BWA. paired reads have different names: "SRR1655713.931913", "SRR1655713.3"

[cahuparo]

Hi @zachary-foster,

I got a new error with the validation dataset. See below:

ERROR ~ Error executing process > 'PATHOGENSURVEILLANCE:VARIANT_ANALYSIS:ALIGN_READS:BWA_MEM (GCA_000513215_1_GCA_001064335_1_ASM106433v1_genomic)'

Caused by:
  Process `PATHOGENSURVEILLANCE:VARIANT_ANALYSIS:ALIGN_READS:BWA_MEM (GCA_000513215_1_GCA_001064335_1_ASM106433v1_genomic)` terminated with an error exit status (1)


Command executed:

  INDEX=`find -L ./ -name "*.amb" | sed 's/\.amb$//'`
 
  bwa mem \
      -M \
      -t 8 \
      $INDEX \
      SRR1655713.fastq.gz SRR1655713_1.fastq.gz \
      | samtools view   --threads 8 -o GCA_000513215_1_GCA_001064335_1_ASM106433v1_genomic.bam -
 
  cat <<-END_VERSIONS > versions.yml
  "PATHOGENSURVEILLANCE:VARIANT_ANALYSIS:ALIGN_READS:BWA_MEM":
      bwa: $(echo $(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*$//')
      samtools: $(echo $(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*$//')
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  [M::bwa_idx_load_from_disk] read 0 ALT contigs
  [M::process] read 418680 sequences (37584179 bp)...
  [W::bseq_read] the 1st file has fewer sequences.
  [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (66, 75, 100, 86)
  [M::mem_pestat] analyzing insert size distribution for orientation FF...
  [M::mem_pestat] (25, 50, 75) percentile: (3342, 5343, 8460)
  [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 18696)
  [M::mem_pestat] mean and std.dev: (5399.29, 2778.03)
  [M::mem_pestat] low and high boundaries for proper pairs: (1, 23814)
  [M::mem_pestat] analyzing insert size distribution for orientation FR...
  [M::mem_pestat] (25, 50, 75) percentile: (1745, 5090, 7342)
  [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 18536)
  [M::mem_pestat] mean and std.dev: (4702.04, 3017.93)
  [M::mem_pestat] low and high boundaries for proper pairs: (1, 24133)
  [M::mem_pestat] analyzing insert size distribution for orientation RF...
  [M::mem_pestat] (25, 50, 75) percentile: (1749, 4499, 7269)
  [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 18309)
  [M::mem_pestat] mean and std.dev: (4653.66, 2944.11)
  [M::mem_pestat] low and high boundaries for proper pairs: (1, 23829)
  [M::mem_pestat] analyzing insert size distribution for orientation RR...
  [M::mem_pestat] (25, 50, 75) percentile: (2349, 5359, 7303)
  [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 17211)
  [M::mem_pestat] mean and std.dev: (4895.87, 2849.74)
  [M::mem_pestat] low and high boundaries for proper pairs: (1, 22165)
  [mem_sam_pe] paired reads have different names: "SRR1655713.931912", "SRR1655713.2"
 
  [mem_sam_pe] paired reads have different names: "SRR1655713.931913", "SRR1655713.3"

Work dir:
  /nfs7/BPP/Chang_Lab/paradarc/ps_pipeline_validation/scripts/pathogensurveillance/work/dc/75a0dd1ccbd69e238aaa44058f2cc3

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

 -- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

 -- Check '.nextflow.log' file for details

I will delete that sample reads and let it try again.

[zachary-foster]

Thats odd. Could it be that it is actually not paired end? Maybe one of those accessions with multiple sequencing runs that is getting misinterpreted as paired end? If you look at the files, is this just one odd read or is it all that way?