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fmalmeida / MpGAP

Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads
https://mpgap.readthedocs.io/en/latest/
GNU General Public License v3.0
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100% missing in Busco #54

Closed scintilla9 closed 7 months ago

scintilla9 commented 8 months ago

Hi Dr Almeida,

I was playing around the pipeline, everything want well, however, I found issue in Busco. The output summary showed no buscos were found in query genome (100% missing) against bacteria_odb9. I also found some issues in quast github, seems related to LD_LIBRARY_PATH (https://github.com/ablab/quast/issues/88).

I also tried on standalone Busco container (v5.4.7) with bacteria_odb10, and got 100% complete single copy. It confirms that the assembled genome is well.

Could you please kindly check if it could be fixed?

Best, CW

fmalmeida commented 8 months ago

Hi @scintilla9 , Thanks for reporting it. I think it might have happened in the last docker image update I made.

I will take a look at this and let you know. Glad tk hear that the assembly is good.

fmalmeida commented 8 months ago

Hi @scintilla9 , Thank you very much for reporting this error. I have found the problem, and realised that I have done a major mistake a few weeks ago, which I have merged a branch with new features (considered dev) in the master branch instead of the dev branch.

Luckly, I was able to use the latest tagged version, v3.1.4 to revert the master branch back to its right version and passed on the developmental code to the dev branch where it always belonged.

So now, things are supposed to be correct:

Once again, thanks for reporting it.

Can you give a try using one of the following options so I can be sure it is fine and close this ticket?

scintilla9 commented 7 months ago

Hi @fmalmeida ,

Sorry for the late reply, I was unavailable for testing the pipeline until yesterday. The master branch / v3.1.4 works fine! I got busco result with 95% completeness.

Thanks for fixing it.

fmalmeida commented 7 months ago

Thanks. I will close the ticket.

Also added some merging rules to only allow PRs to merge code in master to try to avoid this problem in the future.

Thanks for reporting it.