Open lam-c opened 9 months ago
@lam-c thanks for letting us know. We will fix the container and publish a new one, we will also review all the containers as this could also affect other ones.
Thank you for considering. I tried to build singularity images locally, and it worked.
# mash2nwk.def
bootstrap: docker
from: [quay.io/microbiome-informatics/genomes-pipeline.mash2nwk:v1](http://quay.io/microbiome-informatics/genomes-pipeline.mash2nwk:v1)
%post
apt-get update
apt-get install -y procps
rm -rf /var/lib/apt/lists/*
$ singularity build --fakeroot quay.io-microbiome-informatics-genomes-pipeline.mash2nwk-v1.img mash2nwk.def
But soon after this, I met another error prompted by container GAP:AMRFINDER_PLUS
(as below). It seems like the database download from ncbi (ftp://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/3.11/2023-02-23.1) lacking some AMRProt files (e.g. AMRProt.pdb, ...). I tried to update database as amrfinder suggested, then it runned as expected.
Running: amrfinder --plus -n MGYG000299305.fna -p MGYG000299305.faa -g MGYG000299305.gff -d /home/user/databases/AMRFinderPlus_2023-02-23.1 -a prokka --output MGYG000299305_amrfinderplus.tsv --threads 1
Software directory: '/usr/local/bin/'
Software version: 3.11.4
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_1678396575214/_build_env/share/amrfinderplus/data/latest
Database directory: '/home/user/databases/AMRFinderPlus_2023-02-23.1'
*** ERROR ***
The BLAST database for AMRProt was not found. Use amrfinder -u to download and prepare database for AMRFinderPlus
HOSTNAME: ?
SHELL: ?
PWD: /home/user/temp/work/27/2ab8a76f7a43c8690d4a4ba0ecf058
PATH: /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/user/.nextflow/assets/EBI-Metagenomics/genomes-pipeline/bin
Progam name: amrfinder
Command line: amrfinder --plus -n MGYG000299305.fna -p MGYG000299305.faa -g MGYG000299305.gff -d /home/user/databases/AMRFinderPlus_2023-02-23.1 -a prokka --output MGYG000299305_amrfinderplus.tsv --threads 1
@KateSakharova ran into the same error, updating it to v1.1 I get a different architecture mismatch error:
ERROR ~ Error executing process > 'GAP:MASH_TO_NWK (1)'
Caused by:
Process `GAP:MASH_TO_NWK (1)` terminated with an error exit status (1)
Command executed:
mash2nwk1.R -m MGYG000000018_mash.tsv
mv trees/mashtree.nwk MGYG000000018_mash.nwk
Command exit status:
1
Command output:
(empty)
Command error:
WARNING: The requested image's platform (linux/arm64) does not match the detected host platform (linux/amd64/v4) and no specific platform was requested
exec /bin/bash: exec format error
I also had the same issues with amrfinder as Iam-c
@lam-c what was the amrfinder_plus_db
path you used? Still can't get it running even with downloading amrfinder plus and updating the db..
@amardeepranu I updated the database with amrfinder -u
, and then parsed a custom config to the pipeline to bind the amrfinder_plus_db
to the container.
# custom config
process {
withName: AMRFINDER_PLUS {
containerOptions = "--bind ${params.amrfinder_plus_db}"
}
}
# command to run the pipeline
$ nextflow run EBI-Metagenomics/genomes-pipeline -c custom.config ...
@KateSakharova ran into the same error as @amardeepranu after I updated mash2nwk to v1.1, using docker container
exec format error
Hi @amardeepranu and @akques
The problem was that the container was built in a mac with an M2 chip (different architecture), I just replaced the image in quay with a version built for "linux/amd64" so it should work now. Please remove the image and pull it again.
I will run the whole pipeline with the Nextflow with the "-with-report" flag to check if all the containers are working with it. I'll post an update in the next few days.
Cheers
Hi, I caught an error in Process: GAP:MASH_TO_NWK.
I think the container
genomes-pipeline.mash2nwk
might lack an important toolps
. A possible solution could be includedps
into the Dockerfile of mash2nwk (as below). Since docker was not installed on the system I worked on, I had some trouble on transforming dockerfile to singularity image. I would be so grateful if you could publish an updated container on quay.io.