EPA-NG not working about picrust2

[gavinmdouglas]

Hi there, Are you using the version of EPA-NG that’s packaged in the “placement_tools” folder of the picrust2 rep? Best, Gavin

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On Aug 6, 2018, at 11:09 AM, Arghya Mukherjee ***@***.***> wrote: generating best scoring alignments SUCCESS 38.1369 INFO Converting given FASTA file to BFAST format... INFO Resulting bfast file was written to: placement_working/epa_out/study_seqs_papara.fasta.bfast INFO Selected: Output dir: placement_working/epa_out/ INFO Selected: Query file: placement_working/epa_out/study_seqs_papara.fasta.bfast INFO Selected: Tree file: /home/arghya250/Apps/picrust2/default_files/prokaryotic/img_centroid_16S_aligned.tree INFO Selected: Reference MSA: placement_working/ref_seqs_papara.fasta INFO Selected: Specified model: GTR+G INFO Rate heterogeneity: GAMMA (4 cats, mean), alpha: 1 (ML), weights&rates: (0.25,0.136954) (0.25,0.476752) (0.25,1) (0.25,2.38629) Base frequencies (ML): 0.25 0.25 0.25 0.25 Substitution rates (ML): 0.5 0.5 0.5 0.5 0.5 1 INFO Selected: Reading queries in chunks of: 5000 INFO Selected: Using threads: 10 INFO ______ ____ ___ _ __ ______ / // __ \ / | / | / // / / __/ / // // /| | ______ / |/ // / __ / / / // ___ |/_____// /| // // / /_____/// // || // |/ __/ (v0.2.1-beta) INFO Number of ranks: 1 INFO Output file: placement_working/epa_out/epa_result.jplace Error running this command: epa-ng --tree /home/arghya250/Apps/picrust2/default_files/prokaryotic/img_centroid_16S_aligned.tree --ref-msa placement_working/ref_seqs_papara.fasta --query placement_working/epa_out/study_seqs_papara.fasta.bfast --chunk-size 5000 -T 10 -m GTR+G -w placement_working/epa_out

[arghya1611]

Hi,
Yes all prerequisite were installed using versions packaged in picrust2 repo as downloaded en block.
Best,
Arghya

[gavinmdouglas]

Hi again,

Sorry you're running into this issue. What's the error reported when you run the below command?

epa-ng --tree /home/arghya250/Apps/picrust2/default_files/prokaryotic/img_centroid_16S_aligned.tree --ref-msa placement_working/ref_seqs_papara.fasta --query placement_working/epa_out/study_seqs_papara.fasta.bfast --chunk-size 5000 -T 10 -m GTR+G -w placement_working/epa_out

[arghya1611]

Hi
I ran the epa-ng separately as you suggested. I am getting the following VBox error. It seems like a memory issue in VBOx. My Vbox has a memory of 7052 MB dedicated to it as well as 6 processors. I know the recommended memory for picrust2 is 16GB. Having said that, should such a small dataset require so much memory?

[gavinmdouglas]

Hi again,

That command should take around 13 GB. The reason is that it's using the default reference tree and FASTA file, which are very large and take up a lot of memory when running EPA-NG. Sorry I can't be of more help, but currently I'm not sure how to decrease the memory usage without using different reference files.

Gavin