amd64/188979: openjdk 7.55.13_3, 1 IOException Cannot run program "bash"

[Jeremiah H. Savage]

>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 at 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 at 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: