From owner-bio-srs@hgmp.mrc.ac.uk Wed Jun 13 09:39:37 2001 Return-Path: Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id F1CAA17BC6 for ; Wed, 13 Jun 2001 09:39:36 +0100 (BST) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 9337E17BD1 for ; Wed, 13 Jun 2001 09:39:16 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6015) id 866B217BC7; Wed, 13 Jun 2001 09:38:52 +0100 (BST) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id C27D517B20 for ; Wed, 13 Jun 2001 00:30:33 +0100 (BST) Received: from mailbox3.ucsd.edu (mailbox3.ucsd.edu [132.239.1.55]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id AEF6617AB6 for ; Wed, 13 Jun 2001 00:30:22 +0100 (BST) Received: from rowan.netcom.ubc.ca (rowan.netcom.ubc.ca [137.82.1.15]) by mailbox3.ucsd.edu (8.10.1/8.11.0) with ESMTP id f5CNULR22279 for ; Tue, 12 Jun 2001 16:30:21 -0700 (PDT) Received: from nntp.itservices.ubc.ca (nntp.itservices.ubc.ca [137.82.194.1]) by rowan.netcom.ubc.ca (8.11.2/8.11.2) with ESMTP id f5CNUKn28138 for ; Tue, 12 Jun 2001 16:30:20 -0700 (PDT) Received: (from news@localhost) by nntp.itservices.ubc.ca (8.9.3+Sun/8.9.3) id QAA10065 for bionet-software-srs@moderators.isc.org; Tue, 12 Jun 2001 16:30:20 -0700 (PDT) To: bionet-software-srs@moderators.isc.org From: "Yaron S. Butterfield" Newsgroups: bionet.software.srs Subject: indexing embl Organization: Genome Sequence Centre Message-ID: <3B26A60B.83DF3D61@bcgsc.bc.ca> Reply-To: ybutterf@bcgsc.bc.ca Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="------------B4FF810AD5CB5D23DDEAA7F7" X-Trace: nntp.itservices.ubc.ca 992388618 10059 142.103.205.1 (12 Jun 2001 23:30:18 GMT) X-Complaints-To: abuse@interchange.ubc.ca X-Mailer: Mozilla 4.76 [en] (X11; U; Linux 2.2.12-20smp i686) X-Accept-Language: en Date: Wed, 13 Jun 2001 09:38:52 +0100 (BST) Sender: owner-bio-srs@hgmp.mrc.ac.uk Precedence: bulk --------------B4FF810AD5CB5D23DDEAA7F7 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: base64 Hello, If anyone can help me with this problem, it would be greatly appreciated. I have been trying to index EMBL on its own to see if I an do one library and try and detect the problem. It has failed on three separate attempts with various parameters and different systems. Specifically, after numerous error messages during indexing (srsbuild embl) that say: /mnt/disk2/home/srs6/icarus/db/embl.is:160: error: fseek failure, in file "/mnt/disk2/home/srs6/index/embl_ftd.ids" there was a segmentation fault and the indexing of EMBL stopped. Do you know what is causing the problem and how it can be resolved? I assume that the 160 means that the source is at line 160 of embl.is: ftgene: ~ {$In:[ftvals c:qual] $Out} /\/gene="([^"]+)/ {$Wrt:[s:$1]} ~ #" embl_ftd.ids is a binary file so I don't know how to check that. Thanks you! -- Yaron S. Butterfield Computational Biologist http://www.bcgsc.bc.ca Genome Sequence Centre BC Cancer Research Centre 600 West 10th Avenue Vancouver, BC V6R 1T6 --------------B4FF810AD5CB5D23DDEAA7F7 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Hello,
If anyone can help me with this problem, it would be greatly appreciated.

I have been trying to index EMBL on its own to see if I an do one library and try and detect the problem.  It has failed on three separate attempts with various parameters and different systems.  Specifically, after numerous error messages during indexing (srsbuild embl) that say:

/mnt/disk2/home/srs6/icarus/db/embl.is:160: error: fseek failure, in file
"/mnt/disk2/home/srs6/index/embl_ftd.ids"

there was a segmentation fault and the indexing of EMBL stopped.

Do you know what is causing the problem and how it can be resolved?    I assume that the 160 means that the source is at line 160 of embl.is:

 ftgene:     ~ {$In:[ftvals c:qual] $Out}
                  /\/gene="([^"]+)/ {$Wrt:[s:$1]} ~ #"

embl_ftd.ids is a binary file so I don't know how to check that.

Thanks you!
  

-- 
Yaron S. Butterfield
Computational Biologist
http://www.bcgsc.bc.ca
Genome Sequence Centre
BC Cancer Research Centre
600 West 10th Avenue
Vancouver, BC  V6R 1T6
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