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cancerit / telomerecat

Telomerecat: The telomere computational analysis tool
GNU General Public License v3.0
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lots of lines showing "Could not retrieve index file for...." #14

Closed dylanzhao1993 closed 4 years ago

dylanzhao1993 commented 4 years ago

I have also met the same issue as @eb32142 . There are lots of lines showing "Could not retrieve index file for....". So the telomere length cannot be estimated. But I can make sure that the bam file and its index file are under the same path.

byb121 commented 4 years ago

Would you be able to provide me with a minimum file to reproduce the issue?

dylanzhao1993 commented 4 years ago

There are the errors showed in error file.

dylanzhao1993 commented 4 years ago

Hi @byb121 , I have run the program according to your advice for @eb32142 . But it still showed the same error.

dylanzhao1993 commented 4 years ago

And I have also generated a new index file for this job. So I may have the exact same issue as @eb32142 . Did he resolve this issue eventually?

dylanzhao1993 commented 4 years ago

image

byb121 commented 4 years ago

That issue is not solved either.

Does you BAM file have @PG lines in its header? Could you post them here, or probably the whole header if it's ok.

byb121 commented 4 years ago

It's possible that isaac's bgzip level causes the issue. Could you convert your BAM to an uncompressed BAM and run telomerecat again:

samtools view -bu your.bam > new.bam
dylanzhao1993 commented 4 years ago

image

dylanzhao1993 commented 4 years ago

Not work. Same error again.

dylanzhao1993 commented 4 years ago

image

keiranmraine commented 4 years ago

You didn't create a new index for the bam based on that message.

dylanzhao1993 commented 4 years ago

You didn't create a new index for the bam based on that message.

Thank you for your notification. I will try it again.

dylanzhao1993 commented 4 years ago

image

dylanzhao1993 commented 4 years ago

It still cannot work.

byb121 commented 4 years ago

I suspect it's an issue from pysam's new updates. What's your pysam version?

dylanzhao1993 commented 4 years ago

the version is 0.16.0.1

byb121 commented 4 years ago

Thanks, I'll run some tests to confirm it.

byb121 commented 4 years ago

Reverting pysam to version 0.15.3 should eliminate those warnings, and perhaps will eliminate the truncated file error as well. Please have a go and let me know your outcome. Thanks.

dylanzhao1993 commented 4 years ago

@byb121 @keiranmraine It works now. Thank you very much for your help!!!!!!!