========================================
 nf-core/eager v2.0.2
========================================
Run Name: naughty_lorenz

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## nf-core/eager execution completed unsuccessfully! ##

####################################################
The exit status of the task that caused the workflow execution to fail was: 1.
The full error message was:

Error executing process > 'bwa (ABM006.A0101_S0_L002_R1_001)'

Caused by:
  Process `bwa (ABM006.A0101_S0_L002_R1_001)` terminated with an error exit status (1)

Command executed:

  bwa aln -t 1 hg19_MT.fasta ABM006.A0101_S0_L002_R1_001.combined.prefixed.fq.gz -n 0.04 -l 32 -k 2 -f "ABM006.A0101_S0_L002_R1_001.combined.prefixed.fq.sai"
  bwa samse -r "@RG\tID:ILLUMINA-ABM006.A0101_S0_L002_R1_001\tSM:ABM006.A0101_S0_L002_R1_001\tPL:illumina" hg19_MT.fasta "ABM006.A0101_S0_L002_R1_001.combined.prefixed.fq".sai ABM006.A0101_S0_L002_R1_001.combined.prefixed.fq.gz | samtools sort -@ 1 -O bam - > "ABM006.A0101_S0_L002_R1_001".sorted.bam
  samtools index -@ 1 "ABM006.A0101_S0_L002_R1_001".sorted.bam

Command exit status:
  1

Command output:
  (empty)

Command error:
  [bwa_aln_core] calculate SA coordinate... 1.14 sec
  [bwa_aln_core] write to the disk... 0.01 sec
  [bwa_aln_core] 1835008 sequences have been processed.
  [bwa_aln_core] calculate SA coordinate... 0.93 sec
  [bwa_aln_core] write to the disk... 0.01 sec
  [bwa_aln_core] 2027689 sequences have been processed.
  [main] Version: 0.7.12-r1039
  [main] CMD: bwa aln -t 1 -n 0.04 -l 32 -k 2 -f ABM006.A0101_S0_L002_R1_001.combined.prefixed.fq.sai hg19_MT.fasta ABM006.A0101_S0_L002_R1_001.combined.prefixed.fq.gz
  [main] Real time: 13.003 sec; CPU: 12.988 sec
  [bwa_aln_core] convert to sequence coordinate... 0.02 sec
  [bwa_aln_core] refine gapped alignments... 0.02 sec
  [bwa_aln_core] print alignments... 0.21 sec
  [bwa_aln_core] 262144 sequences have been processed.
  [bwa_aln_core] convert to sequence coordinate... 0.04 sec
  [bwa_aln_core] refine gapped alignments... 0.05 sec
  [bwa_aln_core] print alignments... 0.21 sec
  [bwa_aln_core] 524288 sequences have been processed.
  [bwa_aln_core] convert to sequence coordinate... 0.06 sec
  [bwa_aln_core] refine gapped alignments... 0.04 sec
  [bwa_aln_core] print alignments... 0.19 sec
  [bwa_aln_core] 786432 sequences have been processed.
  [bwa_aln_core] convert to sequence coordinate... 0.02 sec
  [bwa_aln_core] refine gapped alignments... 0.02 sec
  [bwa_aln_core] print alignments... 0.19 sec
  [bwa_aln_core] 1048576 sequences have been processed.
  [bwa_aln_core] convert to sequence coordinate... 0.02 sec
  [bwa_aln_core] refine gapped alignments... 0.02 sec
  [bwa_aln_core] print alignments... 0.19 sec
  [bwa_aln_core] 1310720 sequences have been processed.
  [bwa_aln_core] convert to sequence coordinate... 0.02 sec
  [bwa_aln_core] refine gapped alignments... 0.02 sec
  [bwa_aln_core] print alignments... 0.19 sec
  [bwa_aln_core] 1572864 sequences have been processed.
  [bwa_aln_core] convert to sequence coordinate... 0.03 sec
  [bwa_aln_core] refine gapped alignments... 0.05 sec
  [bwa_aln_core] print alignments... 0.21 sec
  [bwa_aln_core] 1835008 sequences have been processed.
  [bwa_aln_core] convert to sequence coordinate... 0.02 sec
  [bwa_aln_core] refine gapped alignments... 0.04 sec
  [bwa_aln_core] print alignments... 0.15 sec
  [bwa_aln_core] 2027689 sequences have been processed.
  [main] Version: 0.7.12-r1039
  [main] CMD: bwa samse -r @RG\tID:ILLUMINA-ABM006.A0101_S0_L002_R1_001\tSM:ABM006.A0101_S0_L002_R1_001\tPL:illumina hg19_MT.fasta ABM006.A0101_S0_L002_R1_001.combined.prefixed.fq.sai ABM006.A0101_S0_L002_R1_001.combined.prefixed.fq.gz
  [main] Real time: 7.227 sec; CPU: 6.184 sec
  index: invalid option -- '@'
  Usage: samtools index [-bc] [-m INT] <in.bam> [out.index]
  Options:
    -b       Generate BAI-format index for BAM files [default]
    -c       Generate CSI-format index for BAM files
    -m INT   Set minimum interval size for CSI indices to 2^INT [14]

Work dir:
  /projects1/users/fellows/nextflow/eager2/my_test/work/09/867e241abeeb78307c9fc618980ca2

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`



####################################################
## nf-core/eager execution completed unsuccessfully! ##
####################################################
The exit status of the task that caused the workflow execution to fail was: 1.
The full error message was:

Error executing process > 'bwa (ABM006.A0101_S0_L002_R1_001)'

Caused by:
  Process `bwa (ABM006.A0101_S0_L002_R1_001)` terminated with an error exit status (1)

Command executed:

  bwa aln -t 1 hg19_MT.fasta ABM006.A0101_S0_L002_R1_001.combined.prefixed.fq.gz -n 0.04 -l 32 -k 2 -f "ABM006.A0101_S0_L002_R1_001.combined.prefixed.fq.sai"
  bwa samse -r "@RG\tID:ILLUMINA-ABM006.A0101_S0_L002_R1_001\tSM:ABM006.A0101_S0_L002_R1_001\tPL:illumina" hg19_MT.fasta "ABM006.A0101_S0_L002_R1_001.combined.prefixed.fq".sai ABM006.A0101_S0_L002_R1_001.combined.prefixed.fq.gz | samtools sort -@ 1 -O bam - > "ABM006.A0101_S0_L002_R1_001".sorted.bam
  samtools index -@ 1 "ABM006.A0101_S0_L002_R1_001".sorted.bam

Command exit status:
  1

Command output:
  (empty)

Command error:
  [bwa_aln_core] calculate SA coordinate... 1.14 sec
  [bwa_aln_core] write to the disk... 0.01 sec
  [bwa_aln_core] 1835008 sequences have been processed.
  [bwa_aln_core] calculate SA coordinate... 0.93 sec
  [bwa_aln_core] write to the disk... 0.01 sec
  [bwa_aln_core] 2027689 sequences have been processed.
  [main] Version: 0.7.12-r1039
  [main] CMD: bwa aln -t 1 -n 0.04 -l 32 -k 2 -f ABM006.A0101_S0_L002_R1_001.combined.prefixed.fq.sai hg19_MT.fasta ABM006.A0101_S0_L002_R1_001.combined.prefixed.fq.gz
  [main] Real time: 13.003 sec; CPU: 12.988 sec
  [bwa_aln_core] convert to sequence coordinate... 0.02 sec
  [bwa_aln_core] refine gapped alignments... 0.02 sec
  [bwa_aln_core] print alignments... 0.21 sec
  [bwa_aln_core] 262144 sequences have been processed.
  [bwa_aln_core] convert to sequence coordinate... 0.04 sec
  [bwa_aln_core] refine gapped alignments... 0.05 sec
  [bwa_aln_core] print alignments... 0.21 sec
  [bwa_aln_core] 524288 sequences have been processed.
  [bwa_aln_core] convert to sequence coordinate... 0.06 sec
  [bwa_aln_core] refine gapped alignments... 0.04 sec
  [bwa_aln_core] print alignments... 0.19 sec
  [bwa_aln_core] 786432 sequences have been processed.
  [bwa_aln_core] convert to sequence coordinate... 0.02 sec
  [bwa_aln_core] refine gapped alignments... 0.02 sec
  [bwa_aln_core] print alignments... 0.19 sec
  [bwa_aln_core] 1048576 sequences have been processed.
  [bwa_aln_core] convert to sequence coordinate... 0.02 sec
  [bwa_aln_core] refine gapped alignments... 0.02 sec
  [bwa_aln_core] print alignments... 0.19 sec
  [bwa_aln_core] 1310720 sequences have been processed.
  [bwa_aln_core] convert to sequence coordinate... 0.02 sec
  [bwa_aln_core] refine gapped alignments... 0.02 sec
  [bwa_aln_core] print alignments... 0.19 sec
  [bwa_aln_core] 1572864 sequences have been processed.
  [bwa_aln_core] convert to sequence coordinate... 0.03 sec
  [bwa_aln_core] refine gapped alignments... 0.05 sec
  [bwa_aln_core] print alignments... 0.21 sec
  [bwa_aln_core] 1835008 sequences have been processed.
  [bwa_aln_core] convert to sequence coordinate... 0.02 sec
  [bwa_aln_core] refine gapped alignments... 0.04 sec
  [bwa_aln_core] print alignments... 0.15 sec
  [bwa_aln_core] 2027689 sequences have been processed.
  [main] Version: 0.7.12-r1039
  [main] CMD: bwa samse -r @RG\tID:ILLUMINA-ABM006.A0101_S0_L002_R1_001\tSM:ABM006.A0101_S0_L002_R1_001\tPL:illumina hg19_MT.fasta ABM006.A0101_S0_L002_R1_001.combined.prefixed.fq.sai ABM006.A0101_S0_L002_R1_001.combined.prefixed.fq.gz
  [main] Real time: 7.227 sec; CPU: 6.184 sec
  index: invalid option -- '@'
  Usage: samtools index [-bc] [-m INT] <in.bam> [out.index]
  Options:
    -b       Generate BAI-format index for BAM files [default]
    -c       Generate CSI-format index for BAM files
    -m INT   Set minimum interval size for CSI indices to 2^INT [14]

Work dir:
  /projects1/users/fellows/nextflow/eager2/my_test/work/09/867e241abeeb78307c9fc618980ca2

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`





The workflow was completed at Wed Nov 14 17:08:40 CET 2018 (duration: 2m 58s)

The command used to launch the workflow was as follows:

  nextflow run nf-core/eager --reads /projects1/users/fellows/nextflow/eager2/my_test/data/ABM006.A0101/*_R{1,2}*fastq.gz --pairedEnd --fasta /projects1/users/fellows/nextflow/eager2/my_test/references/hg19_MT.fasta --outdir /projects1/users/fellows/nextflow/eager2/my_test/output_eager2 -profile singularity --max_cpus 4 --max_memory 16G -r 2.0.2



Pipeline Configuration:
-----------------------
 - Pipeline Name: nf-core/eager
 - Pipeline Version: 2.0.2
 - Run Name: naughty_lorenz
 - Reads: /projects1/users/fellows/nextflow/eager2/my_test/data/ABM006.A0101/*_R{1,2}*fastq.gz
 - Fasta Ref: /projects1/users/fellows/nextflow/eager2/my_test/references/hg19_MT.fasta
 - Data Type: Paired-End
 - Max Memory: 16G
 - Max CPUs: 4
 - Max Time: null
 - Output dir: /projects1/users/fellows/nextflow/eager2/my_test/output_eager2
 - Working dir: /projects1/users/fellows/nextflow/eager2/my_test/work
 - Container Engine: singularity
 - Container: [:]
 - Current home: /projects1/clusterhomes/fellows
 - Current user: fellows
 - Current path: /projects1/users/fellows/nextflow/eager2/my_test
 - Script dir: /projects1/clusterhomes/fellows/.nextflow/assets/nf-core/eager
 - Config Profile: singularity
 - Date Started: Wed Nov 14 17:05:42 CET 2018
 - Date Completed: Wed Nov 14 17:08:40 CET 2018
 - Pipeline script file path: /projects1/clusterhomes/fellows/.nextflow/assets/nf-core/eager/main.nf
 - Pipeline script hash ID: b830dc186a77957a7b56fd9b3a6233ea
 - Pipeline repository Git URL: https://github.com/nf-core/eager.git
 - Pipeline repository Git Commit: c44b88110d7daba8b51c6a0aca96be74b30d8afd
 - Pipeline Git branch/tag: 2.0.2
 - Nextflow Version: 0.32.0
 - Nextflow Build: 4897
 - Nextflow Compile Timestamp: 27-09-2018 10:17 UTC

--
nf-core/eager
https://github.com/nf-core/eager