amd64/188979: openjdk 7.55.13_3, 1 IOException Cannot run program "bash"
Jeremiah H. Savage
jeremiahsavage at gmail.com
Thu Apr 24 23:20:01 UTC 2014
>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:
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