On Thu, May 18, 2017 at 06:35:41PM +0000, Andrew Maksymowsky wrote:
> When I attempt to open a remote file for viewing from the thousand
> genomes project ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/phase1/dat
> a/HG00149/alignment/HG00149.mapped.ILLUMINA.bwa.GBR.low_coverage.201011
> 23.bam I recieve the following error and am unable to view the file:
...
> This only happens with files larger than round 5 Gb. For anything
> smaller the command runs successfully I have tried on multiple machines
> with multiple operating systems from multiple different networks.
> (Centos6.4, Ubuntu 16.04, Centos 7). I have tried on a server with 120
> Gb of RAM which makes me suspect that this is not an insufficient
> memory issue.
The file works for me, so I'm clutching at straws here. Maybe it's a
32-bit large-file support issue, or maybe it's something to do with
knet vs curl.
How did you build samtools/htslib? (straight make or
./configure;make?). If you went the configure route, would you please
email me a copy of the config.log file? Also, what OS version and
hardware are you using please?
James
--
James Bonfield (j...@sanger.ac.uk) | Hora aderat briligi. Nunc et Slythia Tova
| Plurima gyrabant gymbolitare vabo;
A Staden Package developer: | Et Borogovorum mimzebant undique formae,
https://sf.net/projects/staden/ | 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.
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