Command output empty on example dataset

[rmadnantariq]

Hi, I have been trying to work with the example dataset and I got this error is there something I'm doing wrong?

Thanks

Error executing process > 'vibrant (megahit-SRR8652861)'

Caused by: Process vibrant (megahit-SRR8652861) terminated with an error exit status (1)

Command executed:

VIBRANT_run.py -t 16 -i SRR8652861_megahit_contigs.fasta -d /home/crk_tgms5/MetaPhage/db/vibrant/legacy/ -m /home/crktgms5/MetaPhage/db/vibrant/legacy/ -virome mv VIBRANT/ SRR8652861vibrant/ sed 's/^>/>vibrant/' SRR8652861_vibrant/VIBRANT_phages_SRR8652861_megahit_contigs/SRR8652861_megahit_contigs.phages_combined.fna > SRR8652861_vibrant/VIBRANT_phages_SRR8652861_megahit_contigs/SRR8652861_correct_vibrant.fna rm -f temp

Command exit status: 1

Command output: (empty)

Command error: /cm/local/apps/environment-modules/4.0.0//init/bash: line 15: MODULES_USE_COMPAT_VERSION: unbound variable Traceback (most recent call last): File "/home/crk_tgms5/miniconda/envs/MetaPhage/bin/VIBRANT_annotation.py", line 1708, in AMG_dict.update({str(annotations[n]):str(annotations[n+1]).replace("$~&", " ").replace('^@%','"') + '\t' + str(annotations[n+2]) + '\t' + str(ko_name) + '\t' + str(annotations[n+6]) + '\t' + str(pfam_name)}) NameError: name 'pfam_name' is not defined Traceback (most recent call last): File "/home/crk_tgms5/miniconda/envs/MetaPhage/bin/VIBRANT_run.py", line 633, in with open(str(out_folder)+'VIBRANT_AMGindividuals' + str(base) + '.tsv', 'r') as annotations: FileNotFoundError: [Errno 2] No such file or directory: 'VIBRANT_AMG_individuals_SRR8652861_megahit_contigs.tsv'

Work dir: /home/crk_tgms5/MetaPhage/work/0d/98d8f82c8bfa2d1a2073b0c0f57814

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line

[telatin]

Can you please provide your configuration file? Did you use Singularity or created a Conda environment? Did you use a "release" or just cloned the repository?

[rmadnantariq]

demo.txt Hi I used Conda environment and cloned the repository.

[rmadnantariq]

I've just realised I've been sbatch(ing) the command, speaking to a colleague nextflow doesn't need to be sbatched. Although I still get errors mainly in megahit and phigaro it ignores and carries on the pipeline.

Thanks again!