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[bash] No result file is created after hisat2

I can see that hisat2 is working because it shows the result on the terminal, but a result file is not created.

Here is my code.

#!/usr/bin bash

File='abc.txt'
Samples=$(cat $File)
IDX=/mnt/g/refs/wheat/iwgsc_refseqv2.1_assembly.fa
WD=/mnt/g/translocation

for Sample in $Samples
do
    hisat2 -x $IDX -p 16 -1 $WD/"$Sample"_R1.fastq.gz -2 $WD/"$Sample"_R2.fastq.gz | samtools sort > $WD/$Sample.bam
done

Please give me any advices. Thank you.

bash hisat2
• 1,325 views • link
updated by cpad0112 cpad0112 • written by Olajucan • Olajucan

when in doubt, echo every thing and run main function with small sized files.

• 0 views • link
written by cpad0112 cpad0112

1 answer

You can try decompose the pipe in two steps, set bash option -e (stops at first error) and add a few "echo" lines to know where you are in your script. Together, these changes should allow you to debug your code and see where you are getting an error or where the code is stuck. For instance:

set -e #stop script when it encounters an error

for Sample in $Samples
do
    echo ""; echo "processing sample : ${Sample}"; echo "... aligning..."
    hisat2 -x $IDX -p 16 -1 $WD/"$Sample"_R1.fastq.gz -2 $WD/"$Sample"_R2.fastq.gz -S temp.sam
    echo "... done"; echo "... sorting and indexing alignment..."
    samtools sort --write-index temp.sam > $WD/$Sample.bam
    echo "... done"
done
• 0 views • link
written by Carlo Yague Carlo Yague

Thank you. It really helped a lot :)

• 0 views • link
written by Olajucan • Olajucan

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