Error with epa-ng
yliu3089 opened this issue · comments
Hi
I am new to picrust2. I just tried to run through it according to your tutorial https://github.com/picrust/picrust2/wiki/PICRUSt2-Tutorial-(v2.1.4-beta) with v2.5.1. Everything works well until I started to run place_seqs.py -s ../seqs.fna -o out.tre -p 1 \ --intermediate intermediate/place_seqs. It gives me the error message:
Error running this command
epa-ng --tree /home/yzl497/miniconda3/envs/picrust2/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre --ref-msa intermediate/place_seqs/ref_seqs_hmmalign.fasta --query intermediate/place_seqs/study_seqs_hmmalign.fasta --chunk-size 5000 -T 32 -m /home/yzl497/miniconda3/envs/picrust2/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.model -w intermediate/place_seqs/epa_out --filter-acc-lwr 0.99 --filter-max 100 .
I tried to use -p 1, 4, 8, 16, 17, 32, but all gave me the same error message. Do you have any suggestions how to fix it? Thank you.
That normally happens if you don't have sufficient RAM to run EPA-ng, which usually requires at least 16 GB of RAM. You can try using SEPP for placement (--placement_tool sepp) instead, which uses less memory.
I am closing this issue because there hasn't been any additional comments/questions for a long time. Please let me know if it needs to be reopened.