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Old 09-01-2020, 08:33 AM   #1
Kaskere
Junior Member
 
Location: Europe

Join Date: Jul 2018
Posts: 6
Default Samtools is not working

Hello,
I wrote a script for obtaining bam files, however it looks like it is not understanding flags given. I wrote a flag for no header - bS but still keep getting errors. I already feel desperated

#!/bin/bash -x

module load bio/samtools/1.10

export INPATH=/dir/subdir
export INPATH1=/dir/subdir1
export INPATH2=/dir/subdir2
export INPATH3=/dir/subdir3
export INPATH4=/dir/subdir4
export INPATH5=/dir/subdir5
export INPATH6=/dir/subdir6
export INPATH7=/dir/subdir7
export reference=/dir/subdir/refseq.fasta

samtools faidx $reference

for file in $INPATH/*.sam ;
do
bname=$(basename $file ".sam")
echo $bname
file=$INPATH/*.sam
echo file: $file
bamfile=$INPATH1/$bname".bam"
namesort=$INPATH2/$bname"_sorted.bam"
fixmate=$INPATH3/$bname"_sorted_fixmate.bam"
positionsort=$INPATH4/$bname"_sorted_fixmate_position.bam"
markdup=$INPATH5/$bname"_sorted_fixmate_position_markdup.bam"
bai=$INPATH6/$bname".bai"
stats=$INPATH7/$bname".txt"
echo $bamfile $namesort $fixmate $positionsort $markdup

samtools view -bT $reference $file > $bamfile
samtools sort -@ 12 -n $bamfile > $namesort
samtools fixmate -m $namesort > $fixmate
samtools sort -@ 12 $fixmate > $positionsort
samtools markdup $positionsort > $markdup
samtools index > $markdup
samtools flagstat $markdup > $stats
done


this is the error output

./samtools.sh: line 25: 348179 Segmentation fault samtools view -bT $reference $file > $bamfile
+ samtools sort -@ 12 -n file.bam
samtools sort: failed to read header from "file.bam"
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Old 09-01-2020, 02:01 PM   #2
LucyaSmit
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Location: Milwaukie

Join Date: Sep 2020
Posts: 1
Default

So strange that it happened
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