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List:       freebsd-amd64
Subject:    amd64/188979: openjdk 7.55.13_3, 1 IOException Cannot run program "bash"
From:       "Jeremiah H. Savage" <jeremiahsavage () gmail ! com>
Date:       2014-04-24 23:11:28
Message-ID: 201404242311.s3ONBS4k026137 () cgiserv ! freebsd ! org
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> Number:         188979
> Category:       amd64
> Synopsis:       openjdk 7.55.13_3,1 IOException Cannot run program "bash"
> Confidential:   no
> Severity:       non-critical
> Priority:       low
> Responsible:    freebsd-amd64
> State:          open
> Quarter:        
> Keywords:       
> Date-Required:
> Class:          sw-bug
> Submitter-Id:   current-users
> Arrival-Date:   Thu Apr 24 23:20:00 UTC 2014
> Closed-Date:
> Last-Modified:
> Originator:     Jeremiah H. Savage
> Release:        10.0
> Organization:
> Environment:
FreeBSD chdm_stor_001 10.0-RELEASE FreeBSD 10.0-RELEASE #0 r260789: Thu Jan 16 \
22:34:59 UTC 2014     root@snap.freebsd.org:/usr/obj/usr/src/sys/GENERIC  amd64
> Description:
I've downgraded to 2,1 and no longer have the problem below from 3,1

I'm not that informed on java, but perhaps this is the related to the recent bug fix

http://bugs.java.com/view_bug.do?bug_id=8029974 : (process) Use posix_spawn, not \
fork, on S10 to avoid swap exhaustion

as it is listed as part of 7u55
http://www.oracle.com/technetwork/java/javase/2col/7u55-bugfixes-2180733.html

From what I can tell, DeNovoCheck is calling another program (samtools) through the \
shell, and is unable to do so in 3,1. Perhaps process spawning is part of the \
problem.

----
[claudia@chdm_stor_001 ~/TaskForceData/DM615]$ java -Xmx6G -jar \
/home/claudia/bin/DeNovoCheck/DeNovoCheck.jar -properties \
~/TaskForceData/DM615/DNC_Properties_DM615-0001.txt  0 [main] DEBUG DeNovoCheck  - \
[DNC] Read properties from: \
/home/claudia/TaskForceData/DM615/DNC_Properties_DM615-0001.txt 2 [main] INFO \
DeNovoCheck  - [DNC] Reading Mutation file: \
/hdstor/home/claudia/TaskForceData/DM615/DM615-0001.VARFILT3.VARFILE 183 [main] INFO \
RunPipeline.DiffsParser  - [DP] Read 401 mutations from \
/hdstor/home/claudia/TaskForceData/DM615/DM615-0001.VARFILT3.VARFILE 183 [main] INFO \
DeNovoCheck  - [DNC] Read 401 mutations 197 [main] FATAL PileupInterface  - [PI] \
IOException Cannot run program "bash": error=2, No such file or directory 197 [main] \
ERROR DeNovoCheck  - Error in samtools call 197 [main] WARN DeNovoCheck  - Error in \
checking the mutations, halting proccess 197 [main] INFO DeNovoCheck  - DONE, result \
summary:

> How-To-Repeat:
Run DeNovoCheck http://sourceforge.net/projects/denovocheck/

The input files are rather large (16GB bam files).


> Fix:


> Release-Note:
> Audit-Trail:
> Unformatted:
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