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Out of space when running SplitNCigarReads

ttgumpttgump New JerseyMember
edited May 2016 in Ask the GATK team

I know this question has been asked before. I have read the answers of previous post and did fix by the instructions, but this problem keeping occur. I have checked my storage space, there is enough space indeed. Here is my script:

java -d64 -Xmx32g -Djava.io.tmpdif=/home/RNAseq_SCZ/tmp -jar $GATK -T SplitNCigarReads -R /home/hg19seq/hg19.fa -I dedupped.bam -o split.bam -rf ReassignOneMappingQuality -RMQF 255 -RMQT 60 -U ALLOW_N_CIG
AR_READS

The output of error message:

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 3.5-0-g36282e4):
ERROR
ERROR This means that one or more arguments or inputs in your command are incorrect.
ERROR The error message below tells you what is the problem.
ERROR
ERROR If the problem is an invalid argument, please check the online documentation guide
ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
ERROR
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
ERROR
ERROR MESSAGE: Writing failed because there is no space left on the disk or hard drive. Please make some space or specify a different location for writing output files.
ERROR ------------------------------------------------------------------------------------------

Answers

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