SamSort gatk invalid argument / no space left on disk

Question

[Eliveri]

I have a nextflow pipeline which runs the following argument in script for a process using memory '16 GB':

gatk --java-options "-Xmx16g -Xms16g" SortSam -R $ref -I ${pair_id}.clean.bam -O ${pair_id}.sorted.bam -SO coordinate --CREATE_INDEX true

At first the issue was java.io.IOException: No space left on device So I referred to the following posts

• Out Of Disk Space With Picard Tools ?
• Setting temporary directory for GATK4 SortSam

And added the -Djava.io.tmpdir=`pwd`/tmp but now I am still having issues. I get error ERROR: Invalid argument '-R'.

gatk --java-options "-Xmx16g -Xms16g -Djava.io.tmpdir=`pwd`/tmp" SortSam -R $ref -I ${pair_id}.clean.bam -O ${pair_id}.sorted.bam -SO coordinate --CREATE_INDEX true TMP_DIR=`pwd`/tmp

I tried with various combinations

gatk --java-options "-Djava.io.tmpdir=`pwd`/tmp"  "-Xmx16g -Xms16g" SortSam -R $ref -I ${pair_id}.clean.bam -O ${pair_id}.sorted.bam -SO coordinate --CREATE_INDEX true TMP_DIR=`pwd`/tmp

Sometimes it does not recognize the "-Djava.io.tmpdir=.." parameter, sometimes it does not recognize the "-Xmx16g -Xms16g" parameter, and sometimes it does not recognize -R after SamSort.

[iraun]

Hi! What kind of error do you get? Could you copy paste it? Also, could you copy paste the actual nextflow code (not just the gatk command)? When I call gatk within nextflow I don't add quotes in -Xmx${java_memory}m. Regarding the tmp path, maybe it is safer to provide a full path, without calling pwd and such.

[Pierre Lindenbaum]

for a start You put two values for --java-options . Use ${PWD} instead of a call to pwd. Furthermore, why using the slow gatk when you can use samtools sort ?

[Eliveri]

Thank you all, --TMP_DIR . solved the issue