broadinstitute/picard

java.io.FileNotFoundException: /tmp/CSPI.tmp15948393444880722616/7573.tmp (Too many open files)

poojancf opened this issue · 1 comments

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I am trying to use MarkDuplicates
here is the code I am using
java -jar .~/picard.jar MarkDuplicates
INPUT=input.bam \
OUTPUT=ouput.bam
METRICS_FILE=output.metrics.txt CREATE_INDEX=true

The error is in find a tmp file.
Please let me know how to troubleshoot this error.

Thanks

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kockan commented

This looks like the same issue with this: #1911

The most likely scenario is that you need to increase your "maximum open file" limit defined by your operating system.
For example, on my machine this would be ulimit -a 10000 if I wanted to set this limit to 10000.