Closed pdy1084 closed 4 months ago
jfy133
commented
8 months ago Ooof that looks like amrfinder itself borked for some reason... but it doesn't actually report the error message..
@jasmezz @Darcy220606 could you see if you fan replicate?
The other option @pdy1084 is to try downloading the database manually yourself and pass that to the pipeline. Pleas esee https://nf-co.re/funcscan/1.1.4/parameters#arg_amrfinderplus_db
pdy1084
commented
8 months ago Hi again @jfy133,
As you suggested, I have downloaded amrfinderplus_db to a folder, added the path to the nf-core parameters and run again the test. It seems that the error I get now is not related to AMRFINDERPLUS_UPDATE module anymore but instead to AMRFINDERPLUS_RUN. I checked and AMRprot is in the folder. Do you have any suggestions on how to address this?
Thank you!
----------------------- Run command
$ nextflow run nf-core/funcscan -r 1.1.4 \ --outdir /mnt/beegfs/mnt/work/nf_core_funscan/test_funcscan/results/ -profile test,singularity \ -params-file /mnt/beegfs/mnt/work/nf_core_funscan/nf-params_nfcore_test.json
----------------------- Here you can see nf-core/funcscan is reading well the database
... AMP: AMPcombi amp_ampcombi_cutoff : 0
ARG: AMRFinderPlus arg_amrfinderplus_db : /mnt/beegfs/mnt/work/nf_core_funscan/databases/amrfinderplusdb
ARG: DeepARG arg_skip_deeparg : true ...
------------------------ And here I post a chunk of the error message which keeps repeating:
[63/8e3b7a] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [ 0%] 0 of 4 [- ] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... - [66/a4495c] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [ 0%] 0 of 2 [- ] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... - [85/fcb015] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... [ 0%] 0 of 2 [- ] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... - [- ] process > NFCORE_FUNCSCAN:FUNCSCAN:AR... - [- ] process > NFCORE_FUNCSCAN:FUNCSCAN:CU... - [- ] process > NFCORE_FUNCSCAN:FUNCSCAN:MU... - ERROR ~ Error executing process > 'NFCORE_FUNCSCAN:FUNCSCAN:ARG:AMRFINDERPLUS_RUN (sample_2)'
Caused by:
Process NFCORE_FUNCSCAN:FUNCSCAN:ARG:AMRFINDERPLUS_RUN (sample_2) terminated with an error exit status (1)
Command executed:
if [ "false" == "true" ]; then gzip -c -d wastewater_metagenome_contigs_2.fasta > wastewater_metagenome_contigs_2.fasta fi
if [ "false" == "true" ]; then mkdir amrfinderdb tar xzvf amrfinderplusdb -C amrfinderdb else mv amrfinderplusdb amrfinderdb fi
amrfinder \ -n wastewater_metagenome_contigs_2.fasta \ \ --ident_min -1 --coverage_min 0.5 --translation_table 11 \ --database amrfinderdb \ --threads 1 > sample_2.tsv
VER=$(amrfinder --version) DBVER=$(echo $(amrfinder --database amrfinderdb --database_version 2> stdout) | rev | cut -f 1 -d ' ' | rev)
cat <<-END_VERSIONS > versions.yml "NFCORE_FUNCSCAN:FUNCSCAN:ARG:AMRFINDERPLUS_RUN": amrfinderplus: $(amrfinder --version) amrfinderplus-database: $(echo $(echo $(amrfinder --database amrfinderdb --database_version 2> stdout) | rev | cut -f 1 -d ' ' | rev)) END_VERSIONS
Command exit status: 1
Command output: (empty)
Command error: INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred Running: amrfinder -n wastewater_metagenome_contigs_2.fasta --ident_min -1 --coverage_min 0.5 --translation_table 11 --database amrfinderdb --threads 1 Software directory: '/usr/local/bin/' Software version: 3.11.18 WARNING: This was compiled for running under bioconda, but $CONDA_PREFIX was not found Reverting to hard coded directory: /opt/conda/conda-bld/ncbi-amrfinderplus_1691435906550/_build_env/share/amrfinderplus/data/latest Database directory: '/mnt/beegfs/mnt/work/nf_core_funscan/databases/amrfinderplusdb'
ERROR The BLAST database for AMRProt was not found. Use amrfinder -u to download and prepare database for AMRFinderPlus
HOSTNAME: ? SHELL: ? PWD: /mnt/beegfs/mnt/work/nf_core_funscan/test_funcscan/results/work/51/a8e92627ade1063c88a5c46f99506d PATH: /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/pdy23/.nextflow/assets/nf-core/funcscan/bin Progam name: amrfinder Command line: amrfinder -n wastewater_metagenome_contigs_2.fasta --ident_min -1 --coverage_min 0.5 --translation_table 11 --database amrfinderdb --threads 1
Work dir: /mnt/beegfs/mnt/work/nf_core_funscan/test_funcscan/results/work/51/a8e92627ade1063c88a5c46f99506d
Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run
-- Check '.nextflow.log' file for details
jasmezz
commented
8 months ago Update: I could replicate it, the error seems only with the zipped DB version. Not solved yet, though...
jasmezz
commented
4 months ago This should be solved now by #365
Description of the bug
When I run the nf-core/funcscan pipeline with test,singularity as -profile, Amrfinderplus_update does not work properly and the pipeline crashes.
I could run nf-core/mag in the same HPC before and this worked properly.
Command used and terminal output
Relevant files
No response
System information
Nextflow version 23.10.0 HPC Executor Slurm Container engine: Singularity OS Rocky Linux 8.9 (Green Obsidian) Version of nf-core/funcscan: v1.1.4-g274042b