several errors across the execution

[FrAoJm]

Hi, I am new to this kind of simulations and find your tool at the first place very intuitive, but in the end I just get several times blocked.

I am trying to generate fastq files using the following inputs:

tsv

AssemblyInput nb_genomes RelativeProp 287 1 0.119885856945813 562 1 0.179456348063797 1270 1 0.150696032532491 1282 1 0.0995596833513118

I had to change the headers since the tool was giving me errors and this allowed me to keep going.

The yaml

input_table_path: path/to/subj001_V1.tsv community_name: subj001_V1 replicates: 1 sd_read_num: 0 same_dist_rep: False seed: 11 dist: lognormal mu: 1.0 sigma: 0.0 seq_tech: illumina read_status: paired total_reads: 2.561071e+07 illumina_sequencing_system: HSXt illumina_read_len: 150 illumina_mean_frag_len: 200 illumina_sd_frag_len: 10 bam: False NCBI_key: the key I got from NCBI NCBI_email: myNCBIemail complete_assemblies: True reference_assemblies: False representative_assemblies: False exclude_from_metagenomes: True Genbank_assemblies: True Refseq_assemblies: True Rank_to_filter_by: False

And run it like this: mess run -f subj001_V1.yml -c 10

Not sure where the problem is, but is giving me an error: `` Error in rule get_assembly_tables: jobid: 6 output: tables/287-all.tsv, tables/287-filtered.tsv log: logs/find-assemblies/287.log (check log file(s) for error message) conda-env: pathto/miniconda3/envs/mess/0196f5cd3651220e69f7e76b842252bd

RuleException: CalledProcessError in line 46 of pathto/miniconda3/envs/mess/lib/python3.8/site-packages/mess/assembly_finder/rules/find_assemblies.rules: Command 'source pathto/miniconda3/bin/activate 'pathto/miniconda3/envs/mess/0196f5cd3651220e69f7e76b842252bd'; set -euo pipefail; python pathto/test2/.snakemake/scripts/tmpe02brmhj.assembly_table.py' returned non-zero exit status 1. File "pathto/miniconda3/envs/mess/lib/python3.8/site-packages/snakemake/executors/init.py", line 2274, in run_wrapper File "pathto/miniconda3/envs/mess/lib/python3.8/site-packages/mess/assembly_finder/rules/find_assemblies.rules", line 46, in rule_get_assembly_tables File "pathto/miniconda3/envs/mess/lib/python3.8/site-packages/snakemake/executors/init.py", line 569, in _callback File "pathto/miniconda3/envs/mess/lib/python3.8/concurrent/futures/thread.py", line 57, in run File "pathto/miniconda3/envs/mess/lib/python3.8/site-packages/snakemake/executors/init.py", line 555, in cached_or_run File "pathto/miniconda3/envs/mess/lib/python3.8/site-packages/snakemake/executors/init__.py", line 2362, in run_wrapper ``

I would appreciate any help with this! Thanks