problem with a for loop
Heys!
I'm implementing GATK best practises for doing SNP calling and I have a problem in my first for loop. I'm trying to run it through /dev/stdin and /dev/stdout in order to avoid creating intermediate files, but when I run it, the last file (NEW_"$i".fastq) is created but with anything inside.
new_fastq () {
fastq=$1
for i in $(cat $fastq);
do
(java -Xmx2g -Djava.io.tmpdir=`pwd`/tmp -jar ~/softwares/picard/picard.jar FastqToSam FASTQ="$i"1.fastq.gz \
FASTQ2="$i"2.fastq.gz OUTPUT=/dev/stdout SAMPLE_NAME="$i" READ_GROUP_NAME="$i" TMP_DIR=`pwd`/tmp\
java -Xmx2g -Djava.io.tmpdir=`pwd`/tmp -jar ~/softwares/picard/picard.jar SortSam I=/dev/stdin \
O=/dev/stdout SORT_ORDER=queryname TMP_DIR=`pwd`/tmp \
java -Xmx2g -Djava.io.tmpdir=`pwd`/tmp -jar ~/softwares/picard/picard.jar MarkIlluminaAdapters \
I=/dev/stdin O=/dev/stdout METRICS=metrics_"$i".txt TMP_DIR=`pwd`/tmp \
java -Xmx2g -Djava.io.tmpdir=`pwd`/tmp -jar ~/softwares/picard/picard.jar SamToFastq \
I=/dev/stdin FASTQ=NEW_"$i".fastq CLIPPING_ATTRIBUTE=XT CLIPPING_ACTION=2 \
INTERLEAVE=true NON_PF=true TMP_DIR=`pwd`/tmp) &
done
wait
}
new_fastq fastq.txt
What am I missing?
Thanks in advance!
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Add a
set -xto the script and run it. That will print (to STDOUT) the exact commands being run, which you can use to debug.where should I add it? inside the loop?
Save the function to a script and add
set -xto the second line, the first line being#!/bin/bash.Can you try this?
OUTPUT=/dev/stdout/$i.bamon your first command and check the output?Sorry, maybe I did not explain properly want I want to obtain. There are four functions and I want that the output from the first one was to the second one and so on until the end, where this
FASTQ=NEW_"$i".fastqshould be createdIf I have an output in each of the functions it works, but I would like to avoid having intermediate files that in this case I will not use.
Oh, now I got it! You can simply remove the intermediate files as soon as they are used (I do this!) or you can try to use pipe
|between your functions. I've never tried this approach but doesn't hurt to try!