Hi Rob,
Apologies - I got the wrong sample (SC_GMFUL5306366 rather than the file
mentioned, SC_GMFUL5306338). I am now able to replicate the problem.
For information, yes, it was the same file as is on the FTP site.
For the correct sample, I’m seeing this too:
[alignment]:samtools view -H
SC_GMFUL5306338.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov.cram
[E::hts_hopen] fail to open file
'SC_GMFUL5306338.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov.cram'
[E::hts_open] fail to open file
'SC_GMFUL5306338.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov.cram'
samtools: failed to open
"SC_GMFUL5306338.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov.cram" for
reading: Success
I’ll follow up on this and see if we can get it sorted.
Thanks,
Susan.
> On 8 Nov 2017, at 14:00, Robert Davies <r...@sanger.ac.uk> wrote:
>
> On Wed, 8 Nov 2017, Susan Fairley wrote:
>
>> Thanks for letting me know about this.
>>
>> I’ve had a (very) quick look and the samtools view -H command is working for
>> me with v1.2.
>>
>> [alignment]:samtools
>>
>> Program: samtools (Tools for alignments in the SAM format)
>> Version: 1.2 (using htslib 1.2.1)
>>
>>
>> [alignment]:samtools view -H
>> SC_GMFUL5306366.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov.cram
>> @HD VN:1.5 SO:coordinate
>>
>> Any thoughts on what is causing this and the best way to address it are
>> welcome.
>
> Is that the file on the FTP site, or a different copy? If it's a different
> copy, you need to upload it to the FTP site to replace the broken file. It
> would also be a good idea to check the rest for the similar problems.
>
> Rob Davies r...@sanger.ac.uk
> The Sanger Institute http://www.sanger.ac.uk/
> Hinxton, Cambs., Tel. +44 (1223) 834244
> CB10 1SA, U.K. Fax. +44 (1223) 494919
>
>
> --
> 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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