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samtools fixmate: Couldn't write to output file: Broken pipe
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19 months ago
Ric • 240
Australia

I have the below alignment script which uses BWA and I added `sed 's/^/LP1-/' command in order to put LP1- at the front of every line because I would like to use SGSautoSNP pipeline to detect different cultivars.

#!/bin/bash
#usage: sh align_pbs.sh good/ output.racon2.fasta bam-soap

mkdir $3

for r1 in $(find $1 -name "*R1*.gz");
do
  base=${r1%_R1*}
  output=$(basename $(echo $r1 | sed 's/R1//g'))
  r2=$(echo $r1 | sed 's/R1/R2/g') 

  #Get read group infomration:
  #Source: A: bwa mem: Passing a variable to read group
  header=$(zcat $r1 | head -n 1)
  id=$(echo $header | head -n 1 | cut -f 1-4 -d":" | sed 's/@//' | sed 's/:/_/g')
  sm=$(echo $header | head -n 1 | grep -Eo "[ATGCN]+$")
  #echo "Read Group @RG\tID:$id\tSM:$id"_"$sm\tLB:$id"_"$sm\tPL:ILLUMINA"
  echo "@RG\tID:${output}\tSM:${output}\tLB:${output}\tPL:ILLUMINA"

  #cat <

Unfortunatelye, this pipeline cuased the following erros:

samblaster: Version 0.1.24
samblaster: Inputting from stdin
samblaster: Outputting to stdout
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1200000 sequences (120000000 bp)...
[M::process] read 1200000 sequences (120000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 316829, 6, 4)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (432, 474, 509)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (278, 663)
[M::mem_pestat] mean and std.dev: (471.59, 53.66)
[M::mem_pestat] low and high boundaries for proper pairs: (201, 740)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 1200000 reads in 615.287 CPU sec, 58.490 real sec
samblaster: Loaded 19 header sequence entries.
[W::sam_read1] Parse error at line 1
samtools sort: truncated file. Aborting
sed: couldn't write 567 items to stdout: Broken pipe
[E::bgzf_flush] File write failed (wrong size)
samtools fixmate: Couldn't write to output file: Broken pipe
[E::bgzf_close] File write failed
[bam_mating] error while closing output file
samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
samblaster: Unable to write to output file.

How is it possible to fix the above pipeline?

Thank you in advance,

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The pipeline script is truncated.

edit: sorry, I didn't express myself clearly. What I mean is the script is pasted here is incomplete - hence, truncated. Please edit your post to include the complete script.

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How is it possible to fix it?

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You are not showing the whole script, are you?

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I pasted the whole script but it shows only half of it. Meanwhile, I solved the problem.

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