[bash] No result file is created after hisat2

Question

[Olajucan]

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.

[cpad0112]

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

Answer 1

[Carlo Yague]

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

[Olajucan]

Thank you. It really helped a lot :)