Hi Tommy,
I’ve looked into this with the person who generated the file. Unfortunately, we
no longer have a copy of the BAM that was compressed to create the CRAM (or an
intact CRAM). Consequently, it looks like we will have to re-align the data.
In the meantime, I’ll remove the problem file from the FTP site.
Apologies for the inconvenience.
Kind regards,
Susan.
> On 8 Nov 2017, at 14:29, Susan Fairley <fair...@ebi.ac.uk> wrote:
>
> 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
>> <mailto: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 <mailto:r...@sanger.ac.uk>
>> The Sanger Institute http://www.sanger.ac.uk/ <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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