[ensembl-dev] Unable to upload remote BAM file to local site

[Anne Lyle]

Hi Wally

That’s quite an old release of Ensembl (June 2011), and we’ve made a lot of improvements to our code since then, so I would definitely recommend upgrading to a more recent version before looking further into this problem.

Regards

Anne


Anne Lyle
Ensembl Web Developer
European Bioinformatics Institute

On 22 Apr 2014, at 10:25, Jian-Ying Chiu <jychiu at ym.edu.tw> wrote:

> Hi,
> 
> I got an error when I was trying to upload a BAM file to our local
> bacteria ensembl genome browser (version 63). 
> 
> [Error from error_log]========================
> http://.../AN077_AYE_rmdup_rename_sorted.bam open: bad file descriptor at /usr/local/ensembl_bacteria/modules/EnsEMBL/Web/Object/UserData.pm line 113.
> Failed to open BAM http://.../AN077_AYE_rmdup_rename_sorted.bam at /usr/local/ensembl_bacteria/modules/EnsEMBL/Web/Object/UserData.pm line 123.
> 
> Failed to open BAM index for http://.../AN077_AYE_rmdup_rename_sorted.bam at /usr/local/ensembl_bacteria/modules/EnsEMBL/Web/Object/UserData.pm line 124.
> 
> =======================================
> 
> I am very sure that the .bai file was put in the same dir. with BAM file.
> 
> And also, I can open this BAM file in command line. Does anyone know
> 
> where the problem is?  
> 
> Should I upgrade our webcode to newer version for this issue? Besides,
> 
> which version of samtools and Bio::samtools should I use?
> 
> 
> 
> All the Best,
> 
> Wally Chiu  
> 
> 
> 
> -- 
> ======================
> Jian-Ying Chiu, R.A.
> Institute of Biomedical Informatics
> National Yang-Ming University
> Taipei, Taiwan
> Tel: +886-2-28267000 ext 7359
> ======================
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