PPlacer deson't process all genomes it started with.

[SilasK]

I miss 7 genomes in the output of cluster_wf

Environment

• Installed via pip (include the output of pip list)
• Using a conda environment (include the output of conda list && conda list --revisions)
• Using a Docker container (include the IMAGE ID of the container)

v1.7

Server information

• CPU: grep -m 1 "^model name" /proc/cpuinfo && grep -c "^processor" /proc/cpuinfo
• RAM: grep "^MemTotal" /proc/meminfo
• OS: cat /etc/os-release

Debugging information

• gtdbtk.log has been included (drag and drop the file to upload).
• Genomes have been included (if possible, and there are few).

[2021-11-11 06:50:37] TASK: Placing 500 bacterial genomes into reference tree with pplacer using 16 CPUs (be patient).
[2021-11-11 06:50:37] INFO: pplacer version: v1.1.alpha19-0-g807f6f3
[2021-11-11 08:27:57] INFO: Calculating RED values based on reference tree.
[2021-11-11 08:28:10] TASK: Traversing tree to determine classification method.
[2021-11-11 08:28:11] INFO: Completed 493 genomes in 0.48 seconds (1,019.58 genomes/second).
[2021-11-11 08:28:25] TASK: Calculating average nucleotide identity using FastANI (v1.32).
[2021-11-11 08:58:46] INFO: Completed 27,300 comparisons in 30.31 minutes (900.59 comparisons/minute).
[2021-11-11 08:58:49] INFO: 375 genome(s) have been classified using FastANI and pplacer.

Additional comments

gtdbtk. warnings and failed genomes is empty.

[pchaumeil]

Hello,

We recently received a similar issue from another user ( please see ticket #356 ).
It seems pplacer drops genomes during the placement steps.
If you try to re-run the missing genomes my guess is that they will run through pplacer and GTDB-Tk without issue.

Would it be possible to send us your 500 genomes so we can investigate further and see if we can reproduce the problem?

Thanks,
Pierre