error occurred in 3-unzip/2-htigs step of falcon_unzip.

[lee123lee]

Error message
the message in 3-unzip/2-htigs/chunk_002716F/run-P3105148f148918.bash.stderr:
[ERROR 2018-11-05 02:39:40] Failure in generate_haplotigs_for_ctg((u'002716F', u'../../0-phasing/002716F/uow-00/proto', './uow-002716F', u'../../..', False)) Traceback (most recent call last): File "~/miniconda2/envs/assembly/lib/python2.7/site-packages/falcon_unzip/mains/graphs_to_h_tigs_2.py", line 74, in run_generate_haplotigs_for_ctg

.........skipping...........

raise Exception(msg) Exception: Skipping additional subgraphs of the primary contig: 002716F. The graph has multiple primary components.

How can I fix it? Or, how to skip the contig(002716F)? Actually, I have three similar contig that make me can't go on .

[marcopessoa]

Looks like the same issue reported in #31

[lee123lee]

Thanks for your response.
This issue really looks like #31, but I can not find the solution for the repeated issue under #31. So I open the new issue.
Do you have any idea about the issue? Thanks.

[marcopessoa]

Not really, there was no response in #31, I am currently using a previous commit of FALCON-integrate from march 2018 to continue my project.

[lee123lee]

oh! I checked the problem fc_run assembly in my item when I saw your comment under #31. I found the same configure, fc_run is falcon-kit 1.2.4, and fc_unzip is falcon-kit 1.2.3. Interestingly, the cause of all this is that I update the pb-assembly after fc_run as well. So, now I am running a new assembly by the same version pb-assembly.
Maybe this is the solution. good luck to us!

[isovic]

Hi,
Thank you for reporting this issue - it indeed its the same as #31.
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.
Do you manage to finish your assembly process using the latest version?

[marcopessoa]

My run is in the final polishing step with Arrow, so I would say yes. Thanks for the feedback!

[isovic]

Thank you as well!
Ok, I will close both this issue and issue #31. In case there are more failures like this, don't hesitate to reopen one of the two.
Best regards,
Ivan.