Dear James and Martin, Thank you for the pointers. GATK UG gave me a clear "Too many open files" error on the same set of files. Once I increased the limit using "ulimit -n" it all worked fine.
I can confirm that "too many open files" was the issue. Cheers, Hans ----------------------------------------- Dr. Hans Daetwyler | Research Leader Computational Biology Biosciences Research | Agriculture Victoria | DEDJTR Senior Research Fellow | Applied Systems Biology | La Trobe University AgriBio Centre, 5 Ring Rd., Bundoora 3083, Victoria T: 03 9032 7037 | E: [email protected] From: James Bonfield <[email protected]> To: [email protected], Cc: [email protected] Date: 01/12/2016 04:51 AM Subject: Re: [Samtools-help] Limit number of bam files Samtools1.3 On Mon, Nov 28, 2016 at 11:16:55AM +1100, [email protected] wrote: > XXX.bam is the 1995th file, and YYY.bam is the 1996th. When YYY.bam > becomes the 1995th (because I removed an earlier bam file in the list) > file the error passes XXX.bam and prints at YYY.bam. Try the linux "ulimit -a" command to see if this is an OS imposed limitation. Hopefully "ulimit -n" will permit you to adjust the number of open files. If you're unable to raise it, about the only course of action left is to merge groups of, say, 100 files into intermediaries first. (I'm not sure whether this has any impact on mpileup & bcftools results though.) James -- James Bonfield ([email protected]) | Hora aderat briligi. Nunc et Slythia Tova | Plurima gyrabant gymbolitare vabo; A Staden Package developer: | Et Borogovorum mimzebant undique formae, https://urldefense.proofpoint.com/v2/url?u=https-3A__sf.net_projects_staden_&d=DgIBAg&c=JnBkUqWXzx2bz-3a05d47Q&r=w6yf14nyxUbiCn2GwWVtJrXHKyEzgK03GZUj0gEfAIs&m=OJrJK-DFZE_fy8G1q5VHCeSXZeReWlwF5ze4wZ0dPS0&s=SYbphhCQuhjEOXegfKYuql47Zx1VSuEZmcmsKxZJvB8&e= | Momiferique omnes exgrabure Rathi. -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. ******************************************************************************** Department of Economic Development, Jobs, Transport and Resources, Government of Victoria, Victoria, Australia. This email, and any attachments, may contain privileged and confidential information. If you are not the intended recipient, you may not distribute or reproduce this e-mail or the attachments. If you have received this message in error, please notify us by return email. ********************************************************************************
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