Date: Thu, 24 Apr 2014 23:11:28 GMT From: "Jeremiah H. Savage" <jeremiahsavage@gmail.com> To: freebsd-gnats-submit@FreeBSD.org Subject: amd64/188979: openjdk 7.55.13_3, 1 IOException Cannot run program "bash" Message-ID: <201404242311.s3ONBS4k026137@cgiserv.freebsd.org> Resent-Message-ID: <201404242320.s3ONK1CQ090167@freefall.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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