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several errors across the execution #14

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FrAoJm opened this issue Jun 7, 2023 · 0 comments
Open

several errors across the execution #14

FrAoJm opened this issue Jun 7, 2023 · 0 comments
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@FrAoJm
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FrAoJm commented Jun 7, 2023

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

@farchaab farchaab self-assigned this Sep 7, 2023
@farchaab farchaab mentioned this issue Apr 9, 2024
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