PICRUSt2 alpha version - occassional error on guppy step

[Jamie Kwok]

Hello PICRUSt2 developers, not sure if this is the right place to post a question on the alpha version of PICRUSt2 but the GitHub issues page told me to come here.

place_seqs.py (the first step of the workflow) ran successfully on a small dataset with one sample, but today I switched to using a four-sample dataset and got this error:

(...truncated, last lines shown)
INFO     ______ ____   ___           _   __ ______
        / ____// __ \ /   |         / | / // ____/
       / __/  / /_/ // /| | ______ /  |/ // / __
      / /___ / ____// ___ |/_____// /|  // /_/ /
     /_____//_/    /_/  |_|      /_/ |_/ \____/ (v0.2.1-beta)
INFO Number of ranks: 1
INFO Output file: place_seqs_tmp_2026r561/epa_out/epa_result.jplace
INFO 541 Sequences done!
INFO Time spent placing: 11s
INFO Elapsed Time: 14s
guppy tog place_seqs_tmp_2026r561/epa_out/epa_result.jplace -o OUTPUT.tre
Uncaught exception: Failure("Internal edge became -4.62762e-07 when attaching subtrees to 32476")
Fatal error: exception Failure("Internal edge became -4.62762e-07 when attaching subtrees to 32476")
Error running this command:
guppy tog place_seqs_tmp_2026r561/epa_out/epa_result.jplace -o OUTPUT.tre

To provide more info, the study_seqs.fna is actually concatenated from 4 FASTA files, one per sample, so I tested place_seqs.py on per-sample files. The first, second, third sample ran without error, but on the fourth sample, the same error as above occurred. Do you have some idea about this issue? Perhaps I shall ask the guppy or EPA-ng developers as well. Thank you for your attention.

Best regards,
Jamie

[Gavin Douglas]

Hey Jamie,

I haven’t seen that error before. Would you mind emailing me the FASTA file for the 4th sample privately? That would help me figure out the problem. It would also be helpful if you could provide me the temporary file that the intermediate files are in that would be helpful! You can keep this folder with the "—keep_tmp” option.

Best,

Gavin 

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[Gavin Douglas]

In case anyone comes across a similar problem, this was due to guppy (which was written with ppalcer jplace files in mind) being using on a jplace file output from EPA-NG. The tool gappa was written with EPA-NG generated jplace files in mind and I have swapped that tool into the picrust2 pipeline, which fixed this problem.

Also, see a cross-post of this question on the pplacer google group here: https://groups.google.com/forum/#!topic/pplacer-users/jWWVWLLtb6Q