Unicycler
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rrwick
Unicycler hangs when aligning long reads to assembly graph
I've recently run into an issue where Unicycler hangs when trying to aligning long reads to the assembly graph - all of the reads except for one will align, and then I get to:
Aligning reads (2018-11-15 12:44:12)
195,859 / 195,860 (100.0%)
At this point, Unicycler will stall seemingly indefinitely. I have no idea what's going wrong, I haven't had any similar issues when running Unicycler on other samples. Any help is greatly appreciated, the log from this unicycler run is attached.
Thanks!
This looks to be an intermittent bug - I tried running again on the exact same files, and this time assembly completed no problem...
I have the same issue; around 1/4 of my assemblies got stuck during this phase. I've found that renaming the sam file by removing the 'incomplete' suffix and and restarting the assembly allow to complete the assembly process.
Any help would be greatly appreciated since this issue prevent the sequential processing of samples.
Thanks!
I am experiencing the same problem. I am running unicycler through a conda environment inside a docker container, but i dont think this is causing the issue. This error occured two times in a row on the same dataset, other data started in the same batch was working fine.
For what it's worth, I've found that this happens only happens with more recent versions of Unicycler - I was using v0.4.7 when I encountered this issue, I've since downgraded to v0.4.4 and have yet to encounter the same problem.
The same has happened a lot to me since I upgraded to v0.4.7. It is very annoying. I have also seen that returning to v.0.4.4 avoids the issue.
Any update on this issue? Having the same problem with unicycler stalling during read alignment when it reaches 100%
I've found that renaming the sam file by removing the 'incomplete' suffix and and restarting the assembly allow to complete the assembly process.
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