Picard MergeSamFiles Killed java -jar error

[sooheelee]

Any idea what is causing this user's error?

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@shlee Thank you for your answer. The command is MergeSamFiles

[Wed Feb 28 12:35:51 PST 2018] MergeSamFiles INPUT=[/home/bemmo/projects/rrg-jdrouin/bemmo/IAD/results/bwa/005.SS6.AB-Hu-Ex-A107/005.SS6.AB-Hu-Ex-A107.sam, /home/bemmo/projects/rrg-jdrouin/bemmo/IAD/results/bwa/006.SS6.AB-Hu-Ex-A107/006.SS6.AB-Hu-Ex-A107.sam, /home/bemmo/projects/rrg-jdrouin/bemmo/IAD/results/bwa/007.SS6.AB-Hu-Ex-A107/007.SS6.AB-Hu-Ex-A107.sam] OUTPUT=/home/bemmo/projects/rrg-jdrouin/bemmo/IAD/results/variants/AB-Hu-Ex-A107/AB-Hu-Ex-A107.bam USE_JDK_DEFLATER=true USE_JDK_INFLATER=true SORT_ORDER=coordinate ASSUME_SORTED=false MERGE_SEQUENCE_DICTIONARIES=false USE_THREADING=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Wed Feb 28 12:35:51 PST 2018] Executing as bemmo@cdr920.int.cedar.computecanada.ca on Linux 3.10.0-693.11.6.el7.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_121-b13; Deflater: Jdk; Inflater: Jdk; Picard version: 2.17.3-SNAPSHOT INFO 2018-02-28 12:35:51 MergeSamFiles Sorting input files using temp directory [/tmp/bemmo] INFO 2018-02-28 12:35:58 MergeSamFiles Processed 1,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 6s. Last read position: chr15:26,889,500 INFO 2018-02-28 12:36:06 MergeSamFiles Processed 2,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 7s. Last read position: chr6:35,231,712 INFO 2018-02-28 12:36:13 MergeSamFiles Processed 3,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 6s. Last read position: chr3:47,622,264 INFO 2018-02-28 12:36:19 MergeSamFiles Processed 4,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 6s. Last read position: chr7:15,613,034 INFO 2018-02-28 12:36:26 MergeSamFiles Processed 5,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 6s. Last read position: chr17:38,490,029 INFO 2018-02-28 12:36:33 MergeSamFiles Processed 6,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 7s. Last read position: chr15:81,358,297 INFO 2018-02-28 12:36:40 MergeSamFiles Processed 7,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 7s. Last read position: chr1:1,228,522 INFO 2018-02-28 12:36:47 MergeSamFiles Processed 8,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 7s. Last read position: chr6:87,589,803 INFO 2018-02-28 12:36:55 MergeSamFiles Processed 9,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 7s. Last read position: chr1:42,610,992 INFO 2018-02-28 12:37:02 MergeSamFiles Processed 10,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 6s. Last read position: chr1:235,728,122 /var/spool/slurmd/job5614122/slurm_script: line 27: 42247 Killed java -jar /cvmfs/soft.mugqic/CentOS6/software/picard/picard-2.17.3/picard.jar MergeSamFiles $file O=/home/bemmo/projects/rrg-jdrouin/bemmo/IAD/results/variants/AB-Hu-Ex-A107/AB-Hu-Ex-A107.bam USE_JDK_DEFLATER=true USE_JDK_INFLATER=true 12:37:10.830 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/cvmfs/soft.mugqic/CentOS6/software/picard/picard-2.17.3/picard.jar!/com/intel/gkl/native/libgkl_compression.so

This Issue was generated from your forums

[sooheelee]

@lbergelson @yfarjoun?

[lbergelson]

The only error I see is

/var/spool/slurmd/job5614122/slurm_script: line 27: 42247 Killed java -jar 

which implies that slurm killed their job for some reason. Maybe it's running over the memory requirements? Seems like a slurm / cluster configuration issue and not necessarily a picard one.

[sooheelee]

Thanks for the lightning response. I just asked the user what kind of memory are they giving the tool.

[sooheelee]

Another user has enlightened us with:

This is a memory issue of slurm your job exeeds the default settings