If any Picard / Samtools experts can help ... Ran into a picard sortSam libc / python error that is only showing up when launched within Galaxy - AND ONLY WITH SORT_ORDER="queryname" option. I run the same command line as the tool does, but as galaxy user on command line, it runs ok?! Is there some resource limit I need to raise or lower in Galaxy context? The server has tonnes of memory and cores.
After the crash, I get this at bottom of STDERR along with error message. But I presume this may only be a side-effect:
[bam_index_core] the alignment is not sorted (HWI-ST521:273:C4EH9ACXX:4:1101:10000:53458/1): 2632 > 1357 in 75-th chr [bam_index_build2] fail to index the BAM file.
since no such message occurs via command line invocation.
Advice greatly appreciated,
Damion
********************************************* Details...
Galaxy tool run: after a few minutes finally yields this on stderr:
Picked up _JAVA_OPTIONS: -Xmx2048m -Xms256m *** glibc detected *** python: double free or corruption (top): 0x0000000005fb5200 *** ======= Backtrace: ========= /lib64/libc.so.6[0x3f4d675e66] ... /usr/lib64/libpython2.6.so.1.0(Py_Main+0xb62)[0x3f4f2ff8a2] /lib64/libc.so.6(__libc_start_main+0xfd)[0x3f4d61ed5d] python[0x400649] ... /galaxy_data/production1/job_working_directory/003/3583/galaxy_3583.sh: line 21: 46594 Aborted (core dumped) python ...
Command line version:(Taken directly from Galaxy tool execution info; extract below shows with QUIET=false though I get same success with QUIET=true, and I loaded the right picard.jar path into JAVA_JAR_PATH)
-salk tmp]$ _JAVA_OPTIONS=${_JAVA_OPTIONS:-'-Xmx2048m -Xms256m'} && export _JAVA_OPTIONS && java -jar $JAVA_JAR_PATH/picard.jar SortSam INPUT="/galaxy_data/production1/files/004/dataset_4987.dat" OUTPUT="/galaxy_data/production1/files/005/dataset_5408.dat" SORT_ORDER="queryname" VERBOSITY=ERROR VALIDATION_STRINGENCY=LENIENT Picked up _JAVA_OPTIONS: -Xmx2048m -Xms256m [Wed Sep 30 12:29:39 PDT 2015] picard.sam.SortSam INPUT=/galaxy_data/production1/files/004/dataset_4987.dat OUTPUT=/galaxy_data/production1/files/005/dataset_5408.dat SORT_ORDER=queryname VERBOSITY=ERROR VALIDATION_STRINGENCY=LENIENT QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json [Wed Sep 30 12:29:39 PDT 2015] Executing as galaxy@grl-salk on Linux 2.6.32-220.17.1.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.6.0_30-b30; Picard version: 1.136(f187319bf8bbde56892d5b5a1ce3fc0529b71a49_1436805856) IntelDeflater [Wed Sep 30 12:42:51 PDT 2015] picard.sam.SortSam done. Elapsed time: 13.21 minutes. Runtime.totalMemory()=1677066240
Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada