cryptogenomicon
commented
1 year ago It's running out of memory; the alignment you're trying to create must be very large. hmmalign can definitely require >60G on some very large alignments. It would help to have a simpler case, boiled down to just a HMMER command that fails for you, with a minimal number of files and switches, but the main thing is probably going to be the size of the alignment problem. How large is the profile in pro_ref.hmm in consensus states, and how many sequences are in seqs.fna and of what lengths?
Hello!
I was wondering if someone could help me with an issue I have been having running hmmer in QIIME2 for PICRUST - I am running into a realloc error (command and error shown below) Previously, the error was that there was not enough space in my tmp directory which is why I changed it to another location which have over 5TB of space and checked that the command is directing to the new tmp location using echo.
The command: qiime picrust2 full-pipeline --i-table tmp_to_delete/feature-table.qza --i-seq tmp_to_delete/sequences.qza --output-dir q2-picrust2_output_wgs --p-placement-tool sepp --p-threads 1 --p-hsp-method mp --p-edge-exponent 0 --p-max-nsti 2 --verbose
The error:
Error running this command:
place_seqs.py --study_fasta /SAN/tmp/tmp29_2eqcm/seqs.fna --ref_dir /SAN/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/picrust2/default_files/prokaryotic/pro_ref --out_tree /SAN/tmp/tmp29_2eqcm/picrust2_out/out.tre --processes 1 --intermediate /SAN/tmp/tmp29_2eqcm/picrust2_out/intermediate/place_seqs --min_align 0.8 --chunk_size 5000 --placement_tool sepp
Standard error of the above failed command:
Error running this command:
hmmalign --trim --dna --mapali /SAN/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna --informat FASTA -o /SAN/tmp/tmp29_2eqcm/picrust2_out/intermediate/place_seqs/query_align.stockholm /SAN/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.hmm /SAN/tmp/tmp29_2eqcm/seqs.fna
Standard error of the above failed command: Fatal exception (source file p7_omx.c, line 159): realloc for size -1777974705 failed
I am not sure why this is the case - I am running the script with 60G of memory and setting it for 12 hours though it fails in under an hour. Any help would be appreciated!