02:53 ReorderSam SN=14 LN=107349540 INFO 2023-01-30 12:02:53 ReorderSam SN=15 LN=102531392 INFO 2023-01-30 12:02:53 ReorderSam SN=16 LN=90354753 INFO 2023-01-30 12:02:53 ReorderSam SN=17 LN=81195210 INFO 2023-01-30 12:02:53 ReorderSam SN=18 LN=78077248 INFO 2023-01-30 12:02:53 ReorderSam SN=19 LN=59128983 INFO 2023-01-30 12:02:53 ReorderSam SN=2 LN=243199373 INFO 2023-01-30 12:02:53 ReorderSam SN=20 LN=63025520 INFO 2023-01-30 12:02:53 ReorderSam SN=21 LN=48129895 INFO 2023-01-30 12:02:53 ReorderSam SN=22 LN=51304566 INFO 2023-01-30 12:02:53 ReorderSam SN=3 LN=198022430 INFO 2023-01-30 12:02:53 ReorderSam SN=4 LN=191154276 INFO 2023-01-30 12:02:53 ReorderSam SN=5 LN=180915260 INFO 2023-01-30 12:02:53 ReorderSam SN=6 LN=171115067 INFO 2023-01-30 12:02:53 ReorderSam SN=7 LN=159138663 INFO 2023-01-30 12:02:53 ReorderSam SN=8 LN=146364022 INFO 2023-01-30 12:02:53 ReorderSam SN=9 LN=141213431 INFO 2023-01-30 12:02:53 ReorderSam SN=X LN=155270560 INFO 2023-01-30 12:02:53 ReorderSam SN=Y LN=59373566 INFO 2023-01-30 12:02:53 ReorderSam Reference INFO 2023-01-30 12:02:53 ReorderSam SN=21 LN=48129895 INFO 2023-01-30 12:02:53 ReorderSam Reordering SAM/BAM/CRAM file: INFO 2023-01-30 12:02:53 ReorderSam Reordering read contig 21 [index=13] to => ref contig 21 [index=0] INFO 2023-01-30 12:02:53 ReorderSam Writing reads... INFO 2023-01-30 12:02:53 ReorderSam Processing All reads INFO 2023-01-30 12:02:54 ReorderSam Wrote 62690 reads [Mon Jan 30 12:02:55 CET 2023] picard.sam.ReorderSam done. Elapsed time: 0.03 minutes. Runtime.totalMemory()=2113929216 Tool returned: 0 [Mon Jan 30 12:02:55 2023] Finished job 149. 24 of 194 steps (12%) done Removing temporary output /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.dupMarked.out.bam. Select jobs to execute... [Mon Jan 30 12:02:55 2023] rule splitNcigar: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.dupMarked.FAorder.out.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.dupMarked.FAorder.out.bai, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21_ncbi.fa.fai, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21_ncbi.dict output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.dupMarked.split.out.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.dupMarked.split.out.bai log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/logs/splitNcigar/HG00096.log jobid: 148 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.dupMarked.split.out.bai, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.dupMarked.split.out.bam; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.dupMarked.FAorder.out.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.dupMarked.FAorder.out.bai, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21_ncbi.dict wildcards: sample=HG00096 resources: tmpdir=/tmp [Mon Jan 30 12:03:05 2023] Finished job 148. 25 of 194 steps (13%) done Removing temporary output /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.dupMarked.FAorder.out.bam. Removing temporary output /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.dupMarked.FAorder.out.bai. Select jobs to execute... [Mon Jan 30 12:03:05 2023] rule bqsr: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.dupMarked.split.out.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.dupMarked.split.out.bai, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/rnaVariantCalling/pipeline/GATK_BASH/bqsr.sh output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bqsr/HG00096_recal.table log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/logs/bqsr/HG00096.log jobid: 154 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bqsr/HG00096_recal.table; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.dupMarked.split.out.bai, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.dupMarked.split.out.bam wildcards: sample=HG00096 resources: tmpdir=/tmp converting known vcfs from NCBI to UCSC format [W::bcf_hdr_check_sanity] PL should be declared as Number=G starting BaseRecalibrator Using GATK jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Djava.io.tmpdir=/tmp -jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar BaseRecalibrator -I /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.dupMarked.split.out.bam -R /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21_ncbi.fa --known-sites /tmp/tmp.pazkk1NhRn.gz --known-sites /tmp/tmp.xMbZXE8M2K.gz --known-sites /tmp/tmp.6P8OeVAGkv.gz -O /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bqsr/HG00096_recal.table 12:03:09.916 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 12:03:10.112 INFO BaseRecalibrator - ------------------------------------------------------------ 12:03:10.112 INFO BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.3.0.0 12:03:10.112 INFO BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/ 12:03:10.113 INFO BaseRecalibrator - Executing as plassard@flash-node10 on Linux v4.19.0-18-amd64 amd64 12:03:10.113 INFO BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v11.0.1-internal+0-adhoc..src 12:03:10.113 INFO BaseRecalibrator - Start Date/Time: 30 janvier 2023 à 12:03:09 CET 12:03:10.113 INFO BaseRecalibrator - ------------------------------------------------------------ 12:03:10.113 INFO BaseRecalibrator - ------------------------------------------------------------ 12:03:10.114 INFO BaseRecalibrator - HTSJDK Version: 3.0.1 12:03:10.114 INFO BaseRecalibrator - Picard Version: 2.27.5 12:03:10.114 INFO BaseRecalibrator - Built for Spark Version: 2.4.5 12:03:10.115 INFO BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2 12:03:10.115 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 12:03:10.115 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 12:03:10.115 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 12:03:10.115 INFO BaseRecalibrator - Deflater: IntelDeflater 12:03:10.115 INFO BaseRecalibrator - Inflater: IntelInflater 12:03:10.115 INFO BaseRecalibrator - GCS max retries/reopens: 20 12:03:10.116 INFO BaseRecalibrator - Requester pays: disabled 12:03:10.116 INFO BaseRecalibrator - Initializing engine 12:03:10.378 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/tmp.pazkk1NhRn.gz 12:03:10.421 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/tmp.xMbZXE8M2K.gz 12:03:10.438 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/tmp.6P8OeVAGkv.gz 12:03:10.455 INFO BaseRecalibrator - Done initializing engine 12:03:10.460 INFO BaseRecalibrationEngine - The covariates being used here: 12:03:10.460 INFO BaseRecalibrationEngine - ReadGroupCovariate 12:03:10.460 INFO BaseRecalibrationEngine - QualityScoreCovariate 12:03:10.460 INFO BaseRecalibrationEngine - ContextCovariate 12:03:10.460 INFO BaseRecalibrationEngine - CycleCovariate 12:03:10.463 INFO ProgressMeter - Starting traversal 12:03:10.463 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute 12:03:13.580 WARN IntelInflater - Zero Bytes Written : 0 12:03:13.582 INFO BaseRecalibrator - 341 read(s) filtered by: MappingQualityNotZeroReadFilter 0 read(s) filtered by: MappingQualityAvailableReadFilter 0 read(s) filtered by: MappedReadFilter 0 read(s) filtered by: NotSecondaryAlignmentReadFilter 3205 read(s) filtered by: NotDuplicateReadFilter 0 read(s) filtered by: PassesVendorQualityCheckReadFilter 0 read(s) filtered by: WellformedReadFilter 3546 total reads filtered 12:03:13.583 INFO ProgressMeter - 21:48084514 0.1 74183 1427053.5 12:03:13.583 INFO ProgressMeter - Traversal complete. Processed 74183 total reads in 0.1 minutes. 12:03:13.666 INFO BaseRecalibrator - Calculating quantized quality scores... 12:03:13.682 INFO BaseRecalibrator - Writing recalibration report... 12:03:16.990 INFO BaseRecalibrator - ...done! 12:03:16.991 INFO BaseRecalibrator - BaseRecalibrator was able to recalibrate 74183 reads 12:03:16.991 INFO BaseRecalibrator - Shutting down engine [30 janvier 2023 à 12:03:16 CET] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.12 minutes. Runtime.totalMemory()=3116367872 Tool returned: SUCCESS [Mon Jan 30 12:03:17 2023] Finished job 154. 26 of 194 steps (13%) done Select jobs to execute... [Mon Jan 30 12:03:17 2023] rule applyBQSR: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.dupMarked.split.out.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.dupMarked.split.out.bai, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bqsr/HG00096_recal.table output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.dupMarked.split.bqsr.out.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.dupMarked.split.bqsr.out.bai log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/logs/applyBQSR/HG00096.log jobid: 147 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.dupMarked.split.bqsr.out.bai, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.dupMarked.split.bqsr.out.bam; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.dupMarked.split.out.bai, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bqsr/HG00096_recal.table, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.dupMarked.split.out.bam wildcards: sample=HG00096 resources: tmpdir=/tmp [Mon Jan 30 12:03:26 2023] Finished job 147. 27 of 194 steps (14%) done Removing temporary output /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.dupMarked.split.out.bai. Removing temporary output /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.dupMarked.split.out.bam. Select jobs to execute... [Mon Jan 30 12:03:26 2023] rule haplotypeCaller: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.dupMarked.split.bqsr.out.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.dupMarked.split.bqsr.out.bai, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/rnaVariantCalling/pipeline/GATK_BASH/haplotypeCaller.sh output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/sample_vcfs/HG00096/HG00096.g.vcf.gz log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/logs/all_haplocaller/HG00096.log jobid: 146 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/sample_vcfs/HG00096/HG00096.g.vcf.gz; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.dupMarked.split.bqsr.out.bai, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.dupMarked.split.bqsr.out.bam wildcards: sample=HG00096 resources: tmpdir=/tmp converting dbSNP from NCBI to UCSC format starting HaplotypeCaller Using GATK jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Djava.io.tmpdir=/tmp -jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar HaplotypeCaller -I /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.dupMarked.split.bqsr.out.bam -R /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21_ncbi.fa --dont-use-soft-clipped-bases -stand-call-conf 20.0 --dbsnp /tmp/tmp.bCHaPpItjm.vcf.gz --output-mode EMIT_ALL_CONFIDENT_SITES -ERC GVCF -O /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/sample_vcfs/HG00096/HG00096.g.vcf.gz 12:03:30.165 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 12:03:30.369 INFO HaplotypeCaller - ------------------------------------------------------------ 12:03:30.370 INFO HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.3.0.0 12:03:30.370 INFO HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/ 12:03:30.370 INFO HaplotypeCaller - Executing as plassard@flash-node10 on Linux v4.19.0-18-amd64 amd64 12:03:30.370 INFO HaplotypeCaller - Java runtime: OpenJDK 64-Bit Server VM v11.0.1-internal+0-adhoc..src 12:03:30.371 INFO HaplotypeCaller - Start Date/Time: 30 janvier 2023 à 12:03:30 CET 12:03:30.371 INFO HaplotypeCaller - ------------------------------------------------------------ 12:03:30.371 INFO HaplotypeCaller - ------------------------------------------------------------ 12:03:30.372 INFO HaplotypeCaller - HTSJDK Version: 3.0.1 12:03:30.372 INFO HaplotypeCaller - Picard Version: 2.27.5 12:03:30.372 INFO HaplotypeCaller - Built for Spark Version: 2.4.5 12:03:30.372 INFO HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2 12:03:30.372 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 12:03:30.373 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 12:03:30.373 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 12:03:30.373 INFO HaplotypeCaller - Deflater: IntelDeflater 12:03:30.373 INFO HaplotypeCaller - Inflater: IntelInflater 12:03:30.373 INFO HaplotypeCaller - GCS max retries/reopens: 20 12:03:30.373 INFO HaplotypeCaller - Requester pays: disabled 12:03:30.373 INFO HaplotypeCaller - Initializing engine 12:03:30.651 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/tmp.bCHaPpItjm.vcf.gz 12:03:30.689 INFO HaplotypeCaller - Done initializing engine 12:03:30.692 INFO HaplotypeCallerEngine - Tool is in reference confidence mode and the annotation, the following changes will be made to any specified annotations: 'StrandBiasBySample' will be enabled. 'ChromosomeCounts', 'FisherStrand', 'StrandOddsRatio' and 'QualByDepth' annotations have been disabled 12:03:30.701 INFO HaplotypeCallerEngine - Standard Emitting and Calling confidence set to -0.0 for reference-model confidence output 12:03:30.701 INFO HaplotypeCallerEngine - All sites annotated with PLs forced to true for reference-model confidence output 12:03:30.723 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 12:03:30.726 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 12:03:30.765 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 12:03:30.766 INFO IntelPairHmm - Available threads: 1 12:03:30.767 INFO IntelPairHmm - Requested threads: 4 12:03:30.767 WARN IntelPairHmm - Using 1 available threads, but 4 were requested 12:03:30.767 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 12:03:30.828 INFO ProgressMeter - Starting traversal 12:03:30.828 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 12:03:42.135 WARN InbreedingCoeff - InbreedingCoeff will not be calculated at position 21:9907271 and possibly subsequent; at least 10 samples must have called genotypes 12:03:43.102 INFO ProgressMeter - 21:9908030 0.2 33030 161476.4 12:03:53.101 INFO ProgressMeter - 21:12705777 0.4 42390 114192.1 12:04:03.102 INFO ProgressMeter - 21:18778603 0.5 62660 116490.1 12:04:13.103 INFO ProgressMeter - 21:25232888 0.7 84200 119506.1 12:04:23.556 INFO ProgressMeter - 21:28795468 0.9 96140 109399.2 12:04:25.257 WARN DepthPerSampleHC - Annotation will not be calculated at position 21:30261344 and possibly subsequent; genotype for sample HG00096 is not called 12:04:25.257 WARN StrandBiasBySample - Annotation will not be calculated at position 21:30261344 and possibly subsequent; genotype for sample HG00096 is not called 12:04:33.943 INFO ProgressMeter - 21:33871290 1.1 113190 107605.3 12:04:43.946 INFO ProgressMeter - 21:36318110 1.2 121510 99710.1 12:04:53.947 INFO ProgressMeter - 21:41697353 1.4 139610 100779.6 12:05:03.950 INFO ProgressMeter - 21:44825282 1.6 150150 96744.1 12:05:10.375 INFO HaplotypeCaller - 341 read(s) filtered by: MappingQualityReadFilter 0 read(s) filtered by: MappingQualityAvailableReadFilter 0 read(s) filtered by: MappedReadFilter 0 read(s) filtered by: NotSecondaryAlignmentReadFilter 3205 read(s) filtered by: NotDuplicateReadFilter 0 read(s) filtered by: PassesVendorQualityCheckReadFilter 0 read(s) filtered by: NonZeroReferenceLengthAlignmentReadFilter 0 read(s) filtered by: GoodCigarReadFilter 0 read(s) filtered by: WellformedReadFilter 3546 total reads filtered 12:05:10.375 INFO ProgressMeter - 21:48129148 1.7 161442 97306.0 12:05:10.375 INFO ProgressMeter - Traversal complete. Processed 161442 total regions in 1.7 minutes. 12:05:10.448 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.019632372000000002 12:05:10.449 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 10.377106640000001 12:05:10.449 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 11.10 sec 12:05:10.450 INFO HaplotypeCaller - Shutting down engine [30 janvier 2023 à 12:05:10 CET] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 1.67 minutes. Runtime.totalMemory()=5154799616 [Mon Jan 30 12:05:10 2023] Finished job 146. 28 of 194 steps (14%) done Removing temporary output /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.dupMarked.split.bqsr.out.bai. Removing temporary output /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00096/HG00096_Aligned.sortedByCoord.dupMarked.split.bqsr.out.bam. Select jobs to execute... [Mon Jan 30 12:05:10 2023] rule mae_allelicCounts: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/Pipeline/chr_NCBI_UCSC.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/Pipeline/chr_UCSC_NCBI.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/snvs/QC--HG00096.vcf.gz, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00096_ncbi.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21_ncbi.fa, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21_ncbi.dict, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/MonoallelicExpression/pipeline/MAE/ASEReadCounter.sh output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/allelic_counts/QC--HG00096.csv.gz jobid: 133 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/allelic_counts/QC--HG00096.csv.gz; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/snvs/QC--HG00096.vcf.gz, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21_ncbi.dict wildcards: vcf=QC, rna=HG00096 resources: tmpdir=/tmp use NCBI format BAM contains read groups (RG), continuing with ASEReadCounter... Using GATK jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar ASEReadCounter -R /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21_ncbi.fa -I /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00096_ncbi.bam -V /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/snvs/QC--HG00096.vcf.gz -L 21 --verbosity ERROR --QUIET true --disable-sequence-dictionary-validation True contig position variantID refAllele altAllele refCount altCount totalCount lowMAPQDepth lowBaseQDepth rawDepth otherBases improperPairs ID 21 9907416 384348 C T 44 1 45 0 0 46 0 1 QC--HG00096 21 27543049 384878 C G 11 11 22 0 0 22 0 0 QC--HG00096 21 35474410 386074 G A 25 15 40 0 0 40 0 0 QC--HG00096 21 35478063 386087 G T 42 51 93 0 0 94 0 1 QC--HG00096 21 38308911 386499 G A 6 6 12 0 0 12 0 0 QC--HG00096 21 40190443 386756 C T 5 3 8 0 0 9 1 0 QC--HG00096 [Mon Jan 30 12:05:26 2023] Finished job 133. 29 of 194 steps (15%) done Select jobs to execute... [Mon Jan 30 12:05:27 2023] rule combineGVCFs: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/sample_vcfs/HG00096/HG00096.g.vcf.gz, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/params/batches/batch_0_batchParams.csv output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/batch_vcfs/batch_0/batch_0_all_samples.g.vcf.gz, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/batch_vcfs/batch_0/batch_0_all_samples.g.vcf.gz.tbi log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/logs/all_haplocaller/batch_0_combineGVCF.log jobid: 145 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/batch_vcfs/batch_0/batch_0_all_samples.g.vcf.gz.tbi, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/batch_vcfs/batch_0/batch_0_all_samples.g.vcf.gz; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/sample_vcfs/HG00096/HG00096.g.vcf.gz wildcards: dataset=batch_0 resources: tmpdir=/tmp [Mon Jan 30 12:05:35 2023] Finished job 145. 30 of 194 steps (15%) done Select jobs to execute... [Mon Jan 30 12:05:35 2023] rule MonoallelicExpression_pipeline_QC_deseq_qc_R: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/allelic_counts/QC--HG00096.csv.gz, Scripts/MonoallelicExpression/pipeline/QC/deseq_qc.R output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/RNA_GT/HG00096.Rds log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/.drop/tmp/MAE/deseq/QC--HG00096.Rds jobid: 132 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/RNA_GT/HG00096.Rds; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/allelic_counts/QC--HG00096.csv.gz wildcards: rna=HG00096 resources: tmpdir=/tmp Message d'avis : Dans qf(0.99, p, m - p) : Production de NaN [Mon Jan 30 12:05:57 2023] Finished job 132. 31 of 194 steps (16%) done Select jobs to execute... [Mon Jan 30 12:05:57 2023] rule mae_allelicCounts: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/Pipeline/chr_NCBI_UCSC.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/Pipeline/chr_UCSC_NCBI.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/snvs/HG00106--HG00106.vcf.gz, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00106.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21.fa, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21.dict, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/MonoallelicExpression/pipeline/MAE/ASEReadCounter.sh output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/allelic_counts/HG00106--HG00106.csv.gz jobid: 119 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/allelic_counts/HG00106--HG00106.csv.gz; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/snvs/HG00106--HG00106.vcf.gz, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21.dict wildcards: vcf=HG00106, rna=HG00106 resources: tmpdir=/tmp use UCSC format BAM contains read groups (RG), continuing with ASEReadCounter... Using GATK jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar ASEReadCounter -R /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21.fa -I /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00106.bam -V /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/snvs/HG00106--HG00106.vcf.gz -L chr21 --verbosity ERROR --QUIET true --disable-sequence-dictionary-validation True contig position variantID refAllele altAllele refCount altCount totalCount lowMAPQDepth lowBaseQDepth rawDepth otherBases improperPairs ID chr21 9907416 rs574952059 C T 32 9 41 0 0 42 1 0 HG00106--HG00106 chr21 15744767 rs11088017 G A 26 27 53 0 0 53 0 0 HG00106--HG00106 chr21 15745390 rs17208186 T C 14 23 37 0 0 38 0 1 HG00106--HG00106 chr21 27269938 rs572842823 T A 167 0 167 0 0 169 0 2 HG00106--HG00106 chr21 27269939 rs371425292 C A 174 0 174 0 0 176 0 2 HG00106--HG00106 chr21 33371123 rs10775648 C T 0 1 1 0 0 1 0 0 HG00106--HG00106 chr21 33371655 rs2070373 G A 0 2 2 0 0 2 0 0 HG00106--HG00106 chr21 33372446 rs2833598 C T 1 2 3 0 0 3 0 0 HG00106--HG00106 chr21 33373172 rs3787694 G C 0 1 1 0 0 1 0 0 HG00106--HG00106 [Mon Jan 30 12:06:11 2023] Finished job 119. 32 of 194 steps (16%) done Select jobs to execute... [Mon Jan 30 12:06:11 2023] rule aberrantExpression_bamStats: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00116.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/Pipeline/chr_UCSC_NCBI.txt output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00116.txt jobid: 25 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00116.txt wildcards: sampleID=HG00116 resources: tmpdir=/tmp [Mon Jan 30 12:06:11 2023] Finished job 25. 33 of 194 steps (17%) done Select jobs to execute... [Mon Jan 30 12:06:11 2023] rule mae_createSNVs: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/Pipeline/chr_NCBI_UCSC.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/Pipeline/chr_UCSC_NCBI.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/dna_vcf/demo_chr21.vcf.gz, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00103.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/MonoallelicExpression/pipeline/MAE/filterSNVs.sh, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/params/snvs/HG00103_snvParams.csv output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/snvs/HG00103--HG00103.vcf.gz, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/snvs/HG00103--HG00103.vcf.gz.tbi jobid: 117 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/snvs/HG00103--HG00103.vcf.gz wildcards: vcf=HG00103, rna=HG00103 resources: tmpdir=/tmp Filter SNVs Lines total/split/realigned/skipped: 6023/0/0/0 Lines total/split/realigned/skipped: 6023/0/0/0 Using GATK jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar SelectVariants -V /tmp/tmp.Hrrx9VHOIB -sn HG00103 -select vc.getGenotype('HG00103').isHet() -O /tmp/tmp.VKEWX6PTiF 12:06:15.547 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 12:06:15.755 INFO SelectVariants - ------------------------------------------------------------ 12:06:15.756 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.3.0.0 12:06:15.756 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/ 12:06:15.756 INFO SelectVariants - Executing as plassard@flash-node10 on Linux v4.19.0-18-amd64 amd64 12:06:15.756 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v11.0.1-internal+0-adhoc..src 12:06:15.757 INFO SelectVariants - Start Date/Time: 30 janvier 2023 à 12:06:15 CET 12:06:15.757 INFO SelectVariants - ------------------------------------------------------------ 12:06:15.757 INFO SelectVariants - ------------------------------------------------------------ 12:06:15.758 INFO SelectVariants - HTSJDK Version: 3.0.1 12:06:15.758 INFO SelectVariants - Picard Version: 2.27.5 12:06:15.758 INFO SelectVariants - Built for Spark Version: 2.4.5 12:06:15.759 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2 12:06:15.759 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 12:06:15.759 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 12:06:15.759 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 12:06:15.759 INFO SelectVariants - Deflater: IntelDeflater 12:06:15.760 INFO SelectVariants - Inflater: IntelInflater 12:06:15.760 INFO SelectVariants - GCS max retries/reopens: 20 12:06:15.760 INFO SelectVariants - Requester pays: disabled 12:06:15.760 INFO SelectVariants - Initializing engine 12:06:15.975 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/tmp.Hrrx9VHOIB 12:06:16.023 INFO SelectVariants - Done initializing engine 12:06:16.159 INFO SelectVariants - Including sample 'HG00103' 12:06:16.165 WARN GATKVariantContextUtils - Can't determine output variant file format from output file extension "VKEWX6PTiF". Defaulting to VCF. 12:06:16.210 INFO ProgressMeter - Starting traversal 12:06:16.211 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute 12:06:16.723 INFO ProgressMeter - 21:47408915 0.0 5538 650254.4 12:06:16.723 INFO ProgressMeter - Traversal complete. Processed 5538 total variants in 0.0 minutes. 12:06:16.775 INFO SelectVariants - Shutting down engine [30 janvier 2023 à 12:06:16 CET] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=2113929216 Using GATK jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar SelectVariants --restrict-alleles-to BIALLELIC -V /tmp/tmp.VKEWX6PTiF -O /tmp/tmp.Hrrx9VHOIB 12:06:20.781 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 12:06:20.984 INFO SelectVariants - ------------------------------------------------------------ 12:06:20.985 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.3.0.0 12:06:20.985 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/ 12:06:20.986 INFO SelectVariants - Executing as plassard@flash-node10 on Linux v4.19.0-18-amd64 amd64 12:06:20.986 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v11.0.1-internal+0-adhoc..src 12:06:20.986 INFO SelectVariants - Start Date/Time: 30 janvier 2023 à 12:06:20 CET 12:06:20.986 INFO SelectVariants - ------------------------------------------------------------ 12:06:20.986 INFO SelectVariants - ------------------------------------------------------------ 12:06:20.987 INFO SelectVariants - HTSJDK Version: 3.0.1 12:06:20.988 INFO SelectVariants - Picard Version: 2.27.5 12:06:20.988 INFO SelectVariants - Built for Spark Version: 2.4.5 12:06:20.988 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2 12:06:20.988 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 12:06:20.988 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 12:06:20.988 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 12:06:20.989 INFO SelectVariants - Deflater: IntelDeflater 12:06:20.989 INFO SelectVariants - Inflater: IntelInflater 12:06:20.989 INFO SelectVariants - GCS max retries/reopens: 20 12:06:20.989 INFO SelectVariants - Requester pays: disabled 12:06:20.989 INFO SelectVariants - Initializing engine 12:06:21.177 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/tmp.VKEWX6PTiF 12:06:21.230 INFO SelectVariants - Done initializing engine 12:06:21.298 WARN GATKVariantContextUtils - Can't determine output variant file format from output file extension "Hrrx9VHOIB". Defaulting to VCF. 12:06:21.335 INFO ProgressMeter - Starting traversal 12:06:21.336 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute 12:06:21.457 INFO ProgressMeter - unmapped 0.0 527 263500.0 12:06:21.457 INFO ProgressMeter - Traversal complete. Processed 527 total variants in 0.0 minutes. 12:06:21.504 INFO SelectVariants - Shutting down engine [30 janvier 2023 à 12:06:21 CET] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=2113929216 converting from NCBI to UCSC format [Mon Jan 30 12:06:21 2023] Finished job 117. 34 of 194 steps (18%) done Select jobs to execute... [Mon Jan 30 12:06:21 2023] rule AberrantExpression_pipeline_Counting_countReads_R: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00096_ncbi.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/count_ranges.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/params/counts/HG00096_countParams.csv, Scripts/AberrantExpression/pipeline/Counting/countReads.R output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00096.Rds log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/.drop/tmp/AE/v29/counts/HG00096.Rds jobid: 13 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00096.Rds; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/count_ranges.Rds wildcards: annotation=v29, sampleID=HG00096 resources: tmpdir=/tmp Message d'avis : Dans .normarg_seqlevelsStyle(value) : more than one seqlevels style supplied, using the 1st one only input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00096_ncbi.bam output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00096.Rds count mode: IntersectionStrict paired end: TRUE inter.feature: FALSE strand: no strand specific: FALSE 21 counting done [1] "2.371891 secs" [1] 37088 [Mon Jan 30 12:06:39 2023] Finished job 13. 35 of 194 steps (18%) done Select jobs to execute... [Mon Jan 30 12:06:39 2023] rule aberrantExpression_bamStats: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00150.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/Pipeline/chr_UCSC_NCBI.txt output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00150.txt jobid: 23 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00150.txt wildcards: sampleID=HG00150 resources: tmpdir=/tmp [Mon Jan 30 12:06:39 2023] Finished job 23. 36 of 194 steps (19%) done Select jobs to execute... [Mon Jan 30 12:06:39 2023] rule aberrantSplicing_dependency: output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/html/aberrant-splicing-pipeline_dep.svg jobid: 107 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/html/aberrant-splicing-pipeline_dep.svg resources: tmpdir=/tmp WARNING: Less than 30 IDs in DROP_GROUP outrider WARNING: Less than 30 IDs in DROP_GROUP outrider_external WARNING: Less than 30 IDs in DROP_GROUP fraser WARNING: Less than 30 IDs in DROP_GROUP fraser_external check for missing R packages Structuring dependencies... Dependencies file generated at: /tmp/tmp1s5vqrql Building DAG of jobs... Error: Directory cannot be locked. This usually means that another Snakemake instance is running on this directory. Another possibility is that a previous run exited unexpectedly. [Mon Jan 30 12:06:44 2023] Finished job 107. 37 of 194 steps (19%) done Select jobs to execute... [Mon Jan 30 12:06:44 2023] rule AberrantExpression_pipeline_Counting_countReads_R: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00126.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/count_ranges.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/params/counts/HG00126_countParams.csv, Scripts/AberrantExpression/pipeline/Counting/countReads.R output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00126.Rds log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/.drop/tmp/AE/v29/counts/HG00126.Rds jobid: 9 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00126.Rds; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/count_ranges.Rds wildcards: annotation=v29, sampleID=HG00126 resources: tmpdir=/tmp input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00126.bam output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00126.Rds count mode: IntersectionStrict paired end: TRUE inter.feature: FALSE strand: no strand specific: FALSE chr21 counting done [1] "1.597361 secs" [1] 44651 [Mon Jan 30 12:06:58 2023] Finished job 9. 38 of 194 steps (20%) done Select jobs to execute... [Mon Jan 30 12:06:58 2023] rule AberrantExpression_pipeline_Counting_countReads_R: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00149.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/count_ranges.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/params/counts/HG00149_countParams.csv, Scripts/AberrantExpression/pipeline/Counting/countReads.R output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00149.Rds log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/.drop/tmp/AE/v29/counts/HG00149.Rds jobid: 8 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00149.Rds; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/count_ranges.Rds wildcards: annotation=v29, sampleID=HG00149 resources: tmpdir=/tmp input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00149.bam output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00149.Rds count mode: IntersectionStrict paired end: TRUE inter.feature: FALSE strand: no strand specific: FALSE chr21 counting done [1] "1.55693 secs" [1] 39384 [Mon Jan 30 12:07:11 2023] Finished job 8. 39 of 194 steps (20%) done Select jobs to execute... [Mon Jan 30 12:07:11 2023] rule mae_createSNVs: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/Pipeline/chr_NCBI_UCSC.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/Pipeline/chr_UCSC_NCBI.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/qc_vcf_1000G.vcf.gz, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00106.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/MonoallelicExpression/pipeline/MAE/filterSNVs.sh, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/params/snvs/HG00106_snvParams.csv output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/snvs/QC--HG00106.vcf.gz, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/snvs/QC--HG00106.vcf.gz.tbi jobid: 128 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/snvs/QC--HG00106.vcf.gz wildcards: vcf=QC, rna=HG00106 resources: tmpdir=/tmp Filter SNVs Lines total/split/realigned/skipped: 26402/0/0/0 Lines total/split/realigned/skipped: 26402/0/0/0 Using GATK jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar SelectVariants -V /tmp/tmp.PoTnAOiC3o -O /tmp/tmp.vO0n8tEFM7 12:07:16.944 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 12:07:17.156 INFO SelectVariants - ------------------------------------------------------------ 12:07:17.156 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.3.0.0 12:07:17.157 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/ 12:07:17.157 INFO SelectVariants - Executing as plassard@flash-node10 on Linux v4.19.0-18-amd64 amd64 12:07:17.157 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v11.0.1-internal+0-adhoc..src 12:07:17.158 INFO SelectVariants - Start Date/Time: 30 janvier 2023 à 12:07:16 CET 12:07:17.158 INFO SelectVariants - ------------------------------------------------------------ 12:07:17.158 INFO SelectVariants - ------------------------------------------------------------ 12:07:17.159 INFO SelectVariants - HTSJDK Version: 3.0.1 12:07:17.159 INFO SelectVariants - Picard Version: 2.27.5 12:07:17.159 INFO SelectVariants - Built for Spark Version: 2.4.5 12:07:17.159 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2 12:07:17.160 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 12:07:17.160 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 12:07:17.160 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 12:07:17.160 INFO SelectVariants - Deflater: IntelDeflater 12:07:17.160 INFO SelectVariants - Inflater: IntelInflater 12:07:17.160 INFO SelectVariants - GCS max retries/reopens: 20 12:07:17.161 INFO SelectVariants - Requester pays: disabled 12:07:17.161 INFO SelectVariants - Initializing engine 12:07:17.382 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/tmp.PoTnAOiC3o 12:07:17.406 INFO SelectVariants - Done initializing engine 12:07:17.418 WARN GATKVariantContextUtils - Can't determine output variant file format from output file extension "vO0n8tEFM7". Defaulting to VCF. 12:07:17.434 INFO ProgressMeter - Starting traversal 12:07:17.435 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute 12:07:18.336 INFO ProgressMeter - chr22:30163526 0.0 26402 1760133.3 12:07:18.337 INFO ProgressMeter - Traversal complete. Processed 26402 total variants in 0.0 minutes. 12:07:18.542 INFO SelectVariants - Shutting down engine [30 janvier 2023 à 12:07:18 CET] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.03 minutes. Runtime.totalMemory()=2113929216 Using GATK jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar SelectVariants --restrict-alleles-to BIALLELIC -V /tmp/tmp.vO0n8tEFM7 -O /tmp/tmp.PoTnAOiC3o 12:07:22.352 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 12:07:22.555 INFO SelectVariants - ------------------------------------------------------------ 12:07:22.556 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.3.0.0 12:07:22.556 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/ 12:07:22.556 INFO SelectVariants - Executing as plassard@flash-node10 on Linux v4.19.0-18-amd64 amd64 12:07:22.556 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v11.0.1-internal+0-adhoc..src 12:07:22.556 INFO SelectVariants - Start Date/Time: 30 janvier 2023 à 12:07:22 CET 12:07:22.557 INFO SelectVariants - ------------------------------------------------------------ 12:07:22.557 INFO SelectVariants - ------------------------------------------------------------ 12:07:22.558 INFO SelectVariants - HTSJDK Version: 3.0.1 12:07:22.558 INFO SelectVariants - Picard Version: 2.27.5 12:07:22.558 INFO SelectVariants - Built for Spark Version: 2.4.5 12:07:22.558 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2 12:07:22.558 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 12:07:22.559 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 12:07:22.560 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 12:07:22.560 INFO SelectVariants - Deflater: IntelDeflater 12:07:22.560 INFO SelectVariants - Inflater: IntelInflater 12:07:22.560 INFO SelectVariants - GCS max retries/reopens: 20 12:07:22.560 INFO SelectVariants - Requester pays: disabled 12:07:22.560 INFO SelectVariants - Initializing engine 12:07:22.753 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/tmp.vO0n8tEFM7 12:07:22.791 INFO SelectVariants - Done initializing engine 12:07:22.807 WARN GATKVariantContextUtils - Can't determine output variant file format from output file extension "PoTnAOiC3o". Defaulting to VCF. 12:07:22.818 INFO ProgressMeter - Starting traversal 12:07:22.818 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute 12:07:23.701 INFO ProgressMeter - chr22:30163526 0.0 26402 1798093.1 12:07:23.702 INFO ProgressMeter - Traversal complete. Processed 26402 total variants in 0.0 minutes. 12:07:23.913 INFO SelectVariants - Shutting down engine [30 janvier 2023 à 12:07:23 CET] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.03 minutes. Runtime.totalMemory()=3191865344 [Mon Jan 30 12:07:24 2023] Finished job 128. 40 of 194 steps (21%) done Select jobs to execute... [Mon Jan 30 12:07:24 2023] rule mae_allelicCounts: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/Pipeline/chr_NCBI_UCSC.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/Pipeline/chr_UCSC_NCBI.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/snvs/QC--HG00106.vcf.gz, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00106.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21.fa, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21.dict, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/MonoallelicExpression/pipeline/MAE/ASEReadCounter.sh output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/allelic_counts/QC--HG00106.csv.gz jobid: 127 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/allelic_counts/QC--HG00106.csv.gz; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21.dict, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/snvs/QC--HG00106.vcf.gz wildcards: vcf=QC, rna=HG00106 resources: tmpdir=/tmp use UCSC format BAM contains read groups (RG), continuing with ASEReadCounter... Using GATK jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar ASEReadCounter -R /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21.fa -I /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00106.bam -V /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/snvs/QC--HG00106.vcf.gz -L chr21 --verbosity ERROR --QUIET true --disable-sequence-dictionary-validation True contig position variantID refAllele altAllele refCount altCount totalCount lowMAPQDepth lowBaseQDepth rawDepth otherBases improperPairs ID chr21 9907416 384348 C T 32 9 41 0 0 42 1 0 QC--HG00106 chr21 27543049 384878 C G 7 0 7 0 0 7 0 0 QC--HG00106 chr21 35474410 386074 G A 0 26 26 0 0 26 0 0 QC--HG00106 chr21 35478063 386087 G T 44 56 100 0 0 100 0 0 QC--HG00106 chr21 38308911 386499 G A 8 0 8 0 0 8 0 0 QC--HG00106 chr21 40190443 386756 C T 7 0 7 0 0 7 0 0 QC--HG00106 [Mon Jan 30 12:07:39 2023] Finished job 127. 41 of 194 steps (21%) done Select jobs to execute... [Mon Jan 30 12:07:39 2023] rule AberrantSplicing_pipeline_Counting_00_define_datasets_from_anno_R: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/sample_annotation.tsv, Scripts/AberrantSplicing/pipeline/Counting/00_define_datasets_from_anno.R output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/annotations/fraser_external.tsv, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/html/AberrantSplicing/annotations/fraser_external.html log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/.drop/tmp/AS/fraser_external/00_defineDataset.Rds jobid: 80 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/annotations/fraser_external.tsv wildcards: dataset=fraser_external resources: tmpdir=/tmp Le chargement a nécessité le package : knitr Le chargement a nécessité le package : rmarkdown [1] TRUE processing file: /tmp/Rtmp3ZLuJP/fileaf7d42be3e6b/00_define_datasets_from_anno.spin.Rmd | | | 0% | |.......... | 11% | |.................... | 22% (unnamed-chunk-1) | |............................... | 33% (input) | |......................................... | 44% (dataset name) | |................................................... | 56% | |............................................................. | 67% (unnamed-chunk-2) | |........................................................................ | 78% | |.................................................................................. | 89% (savetable) | |............................................................................................| 100% output file: /tmp/Rtmp3ZLuJP/fileaf7d42be3e6b/00_define_datasets_from_anno.knit.md /shared/ifs/home/plassard/Conda/envs_conda_flash/drop_env/bin/pandoc +RTS -K512m -RTS /tmp/Rtmp3ZLuJP/fileaf7d42be3e6b/00_define_datasets_from_anno.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/Rtmp3ZLuJP/fileaf7d795b7f75/fraser_external.html --lua-filter /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/lib/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/lib/R/library/rmarkdown/rmarkdown/lua/latex-div.lua --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/lib/R/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --css lib/add_content_table.css --css lib/leo_style.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/Rtmp3ZLuJP/rmarkdown-straf7d435f0a16.html --variable code_folding=hide --variable source_embed=00_define_datasets_from_anno.R --include-after-body /tmp/Rtmp3ZLuJP/fileaf7d4d4b9717.html --variable code_menu=1 Output created: /tmp/Rtmp3ZLuJP/fileaf7d795b7f75/fraser_external.html [1] TRUE TRUE TRUE [Mon Jan 30 12:08:11 2023] Finished job 80. 42 of 194 steps (22%) done Select jobs to execute... [Mon Jan 30 12:08:11 2023] rule AberrantSplicing_pipeline_Counting_01_0_countRNA_init_R: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/annotations/fraser_external.tsv, Scripts/AberrantSplicing/pipeline/Counting/01_0_countRNA_init.R output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/savedObjects/raw-local-fraser_external/fds-object.RDS, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/fds.done log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/.drop/tmp/AS/fraser_external/01_0_init.Rds jobid: 79 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/fds.done; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/annotations/fraser_external.tsv wildcards: dataset=fraser_external resources: tmpdir=/tmp Load packages Mon Jan 30 12:08:45 2023: Writing final FRASER object ('/shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets//savedObjects/raw-local-fraser_external/fds-object.RDS'). Mon Jan 30 12:08:45 2023: FRASER object initialized for fraser_external [1] TRUE [Mon Jan 30 12:08:45 2023] Finished job 79. 43 of 194 steps (22%) done Select jobs to execute... [Mon Jan 30 12:08:45 2023] rule AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/fds.done, Scripts/AberrantSplicing/pipeline/Counting/01_1_countRNA_splitReads_samplewise.R output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/sample_tmp/splitCounts/sample_HG00116.done log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/.drop/tmp/AS/fraser_external/splitReads/HG00116.Rds jobid: 85 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/sample_tmp/splitCounts/sample_HG00116.done; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/fds.done wildcards: dataset=fraser_external, sample_id=HG00116 resources: tmpdir=/tmp Load packages Le chargement a nécessité le package : rtracklayer Mon Jan 30 12:09:13 2023: Count split reads for sample: HG00116 Message d'avis : Dans .infer_intron_strand(unoriented_intron_motif) : For some junctions, the dinucleotides found at the intron boundaries don't match any of the natural intron motifs stored in predefined character vector 'NATURAL_INTRON_MOTIFS'. For these junctions, the intron_motif and intron_strand metadata columns were set to NA and *, respectively. Mon Jan 30 12:09:17 2023: fraser_external, HG00116 no. splice junctions (split counts) = 477 [1] TRUE [Mon Jan 30 12:09:17 2023] Finished job 85. 44 of 194 steps (23%) done Select jobs to execute... [Mon Jan 30 12:09:17 2023] rule AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/fds.done, Scripts/AberrantSplicing/pipeline/Counting/01_1_countRNA_splitReads_samplewise.R output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/sample_tmp/splitCounts/sample_HG00149.done log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/.drop/tmp/AS/fraser_external/splitReads/HG00149.Rds jobid: 81 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/sample_tmp/splitCounts/sample_HG00149.done; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/fds.done wildcards: dataset=fraser_external, sample_id=HG00149 resources: tmpdir=/tmp Load packages Le chargement a nécessité le package : rtracklayer Mon Jan 30 12:09:49 2023: Count split reads for sample: HG00149 Mon Jan 30 12:09:52 2023: fraser_external, HG00149 no. splice junctions (split counts) = 523 [1] TRUE [Mon Jan 30 12:09:52 2023] Finished job 81. 45 of 194 steps (23%) done Select jobs to execute... [Mon Jan 30 12:09:53 2023] rule AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/fds.done, Scripts/AberrantSplicing/pipeline/Counting/01_1_countRNA_splitReads_samplewise.R output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/sample_tmp/splitCounts/sample_HG00126.done log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/.drop/tmp/AS/fraser_external/splitReads/HG00126.Rds jobid: 82 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/sample_tmp/splitCounts/sample_HG00126.done; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/fds.done wildcards: dataset=fraser_external, sample_id=HG00126 resources: tmpdir=/tmp Load packages Le chargement a nécessité le package : rtracklayer Mon Jan 30 12:10:24 2023: Count split reads for sample: HG00126 Mon Jan 30 12:10:28 2023: fraser_external, HG00126 no. splice junctions (split counts) = 511 [1] TRUE [Mon Jan 30 12:10:28 2023] Finished job 82. 46 of 194 steps (24%) done Select jobs to execute... [Mon Jan 30 12:10:28 2023] rule AberrantExpression_pipeline_Counting_countReads_R: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00103.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/count_ranges.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/params/counts/HG00103_countParams.csv, Scripts/AberrantExpression/pipeline/Counting/countReads.R output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00103.Rds log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/.drop/tmp/AE/v29/counts/HG00103.Rds jobid: 11 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00103.Rds; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/count_ranges.Rds wildcards: annotation=v29, sampleID=HG00103 resources: tmpdir=/tmp input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00103.bam output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00103.Rds count mode: IntersectionStrict paired end: TRUE inter.feature: FALSE strand: no strand specific: FALSE chr21 counting done [1] "2.408817 secs" [1] 36655 [Mon Jan 30 12:10:46 2023] Finished job 11. 47 of 194 steps (24%) done Select jobs to execute... [Mon Jan 30 12:10:46 2023] rule AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/fds.done, Scripts/AberrantSplicing/pipeline/Counting/01_1_countRNA_splitReads_samplewise.R output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/sample_tmp/splitCounts/sample_HG00106.done log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/.drop/tmp/AS/fraser_external/splitReads/HG00106.Rds jobid: 86 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/sample_tmp/splitCounts/sample_HG00106.done; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/fds.done wildcards: dataset=fraser_external, sample_id=HG00106 resources: tmpdir=/tmp Load packages Le chargement a nécessité le package : rtracklayer Mon Jan 30 12:11:23 2023: Count split reads for sample: HG00106 Message d'avis : Dans .infer_intron_strand(unoriented_intron_motif) : For some junctions, the dinucleotides found at the intron boundaries don't match any of the natural intron motifs stored in predefined character vector 'NATURAL_INTRON_MOTIFS'. For these junctions, the intron_motif and intron_strand metadata columns were set to NA and *, respectively. Mon Jan 30 12:11:27 2023: fraser_external, HG00106 no. splice junctions (split counts) = 500 [1] TRUE [Mon Jan 30 12:11:27 2023] Finished job 86. 48 of 194 steps (25%) done Select jobs to execute... [Mon Jan 30 12:11:28 2023] rule AberrantExpression_pipeline_aberrant_expression_readme_md: input: Scripts/AberrantExpression/pipeline/aberrant_expression_readme.md output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/html/Scripts_AberrantExpression_pipeline_aberrant_expression_readme.html jobid: 32 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/html/Scripts_AberrantExpression_pipeline_aberrant_expression_readme.html resources: tmpdir=/tmp [WARNING] Deprecated: --self-contained. use --embed-resources --standalone [Mon Jan 30 12:11:28 2023] Finished job 32. 49 of 194 steps (25%) done Select jobs to execute... [Mon Jan 30 12:11:28 2023] rule aberrantExpression_bamStats: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00106.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/Pipeline/chr_UCSC_NCBI.txt output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00106.txt jobid: 26 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00106.txt wildcards: sampleID=HG00106 resources: tmpdir=/tmp [Mon Jan 30 12:11:28 2023] Finished job 26. 50 of 194 steps (26%) done Select jobs to execute... [Mon Jan 30 12:11:28 2023] rule AberrantExpression_pipeline_Counting_countReads_R: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00111.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/count_ranges.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/params/counts/HG00111_countParams.csv, Scripts/AberrantExpression/pipeline/Counting/countReads.R output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00111.Rds log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/.drop/tmp/AE/v29/counts/HG00111.Rds jobid: 6 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00111.Rds; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/count_ranges.Rds wildcards: annotation=v29, sampleID=HG00111 resources: tmpdir=/tmp input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00111.bam output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00111.Rds count mode: IntersectionStrict paired end: TRUE inter.feature: FALSE strand: no strand specific: FALSE chr21 counting done [1] "2.763848 secs" [1] 49223 [Mon Jan 30 12:11:46 2023] Finished job 6. 51 of 194 steps (26%) done Select jobs to execute... [Mon Jan 30 12:11:46 2023] rule AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/fds.done, Scripts/AberrantSplicing/pipeline/Counting/01_1_countRNA_splitReads_samplewise.R output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/sample_tmp/splitCounts/sample_HG00132.done log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/.drop/tmp/AS/fraser_external/splitReads/HG00132.Rds jobid: 87 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/sample_tmp/splitCounts/sample_HG00132.done; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/fds.done wildcards: dataset=fraser_external, sample_id=HG00132 resources: tmpdir=/tmp Load packages Le chargement a nécessité le package : rtracklayer Mon Jan 30 12:12:19 2023: Count split reads for sample: HG00132 Message d'avis : Dans .infer_intron_strand(unoriented_intron_motif) : For some junctions, the dinucleotides found at the intron boundaries don't match any of the natural intron motifs stored in predefined character vector 'NATURAL_INTRON_MOTIFS'. For these junctions, the intron_motif and intron_strand metadata columns were set to NA and *, respectively. Mon Jan 30 12:12:23 2023: fraser_external, HG00132 no. splice junctions (split counts) = 469 [1] TRUE [Mon Jan 30 12:12:24 2023] Finished job 87. 52 of 194 steps (27%) done Select jobs to execute... [Mon Jan 30 12:12:24 2023] rule AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/fds.done, Scripts/AberrantSplicing/pipeline/Counting/01_1_countRNA_splitReads_samplewise.R output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/sample_tmp/splitCounts/sample_HG00176.done log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/.drop/tmp/AS/fraser_external/splitReads/HG00176.Rds jobid: 83 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/sample_tmp/splitCounts/sample_HG00176.done; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/fds.done wildcards: dataset=fraser_external, sample_id=HG00176 resources: tmpdir=/tmp Load packages Le chargement a nécessité le package : rtracklayer Mon Jan 30 12:12:58 2023: Count split reads for sample: HG00176 Message d'avis : Dans .infer_intron_strand(unoriented_intron_motif) : For some junctions, the dinucleotides found at the intron boundaries don't match any of the natural intron motifs stored in predefined character vector 'NATURAL_INTRON_MOTIFS'. For these junctions, the intron_motif and intron_strand metadata columns were set to NA and *, respectively. Mon Jan 30 12:13:01 2023: fraser_external, HG00176 no. splice junctions (split counts) = 469 [1] TRUE [Mon Jan 30 12:13:01 2023] Finished job 83. 53 of 194 steps (27%) done Select jobs to execute... [Mon Jan 30 12:13:02 2023] rule mae_allelicCounts: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/Pipeline/chr_NCBI_UCSC.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/Pipeline/chr_UCSC_NCBI.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/snvs/HG00103--HG00103.vcf.gz, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00103.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21.fa, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21.dict, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/MonoallelicExpression/pipeline/MAE/ASEReadCounter.sh output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/allelic_counts/HG00103--HG00103.csv.gz jobid: 116 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/allelic_counts/HG00103--HG00103.csv.gz; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/snvs/HG00103--HG00103.vcf.gz, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21.dict wildcards: vcf=HG00103, rna=HG00103 resources: tmpdir=/tmp use UCSC format BAM contains read groups (RG), continuing with ASEReadCounter... Using GATK jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar ASEReadCounter -R /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21.fa -I /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00103.bam -V /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/snvs/HG00103--HG00103.vcf.gz -L chr21 --verbosity ERROR --QUIET true --disable-sequence-dictionary-validation True contig position variantID refAllele altAllele refCount altCount totalCount lowMAPQDepth lowBaseQDepth rawDepth otherBases improperPairs ID chr21 9907416 rs574952059 C T 29 2 31 0 0 42 1 10 HG00103--HG00103 chr21 15744389 rs3178188 T C 29 20 49 0 0 50 1 0 HG00103--HG00103 chr21 15744530 rs17002662 A G 22 22 44 0 0 44 0 0 HG00103--HG00103 chr21 15744594 rs17306192 T C 16 17 33 0 0 33 0 0 HG00103--HG00103 chr21 15745106 rs2822638 C T 15 19 34 0 0 36 0 2 HG00103--HG00103 chr21 15745176 rs2822639 A G 18 16 34 0 0 34 0 0 HG00103--HG00103 chr21 15745269 rs12479 T C 20 28 48 0 0 49 0 1 HG00103--HG00103 chr21 15745410 rs147050202 A C 10 14 24 0 0 24 0 0 HG00103--HG00103 chr21 16334027 rs76206782 T A 10 5 15 0 0 15 0 0 HG00103--HG00103 [Mon Jan 30 12:13:17 2023] Finished job 116. 54 of 194 steps (28%) done Select jobs to execute... [Mon Jan 30 12:13:17 2023] rule MonoallelicExpression_pipeline_MAE_deseq_mae_R: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/allelic_counts/HG00103--HG00103.csv.gz, Scripts/MonoallelicExpression/pipeline/MAE/deseq_mae.R output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_results/mae/samples/HG00103--HG00103_res.Rds log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/.drop/tmp/MAE/deseq/HG00103--HG00103.Rds jobid: 115 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_results/mae/samples/HG00103--HG00103_res.Rds; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/allelic_counts/HG00103--HG00103.csv.gz wildcards: vcf=HG00103, rna=HG00103 resources: tmpdir=/tmp Started with deseq [1] "Running DESeq..." Message d'avis : Dans qf(0.99, p, m - p) : Production de NaN [Mon Jan 30 12:13:42 2023] Finished job 115. 55 of 194 steps (28%) done Select jobs to execute... [Mon Jan 30 12:13:43 2023] rule MonoallelicExpression_pipeline_QC_deseq_qc_R: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/allelic_counts/QC--HG00106.csv.gz, Scripts/MonoallelicExpression/pipeline/QC/deseq_qc.R output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/RNA_GT/HG00106.Rds log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/.drop/tmp/MAE/deseq/QC--HG00106.Rds jobid: 126 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/RNA_GT/HG00106.Rds; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/allelic_counts/QC--HG00106.csv.gz wildcards: rna=HG00106 resources: tmpdir=/tmp Message d'avis : Dans qf(0.99, p, m - p) : Production de NaN [Mon Jan 30 12:14:07 2023] Finished job 126. 56 of 194 steps (29%) done Select jobs to execute... [Mon Jan 30 12:14:07 2023] rule AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/fds.done, Scripts/AberrantSplicing/pipeline/Counting/01_1_countRNA_splitReads_samplewise.R output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/sample_tmp/splitCounts/sample_HG00150.done log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/.drop/tmp/AS/fraser_external/splitReads/HG00150.Rds jobid: 84 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/sample_tmp/splitCounts/sample_HG00150.done; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/fds.done wildcards: dataset=fraser_external, sample_id=HG00150 resources: tmpdir=/tmp Load packages Le chargement a nécessité le package : rtracklayer Mon Jan 30 12:14:41 2023: Count split reads for sample: HG00150 Mon Jan 30 12:14:45 2023: fraser_external, HG00150 no. splice junctions (split counts) = 472 [1] TRUE [Mon Jan 30 12:14:45 2023] Finished job 84. 57 of 194 steps (29%) done Select jobs to execute... [Mon Jan 30 12:14:45 2023] rule mae_allelicCounts: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/Pipeline/chr_NCBI_UCSC.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/Pipeline/chr_UCSC_NCBI.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/snvs/HG00096--HG00096.vcf.gz, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00096_ncbi.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21_ncbi.fa, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21_ncbi.dict, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/MonoallelicExpression/pipeline/MAE/ASEReadCounter.sh output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/allelic_counts/HG00096--HG00096.csv.gz jobid: 112 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/allelic_counts/HG00096--HG00096.csv.gz; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/snvs/HG00096--HG00096.vcf.gz, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21_ncbi.dict wildcards: vcf=HG00096, rna=HG00096 resources: tmpdir=/tmp use NCBI format BAM contains read groups (RG), continuing with ASEReadCounter... Using GATK jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar ASEReadCounter -R /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21_ncbi.fa -I /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00096_ncbi.bam -V /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/snvs/HG00096--HG00096.vcf.gz -L 21 --verbosity ERROR --QUIET true --disable-sequence-dictionary-validation True contig position variantID refAllele altAllele refCount altCount totalCount lowMAPQDepth lowBaseQDepth rawDepth otherBases improperPairs ID 21 9907416 rs574952059 C T 44 1 45 0 0 46 0 1 HG00096--HG00096 21 15744767 rs11088017 G A 30 37 67 0 0 68 0 1 HG00096--HG00096 21 27543049 rs459543 C G 11 11 22 0 0 22 0 0 HG00096--HG00096 21 33370900 rs9305483 T C 0 1 1 0 0 1 0 0 HG00096--HG00096 21 33372446 rs2833598 C T 0 1 1 0 0 1 0 0 HG00096--HG00096 21 33372749 rs3746856 T C 0 1 1 0 0 1 0 0 HG00096--HG00096 21 33373930 rs3787697 A C 0 1 1 0 0 1 0 0 HG00096--HG00096 21 33374102 rs3578 C T 0 2 2 0 0 2 0 0 HG00096--HG00096 21 33374112 rs3576 G A 0 2 2 0 0 2 0 0 HG00096--HG00096 [Mon Jan 30 12:15:04 2023] Finished job 112. 58 of 194 steps (30%) done Select jobs to execute... [Mon Jan 30 12:15:04 2023] rule MonoallelicExpression_pipeline_MAE_deseq_mae_R: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/allelic_counts/HG00096--HG00096.csv.gz, Scripts/MonoallelicExpression/pipeline/MAE/deseq_mae.R output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_results/mae/samples/HG00096--HG00096_res.Rds log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/.drop/tmp/MAE/deseq/HG00096--HG00096.Rds jobid: 111 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_results/mae/samples/HG00096--HG00096_res.Rds; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/allelic_counts/HG00096--HG00096.csv.gz wildcards: vcf=HG00096, rna=HG00096 resources: tmpdir=/tmp Started with deseq [1] "Running DESeq..." Message d'avis : Dans qf(0.99, p, m - p) : Production de NaN [Mon Jan 30 12:15:31 2023] Finished job 111. 59 of 194 steps (30%) done Select jobs to execute... [Mon Jan 30 12:15:31 2023] rule aberrantExpression_dependency: output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/html/aberrant-expression-pipeline_dep.svg jobid: 40 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/html/aberrant-expression-pipeline_dep.svg resources: tmpdir=/tmp WARNING: Less than 30 IDs in DROP_GROUP outrider WARNING: Less than 30 IDs in DROP_GROUP outrider_external WARNING: Less than 30 IDs in DROP_GROUP fraser WARNING: Less than 30 IDs in DROP_GROUP fraser_external check for missing R packages Structuring dependencies... Dependencies file generated at: /tmp/tmpuc10olw7 Building DAG of jobs... Error: Directory cannot be locked. This usually means that another Snakemake instance is running on this directory. Another possibility is that a previous run exited unexpectedly. [Mon Jan 30 12:15:49 2023] Finished job 40. 60 of 194 steps (31%) done Select jobs to execute... [Mon Jan 30 12:15:49 2023] rule AberrantExpression_pipeline_Counting_countReads_R: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00150.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/count_ranges.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/params/counts/HG00150_countParams.csv, Scripts/AberrantExpression/pipeline/Counting/countReads.R output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00150.Rds log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/.drop/tmp/AE/v29/counts/HG00150.Rds jobid: 12 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00150.Rds; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/count_ranges.Rds wildcards: annotation=v29, sampleID=HG00150 resources: tmpdir=/tmp input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00150.bam output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00150.Rds count mode: IntersectionStrict paired end: TRUE inter.feature: FALSE strand: no strand specific: FALSE chr21 counting done [1] "2.302631 secs" [1] 45629 [Mon Jan 30 12:16:06 2023] Finished job 12. 61 of 194 steps (31%) done Select jobs to execute... [Mon Jan 30 12:16:06 2023] rule AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/fds.done, Scripts/AberrantSplicing/pipeline/Counting/01_1_countRNA_splitReads_samplewise.R output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/sample_tmp/splitCounts/sample_HG00111.done log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/.drop/tmp/AS/fraser_external/splitReads/HG00111.Rds jobid: 78 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/sample_tmp/splitCounts/sample_HG00111.done; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/fds.done wildcards: dataset=fraser_external, sample_id=HG00111 resources: tmpdir=/tmp Load packages Le chargement a nécessité le package : rtracklayer Mon Jan 30 12:16:42 2023: Count split reads for sample: HG00111 Message d'avis : Dans .infer_intron_strand(unoriented_intron_motif) : For some junctions, the dinucleotides found at the intron boundaries don't match any of the natural intron motifs stored in predefined character vector 'NATURAL_INTRON_MOTIFS'. For these junctions, the intron_motif and intron_strand metadata columns were set to NA and *, respectively. Mon Jan 30 12:16:46 2023: fraser_external, HG00111 no. splice junctions (split counts) = 468 [1] TRUE [Mon Jan 30 12:16:46 2023] Finished job 78. 62 of 194 steps (32%) done Select jobs to execute... [Mon Jan 30 12:16:47 2023] rule AberrantSplicing_pipeline_Counting_01_2_countRNA_splitReads_merge_R: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/sample_tmp/splitCounts/sample_HG00111.done, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/sample_tmp/splitCounts/sample_HG00149.done, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/sample_tmp/splitCounts/sample_HG00126.done, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/sample_tmp/splitCounts/sample_HG00176.done, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/sample_tmp/splitCounts/sample_HG00150.done, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/sample_tmp/splitCounts/sample_HG00116.done, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/sample_tmp/splitCounts/sample_HG00106.done, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/sample_tmp/splitCounts/sample_HG00132.done, Scripts/AberrantSplicing/pipeline/Counting/01_2_countRNA_splitReads_merge.R output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/savedObjects/raw-local-fraser_external/rawCountsJ.h5, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/gRanges_splitCounts.rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/gRanges_NonSplitCounts.rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/spliceSites_splitCounts.rds log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/.drop/tmp/AS/fraser_external/01_2_splitReadsMerge.Rds jobid: 77 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/gRanges_splitCounts.rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/spliceSites_splitCounts.rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/gRanges_NonSplitCounts.rds; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/sample_tmp/splitCounts/sample_HG00116.done, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/sample_tmp/splitCounts/sample_HG00150.done, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/sample_tmp/splitCounts/sample_HG00111.done, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/sample_tmp/splitCounts/sample_HG00132.done, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/sample_tmp/splitCounts/sample_HG00106.done, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/sample_tmp/splitCounts/sample_HG00126.done, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/sample_tmp/splitCounts/sample_HG00176.done, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/sample_tmp/splitCounts/sample_HG00149.done wildcards: dataset=fraser_external resources: tmpdir=/tmp Load packages Mon Jan 30 12:17:25 2023: Start counting the split reads ... Mon Jan 30 12:17:25 2023: Using existing split read counts for sample: HG00106 Mon Jan 30 12:17:25 2023: Using existing split read counts for sample: HG00111 Mon Jan 30 12:17:25 2023: Using existing split read counts for sample: HG00116 Mon Jan 30 12:17:25 2023: Using existing split read counts for sample: HG00126 Mon Jan 30 12:17:25 2023: Using existing split read counts for sample: HG00132 Mon Jan 30 12:17:26 2023: Using existing split read counts for sample: HG00149 Mon Jan 30 12:17:26 2023: Using existing split read counts for sample: HG00150 Mon Jan 30 12:17:26 2023: Using existing split read counts for sample: HG00176 Mon Jan 30 12:17:30 2023 : count ranges need to be merged ... Mon Jan 30 12:17:32 2023: Create splice site indices ... Mon Jan 30 12:17:33 2023: Writing split counts to folder: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/savedObjects/raw-local-fraser_external/splitCounts Mon Jan 30 12:17:33 2023: Create splice site indices ... Mon Jan 30 12:17:33 2023: fraser_external total no. splice junctions = 1086 [Mon Jan 30 12:17:33 2023] Finished job 77. 63 of 194 steps (32%) done Select jobs to execute... [Mon Jan 30 12:17:34 2023] rule AberrantSplicing_pipeline_Counting_01_3_countRNA_nonSplitReads_samplewise_R: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/spliceSites_splitCounts.rds, Scripts/AberrantSplicing/pipeline/Counting/01_3_countRNA_nonSplitReads_samplewise.R output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/sample_tmp/nonSplitCounts/sample_HG00116.done log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/.drop/tmp/AS/fraser_external/nonsplitReads/HG00116.Rds jobid: 92 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/sample_tmp/nonSplitCounts/sample_HG00116.done; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/spliceSites_splitCounts.rds wildcards: dataset=fraser_external, sample_id=HG00116 resources: tmpdir=/tmp Load packages Mon Jan 30 12:18:08 2023: Count non spliced reads for sample: HG00116 ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ Rsubread 2.12.0 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || || || HG00116.bam || || || || Paired-end : yes || || Count read pairs : yes || || Annotation : R data.frame || || Dir for temp files : /shared/ngs/illumina/plassard/Project/RNAseq ... || || Threads : 1 || || Level : meta-feature level || || Multimapping reads : counted || || Multi-overlapping reads : counted || || Min overlapping bases : 10 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file .Rsubread_UserProvidedAnnotation_pid46737 ... || || Features : 377 || || Meta-features : 377 || || Chromosomes/contigs : 1 || || || || Process BAM file HG00116.bam... || || Paired-end reads are included. || || Total alignments : 32671 || || Successfully assigned alignments : 990 (3.0%) || || Running time : 0.00 minutes || || || || Write the final count table. || || Write the read assignment summary. || || || \\============================================================================// Saving splice site cache ... Mon Jan 30 12:18:08 2023: fraser_external, HG00116 no. splice junctions (non split counts) = 377 [1] TRUE [Mon Jan 30 12:18:09 2023] Finished job 92. 64 of 194 steps (33%) done Select jobs to execute... [Mon Jan 30 12:18:09 2023] rule AberrantSplicing_pipeline_Counting_01_3_countRNA_nonSplitReads_samplewise_R: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/spliceSites_splitCounts.rds, Scripts/AberrantSplicing/pipeline/Counting/01_3_countRNA_nonSplitReads_samplewise.R output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/sample_tmp/nonSplitCounts/sample_HG00149.done log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/.drop/tmp/AS/fraser_external/nonsplitReads/HG00149.Rds jobid: 88 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/sample_tmp/nonSplitCounts/sample_HG00149.done; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/spliceSites_splitCounts.rds wildcards: dataset=fraser_external, sample_id=HG00149 resources: tmpdir=/tmp Load packages Mon Jan 30 12:18:42 2023: Count non spliced reads for sample: HG00149 ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ Rsubread 2.12.0 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || || || HG00149.bam || || || || Paired-end : yes || || Count read pairs : yes || || Annotation : R data.frame || || Dir for temp files : /shared/ngs/illumina/plassard/Project/RNAseq ... || || Threads : 1 || || Level : meta-feature level || || Multimapping reads : counted || || Multi-overlapping reads : counted || || Min overlapping bases : 10 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file .Rsubread_UserProvidedAnnotation_pid46811 ... || || Features : 377 || || Meta-features : 377 || || Chromosomes/contigs : 1 || || || || Process BAM file HG00149.bam... || || Paired-end reads are included. || || Total alignments : 35133 || || Successfully assigned alignments : 1350 (3.8%) || || Running time : 0.00 minutes || || || || Write the final count table. || || Write the read assignment summary. || || || \\============================================================================// Saving splice site cache ... Mon Jan 30 12:18:43 2023: fraser_external, HG00149 no. splice junctions (non split counts) = 377 [1] TRUE [Mon Jan 30 12:18:43 2023] Finished job 88. 65 of 194 steps (34%) done Select jobs to execute... [Mon Jan 30 12:18:44 2023] rule AberrantSplicing_pipeline_Counting_01_3_countRNA_nonSplitReads_samplewise_R: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/spliceSites_splitCounts.rds, Scripts/AberrantSplicing/pipeline/Counting/01_3_countRNA_nonSplitReads_samplewise.R output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/sample_tmp/nonSplitCounts/sample_HG00126.done log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/.drop/tmp/AS/fraser_external/nonsplitReads/HG00126.Rds jobid: 89 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/sample_tmp/nonSplitCounts/sample_HG00126.done; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/spliceSites_splitCounts.rds wildcards: dataset=fraser_external, sample_id=HG00126 resources: tmpdir=/tmp Load packages Mon Jan 30 12:19:18 2023: Count non spliced reads for sample: HG00126 ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ Rsubread 2.12.0 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || || || HG00126.bam || || || || Paired-end : yes || || Count read pairs : yes || || Annotation : R data.frame || || Dir for temp files : /shared/ngs/illumina/plassard/Project/RNAseq ... || || Threads : 1 || || Level : meta-feature level || || Multimapping reads : counted || || Multi-overlapping reads : counted || || Min overlapping bases : 10 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file .Rsubread_UserProvidedAnnotation_pid46880 ... || || Features : 377 || || Meta-features : 377 || || Chromosomes/contigs : 1 || || || || Process BAM file HG00126.bam... || || Paired-end reads are included. || || Total alignments : 38521 || || Successfully assigned alignments : 1264 (3.3%) || || Running time : 0.01 minutes || || || || Write the final count table. || || Write the read assignment summary. || || || \\============================================================================// Saving splice site cache ... Mon Jan 30 12:19:18 2023: fraser_external, HG00126 no. splice junctions (non split counts) = 377 [1] TRUE [Mon Jan 30 12:19:18 2023] Finished job 89. 66 of 194 steps (34%) done Select jobs to execute... [Mon Jan 30 12:19:19 2023] localrule dependencyGraph: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/html/aberrant-expression-pipeline_dep.svg, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/html/aberrant-splicing-pipeline_dep.svg, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/html/mae-pipeline_dep.svg, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/html/rvc-pipeline_dep.svg output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/html/dependency.done jobid: 195 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/html/dependency.done; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/html/aberrant-splicing-pipeline_dep.svg, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/html/mae-pipeline_dep.svg, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/html/rvc-pipeline_dep.svg, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/html/aberrant-expression-pipeline_dep.svg resources: tmpdir=/tmp Touching output file /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/html/dependency.done. [Mon Jan 30 12:19:19 2023] Finished job 195. 67 of 194 steps (35%) done Select jobs to execute... [Mon Jan 30 12:19:19 2023] rule AberrantExpression_pipeline_Counting_countReads_R: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00106.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/count_ranges.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/params/counts/HG00106_countParams.csv, Scripts/AberrantExpression/pipeline/Counting/countReads.R output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00106.Rds log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/.drop/tmp/AE/v29/counts/HG00106.Rds jobid: 15 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00106.Rds; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/count_ranges.Rds wildcards: annotation=v29, sampleID=HG00106 resources: tmpdir=/tmp input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00106.bam output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00106.Rds count mode: IntersectionStrict paired end: TRUE inter.feature: FALSE strand: no strand specific: FALSE chr21 counting done [1] "1.563934 secs" [1] 39291 [Mon Jan 30 12:19:35 2023] Finished job 15. 68 of 194 steps (35%) done Select jobs to execute... [Mon Jan 30 12:19:35 2023] rule AberrantExpression_pipeline_Counting_mergeCounts_R: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00111.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00149.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00126.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00176.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00103.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00150.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00096.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00116.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00106.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00132.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/count_ranges.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/params/merge/outrider_mergeParams.csv, Scripts/AberrantExpression/pipeline/Counting/mergeCounts.R output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/outrider/outrider/total_counts.Rds log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/.drop/tmp/AE/v29/outrider/merge.Rds jobid: 5 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/outrider/outrider/total_counts.Rds; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00126.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00176.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00111.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00096.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00116.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/count_ranges.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00150.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00106.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00149.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00103.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00132.Rds wildcards: annotation=v29, dataset=outrider resources: tmpdir=/tmp read 10 files [Mon Jan 30 12:19:50 2023] Finished job 5. 69 of 194 steps (36%) done Select jobs to execute... [Mon Jan 30 12:19:51 2023] rule AberrantExpression_pipeline_Counting_filterCounts_R: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/outrider/outrider/total_counts.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/preprocess/v29/txdb.db, Scripts/AberrantExpression/pipeline/Counting/filterCounts.R output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_results/aberrant_expression/v29/outrider/outrider/ods_unfitted.Rds log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/.drop/tmp/AE/v29/outrider/filter.Rds jobid: 4 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_results/aberrant_expression/v29/outrider/outrider/ods_unfitted.Rds; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/outrider/outrider/total_counts.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/preprocess/v29/txdb.db wildcards: annotation=v29, dataset=outrider resources: tmpdir=/tmp Message d'avis : Dans OutriderDataSet(counts) : No sampleID was specified. We will generate a generic one. 644 genes did not pass the filter. This is 80% of the genes. [Mon Jan 30 12:20:17 2023] Finished job 4. 70 of 194 steps (36%) done Select jobs to execute... [Mon Jan 30 12:20:18 2023] rule AberrantExpression_pipeline_OUTRIDER_runOutrider_R: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_results/aberrant_expression/v29/outrider/outrider/ods_unfitted.Rds, Scripts/AberrantExpression/pipeline/OUTRIDER/runOutrider.R output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_results/aberrant_expression/v29/outrider/outrider/ods.Rds log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/.drop/tmp/AE/v29/outrider/runOUTRIDER.Rds jobid: 35 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_results/aberrant_expression/v29/outrider/outrider/ods.Rds; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_results/aberrant_expression/v29/outrider/outrider/ods_unfitted.Rds wildcards: annotation=v29, dataset=outrider resources: tmpdir=/tmp Mon Jan 30 12:20:53 2023: SizeFactor estimation ... Mon Jan 30 12:20:53 2023: Controlling for confounders ... Mon Jan 30 12:20:53 2023: Using the autoencoder implementation for controlling. [1] "Mon Jan 30 12:20:53 2023: Initial PCA loss: 3.0480807090553" [1] "Mon Jan 30 12:20:55 2023: Iteration: 1 loss: 2.55811808733088" [1] "Mon Jan 30 12:20:55 2023: Iteration: 2 loss: 2.55653399195789" [1] "Mon Jan 30 12:20:56 2023: Iteration: 3 loss: 2.55536587019002" [1] "Mon Jan 30 12:20:57 2023: Iteration: 4 loss: 2.55449319265868" [1] "Mon Jan 30 12:20:57 2023: Iteration: 5 loss: 2.55369964178543" [1] "Mon Jan 30 12:20:58 2023: Iteration: 6 loss: 2.55302452937001" [1] "Mon Jan 30 12:20:59 2023: Iteration: 7 loss: 2.55264140914583" [1] "Mon Jan 30 12:21:00 2023: Iteration: 8 loss: 2.55228068304973" [1] "Mon Jan 30 12:21:00 2023: Iteration: 9 loss: 2.55154177863456" [1] "Mon Jan 30 12:21:01 2023: Iteration: 10 loss: 2.55107192118911" [1] "Mon Jan 30 12:21:02 2023: Iteration: 11 loss: 2.54954214042724" [1] "Mon Jan 30 12:21:03 2023: Iteration: 12 loss: 2.54948378811495" [1] "Mon Jan 30 12:21:03 2023: Iteration: 13 loss: 2.54943032741133" [1] "Mon Jan 30 12:21:03 2023: Iteration: 14 loss: 2.54941292378367" [1] "Mon Jan 30 12:21:04 2023: Iteration: 15 loss: 2.54924725660606" Time difference of 10.05531 secs [1] "Mon Jan 30 12:21:04 2023: 15 Final nb-AE loss: 2.54924725660606" Mon Jan 30 12:21:04 2023: Used the autoencoder implementation for controlling. Mon Jan 30 12:21:04 2023: P-value calculation ... Mon Jan 30 12:21:04 2023: Zscore calculation ... [1] "Evaluation loss: 0.017150435416462 for q=5" Mon Jan 30 12:21:04 2023: SizeFactor estimation ... Mon Jan 30 12:21:04 2023: Controlling for confounders ... Mon Jan 30 12:21:04 2023: Using the autoencoder implementation for controlling. [1] "Mon Jan 30 12:21:05 2023: Initial PCA loss: 3.0845556564237" [1] "Mon Jan 30 12:21:06 2023: Iteration: 1 loss: 2.66395551290414" [1] "Mon Jan 30 12:21:06 2023: Iteration: 2 loss: 2.66155022496144" [1] "Mon Jan 30 12:21:07 2023: Iteration: 3 loss: 2.66020366962798" [1] "Mon Jan 30 12:21:08 2023: Iteration: 4 loss: 2.65884414776526" [1] "Mon Jan 30 12:21:08 2023: Iteration: 5 loss: 2.65778224155268" [1] "Mon Jan 30 12:21:09 2023: Iteration: 6 loss: 2.65727536354192" [1] "Mon Jan 30 12:21:09 2023: Iteration: 7 loss: 2.65649983682889" [1] "Mon Jan 30 12:21:10 2023: Iteration: 8 loss: 2.65605953433494" [1] "Mon Jan 30 12:21:11 2023: Iteration: 9 loss: 2.65563577135871" [1] "Mon Jan 30 12:21:11 2023: Iteration: 10 loss: 2.65497041572818" [1] "Mon Jan 30 12:21:12 2023: Iteration: 11 loss: 2.65460140093735" [1] "Mon Jan 30 12:21:12 2023: Iteration: 12 loss: 2.65432513832311" [1] "Mon Jan 30 12:21:13 2023: Iteration: 13 loss: 2.65395272363309" [1] "Mon Jan 30 12:21:13 2023: Iteration: 14 loss: 2.65361556325181" [1] "Mon Jan 30 12:21:14 2023: Iteration: 15 loss: 2.6533759362191" Time difference of 8.356832 secs [1] "Mon Jan 30 12:21:14 2023: 15 Final nb-AE loss: 2.6533759362191" Mon Jan 30 12:21:14 2023: Used the autoencoder implementation for controlling. Mon Jan 30 12:21:14 2023: P-value calculation ... Mon Jan 30 12:21:14 2023: Zscore calculation ... [1] "Evaluation loss: 0.0214471353538572 for q=4" Mon Jan 30 12:21:14 2023: SizeFactor estimation ... Mon Jan 30 12:21:14 2023: Controlling for confounders ... Mon Jan 30 12:21:14 2023: Using the autoencoder implementation for controlling. [1] "Mon Jan 30 12:21:14 2023: Initial PCA loss: 3.11968866910155" [1] "Mon Jan 30 12:21:15 2023: Iteration: 1 loss: 2.76511818226318" [1] "Mon Jan 30 12:21:16 2023: Iteration: 2 loss: 2.76136383468325" [1] "Mon Jan 30 12:21:17 2023: Iteration: 3 loss: 2.75902140476441" [1] "Mon Jan 30 12:21:17 2023: Iteration: 4 loss: 2.75678585243418" [1] "Mon Jan 30 12:21:18 2023: Iteration: 5 loss: 2.7548581413846" [1] "Mon Jan 30 12:21:18 2023: Iteration: 6 loss: 2.75221200079154" [1] "Mon Jan 30 12:21:19 2023: Iteration: 7 loss: 2.75051260245144" [1] "Mon Jan 30 12:21:19 2023: Iteration: 8 loss: 2.7487343199323" [1] "Mon Jan 30 12:21:20 2023: Iteration: 9 loss: 2.74705092123778" [1] "Mon Jan 30 12:21:20 2023: Iteration: 10 loss: 2.7458699198188" [1] "Mon Jan 30 12:21:21 2023: Iteration: 11 loss: 2.74505059599402" [1] "Mon Jan 30 12:21:21 2023: Iteration: 12 loss: 2.744939673895" [1] "Mon Jan 30 12:21:22 2023: Iteration: 13 loss: 2.74483811692356" [1] "Mon Jan 30 12:21:22 2023: Iteration: 14 loss: 2.74425314098336" [1] "Mon Jan 30 12:21:23 2023: Iteration: 15 loss: 2.74377967923243" Time difference of 8.32986 secs [1] "Mon Jan 30 12:21:23 2023: 15 Final nb-AE loss: 2.74377967923243" Mon Jan 30 12:21:23 2023: Used the autoencoder implementation for controlling. Mon Jan 30 12:21:23 2023: P-value calculation ... Mon Jan 30 12:21:23 2023: Zscore calculation ... [1] "Evaluation loss: 0.0209938460270327 for q=3" Mon Jan 30 12:21:23 2023: SizeFactor estimation ... Mon Jan 30 12:21:24 2023: Controlling for confounders ... Using provided q with: 4 Mon Jan 30 12:21:24 2023: Using the autoencoder implementation for controlling. [1] "Mon Jan 30 12:21:25 2023: Initial PCA loss: 3.0578866564983" [1] "Mon Jan 30 12:21:34 2023: Iteration: 1 loss: 2.63260188759247" [1] "Mon Jan 30 12:21:40 2023: Iteration: 2 loss: 2.62852994711954" [1] "Mon Jan 30 12:21:45 2023: Iteration: 3 loss: 2.62553491988016" [1] "Mon Jan 30 12:21:50 2023: Iteration: 4 loss: 2.62351657874535" [1] "Mon Jan 30 12:21:55 2023: Iteration: 5 loss: 2.62229695868298" [1] "Mon Jan 30 12:21:59 2023: Iteration: 6 loss: 2.62117651333932" [1] "Mon Jan 30 12:22:04 2023: Iteration: 7 loss: 2.61922393028289" [1] "Mon Jan 30 12:22:09 2023: Iteration: 8 loss: 2.61866173798602" [1] "Mon Jan 30 12:22:15 2023: Iteration: 9 loss: 2.61799942342301" [1] "Mon Jan 30 12:22:19 2023: Iteration: 10 loss: 2.6175649841018" [1] "Mon Jan 30 12:22:24 2023: Iteration: 11 loss: 2.61708460871024" [1] "Mon Jan 30 12:22:29 2023: Iteration: 12 loss: 2.61703511996359" [1] "Mon Jan 30 12:22:34 2023: Iteration: 13 loss: 2.61658885958245" [1] "Mon Jan 30 12:22:39 2023: Iteration: 14 loss: 2.61625060343763" [1] "Mon Jan 30 12:22:44 2023: Iteration: 15 loss: 2.61586725860883" Time difference of 1.228021 mins [1] "Mon Jan 30 12:22:44 2023: 15 Final nb-AE loss: 2.61586725860883" Mon Jan 30 12:22:44 2023: Used the autoencoder implementation for controlling. Mon Jan 30 12:22:44 2023: P-value calculation ... Mon Jan 30 12:22:47 2023: Zscore calculation ... outrider fitting finished [Mon Jan 30 12:22:47 2023] Finished job 35. 71 of 194 steps (37%) done Select jobs to execute... [Mon Jan 30 12:22:47 2023] rule MonoallelicExpression_pipeline_MAE_deseq_mae_R: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/allelic_counts/HG00106--HG00106.csv.gz, Scripts/MonoallelicExpression/pipeline/MAE/deseq_mae.R output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_results/mae/samples/HG00106--HG00106_res.Rds log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/.drop/tmp/MAE/deseq/HG00106--HG00106.Rds jobid: 118 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_results/mae/samples/HG00106--HG00106_res.Rds; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/allelic_counts/HG00106--HG00106.csv.gz wildcards: vcf=HG00106, rna=HG00106 resources: tmpdir=/tmp Started with deseq [1] "Running DESeq..." Message d'avis : Dans qf(0.99, p, m - p) : Production de NaN [Mon Jan 30 12:23:13 2023] Finished job 118. 72 of 194 steps (37%) done Select jobs to execute... [Mon Jan 30 12:23:13 2023] rule MonoallelicExpression_pipeline_MAE_Results_R: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_results/mae/samples/HG00096--HG00096_res.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_results/mae/samples/HG00103--HG00103_res.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_results/mae/samples/HG00106--HG00106_res.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/gene_name_mapping_v29.tsv, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/params/results/mae_resultParams.csv, Scripts/MonoallelicExpression/pipeline/MAE/Results.R output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_results/mae/mae/MAE_results_all_v29.tsv.gz, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_results/mae/mae/MAE_results_v29.tsv, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_results/mae/mae/MAE_results_v29_rare.tsv, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/html/MonoallelicExpression/mae--v29_results.html log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/.drop/tmp/MAE/mae/v29_results.Rds jobid: 110 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/html/MonoallelicExpression/mae--v29_results.html, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_results/mae/mae/MAE_results_v29.tsv; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/gene_name_mapping_v29.tsv, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_results/mae/samples/HG00103--HG00103_res.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_results/mae/samples/HG00096--HG00096_res.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_results/mae/samples/HG00106--HG00106_res.Rds wildcards: dataset=mae, annotation=v29 resources: tmpdir=/tmp Le chargement a nécessité le package : knitr Le chargement a nécessité le package : rmarkdown [1] TRUE processing file: /tmp/RtmpEWeIUq/fileb94c667c4074/Results.spin.Rmd | | | 0% | |....... | 8% | |.............. | 15% (unnamed-chunk-1) | |..................... | 23% | |............................ | 31% (unnamed-chunk-2) | |................................... | 38% | |.......................................... | 46% (unnamed-chunk-3) | |.................................................. | 54% | |......................................................... | 62% (unnamed-chunk-4) | |................................................................ | 69% | |....................................................................... | 77% (unnamed-chunk-5) | |.............................................................................. | 85% | |..................................................................................... | 92% (unnamed-chunk-6) | |............................................................................................| 100% output file: /tmp/RtmpEWeIUq/fileb94c667c4074/Results.knit.md /shared/ifs/home/plassard/Conda/envs_conda_flash/drop_env/bin/pandoc +RTS -K512m -RTS /tmp/RtmpEWeIUq/fileb94c667c4074/Results.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpEWeIUq/fileb94c5815465d/mae--v29_results.html --lua-filter /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/lib/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/lib/R/library/rmarkdown/rmarkdown/lua/latex-div.lua --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/lib/R/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --css lib/add_content_table.css --css lib/leo_style.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpEWeIUq/rmarkdown-strb94c30a7d27a.html --variable code_folding=hide --variable code_menu=1 Output created: /tmp/RtmpEWeIUq/fileb94c5815465d/mae--v29_results.html [1] TRUE TRUE TRUE TRUE [Mon Jan 30 12:23:33 2023] Finished job 110. 73 of 194 steps (38%) done Select jobs to execute... [Mon Jan 30 12:23:34 2023] rule AberrantSplicing_pipeline_Counting_01_3_countRNA_nonSplitReads_samplewise_R: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/spliceSites_splitCounts.rds, Scripts/AberrantSplicing/pipeline/Counting/01_3_countRNA_nonSplitReads_samplewise.R output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/sample_tmp/nonSplitCounts/sample_HG00132.done log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/.drop/tmp/AS/fraser_external/nonsplitReads/HG00132.Rds jobid: 94 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/sample_tmp/nonSplitCounts/sample_HG00132.done; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/spliceSites_splitCounts.rds wildcards: dataset=fraser_external, sample_id=HG00132 resources: tmpdir=/tmp Load packages Mon Jan 30 12:24:06 2023: Count non spliced reads for sample: HG00132 ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ Rsubread 2.12.0 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || || || HG00132.bam || || || || Paired-end : yes || || Count read pairs : yes || || Annotation : R data.frame || || Dir for temp files : /shared/ngs/illumina/plassard/Project/RNAseq ... || || Threads : 1 || || Level : meta-feature level || || Multimapping reads : counted || || Multi-overlapping reads : counted || || Min overlapping bases : 10 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file .Rsubread_UserProvidedAnnotation_pid47527 ... || || Features : 377 || || Meta-features : 377 || || Chromosomes/contigs : 1 || || || || Process BAM file HG00132.bam... || || Paired-end reads are included. || || Total alignments : 42377 || || Successfully assigned alignments : 1268 (3.0%) || || Running time : 0.01 minutes || || || || Write the final count table. || || Write the read assignment summary. || || || \\============================================================================// Saving splice site cache ... Mon Jan 30 12:24:06 2023: fraser_external, HG00132 no. splice junctions (non split counts) = 377 [1] TRUE [Mon Jan 30 12:24:06 2023] Finished job 94. 74 of 194 steps (38%) done Select jobs to execute... [Mon Jan 30 12:24:07 2023] rule aberrantExpression_bamStats: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00103.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/Pipeline/chr_UCSC_NCBI.txt output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00103.txt jobid: 22 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00103.txt wildcards: sampleID=HG00103 resources: tmpdir=/tmp [Mon Jan 30 12:24:07 2023] Finished job 22. 75 of 194 steps (39%) done Select jobs to execute... [Mon Jan 30 12:24:07 2023] rule genotypeGVCFs: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/batch_vcfs/batch_0/batch_0_all_samples.g.vcf.gz, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/batch_vcfs/batch_0/batch_0_all_samples.g.vcf.gz.tbi, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/params/batches/batch_0_batchParams.csv output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/batch_vcfs/batch_0/batch_0_all_samples.genotyped.raw.vcf.gz, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/batch_vcfs/batch_0/batch_0_all_samples.genotyped.raw.vcf.gz.tbi log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/logs/all_haplocaller/batch_0_genotypeGVCFs.log jobid: 144 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/batch_vcfs/batch_0/batch_0_all_samples.genotyped.raw.vcf.gz, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/batch_vcfs/batch_0/batch_0_all_samples.genotyped.raw.vcf.gz.tbi; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/batch_vcfs/batch_0/batch_0_all_samples.g.vcf.gz.tbi, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/batch_vcfs/batch_0/batch_0_all_samples.g.vcf.gz wildcards: dataset=batch_0 resources: tmpdir=/tmp [Mon Jan 30 12:24:16 2023] Finished job 144. 76 of 194 steps (39%) done Select jobs to execute... [Mon Jan 30 12:24:16 2023] rule filterVCF: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/batch_vcfs/batch_0/batch_0_all_samples.genotyped.raw.vcf.gz, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/batch_vcfs/batch_0/batch_0_all_samples.genotyped.raw.vcf.gz.tbi output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/batch_vcfs/batch_0/TEMP.batch_0_all_samples.genotyped.filtered.vcf.gz, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/batch_vcfs/batch_0/TEMP.batch_0_all_samples.genotyped.filtered.vcf.gz.tbi, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/batch_vcfs/batch_0/batch_0_all_samples.genotyped.filtered.vcf.gz, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/batch_vcfs/batch_0/batch_0_all_samples.genotyped.filtered.vcf.gz.tbi log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/logs/all_haplocaller/batch_0_filterVariants.log jobid: 143 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/batch_vcfs/batch_0/batch_0_all_samples.genotyped.filtered.vcf.gz, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/batch_vcfs/batch_0/batch_0_all_samples.genotyped.filtered.vcf.gz.tbi; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/batch_vcfs/batch_0/batch_0_all_samples.genotyped.raw.vcf.gz, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/batch_vcfs/batch_0/batch_0_all_samples.genotyped.raw.vcf.gz.tbi wildcards: dataset=batch_0 resources: tmpdir=/tmp [Mon Jan 30 12:24:22 2023] Finished job 143. 77 of 194 steps (40%) done Removing temporary output /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/batch_vcfs/batch_0/batch_0_all_samples.genotyped.raw.vcf.gz. Removing temporary output /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/batch_vcfs/batch_0/batch_0_all_samples.genotyped.raw.vcf.gz.tbi. Removing temporary output /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/batch_vcfs/batch_0/TEMP.batch_0_all_samples.genotyped.filtered.vcf.gz. Removing temporary output /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/batch_vcfs/batch_0/TEMP.batch_0_all_samples.genotyped.filtered.vcf.gz.tbi. Select jobs to execute... [Mon Jan 30 12:24:22 2023] rule MonoallelicExpression_pipeline_MAE_Datasets_R: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/html/MonoallelicExpression/mae--v29_results.html, Scripts/MonoallelicExpression/pipeline/MAE/Datasets.R output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/html/Scripts_MonoallelicExpression_pipeline_MAE_Datasets.html log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/.drop/tmp/MAE/overview.Rds jobid: 109 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/html/Scripts_MonoallelicExpression_pipeline_MAE_Datasets.html; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/html/MonoallelicExpression/mae--v29_results.html resources: tmpdir=/tmp Le chargement a nécessité le package : knitr Le chargement a nécessité le package : rmarkdown [1] TRUE processing file: /tmp/Rtmpr1IKAb/filebb23488314d3/Datasets.spin.Rmd | | | 0% | |....................... | 25% | |.............................................. | 50% (unnamed-chunk-1) | |..................................................................... | 75% (unnamed-chunk-2) | |............................................................................................| 100% output file: /tmp/Rtmpr1IKAb/filebb23488314d3/Datasets.knit.md /shared/ifs/home/plassard/Conda/envs_conda_flash/drop_env/bin/pandoc +RTS -K512m -RTS /tmp/Rtmpr1IKAb/filebb23488314d3/Datasets.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/Rtmpr1IKAb/filebb234f833914/Scripts_MonoallelicExpression_pipeline_MAE_Datasets.html --lua-filter /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/lib/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/lib/R/library/rmarkdown/rmarkdown/lua/latex-div.lua --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/lib/R/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --css lib/add_content_table.css --css lib/leo_style.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/Rtmpr1IKAb/rmarkdown-strbb2320fb5365.html --variable code_folding=hide --variable code_menu=1 Output created: /tmp/Rtmpr1IKAb/filebb234f833914/Scripts_MonoallelicExpression_pipeline_MAE_Datasets.html [1] TRUE TRUE TRUE [Mon Jan 30 12:24:26 2023] Finished job 109. 78 of 194 steps (40%) done Select jobs to execute... [Mon Jan 30 12:24:26 2023] rule AberrantSplicing_pipeline_Counting_01_3_countRNA_nonSplitReads_samplewise_R: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/spliceSites_splitCounts.rds, Scripts/AberrantSplicing/pipeline/Counting/01_3_countRNA_nonSplitReads_samplewise.R output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/sample_tmp/nonSplitCounts/sample_HG00150.done log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/.drop/tmp/AS/fraser_external/nonsplitReads/HG00150.Rds jobid: 91 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/sample_tmp/nonSplitCounts/sample_HG00150.done; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/spliceSites_splitCounts.rds wildcards: dataset=fraser_external, sample_id=HG00150 resources: tmpdir=/tmp Load packages Mon Jan 30 12:25:01 2023: Count non spliced reads for sample: HG00150 ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ Rsubread 2.12.0 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || || || HG00150.bam || || || || Paired-end : yes || || Count read pairs : yes || || Annotation : R data.frame || || Dir for temp files : /shared/ngs/illumina/plassard/Project/RNAseq ... || || Threads : 1 || || Level : meta-feature level || || Multimapping reads : counted || || Multi-overlapping reads : counted || || Min overlapping bases : 10 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file .Rsubread_UserProvidedAnnotation_pid47974 ... || || Features : 377 || || Meta-features : 377 || || Chromosomes/contigs : 1 || || || || Process BAM file HG00150.bam... || || Paired-end reads are included. || || Total alignments : 37872 || || Successfully assigned alignments : 1178 (3.1%) || || Running time : 0.00 minutes || || || || Write the final count table. || || Write the read assignment summary. || || || \\============================================================================// Saving splice site cache ... Mon Jan 30 12:25:02 2023: fraser_external, HG00150 no. splice junctions (non split counts) = 377 [1] TRUE [Mon Jan 30 12:25:02 2023] Finished job 91. 79 of 194 steps (41%) done Select jobs to execute... [Mon Jan 30 12:25:02 2023] rule AberrantSplicing_pipeline_Counting_01_3_countRNA_nonSplitReads_samplewise_R: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/spliceSites_splitCounts.rds, Scripts/AberrantSplicing/pipeline/Counting/01_3_countRNA_nonSplitReads_samplewise.R output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/sample_tmp/nonSplitCounts/sample_HG00106.done log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/.drop/tmp/AS/fraser_external/nonsplitReads/HG00106.Rds jobid: 93 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/sample_tmp/nonSplitCounts/sample_HG00106.done; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/spliceSites_splitCounts.rds wildcards: dataset=fraser_external, sample_id=HG00106 resources: tmpdir=/tmp Load packages Mon Jan 30 12:25:35 2023: Count non spliced reads for sample: HG00106 ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ Rsubread 2.12.0 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || || || HG00106.bam || || || || Paired-end : yes || || Count read pairs : yes || || Annotation : R data.frame || || Dir for temp files : /shared/ngs/illumina/plassard/Project/RNAseq ... || || Threads : 1 || || Level : meta-feature level || || Multimapping reads : counted || || Multi-overlapping reads : counted || || Min overlapping bases : 10 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file .Rsubread_UserProvidedAnnotation_pid48055 ... || || Features : 377 || || Meta-features : 377 || || Chromosomes/contigs : 1 || || || || Process BAM file HG00106.bam... || || Paired-end reads are included. || || Total alignments : 33433 || || Successfully assigned alignments : 1152 (3.4%) || || Running time : 0.00 minutes || || || || Write the final count table. || || Write the read assignment summary. || || || \\============================================================================// Saving splice site cache ... Mon Jan 30 12:25:35 2023: fraser_external, HG00106 no. splice junctions (non split counts) = 377 [1] TRUE [Mon Jan 30 12:25:36 2023] Finished job 93. 80 of 194 steps (41%) done Select jobs to execute... [Mon Jan 30 12:25:36 2023] rule rnaVariantCalling_pipeline_rvc_readme_md: input: Scripts/rnaVariantCalling/pipeline/rvc_readme.md output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/html/Scripts_rnaVariantCalling_pipeline_rvc_readme.html jobid: 181 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/html/Scripts_rnaVariantCalling_pipeline_rvc_readme.html resources: tmpdir=/tmp [WARNING] Deprecated: --self-contained. use --embed-resources --standalone [Mon Jan 30 12:25:36 2023] Finished job 181. 81 of 194 steps (42%) done Select jobs to execute... [Mon Jan 30 12:25:36 2023] rule MonoallelicExpression_pipeline_mae_readme_md: input: Scripts/MonoallelicExpression/pipeline/mae_readme.md output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/html/Scripts_MonoallelicExpression_pipeline_mae_readme.html jobid: 122 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/html/Scripts_MonoallelicExpression_pipeline_mae_readme.html resources: tmpdir=/tmp [WARNING] Deprecated: --self-contained. use --embed-resources --standalone [Mon Jan 30 12:25:36 2023] Finished job 122. 82 of 194 steps (42%) done Select jobs to execute... [Mon Jan 30 12:25:36 2023] rule AberrantSplicing_pipeline_Counting_01_3_countRNA_nonSplitReads_samplewise_R: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/spliceSites_splitCounts.rds, Scripts/AberrantSplicing/pipeline/Counting/01_3_countRNA_nonSplitReads_samplewise.R output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/sample_tmp/nonSplitCounts/sample_HG00176.done log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/.drop/tmp/AS/fraser_external/nonsplitReads/HG00176.Rds jobid: 90 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/sample_tmp/nonSplitCounts/sample_HG00176.done; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-fraser_external/spliceSites_splitCounts.rds wildcards: dataset=fraser_external, sample_id=HG00176 resources: tmpdir=/tmp Load packages Mon Jan 30 12:26:10 2023: Count non spliced reads for sample: HG00176 ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ Rsubread 2.12.0 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || || || HG00176.bam || || || || Paired-end : yes || || Count read pairs : yes || || Annotation : R data.frame || || Dir for temp files : /shared/ngs/illumina/plassard/Project/RNAseq ... || || Threads : 1 || || Level : meta-feature level || || Multimapping reads : counted || || Multi-overlapping reads : counted || || Min overlapping bases : 10 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file .Rsubread_UserProvidedAnnotation_pid48218 ... || || Features : 377 || || Meta-features : 377 || || Chromosomes/contigs : 1 || || || || Process BAM file HG00176.bam... || || Paired-end reads are included. || || Total alignments : 31505 || || Successfully assigned alignments : 927 (2.9%) || || Running time : 0.00 minutes || || || || Write the final count table. || || Write the read assignment summary. || || || \\============================================================================// Saving splice site cache ... Mon Jan 30 12:26:11 2023: fraser_external, HG00176 no. splice junctions (non split counts) = 377 [1] TRUE [Mon Jan 30 12:26:11 2023] Finished job 90. 83 of 194 steps (43%) done Select jobs to execute... [Mon Jan 30 12:26:12 2023] rule AberrantExpression_pipeline_Counting_mergeCounts_R: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00111.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00149.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00126.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00176.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00150.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00116.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00106.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00132.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/external_count_data/geneCounts.tsv.gz, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/count_ranges.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/params/merge/outrider_external_mergeParams.csv, Scripts/AberrantExpression/pipeline/Counting/mergeCounts.R output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/outrider/outrider_external/total_counts.Rds log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/.drop/tmp/AE/v29/outrider_external/merge.Rds jobid: 30 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/outrider/outrider_external/total_counts.Rds; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00126.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00176.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00111.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00116.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/count_ranges.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00150.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00106.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00149.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/counts/HG00132.Rds wildcards: annotation=v29, dataset=outrider_external resources: tmpdir=/tmp HG00178 HG00181 ENSG00000141956.13_3 453 479 ENSG00000141959.16_1 5569 4506 ENSG00000142149.8_3 23 6 ENSG00000142156.14_2 5 8 ENSG00000142166.12_3 1792 1843 ENSG00000142168.14_2 2893 1980 read 9 files [Mon Jan 30 12:26:29 2023] Finished job 30. 84 of 194 steps (43%) done Select jobs to execute... [Mon Jan 30 12:26:29 2023] rule AberrantExpression_pipeline_Counting_filterCounts_R: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/outrider/outrider_external/total_counts.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/preprocess/v29/txdb.db, Scripts/AberrantExpression/pipeline/Counting/filterCounts.R output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_results/aberrant_expression/v29/outrider/outrider_external/ods_unfitted.Rds log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/.drop/tmp/AE/v29/outrider_external/filter.Rds jobid: 29 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_results/aberrant_expression/v29/outrider/outrider_external/ods_unfitted.Rds; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/preprocess/v29/txdb.db, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/outrider/outrider_external/total_counts.Rds wildcards: annotation=v29, dataset=outrider_external resources: tmpdir=/tmp Message d'avis : Dans OutriderDataSet(counts) : No sampleID was specified. We will generate a generic one. 416 genes did not pass the filter. This is 51.7% of the genes. [Mon Jan 30 12:26:55 2023] Finished job 29. 85 of 194 steps (44%) done Select jobs to execute... [Mon Jan 30 12:26:56 2023] rule sortIndexRepeatMask: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/repeat_mask_chr21.bed output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/repeat_mask_chr21_sorted.bed, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/repeat_mask_chr21_sorted.bed.idx jobid: 155 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/repeat_mask_chr21_sorted.bed resources: tmpdir=/tmp Using GATK jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Djava.io.tmpdir=/tmp -jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar IndexFeatureFile -I /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/repeat_mask_chr21_sorted.bed 12:27:01.621 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 12:27:01.943 INFO IndexFeatureFile - ------------------------------------------------------------ 12:27:01.944 INFO IndexFeatureFile - The Genome Analysis Toolkit (GATK) v4.3.0.0 12:27:01.944 INFO IndexFeatureFile - For support and documentation go to https://software.broadinstitute.org/gatk/ 12:27:01.944 INFO IndexFeatureFile - Executing as plassard@flash-node10 on Linux v4.19.0-18-amd64 amd64 12:27:01.944 INFO IndexFeatureFile - Java runtime: OpenJDK 64-Bit Server VM v11.0.1-internal+0-adhoc..src 12:27:01.945 INFO IndexFeatureFile - Start Date/Time: 30 janvier 2023 à 12:27:01 CET 12:27:01.945 INFO IndexFeatureFile - ------------------------------------------------------------ 12:27:01.945 INFO IndexFeatureFile - ------------------------------------------------------------ 12:27:01.946 INFO IndexFeatureFile - HTSJDK Version: 3.0.1 12:27:01.946 INFO IndexFeatureFile - Picard Version: 2.27.5 12:27:01.946 INFO IndexFeatureFile - Built for Spark Version: 2.4.5 12:27:01.946 INFO IndexFeatureFile - HTSJDK Defaults.COMPRESSION_LEVEL : 2 12:27:01.959 INFO IndexFeatureFile - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 12:27:01.960 INFO IndexFeatureFile - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 12:27:01.960 INFO IndexFeatureFile - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 12:27:01.960 INFO IndexFeatureFile - Deflater: IntelDeflater 12:27:01.960 INFO IndexFeatureFile - Inflater: IntelInflater 12:27:01.960 INFO IndexFeatureFile - GCS max retries/reopens: 20 12:27:01.960 INFO IndexFeatureFile - Requester pays: disabled 12:27:01.960 INFO IndexFeatureFile - Initializing engine 12:27:01.960 INFO IndexFeatureFile - Done initializing engine 12:27:02.123 INFO FeatureManager - Using codec BEDCodec to read file file:///shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/repeat_mask_chr21_sorted.bed 12:27:02.129 INFO ProgressMeter - Starting traversal 12:27:02.130 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 12:27:02.331 INFO ProgressMeter - chr21:46688832 0.0 10000 3061224.5 12:27:02.331 INFO ProgressMeter - Traversal complete. Processed 10000 total records in 0.0 minutes. 12:27:02.390 INFO IndexFeatureFile - Successfully wrote index to /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/repeat_mask_chr21_sorted.bed.idx 12:27:02.390 INFO IndexFeatureFile - Shutting down engine [30 janvier 2023 à 12:27:02 CET] org.broadinstitute.hellbender.tools.IndexFeatureFile done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=2113929216 Tool returned: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/repeat_mask_chr21_sorted.bed.idx [Mon Jan 30 12:27:02 2023] Finished job 155. 86 of 194 steps (44%) done Select jobs to execute... [Mon Jan 30 12:27:02 2023] rule aberrantExpression_bamStats: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00176.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/Pipeline/chr_UCSC_NCBI.txt output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00176.txt jobid: 21 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00176.txt wildcards: sampleID=HG00176 resources: tmpdir=/tmp [Mon Jan 30 12:27:02 2023] Finished job 21. 87 of 194 steps (45%) done Select jobs to execute... [Mon Jan 30 12:27:02 2023] rule changeHeader: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00103.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00103.bam.bai, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/rnaVariantCalling/pipeline/GATK_BASH/changeHeader.sh output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_dropHeader.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_dropHeader.bam.bai, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_newDropHeader.txt log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/logs/changeHeader/HG00103.log jobid: 170 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_dropHeader.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_dropHeader.bam.bai wildcards: sample=HG00103 resources: tmpdir=/tmp WARNING Internal Header is designated: 0 SampleID is HG00103 Forcing 0 to match HG00103 new header can be found here:/shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_newDropHeader.txt [Mon Jan 30 12:27:03 2023] Finished job 170. 88 of 194 steps (45%) done Select jobs to execute... [Mon Jan 30 12:27:03 2023] rule sortBam: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_dropHeader.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_dropHeader.bam.bai output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.out.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.out.bam.bai log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/logs/sortBam/HG00103.log jobid: 169 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.out.bam.bai, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.out.bam; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_dropHeader.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_dropHeader.bam.bai wildcards: sample=HG00103 resources: tmpdir=/tmp [Mon Jan 30 12:27:03 2023] Finished job 169. 89 of 194 steps (46%) done Removing temporary output /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_dropHeader.bam. Removing temporary output /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_dropHeader.bam.bai. Select jobs to execute... [Mon Jan 30 12:27:03 2023] rule markDuplicates: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.out.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.out.bam.bai output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.dupMarked.out.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.dupMarked.out.bai log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/logs/markDuplicates/HG00103.log jobid: 168 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.dupMarked.out.bam; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.out.bam.bai, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.out.bam wildcards: sample=HG00103 resources: tmpdir=/tmp Tool returned: 0 [Mon Jan 30 12:27:12 2023] Finished job 168. 90 of 194 steps (46%) done Removing temporary output /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.out.bam.bai. Removing temporary output /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.out.bam. Removing temporary output /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.dupMarked.out.bai. Select jobs to execute... [Mon Jan 30 12:27:12 2023] rule reorderBAM: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.dupMarked.out.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21.dict output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.dupMarked.FAorder.out.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.dupMarked.FAorder.out.bai jobid: 167 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.dupMarked.FAorder.out.bai, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.dupMarked.FAorder.out.bam; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.dupMarked.out.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21.dict wildcards: sample=HG00103 resources: tmpdir=/tmp ReorderSam Using GATK jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Djava.io.tmpdir=/tmp -jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar ReorderSam -I /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.dupMarked.out.bam -O /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.dupMarked.FAorder.out.bam --SEQUENCE_DICTIONARY /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21.dict -S true --CREATE_INDEX true 12:27:17.371 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so [Mon Jan 30 12:27:17 CET 2023] ReorderSam --INPUT /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.dupMarked.out.bam --OUTPUT /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.dupMarked.FAorder.out.bam --SEQUENCE_DICTIONARY /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21.dict --ALLOW_INCOMPLETE_DICT_CONCORDANCE true --CREATE_INDEX true --ALLOW_CONTIG_LENGTH_DISCORDANCE false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Mon Jan 30 12:27:17 CET 2023] Executing as plassard@flash-node10 on Linux 4.19.0-18-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.1-internal+0-adhoc..src; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.3.0.0 INFO 2023-01-30 12:27:17 ReorderSam SAM/BAM/CRAM file INFO 2023-01-30 12:27:17 ReorderSam SN=chr1 LN=249250621 INFO 2023-01-30 12:27:17 ReorderSam SN=chr10 LN=135534747 INFO 2023-01-30 12:27:17 ReorderSam SN=chr11 LN=135006516 INFO 2023-01-30 12:27:17 ReorderSam SN=chr12 LN=133851895 INFO 2023-01-30 12:27:17 ReorderSam SN=chr13 LN=115169878 INFO 2023-01-30 12:27:17 ReorderSam SN=chr14 LN=107349540 INFO 2023-01-30 12:27:17 ReorderSam SN=chr15 LN=102531392 INFO 2023-01-30 12:27:17 ReorderSam SN=chr16 LN=90354753 INFO 2023-01-30 12:27:17 ReorderSam SN=chr17 LN=81195210 INFO 2023-01-30 12:27:17 ReorderSam SN=chr18 LN=78077248 INFO 2023-01-30 12:27:17 ReorderSam SN=chr19 LN=59128983 INFO 2023-01-30 12:27:17 ReorderSam SN=chr2 LN=243199373 INFO 2023-01-30 12:27:17 ReorderSam SN=chr20 LN=63025520 INFO 2023-01-30 12:27:17 ReorderSam SN=chr21 LN=48129895 INFO 2023-01-30 12:27:17 ReorderSam SN=chr22 LN=51304566 INFO 2023-01-30 12:27:17 ReorderSam SN=chr3 LN=198022430 INFO 2023-01-30 12:27:17 ReorderSam SN=chr4 LN=191154276 INFO 2023-01-30 12:27:17 ReorderSam SN=chr5 LN=180915260 INFO 2023-01-30 12:27:17 ReorderSam SN=chr6 LN=171115067 INFO 2023-01-30 12:27:17 ReorderSam SN=chr7 LN=159138663 INFO 2023-01-30 12:27:17 ReorderSam SN=chr8 LN=146364022 INFO 2023-01-30 12:27:17 ReorderSam SN=chr9 LN=141213431 INFO 2023-01-30 12:27:17 ReorderSam SN=chrX LN=155270560 INFO 2023-01-30 12:27:17 ReorderSam SN=chrY LN=59373566 INFO 2023-01-30 12:27:17 ReorderSam Reference INFO 2023-01-30 12:27:17 ReorderSam SN=chr21 LN=48129895 INFO 2023-01-30 12:27:17 ReorderSam Reordering SAM/BAM/CRAM file: INFO 2023-01-30 12:27:17 ReorderSam Reordering read contig chr21 [index=13] to => ref contig chr21 [index=0] INFO 2023-01-30 12:27:17 ReorderSam Writing reads... INFO 2023-01-30 12:27:17 ReorderSam Processing All reads INFO 2023-01-30 12:27:18 ReorderSam Wrote 58640 reads [Mon Jan 30 12:27:18 CET 2023] picard.sam.ReorderSam done. Elapsed time: 0.03 minutes. Runtime.totalMemory()=2113929216 Tool returned: 0 [Mon Jan 30 12:27:19 2023] Finished job 167. 91 of 194 steps (47%) done Removing temporary output /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.dupMarked.out.bam. Select jobs to execute... [Mon Jan 30 12:27:19 2023] rule splitNcigar: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.dupMarked.FAorder.out.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.dupMarked.FAorder.out.bai, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21.fa.fai, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21.dict output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.dupMarked.split.out.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.dupMarked.split.out.bai log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/logs/splitNcigar/HG00103.log jobid: 166 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.dupMarked.split.out.bai, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.dupMarked.split.out.bam; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21.dict, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.dupMarked.FAorder.out.bai, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.dupMarked.FAorder.out.bam wildcards: sample=HG00103 resources: tmpdir=/tmp [Mon Jan 30 12:27:29 2023] Finished job 166. 92 of 194 steps (47%) done Removing temporary output /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.dupMarked.FAorder.out.bai. Removing temporary output /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.dupMarked.FAorder.out.bam. Select jobs to execute... [Mon Jan 30 12:27:30 2023] rule bqsr: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.dupMarked.split.out.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.dupMarked.split.out.bai, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/rnaVariantCalling/pipeline/GATK_BASH/bqsr.sh output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bqsr/HG00103_recal.table log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/logs/bqsr/HG00103.log jobid: 172 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bqsr/HG00103_recal.table; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.dupMarked.split.out.bai, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.dupMarked.split.out.bam wildcards: sample=HG00103 resources: tmpdir=/tmp chromosome styles match starting BaseRecalibrator Using GATK jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Djava.io.tmpdir=/tmp -jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar BaseRecalibrator -I /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.dupMarked.split.out.bam -R /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21.fa --known-sites /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/high_confidence_indels.vcf.gz --known-sites /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/high_confidence_snps.vcf.gz --known-sites /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/dbSNP_chr21.vcf.gz -O /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bqsr/HG00103_recal.table 12:27:35.093 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 12:27:35.295 INFO BaseRecalibrator - ------------------------------------------------------------ 12:27:35.295 INFO BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.3.0.0 12:27:35.296 INFO BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/ 12:27:35.296 INFO BaseRecalibrator - Executing as plassard@flash-node10 on Linux v4.19.0-18-amd64 amd64 12:27:35.296 INFO BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v11.0.1-internal+0-adhoc..src 12:27:35.296 INFO BaseRecalibrator - Start Date/Time: 30 janvier 2023 à 12:27:35 CET 12:27:35.296 INFO BaseRecalibrator - ------------------------------------------------------------ 12:27:35.296 INFO BaseRecalibrator - ------------------------------------------------------------ 12:27:35.297 INFO BaseRecalibrator - HTSJDK Version: 3.0.1 12:27:35.297 INFO BaseRecalibrator - Picard Version: 2.27.5 12:27:35.298 INFO BaseRecalibrator - Built for Spark Version: 2.4.5 12:27:35.298 INFO BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2 12:27:35.298 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 12:27:35.298 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 12:27:35.298 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 12:27:35.298 INFO BaseRecalibrator - Deflater: IntelDeflater 12:27:35.298 INFO BaseRecalibrator - Inflater: IntelInflater 12:27:35.298 INFO BaseRecalibrator - GCS max retries/reopens: 20 12:27:35.299 INFO BaseRecalibrator - Requester pays: disabled 12:27:35.299 INFO BaseRecalibrator - Initializing engine 12:27:35.535 INFO FeatureManager - Using codec VCFCodec to read file file:///shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/high_confidence_indels.vcf.gz 12:27:35.585 INFO FeatureManager - Using codec VCFCodec to read file file:///shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/high_confidence_snps.vcf.gz 12:27:35.601 INFO FeatureManager - Using codec VCFCodec to read file file:///shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/dbSNP_chr21.vcf.gz 12:27:35.613 WARN IndexUtils - Feature file "file:///shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/dbSNP_chr21.vcf.gz" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file 12:27:35.618 WARN IntelInflater - Zero Bytes Written : 0 12:27:35.630 INFO BaseRecalibrator - Done initializing engine 12:27:35.633 INFO BaseRecalibrationEngine - The covariates being used here: 12:27:35.633 INFO BaseRecalibrationEngine - ReadGroupCovariate 12:27:35.633 INFO BaseRecalibrationEngine - QualityScoreCovariate 12:27:35.633 INFO BaseRecalibrationEngine - ContextCovariate 12:27:35.633 INFO BaseRecalibrationEngine - CycleCovariate 12:27:35.635 INFO ProgressMeter - Starting traversal 12:27:35.635 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute 12:27:38.603 WARN IntelInflater - Zero Bytes Written : 0 12:27:38.605 INFO BaseRecalibrator - 459 read(s) filtered by: MappingQualityNotZeroReadFilter 0 read(s) filtered by: MappingQualityAvailableReadFilter 0 read(s) filtered by: MappedReadFilter 0 read(s) filtered by: NotSecondaryAlignmentReadFilter 5943 read(s) filtered by: NotDuplicateReadFilter 0 read(s) filtered by: PassesVendorQualityCheckReadFilter 0 read(s) filtered by: WellformedReadFilter 6402 total reads filtered 12:27:38.606 INFO ProgressMeter - chr21:48084754 0.0 65062 1314383.8 12:27:38.606 INFO ProgressMeter - Traversal complete. Processed 65062 total reads in 0.0 minutes. 12:27:38.710 INFO BaseRecalibrator - Calculating quantized quality scores... 12:27:38.730 INFO BaseRecalibrator - Writing recalibration report... 12:27:42.343 INFO BaseRecalibrator - ...done! 12:27:42.344 INFO BaseRecalibrator - BaseRecalibrator was able to recalibrate 65062 reads 12:27:42.344 INFO BaseRecalibrator - Shutting down engine [30 janvier 2023 à 12:27:42 CET] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.12 minutes. Runtime.totalMemory()=2709520384 Tool returned: SUCCESS [Mon Jan 30 12:27:42 2023] Finished job 172. 93 of 194 steps (48%) done Select jobs to execute... [Mon Jan 30 12:27:42 2023] rule applyBQSR: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.dupMarked.split.out.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.dupMarked.split.out.bai, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bqsr/HG00103_recal.table output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.dupMarked.split.bqsr.out.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.dupMarked.split.bqsr.out.bai log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/logs/applyBQSR/HG00103.log jobid: 165 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.dupMarked.split.bqsr.out.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.dupMarked.split.bqsr.out.bai; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.dupMarked.split.out.bai, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bqsr/HG00103_recal.table, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.dupMarked.split.out.bam wildcards: sample=HG00103 resources: tmpdir=/tmp [Mon Jan 30 12:27:51 2023] Finished job 165. 94 of 194 steps (48%) done Removing temporary output /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.dupMarked.split.out.bai. Removing temporary output /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.dupMarked.split.out.bam. Select jobs to execute... [Mon Jan 30 12:27:51 2023] rule haplotypeCaller: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.dupMarked.split.bqsr.out.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.dupMarked.split.bqsr.out.bai, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/rnaVariantCalling/pipeline/GATK_BASH/haplotypeCaller.sh output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/sample_vcfs/HG00103/HG00103.g.vcf.gz log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/logs/all_haplocaller/HG00103.log jobid: 164 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/sample_vcfs/HG00103/HG00103.g.vcf.gz; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.dupMarked.split.bqsr.out.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.dupMarked.split.bqsr.out.bai wildcards: sample=HG00103 resources: tmpdir=/tmp chromosome styles match starting HaplotypeCaller Using GATK jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Djava.io.tmpdir=/tmp -jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar HaplotypeCaller -I /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.dupMarked.split.bqsr.out.bam -R /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21.fa --dont-use-soft-clipped-bases -stand-call-conf 20.0 --dbsnp /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/dbSNP_chr21.vcf.gz --output-mode EMIT_ALL_CONFIDENT_SITES -ERC GVCF -O /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/sample_vcfs/HG00103/HG00103.g.vcf.gz 12:27:55.623 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 12:27:55.838 INFO HaplotypeCaller - ------------------------------------------------------------ 12:27:55.839 INFO HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.3.0.0 12:27:55.839 INFO HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/ 12:27:55.839 INFO HaplotypeCaller - Executing as plassard@flash-node10 on Linux v4.19.0-18-amd64 amd64 12:27:55.839 INFO HaplotypeCaller - Java runtime: OpenJDK 64-Bit Server VM v11.0.1-internal+0-adhoc..src 12:27:55.839 INFO HaplotypeCaller - Start Date/Time: 30 janvier 2023 à 12:27:55 CET 12:27:55.839 INFO HaplotypeCaller - ------------------------------------------------------------ 12:27:55.840 INFO HaplotypeCaller - ------------------------------------------------------------ 12:27:55.841 INFO HaplotypeCaller - HTSJDK Version: 3.0.1 12:27:55.841 INFO HaplotypeCaller - Picard Version: 2.27.5 12:27:55.841 INFO HaplotypeCaller - Built for Spark Version: 2.4.5 12:27:55.841 INFO HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2 12:27:55.841 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 12:27:55.841 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 12:27:55.841 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 12:27:55.842 INFO HaplotypeCaller - Deflater: IntelDeflater 12:27:55.842 INFO HaplotypeCaller - Inflater: IntelInflater 12:27:55.842 INFO HaplotypeCaller - GCS max retries/reopens: 20 12:27:55.842 INFO HaplotypeCaller - Requester pays: disabled 12:27:55.842 INFO HaplotypeCaller - Initializing engine 12:27:56.123 INFO FeatureManager - Using codec VCFCodec to read file file:///shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/dbSNP_chr21.vcf.gz 12:27:56.146 WARN IndexUtils - Feature file "file:///shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/dbSNP_chr21.vcf.gz" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file 12:27:56.151 WARN IntelInflater - Zero Bytes Written : 0 12:27:56.188 INFO HaplotypeCaller - Done initializing engine 12:27:56.192 INFO HaplotypeCallerEngine - Tool is in reference confidence mode and the annotation, the following changes will be made to any specified annotations: 'StrandBiasBySample' will be enabled. 'ChromosomeCounts', 'FisherStrand', 'StrandOddsRatio' and 'QualByDepth' annotations have been disabled 12:27:56.203 INFO HaplotypeCallerEngine - Standard Emitting and Calling confidence set to -0.0 for reference-model confidence output 12:27:56.203 INFO HaplotypeCallerEngine - All sites annotated with PLs forced to true for reference-model confidence output 12:27:56.229 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 12:27:56.234 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 12:27:56.271 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 12:27:56.272 INFO IntelPairHmm - Available threads: 1 12:27:56.272 INFO IntelPairHmm - Requested threads: 4 12:27:56.273 WARN IntelPairHmm - Using 1 available threads, but 4 were requested 12:27:56.273 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 12:27:56.330 INFO ProgressMeter - Starting traversal 12:27:56.331 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 12:28:06.339 INFO ProgressMeter - chr21:9860264 0.2 32870 197200.3 12:28:06.984 WARN InbreedingCoeff - InbreedingCoeff will not be calculated at position chr21:9907271 and possibly subsequent; at least 10 samples must have called genotypes 12:28:16.337 INFO ProgressMeter - chr21:13861964 0.3 46240 138685.3 12:28:26.336 INFO ProgressMeter - chr21:21490067 0.5 71720 143416.1 12:28:36.338 INFO ProgressMeter - chr21:28790232 0.7 96130 144173.4 12:28:43.129 WARN DepthPerSampleHC - Annotation will not be calculated at position chr21:30259667 and possibly subsequent; genotype for sample HG00103 is not called 12:28:43.130 WARN StrandBiasBySample - Annotation will not be calculated at position chr21:30259667 and possibly subsequent; genotype for sample HG00103 is not called 12:28:47.014 INFO ProgressMeter - chr21:31638617 0.8 105640 125059.7 12:28:57.014 INFO ProgressMeter - chr21:35254970 1.0 117850 116523.6 12:29:07.031 INFO ProgressMeter - chr21:38437968 1.2 128570 109111.7 12:29:17.044 INFO ProgressMeter - chr21:44441451 1.3 148740 110569.5 12:29:27.049 INFO ProgressMeter - chr21:47387582 1.5 158790 105022.2 12:29:29.293 INFO HaplotypeCaller - 459 read(s) filtered by: MappingQualityReadFilter 0 read(s) filtered by: MappingQualityAvailableReadFilter 0 read(s) filtered by: MappedReadFilter 0 read(s) filtered by: NotSecondaryAlignmentReadFilter 5943 read(s) filtered by: NotDuplicateReadFilter 0 read(s) filtered by: PassesVendorQualityCheckReadFilter 0 read(s) filtered by: NonZeroReferenceLengthAlignmentReadFilter 0 read(s) filtered by: GoodCigarReadFilter 0 read(s) filtered by: WellformedReadFilter 6402 total reads filtered 12:29:29.293 INFO ProgressMeter - chr21:48129120 1.5 161362 104147.1 12:29:29.293 INFO ProgressMeter - Traversal complete. Processed 161362 total regions in 1.5 minutes. 12:29:29.350 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.018706957 12:29:29.350 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 6.675012757 12:29:29.351 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 10.01 sec 12:29:29.352 INFO HaplotypeCaller - Shutting down engine [30 janvier 2023 à 12:29:29 CET] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 1.56 minutes. Runtime.totalMemory()=4173332480 [Mon Jan 30 12:29:29 2023] Finished job 164. 95 of 194 steps (49%) done Removing temporary output /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.dupMarked.split.bqsr.out.bam. Removing temporary output /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/bam/HG00103/HG00103_Aligned.sortedByCoord.dupMarked.split.bqsr.out.bai. Select jobs to execute... [Mon Jan 30 12:29:29 2023] rule mae_createSNVs: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/Pipeline/chr_NCBI_UCSC.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/Pipeline/chr_UCSC_NCBI.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/qc_vcf_1000G.vcf.gz, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/rna_bam/HG00103.bam, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Scripts/MonoallelicExpression/pipeline/MAE/filterSNVs.sh, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/params/snvs/HG00103_snvParams.csv output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/snvs/QC--HG00103.vcf.gz, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/snvs/QC--HG00103.vcf.gz.tbi jobid: 131 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/mae/snvs/QC--HG00103.vcf.gz wildcards: vcf=QC, rna=HG00103 resources: tmpdir=/tmp Filter SNVs Lines total/split/realigned/skipped: 26402/0/0/0 Lines total/split/realigned/skipped: 26402/0/0/0 Using GATK jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar SelectVariants -V /tmp/tmp.6k7vlQRhXQ -O /tmp/tmp.Vn8Rs0pMp0 12:29:35.498 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 12:29:35.819 INFO SelectVariants - ------------------------------------------------------------ 12:29:35.819 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.3.0.0 12:29:35.819 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/ 12:29:35.820 INFO SelectVariants - Executing as plassard@flash-node10 on Linux v4.19.0-18-amd64 amd64 12:29:35.820 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v11.0.1-internal+0-adhoc..src 12:29:35.820 INFO SelectVariants - Start Date/Time: 30 janvier 2023 à 12:29:35 CET 12:29:35.820 INFO SelectVariants - ------------------------------------------------------------ 12:29:35.820 INFO SelectVariants - ------------------------------------------------------------ 12:29:35.821 INFO SelectVariants - HTSJDK Version: 3.0.1 12:29:35.822 INFO SelectVariants - Picard Version: 2.27.5 12:29:35.822 INFO SelectVariants - Built for Spark Version: 2.4.5 12:29:35.822 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2 12:29:35.822 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 12:29:35.822 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 12:29:35.822 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 12:29:35.823 INFO SelectVariants - Deflater: IntelDeflater 12:29:35.823 INFO SelectVariants - Inflater: IntelInflater 12:29:35.823 INFO SelectVariants - GCS max retries/reopens: 20 12:29:35.823 INFO SelectVariants - Requester pays: disabled 12:29:35.823 INFO SelectVariants - Initializing engine 12:29:36.019 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/tmp.6k7vlQRhXQ 12:29:36.047 INFO SelectVariants - Done initializing engine 12:29:36.082 WARN GATKVariantContextUtils - Can't determine output variant file format from output file extension "Vn8Rs0pMp0". Defaulting to VCF. 12:29:36.098 INFO ProgressMeter - Starting traversal 12:29:36.099 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute 12:29:36.966 INFO ProgressMeter - chr22:30163526 0.0 26402 1829237.9 12:29:36.966 INFO ProgressMeter - Traversal complete. Processed 26402 total variants in 0.0 minutes. 12:29:37.148 INFO SelectVariants - Shutting down engine [30 janvier 2023 à 12:29:37 CET] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.03 minutes. Runtime.totalMemory()=2113929216 Using GATK jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar SelectVariants --restrict-alleles-to BIALLELIC -V /tmp/tmp.Vn8Rs0pMp0 -O /tmp/tmp.6k7vlQRhXQ 12:29:40.980 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 12:29:41.219 INFO SelectVariants - ------------------------------------------------------------ 12:29:41.219 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.3.0.0 12:29:41.219 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/ 12:29:41.219 INFO SelectVariants - Executing as plassard@flash-node10 on Linux v4.19.0-18-amd64 amd64 12:29:41.220 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v11.0.1-internal+0-adhoc..src 12:29:41.220 INFO SelectVariants - Start Date/Time: 30 janvier 2023 à 12:29:40 CET 12:29:41.220 INFO SelectVariants - ------------------------------------------------------------ 12:29:41.222 INFO SelectVariants - ------------------------------------------------------------ 12:29:41.223 INFO SelectVariants - HTSJDK Version: 3.0.1 12:29:41.223 INFO SelectVariants - Picard Version: 2.27.5 12:29:41.223 INFO SelectVariants - Built for Spark Version: 2.4.5 12:29:41.223 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2 12:29:41.223 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 12:29:41.223 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 12:29:41.224 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 12:29:41.224 INFO SelectVariants - Deflater: IntelDeflater 12:29:41.224 INFO SelectVariants - Inflater: IntelInflater 12:29:41.224 INFO SelectVariants - GCS max retries/reopens: 20 12:29:41.224 INFO SelectVariants - Requester pays: disabled 12:29:41.224 INFO SelectVariants - Initializing engine 12:29:41.419 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/tmp.Vn8Rs0pMp0 12:29:41.463 INFO SelectVariants - Done initializing engine 12:29:41.482 WARN GATKVariantContextUtils - Can't determine output variant file format from output file extension "6k7vlQRhXQ". Defaulting to VCF. 12:29:41.495 INFO ProgressMeter - Starting traversal 12:29:41.495 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute 12:29:42.376 INFO ProgressMeter - chr22:30163526 0.0 26402 1800136.4 12:29:42.377 INFO ProgressMeter - Traversal complete. Processed 26402 total variants in 0.0 minutes. 12:29:42.556 INFO SelectVariants - Shutting down engine [30 janvier 2023 à 12:29:42 CET] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.03 minutes. Runtime.totalMemory()=2113929216 [Mon Jan 30 12:29:43 2023] Finished job 131. 96 of 194 steps (49%) done Select jobs to execute... [Mon Jan 30 12:29:43 2023] rule aberrantExpression_mergeBamStats: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00111.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00149.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00126.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00176.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00103.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00150.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00096.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00116.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00106.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00132.txt output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/outrider.tsv jobid: 17 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/outrider.tsv; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00106.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00149.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00126.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00111.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00103.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00096.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00150.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00176.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00132.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00116.txt wildcards: dataset=outrider resources: tmpdir=/tmp WARNING: Less than 30 IDs in DROP_GROUP outrider WARNING: Less than 30 IDs in DROP_GROUP outrider_external WARNING: Less than 30 IDs in DROP_GROUP fraser WARNING: Less than 30 IDs in DROP_GROUP fraser_external check for missing R packages Structuring dependencies... Dependencies file generated at: /tmp/tmpr1s2e4dn Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Select jobs to execute... [Mon Jan 30 12:29:51 2023] Finished job 17. 97 of 194 steps (50%) done Select jobs to execute... [Mon Jan 30 12:29:52 2023] rule AberrantExpression_pipeline_OUTRIDER_results_R: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/.drop/helpers/add_HPO_cols.R, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_results/aberrant_expression/v29/outrider/outrider/ods.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/preprocess/v29/gene_name_mapping_v29.tsv, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/v29/params/results/outrider_resultParams.csv, Scripts/AberrantExpression/pipeline/OUTRIDER/results.R output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_results/aberrant_expression/v29/outrider/outrider/OUTRIDER_results.tsv, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_results/aberrant_expression/v29/outrider/outrider/OUTRIDER_results_all.Rds log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/.drop/tmp/AE/v29/outrider/OUTRIDER_results.Rds jobid: 36 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_results/aberrant_expression/v29/outrider/outrider/OUTRIDER_results.tsv; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_results/aberrant_expression/v29/outrider/outrider/ods.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/preprocess/v29/gene_name_mapping_v29.tsv wildcards: annotation=v29, dataset=outrider resources: tmpdir=/tmp [Mon Jan 30 12:30:23 2023] Finished job 36. 98 of 194 steps (51%) done Select jobs to execute... [Mon Jan 30 12:30:24 2023] rule AberrantExpression_pipeline_OUTRIDER_Summary_R: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_results/aberrant_expression/v29/outrider/outrider/ods.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_results/aberrant_expression/v29/outrider/outrider/OUTRIDER_results.tsv, Scripts/AberrantExpression/pipeline/OUTRIDER/Summary.R output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/html/AberrantExpression/Outrider/v29/Summary_outrider.html, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/html/AberrantExpression/Outrider/v29/OUTRIDER_results_outrider.tsv log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/.drop/tmp/AE/v29/outrider/OUTRIDER_summary.Rds jobid: 34 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/html/AberrantExpression/Outrider/v29/Summary_outrider.html; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_results/aberrant_expression/v29/outrider/outrider/ods.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_results/aberrant_expression/v29/outrider/outrider/OUTRIDER_results.tsv wildcards: annotation=v29, dataset=outrider resources: tmpdir=/tmp Le chargement a nécessité le package : knitr Le chargement a nécessité le package : rmarkdown [1] TRUE processing file: /tmp/RtmpiG82aw/file51f54bffe83/Summary.spin.Rmd | | | 0% | |.... | 5% | |......... | 10% (unnamed-chunk-1) | |............. | 14% | |................. | 19% (unnamed-chunk-2) | |..................... | 24% | |.......................... | 29% (unnamed-chunk-3) | |.............................. | 33% | |.................................. | 38% (countCorHeatmap) | |....................................... | 43% | |........................................... | 48% (geneSampleHeatmap) | |............................................... | 52% | |................................................... | 57% (unnamed-chunk-4) | |........................................................ | 62% (BCV) | |............................................................ | 67% | |................................................................ | 71% (unnamed-chunk-5) | |..................................................................... | 76% | |......................................................................... | 81% (unnamed-chunk-6) | |............................................................................. | 86% | |................................................................................. | 90% (unnamed-chunk-7) | |...................................................................................... | 95% (unnamed-chunk-8) | |..........................................................................................| 100% output file: /tmp/RtmpiG82aw/file51f54bffe83/Summary.knit.md /shared/ifs/home/plassard/Conda/envs_conda_flash/drop_env/bin/pandoc +RTS -K512m -RTS /tmp/RtmpiG82aw/file51f54bffe83/Summary.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpiG82aw/file51f2c2e8326/Summary_outrider.html --lua-filter /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/lib/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/lib/R/library/rmarkdown/rmarkdown/lua/latex-div.lua --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/lib/R/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --css lib/add_content_table.css --css lib/leo_style.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpiG82aw/rmarkdown-str51f77265b1d.html --variable code_folding=hide --variable source_embed=Summary.R --include-after-body /tmp/RtmpiG82aw/file51f2df7f24c.html --variable code_menu=1 Output created: /tmp/RtmpiG82aw/file51f2c2e8326/Summary_outrider.html [1] TRUE TRUE TRUE TRUE [Mon Jan 30 12:31:05 2023] Finished job 34. 99 of 194 steps (51%) done Select jobs to execute... [Mon Jan 30 12:31:05 2023] rule aberrantExpression_mergeBamStats: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00111.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00149.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00126.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00176.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00150.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00116.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00106.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00132.txt output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/outrider_external.tsv jobid: 31 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/outrider_external.tsv; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00106.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00149.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00116.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00150.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00176.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00126.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00132.txt, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/HG00111.txt wildcards: dataset=outrider_external resources: tmpdir=/tmp WARNING: Less than 30 IDs in DROP_GROUP outrider WARNING: Less than 30 IDs in DROP_GROUP outrider_external WARNING: Less than 30 IDs in DROP_GROUP fraser WARNING: Less than 30 IDs in DROP_GROUP fraser_external check for missing R packages Structuring dependencies... Dependencies file generated at: /tmp/tmpu0e1qbcc Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Select jobs to execute... [Mon Jan 30 12:31:12 2023] Finished job 31. 100 of 194 steps (52%) done Select jobs to execute... [Mon Jan 30 12:31:12 2023] rule AberrantExpression_pipeline_Counting_Summary_R: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_results/aberrant_expression/v29/outrider/outrider_external/ods_unfitted.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/outrider_external.tsv, Scripts/AberrantExpression/pipeline/Counting/Summary.R output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/html/AberrantExpression/Counting/v29/Summary_outrider_external.html log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/.drop/tmp/AE/v29/outrider_external/count_summary.Rds jobid: 28 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/html/AberrantExpression/Counting/v29/Summary_outrider_external.html; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_results/aberrant_expression/v29/outrider/outrider_external/ods_unfitted.Rds, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/aberrant_expression/bam_stats/outrider_external.tsv wildcards: annotation=v29, dataset=outrider_external resources: tmpdir=/tmp Le chargement a nécessité le package : knitr Le chargement a nécessité le package : rmarkdown [1] TRUE processing file: /tmp/Rtmp4wCLUY/file684a961c0c/Summary.spin.Rmd | | | 0% | |....... | 8% | |.............. | 15% (unnamed-chunk-1) | |..................... | 23% | |............................ | 31% (unnamed-chunk-2) | |................................... | 38% | |.......................................... | 46% (unnamed-chunk-3) | |.................................................. | 54% (meanCounts) | |......................................................... | 62% | |................................................................ | 69% (unnamed-chunk-4) | |....................................................................... | 77% (expressedGenes) | |.............................................................................. | 85% | |..................................................................................... | 92% (unnamed-chunk-5) | |............................................................................................| 100% output file: /tmp/Rtmp4wCLUY/file684a961c0c/Summary.knit.md /shared/ifs/home/plassard/Conda/envs_conda_flash/drop_env/bin/pandoc +RTS -K512m -RTS /tmp/Rtmp4wCLUY/file684a961c0c/Summary.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/Rtmp4wCLUY/file6846ce473a2/Summary_outrider_external.html --lua-filter /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/lib/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/lib/R/library/rmarkdown/rmarkdown/lua/latex-div.lua --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /shared/ngs/home/plassard/Conda/envs_conda_flash/drop_env/lib/R/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --css lib/add_content_table.css --css lib/leo_style.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/Rtmp4wCLUY/rmarkdown-str68415b5f5a8.html --variable code_folding=hide --variable source_embed=Summary.R --include-after-body /tmp/Rtmp4wCLUY/file684133d3cc6.html --variable code_menu=1 Output created: /tmp/Rtmp4wCLUY/file6846ce473a2/Summary_outrider_external.html [1] TRUE TRUE TRUE TRUE [Mon Jan 30 12:31:49 2023] Finished job 28. 101 of 194 steps (52%) done Select jobs to execute... [Mon Jan 30 12:31:49 2023] rule leftNormalVCF: input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/batch_vcfs/batch_0/batch_0_all_samples.genotyped.filtered.vcf.gz, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/batch_vcfs/batch_0/batch_0_all_samples.genotyped.filtered.vcf.gz.tbi output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/batch_vcfs/batch_0/batch_0_all_samples.genotyped.filtered_clean.vcf.gz, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/batch_vcfs/batch_0/batch_0_all_samples.genotyped.filtered_clean.vcf.gz.tbi log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/logs/all_haplocaller/batch_0_split_norm.log jobid: 142 reason: Missing output files: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/batch_vcfs/batch_0/batch_0_all_samples.genotyped.filtered_clean.vcf.gz.tbi, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/batch_vcfs/batch_0/batch_0_all_samples.genotyped.filtered_clean.vcf.gz; Input files updated by another job: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/batch_vcfs/batch_0/batch_0_all_samples.genotyped.filtered.vcf.gz, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/batch_vcfs/batch_0/batch_0_all_samples.genotyped.filtered.vcf.gz.tbi wildcards: dataset=batch_0 resources: tmpdir=/tmp Lines total/split/realigned/skipped: 584/2/0/0 [W::vcf_parse] Contig 'Fichier binaire (entrée standard) correspondant' is not defined in the header. (Quick workaround: index the file with tabix.) [W::bcf_hrec_check] Invalid contig name: "Fichier binaire (entrée standard) correspondant" [E::faidx_adjust_position] The sequence "Fichier binaire (entrée standard) correspondant" was not found faidx_fetch_seq failed at Fichier binaire (entrée standard) correspondant:1 [Mon Jan 30 12:31:49 2023] Error in rule leftNormalVCF: jobid: 142 input: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/batch_vcfs/batch_0/batch_0_all_samples.genotyped.filtered.vcf.gz, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/batch_vcfs/batch_0/batch_0_all_samples.genotyped.filtered.vcf.gz.tbi output: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/batch_vcfs/batch_0/batch_0_all_samples.genotyped.filtered_clean.vcf.gz, /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/batch_vcfs/batch_0/batch_0_all_samples.genotyped.filtered_clean.vcf.gz.tbi log: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/logs/all_haplocaller/batch_0_split_norm.log (check log file(s) for error details) shell: bcftools norm -m-both /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/batch_vcfs/batch_0/batch_0_all_samples.genotyped.filtered.vcf.gz | grep -v -w "*" | bcftools norm -f /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Data/chr21_ncbi.fa | bgzip -c > /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/batch_vcfs/batch_0/batch_0_all_samples.genotyped.filtered_clean.vcf.gz tabix -f -p vcf /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/batch_vcfs/batch_0/batch_0_all_samples.genotyped.filtered_clean.vcf.gz (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) Removing output files of failed job leftNormalVCF since they might be corrupted: /shared/ngs/illumina/plassard/Project/RNAseq/S17001_Mattioli/230130_DROP/drop_demo/Output/processed_data/rnaVariantCalling/out/batch_vcfs/batch_0/batch_0_all_samples.genotyped.filtered_clean.vcf.gz Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2023-01-30T115916.955496.snakemake.log