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  • 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"

  • #2
    So strange that it happened

    Comment

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