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eggnogdb / eggnog-mapper

Fast genome-wide functional annotation through orthology assignment
http://eggnog-mapper.embl.de
GNU Affero General Public License v3.0
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eggnog-mapper stuck in pfam annotation #478

Open x-rv opened 1 year ago

x-rv commented 1 year ago

I'm trying to run eggnog-mapper in a computing cluster that I've never used before have eggnog-mapper v2.1.10 stuck forever in the pfam annotation step. I've used v2.1.9 in another cluster with the same settings and had no issue with it. This is the .out file:

#  emapper-2.1.10
# emapper.py  --cpu 24 --pfam_realign denovo -i REMEI100_ass_metaspades_bin.126.faa --output REMEI100_ass_metaspades_bin.126
ESC[1;33m  /opt/cesga/2020/software/Core/diamond/2.1.8/bin/diamond blastp -d '/mnt/netapp1/Optcesga_FT2_RHEL7/2020/software/Compiler/gcccore/system/eggnog-mapper/2.1.10/eggnog-mapper-data/eggnog_proteins.dmnd' -q '/mnt/lustre/scratch/nlsas/home/csic/eyg/xrv/genomas/prokka/REMEI100_ass_metaspades_bin.126.prokka.d/REMEI100_ass_metaspades_bin.126.faa' --threads 24 -o '/mnt/lustre/scratch/nlsas/home/csic/eyg/xrv/genomas/eggnogmapper/REMEI100_ass_metaspades_bin.126.emapper.hits' --tmpdir '/mnt/lustre/scratch/nlsas/home/csic/eyg/xrv/genomas/eggnogmapper/emappertmp_dmdn_x4kpxp1i' --sensitive --iterate -e 0.001 --top 3  --outfmt 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qcovhsp scovhspESC[0m
ESC[1;32mDe novo scan of PFAM domainsESC[0m
Namespace(Z=40000000, call_info='## Thu Sep  7 18:30:35 2023\n## emapper-2.1.10\n## /opt/cesga/2020/software/Compiler/gcccore/system/eggnog-mapper/2.1.10/bin/emapper.py --cpu 24 --pfam_realign denovo -i REMEI100_ass_metaspades_bin.126.faa --output REMEI100_ass_metaspades_bin.126\n##', clean_overlaps='clans', cpu=24, cpus_per_worker=24, cut_ga=True, db='/mnt/netapp1/Optcesga_FT2_RHEL7/2020/software/Compiler/gcccore/system/eggnog-mapper/2.1.10/eggnog-mapper-data/pfam/Pfam-A.hmm', dbtype='hmmdb', end_port=53200, evalue=1e-10, excluded_taxa=None, maxhits=0, maxseqlen=None, no_file_comments=False, num_servers=1, num_workers=1, port=51700, qcov=0, qtype='seq', report_no_hits=False, resume=False, scan_type='mem', score=None, servers_list=None, temp_dir='/mnt/lustre/scratch/nlsas/home/csic/eyg/xrv/genomas/eggnogmapper', timeout_load_server=10, trans_table=None, translate=False, usemem=True)

It gives no errors, just stays like this. Any idea about why could this be happening? Thanks!

Cantalapiedra commented 1 year ago

Hi @x-rv ,

It may be stuck trying to load the PFAM DB into memory using hmmpgmd. You may try loading it yourself with hmmpgmd or with hmm_server.py, to see if there is a problem in that step.

Best, Carlos