Hi there,
I am trying to create a loop to run multiple sorted bam files through picard to mark duplicates. My bash script is not working, and I'm at a loss.
#! /bin/bash
picard=/home/picard/picard.jar
sbam=/data/B_bam
for bamfile in *_sorted.bam
do
java -jar "$picard" MarkDuplicates INPUT="$sbam"/"$bamfile" OUTPUT="$sbam"/"${bamfile%_sorted.bam}"_md.bam METRICS_FILE="$sbam"/"${sbam%_sorted.bam}"_metrix
samtools index "$sbam"/"${bamfile%_sorted.bam}"_md.bam
done
Error Message:
Cannot read non-existent file: /data/B_bam/*_sorted.bam
•
written
by
brandnewatthis •
METRICS_FILE="$sbam"/"${bamfile%_sorted.bam}"_metrix
instead of
METRICS_FILE="$sbam"/"${sbam%_sorted.bam}"_metrix
also check there is a bam file under in the CURRENT WORKING directory: for bamfile in *_sorted.bam
but may be you wanted for bamfile in /data/B_bam/*_sorted.bam
also don't use a loop in a script shell when you can use Snakemake or Nextflow
don't use a loop in a script shell when you can use Snakemake or Nextflow
People need to start somewhere. Loops -> xargs/parallel -> snakemake/nextflow is the logical progression in learning automation IMO.
I find it weird that OP uses a mix of ${} and "..."/"...." (multiple quoted strings interleaved with multiple unquoted strings). Why not simply "${sbam}/${bamfile%_sorted.bam}_metrix"?
Sorry, I am very new at this and am just learning my way around these symbols! Thanks for the help :)
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