Faillure : Stopping in STEP18 -> 17.checkM_batch.pl

[bbalog87]

Hi @jtamames,

While running the pipeline, I encountered a recurring issue at the chemM.batch.pl step, as indicated by the log file. Specifically, the file 17.human_metagenome.checkM was not generated as expected.

Currently, I do not have a clear understanding of what might be causing this problem.

syslog.zip

  Using profile for genus rank : Malassezia

  Using profile for family rank : Malasseziaceae
  Using profile for order rank : Malasseziales
  Using profile for class rank : Malasseziomycetes
  Using profile for phylum rank : Basidiomycota
  Using profile for domain rank : Eukaryota

  Storing results for DAS in /home/nguinkal/human_metagenome/intermediate/17.human_metagenome.checkM
Can't find /home/nguinkal/human_metagenome/intermediate/17.human_metagenome.checkM
Stopping in STEP18 -> 17.checkM_batch.pl
Died at /home/nguinkal/amrFlow/Miniconda3/envs/SqueezeMeta/bin/SqueezeMeta.pl line 811.

Best, J

[jtamames]

Hello All your bins are from Eukaryotes. Notice that checkM only works for Prokaryotes. That's why it cannot evaluate any bins in your dataset, and dies in frustration. If you restart in step 19 I bet it will conclude happily (but you won't get any statistics on bins) Best, J

[bbalog87]

Hello @jtamames ,

Okay, I see...but it's weird, because I have only viruses/phages (metavirome). Maybe the samples were contaminated with eukaryotes host. In such cases, would it be possible to just skip the step with a warning note, instead of stoping the whole pipeline? Best, Julien

[jtamames]

Yes, I will introduce that modification in upcoming versions. Best, J

[jtamames]

And regarding the results, the most likely explanation is that these viruses are annotated as Eukaryotes in the databases (either because of prophages or contamination). Not easy solution for that. Best, J

[fpusan]

Closing due to lack of activity, feel free to reopen