sortsamrefname stalling at end for hours

[antmarge]

Subject of the issue

sortsamrefname Makes consistent progress but then stalls at "1 minute remaining"

Environment

• version of jvarkit: 2d33719edc69a979a2b6366351ca6f0b59959755
• version of java: 1.8.0_131
• the value of ${JAVA_HOME}: /share/software/user/open/java/1.8.0_131
• which OS: Linux 7.3.1611

Steps to reproduce

input=/abs/path/to/bamfile.bam (is a valid bam file as verified by samtools) output=/abs/path/to/bamfile.sorted.bam SORT_SAM_REFNAME=/abs/path/to/bin/jvarkit/dist/sortsamrefname.jar

Run java -jar $SORT_SAM_REFNAME $input -o $output

Stalled output

Makes consistent progress for the first 45 minutes, then stalls at last chromosome, at "1 minute remaining" for hours [INFO][SAMSequenceDictionaryProgress]Count: 803650002 Elapsed: 45 minutes(96.82%) Remains: 1 minute(3.18%) Last: 21:41150167

[antmarge]

Update: It finished at about 3 hours, Staying on the last step for over 2 hours. Any idea as to why this is the case?

[lindenb]

no idea, could be a memory problem or too many files open or no more space on device ? isn't there an error message ? Try to increase the jvm memory with xmx or maxRecordsInRam(http://lindenb.github.io/jvarkit/SortSamRefName.html)

java -Xmx3g -jar sortsamrefname --maxRecordsInRam 1000000 --tmpDir . -o out.bam in.bam

[lindenb]

It finished at about 3 hours

does that mean that it ends with success or with failure ?

[antmarge]

Finished with success.

[lindenb]

Any idea as to why this is the case?

the progress bar stops after all the reads have been loaded in the temporary directory. At this point, the program looks over all the temporary files and starts writing...