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MikkelSchubert / paleomix

Pipelines and tools for the processing of ancient and modern HTS data.
https://paleomix.readthedocs.io/en/stable/
MIT License
43 stars 19 forks source link

Issue running the example bam_pipeline #19

Closed ldutoit closed 5 years ago

ldutoit commented 5 years ago

Hi,

we are trying to run the latest paleomix version. Everything is installed but we cannot troubleshoot the error we get back trying to run:

paleomix bam_pipeline run 000_makefile.yaml

pipe_python_46912708195856.stderr.txt

error.log

Basically we get a truncated bam out of BWA ( see error log and attached .stderr file).

Could you maybe help us with that? Thank you so much for your help!

Ludovic Dutoit & Alex Verry University of Otago, New Zealand

MikkelSchubert commented 5 years ago

Dear Ludovic and Alex,

Please try to upgrade your copy of PALEOMIX and let me know if that fixes your problem. This particular bug should have been fixed in PALEOMIX v1.2.13, while you appear to be running v1.2.4.

Best regards, Mikkel

On Wed, Nov 28, 2018 at 2:49 AM Ludovic Dutoit notifications@github.com wrote:

Hi,

we are trying to run the latest paleomix version. Everything is installed but we cannot troubleshoot the error we get back trying to run: ''' paleomix bam_pipeline run 000_makefile.yam ''' error.log https://github.com/MikkelSchubert/paleomix/files/2622508/error.log

Basically we get a truncated bam out of BWA ( see error log and attached .stderr file).

Could you maybe help us with that? Thank you so much for your help!

Ludovic Dutoit & Alex Verry University of Otago, New Zealand

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/MikkelSchubert/paleomix/issues/19, or mute the thread https://github.com/notifications/unsubscribe-auth/ACTMa--wHALoFfa8N5v6hPRamM4Ci1guks5uzeu-gaJpZM4Y2sAM .

ldutoit commented 5 years ago

Hi Mikkel,

thank you very much for your quick reply.

Ludo

On Wed, 28 Nov 2018 at 20:14, Mikkel Schubert notifications@github.com wrote:

Dear Ludovic and Alex,

Please try to upgrade your copy of PALEOMIX and let me know if that fixes your problem. This particular bug should have been fixed in PALEOMIX v1.2.13, while you appear to be running v1.2.4.

Best regards, Mikkel

On Wed, Nov 28, 2018 at 2:49 AM Ludovic Dutoit notifications@github.com wrote:

Hi,

we are trying to run the latest paleomix version. Everything is installed but we cannot troubleshoot the error we get back trying to run: ''' paleomix bam_pipeline run 000_makefile.yam ''' error.log https://github.com/MikkelSchubert/paleomix/files/2622508/error.log

Basically we get a truncated bam out of BWA ( see error log and attached .stderr file).

Could you maybe help us with that? Thank you so much for your help!

Ludovic Dutoit & Alex Verry University of Otago, New Zealand

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/MikkelSchubert/paleomix/issues/19, or mute the thread < https://github.com/notifications/unsubscribe-auth/ACTMa--wHALoFfa8N5v6hPRamM4Ci1guks5uzeu-gaJpZM4Y2sAM

.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/MikkelSchubert/paleomix/issues/19#issuecomment-442344094, or mute the thread https://github.com/notifications/unsubscribe-auth/AELGAXG-bbNzEB3lOco9mLFrJQg6bRlTks5uzjfxgaJpZM4Y2sAM .