Stopping in STEP5

[guianrey]

Hi jtamames

Could you help with this issue, I don't understand what is happening, the database is well installed, I have 128 cores with 256 GB RAM in a cluster to run this pipeline (SqueezeMeta v1.6.3, September 2023).

[52 seconds]: STEP5 -> HMMER/PFAM: 05.run_hmmer.pl Running HMMER3 (Eddy 2009, Genome Inform 23, 205-11) for Pfam Error running command: /home/guillermo.reyes/miniconda3/envs/SqueezeMeta/SqueezeMeta/bin/hmmer/hmmsearch --domtblout /home/guillermo.reyes/CEDIA_Microbiomas/Shotgun_Metagenomics_1er_muestreo/Analisis/01.RawData/Mar_ingreso_M1/intermediate/05.Mar_ingreso_M1.pfam.hmm -E 1e-10 --cpu 128 /home/guillermo.reyes/SqueezeDataBase/db/Pfam-A.hmm /home/guillermo.reyes/CEDIA_Microbiomas/Shotgun_Metagenomics_1er_muestreo/Analisis/01.RawData/Mar_ingreso_M1/results/03.Mar_ingreso_M1.faa > /dev/null 2>&1 at /home/guillermo.reyes/miniconda3/envs/SqueezeMeta/SqueezeMeta/scripts/05.run_hmmer.pl line 31. Stopping in STEP5 -> 05.run_hmmer.pl. Program finished abnormally

---

I checked the installed database with test_install.pl

Scalar value @args[-1] better written as $args[-1] at /home/guillermo.reyes/miniconda3/envs/SqueezeMeta/bin/test_install.pl line 208.

Checking the OS linux OK

Checking that tree is installed tree --help OK

Checking that ruby is installed ruby -h OK

Checking that java is installed java -h OK

Checking that all the required perl libraries are available in this environment perl -e 'use Term::ANSIColor' OK perl -e 'use DBI' OK perl -e 'use DBD::SQLite::Constants' OK perl -e 'use Time::Seconds' OK perl -e 'use Tie::IxHash' OK perl -e 'use Linux::MemInfo' OK perl -e 'use Getopt::Long' OK perl -e 'use File::Basename' OK perl -e 'use DBD::SQLite' OK perl -e 'use Data::Dumper' OK perl -e 'use Cwd' OK perl -e 'use XML::LibXML' OK perl -e 'use XML::Parser' OK perl -e 'use Term::ANSIColor' OK

Checking that all the required python libraries are available in this environment python3 -h OK python3 -c 'import numpy' OK python3 -c 'import scipy' OK python3 -c 'import matplotlib' OK python3 -c 'import dendropy' OK python3 -c 'import pysam' OK python3 -c 'import Bio.Seq' OK python3 -c 'import pandas' OK python3 -c 'import sklearn' OK python3 -c 'import nose' OK python3 -c 'import cython' OK python3 -c 'import future' OK

Checking that all the required R libraries are available in this environment R -h OK R -e 'library(doMC)' OK R -e 'library(ggplot2)' OK R -e 'library(data.table)' OK R -e 'library(reshape2)' OK R -e 'library(pathview)' OK R -e 'library(DASTool)' OK R -e 'library(SQMtools)' OK

Checking binaries spades.py OK metabat2 OK jgi_summarize_bam_contig_depths OK samtools OK bwa OK minimap2 OK diamond OK hmmsearch OK cd-hit-est OK kmer-db OK aragorn OK mothur OK

Checking that SqueezeMeta is properly configured... checking database in /home/guillermo.reyes/SqueezeDataBase/db nr.db OK CheckM manifest OK LCA_tax DB OK

All checks successful