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

[Jian-Ying Chiu]

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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