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Output variability between runs/systems? #286
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Thanks for adding ganon2 to the pipeline! Is the difference in results between machines happening with the same data? It should indeed always add up to 100%. With access to the files and commands used I can gladly check what is the issue. |
Yes the data are the same. Tried to upload them but the file is too big. Can be found here. ganon_GHA.zip Results by running ganon 2 through GHA |
Could you also send the |
This is the db used. |
I did some investigation. Using the reads 2612_pe against the provided database using the default parameters (v2.1.0): I get the following output (
From the files you sent me,
The report above has inconsistencies, therefore creating the issues reported here. I have some clues for what is happening (probably repeated headers) but I need to replicate it to be able to identify it and fix it. Could you please confirm if this data is correct and tell me is the exact command that taxprofiler is running? |
Thank you for looking into that. Yes, the data is correct. Regarding the command, I clone this branch and then I run:
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Thanks. I actually meant what is the ganon command generated by the taxprofiler. |
@sofstam probably the |
Sorry, I misread your comment above. Both commands:
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Can you also send the command used for the specific run |
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Thanks for the commands.
From the files you sent, 2 have problems, one in the local ( For the local ( For the GHA ( Before I go into any further debugging, can you double check if the |
Thanks for your reply. We only updated the module and we did not change anything in taxprofiler. Is this what you mean if the |
I mean to double check that all the inputs are correct, for example, the files are not corrupted or somehow duplicated. If not, I would need some more information to try understand what is happening. Could you re-run the 2 problematic files I mentioned above (just |
Sorry for my late reply. |
Thanks, the logs are looking alright. Can I also have the |
Had to rename to |
Thanks again. I could not detect any issue in those files and reports generated with them will add up to 100%. Note that they are different from the ones you sent before. The only way for me to try detect a possible bug would be to have the
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We are in the process in updating nf-core/taxprofiler to include ganon 2.0
During the establishment of CI tests we found there is slight variability in the output (where ganon 1 did not).
More specifically, @sofstam identified that while ganon v2 output compositionally was OK on our local machines, when the tests ran again but on GitHub Actions, the output appeared to not add up to 100% (99.64%)
Is this to be expected with the new update?
@sofstam can provide more info if necessary :)
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