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picrust / picrust2

Code, unit tests, and tutorials for running PICRUSt2
GNU General Public License v3.0
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Job gets killed when attempting pathway_pipeline.py #154

Closed afOSU-dot closed 3 years ago

afOSU-dot commented 3 years ago

Hello,

I'm trying to do a picrust analysis on some old 16s data (done in Qiime in 2014). Whenever I try to run the picrust analysis using the single script (picrust2_pipeline.py -s study_seqs.fna -i study_seqs.biom -o picrust2_out_pipeline -p 1), it stops right before the metagenomics prediction part. I was able to run the metagenomics prediction step manually and I got the unstrat outputs (EC_metagenome_out). When I moved on to the pathway output script, my job would say "completed" but I don't find any outputs in my directory. I tried doing it in terminal and then I get "job killed". I have little experience with picrust and supercomputers so I would appreciate any help.

My inputs were a fasta file with all denovos and their corresponding sequences (~40,000 denovos). My first input was rarefied OTU table but then I changed it to another OTU table that was not rarefied. Is my file too large or something?

afOSU-dot commented 3 years ago

I think I figured it out! I had -p 20 initially for the script. I changed it to -p 1 for one process and I have all of the outputs in my directory. It did take longer than the script with 20 but I'm glad it worked this time!