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
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