Failure in generate_haplotigs_for_ctg((u'000519F', u'../../0-phasing/000519F/uow-00/proto', './uow-000519F', u'../../..', False)) about pbbioconda

[isovic]

Ok, thank you!
Closing this issue then.
Best regards,
Ivan.

[marcopessoa]

Same issue here. Exception message states "Exception: Skipping additional subgraphs of the primary contig: XXXXXXX. The graph has multiple primary components."

Subscribing to thread and hoping this gets fixed soon.

[marcopessoa]

Not sure if this could be the cause, but when I ran fc_run for assembly I had falcon-kit 1.2.2 installed. Then I updated pb-assembly, and when running fc_unzip.py I had falcon-kit 1.2.3. I am running a new assembly with falcon-kit 1.2.4 and falcon-unzip 1.1.4 with the same dataset and will check if this happens again.

[isovic]

Hi,
Thank you for reporting this issue.
We addressed it and it should have been resolved in falcon-unzip 1.1.4 available in pb-falcon>=0.2.4 and pb-assembly>=0.0.2.
It looks like you have tried the latest version recently - could you confirm whether it worked for you well?

[marcopessoa]

I got to the polishing step with Arrow, so Unzip worked fine. No issues so far.