BAI Index file issue

[Salavati, Mazdak]

Dear Developer,

I’m trying to use your bamCorrelate package (deepTools) to compare bamfiles and although I have indexed all my files using Samtools (index) I’m still facing this error :

 

mazdax@mazdax-biolinux8[Cow] bamCorrelate bins --bamfiles ./68_RO_RGID_undp.bam 134_RO_RGID_undp.bam 838_RO_RGID_undp.bam --outFileName ./polyA_vs_ribominus.png

 

/usr/local/lib/python2.7/dist-packages/deeptools/config/__init__.py:60: UserWarning: Module pysam was already imported from /usr/local/lib/python2.7/dist-packages/pysam-0.8.4pre-py2.7-linux-x86_64.egg/pysam/__init__.pyc, but /usr/local/lib/python2.7/dist-packages/RSeQC-2.6.3-py2.7-linux-x86_64.egg is being added to sys.path

  import pkg_resources

 

./68_RO_RGID_undp.bam does not appear to have an index. You MUST index the file first!

 

I place the .bam and .bam.bai files in the same folder. I would appreciate your help on this issue.

 

Kind regards,

Mazdak

------------------------------------------

Dr. Mazdak Salavati   D.V.M , Ph.D

Postdoctoral Researcher

Production and Population Health

 

105 TARC

Royal Veterinary College

Hawkshead Lane

North Mymms, Hatfield

Herts. AL9 7TA

T: +44 (0)1707 66 6811

Email : msal...@rvc.ac.uk

 

                    

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[Fidel Ramirez]

Hi,

There must be a problem with your files. Did you check that the .bai files are not empty or not readable? What is the output of ls -l | grep bam ?

-fidel

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> Fidel Ramirez

Hello! I am having this same issue. My .bam and .bam.bai files are in the same folder, and I think that the files are okay because I have loaded them into the genome browser and they work there. I have tried re-making and re-indexing the files, but nothing has worked. Do you have any ideas what could be wrong?

Thanks!

[Fidel Ramirez]

Honestly, I don't know what could be wrong. Maybe you can simply try to open a python shell and type:

>>> import pysam

>>> pysam.Samfile("(name of bam file")

And see what sort of error message you get.

Best,

Fidel