stuck at ...started mapping

[Joseph Mudd]

Hi Alex,

I have a run that is stalled at the mapping stage.  I'm needing some advice because the day before, I successfully completed a similar run with essentially the same effective command.  Would you be able to help?

I have attached the Log.out files of the successful and unsuccessful runs.  Please let me know if you need anything else.

thanks

jc

[Alexander Dobin]

Hi Joseph,

something went wrong with loading the genome and/or loading of the GTF file.

In the successful case:

Apr 09 17:05:16 ..... inserting junctions into the genome indices

Apr 09 17:05:18   Finished SA search: number of new junctions=0, old junctions=348621

This is correct as you used the same gtf as you used at the genome generation.

Unsuccessful:

Apr 11 12:08:59 ..... inserting junctions into the genome indices

Apr 11 12:18:53   Finished SA search: number of new junctions=315255, old junctions=33405

Somehow the junctions from the GTF do not match the junctions from the genome.

First, please run the mapping again to see if the problem persists.

Then, check that your genome directory did not get corrupted somehow. I would recommend re-generating the genome in from scratch.

Actually, you do not need to specify GTF at the mapping stage if you already used it at genome generation step.

Cheers

Alex