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Pangolin v4.2 stuck on "Using UShER as inference engine." #500
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Sorry to hear that @VinceLiAB. If you run ' |
The usher version was definitely the culprit. I updated to v0.6.1 from v0.6.0 and it is working again. Thanks for the quick response! |
Great, glad it's working for you now! |
@AngieHinrichs v0.6.1 still seems to have a problem with small test input. This is why the tests for the bioconda recipe update are failing. |
Oof, thanks @wm75! I tested with tests/test-data/sequence1.fasta which has a single sequence... but I did not test with reference.fasta! -- which leads to a VCF file with no data lines (no mutations), which might be triggering some corner case in usher-sampled. @yceh can you please take a look? Here is the header-only VCF file that is causing usher-sampled to hang:
|
Ah, that makes a lot of sense, thanks! Unfortunately, the bioconda test cannot use the test-data sequence because that's not getting installed. |
Yes, it is sufficient to change just a single base in the sequence before using it as a test input! |
Ah, nice idea with the patch! Something like this should work:
[Edit: NM I see you found your own 😁] |
@yceh and @yatisht have already fixed it and released usher v0.6.2: https://github.com/yatisht/usher/releases/tag/v0.6.2 |
Thanks @AngieHinrichs @yceh @yatisht! pangolin 4.2 will also appear on usegalaxy.eu later today, together with pangolin 4.1.3 pinned to the same core dependencies, i.e. both Galaxy tool versions will use:
This way comparisons between usher and usher-sampled should be relatively simple. |
Great, thanks so much @wm75!
Just for the record, results should be overall very consistent but not identical, especially when sequences have Ns in lineage-defining positions. usher may place a sequence on a node that starts a lineage even if it has only Ns at the defining mutations (the mutations on the node that starts the lineage), but usher-sampled doesn't match all-Ns on the node at the end of the path -- it places it on the parent of that node, so in cases like that the sample will be assigned the parental lineage by usher-sampled. Also, usher would find some redundant equally parsimonious placements (EPPs) while usher-sampled is more stringent, so in cases where multiple EPPs would cause different assignments and pangolin takes a vote, the outcomes can be different. [Next on my list: get rid of the voting; with amplicon dropout issues it's looking like a bad idea now, see #492.] |
Hi,
Pangolin v4.2 analysis seems to be stuck on the step "Using UShER as inference engine.". I have tried analyzing different sets of data ranging from 20 to 90 samples and they all stop at the same step.
No error messages are given and I didn't encounter this issue prior to the update.
Thank you.
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