Hi, I seem to have a problem getting my output in the right location. Using the following call..
workdir="$1"
files=($(awk '{print $1}' $2 ))
infile="$workdir"/bam/${files[$SGE_TASK_ID]}.sorted.dedup.bam
macs2 predictd -i $infile -f BAM -g mm -m 5 50 --outdir "$workdir"/macs2/qc --rfile ${$infile%.sorted.dedup.bam}_model.r
..my input goes to $workdir/bam
Any suggestions? Thanks!
Your quoting is off by a bit. Here is some cleaned up code:
workdir="$1"
files=($(awk '{print $1}' $2 ))
infile="${workdir}/bam/${files[$SGE_TASK_ID]}.sorted.dedup.bam"
macs2 predictd -i ${infile} -f BAM -g mm -m 5 50 --outdir "${workdir}/macs2/qc" --rfile ${$infile%.sorted.dedup.bam}_model.r
The double quotes should work with the parameter expansion quotes ({}), not isolate the variable to an extent that it renders the context meaningless. EDIT: Your style of quoting is not wrong, it's just different. Sorry!
Thanks for your suggestions, always happy to improve my quoting. Unfortunately, this didn't seem to solve the issue:
INFO @ Tue, 04 Sep 2018 08:41:05: # Generate R script for model : /mnt/iscsi_speed/bam/SRR1202461_model.r
Any other ideas? Do you think it is a quoting issue?
Can you verify that the command looks OK? Change the last line to
echo "macs2 predictd -i ${infile} -f BAM -g mm -m 5 50 --outdir \"${workdir}/macs2/qc\" --rfile ${$infile%.sorted.dedup.bam}_model.r"
Also, it would help if you could give an example of how you invoke the script, with actual parameters.
I get the following error:
/opt/sge625/sge/default/spool/go-node-38/job_scripts/114466: line 17: macs2 predictd -i ${infile} -f BAM -g mm -m 5 50 --outdir "${workdir}/macs2/qc" --rfile ${$infile%.sorted.dedup.bam}_model.r: bad substitution
Here an attempt to clarify my parameters:
workdir="/mnt/iscsi_speed"
samples="${workdir}/samplesheet.txt" #tab-separated text file with file basename in first column
files=($(awk '{print $1}' $samples ))
infile="${workdir}/bam/${files[0]}.sorted.dedup.bam"
macs2 predictd -i ${infile} -f BAM -g mm -m 5 50 --outdir "${workdir}/macs2/qc" --rfile ${$infile%.sorted.dedup.bam}_model.r
That echo call made me realize what is wrong:
the $infile variable seems to overwrite the output dir because it contains an absolute path. Changing the call option to:
--rfile $(basename ${infile%.sorted.dedup.bam}_model.r)
solves the problem.
Thanks for pointing me towards the answer!
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