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dib-lab / charcoal

Remove contaminated contigs from genomes using k-mers and taxonomies.
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charcoal targets won't start running with latest version of charcoal v0.1.dev327+gde4bd52 #193

Closed taylorreiter closed 3 years ago

taylorreiter commented 3 years ago

No matter how i try to invoke the command line, all I get is this printed:

tereiter@bm2:~/github/2020-ibd$ python -m charcoal run inputs/charcoal-conf.yml report -n

This is charcoal v0.1.dev327+gde4bd52.

Usage:

   charcoal run <conf file> <target> [ <target 2>... ] [ <snakemake args> ]

Recommended targets:

 * stage1 - produce summary of genome taxonomies and potential contamination
 * stage2 - produce alignments summary and report
 * report - produce summary reports in HTML, under {output_dir}/report/
 * clean - produce clean contigs under {output_dir}/*.clean.fa.gz

Debug and config targets:
 * check - verify the basic config
 * showconf - show configuration

Please see https://github.com/dib-lab/charcoal for quickstart docs.

Please post questions at https://github.com/dib-lab/charcoal/issues!

I've been able to get showconf to work:

(/home/tereiter/github/2020-ibd/.snakemake/conda/eed1ece9) tereiter@bm2:~/github/2020-ibd$ python -m charcoal showconf inputs/charcoal-conf.yml
** read 54 provided lineages
** config file checks PASSED!
** from here on out, it's all snakemake...
Building DAG of jobs...
Using shell: /bin/bash
Provided cores: 1 (use --cores to define parallelism)
Rules claiming more threads will be scaled down.
Job counts:
        count   jobs
        1       showconf
        1
Select jobs to execute...

[Wed Jul  7 13:41:36 2021]
rule showconf:
    input: /home/tereiter/github/2020-ibd/outputs/charcoal_conf/charcoal.genome-list.txt
    jobid: 0

** read 54 provided lineages
** config file checks PASSED!
** from here on out, it's all snakemake...
Job counts:
        count   jobs
        1       showconf
        1
# full aggregated configuration:
force: 0
gather_db:
- /group/ctbrowngrp/gtdb/databases/gtdb-rs202.genomic.k31.zip
gather_scaled: 1000
genome_dir: /home/tereiter/github/2020-ibd/genbank_genomes
genome_list: /home/tereiter/github/2020-ibd/outputs/charcoal_conf/charcoal.genome-list.txt
ksize: 31
lineages_csv: /group/ctbrowngrp/gtdb/gtdb-rs202.taxonomy.csv
match_rank: order
min_align_pident: 95
min_f_ident: 0.1
min_f_major: 0.2
min_query_coverage: 0.5
moltype: DNA
output_dir: /home/tereiter/github/2020-ibd/outputs/charcoal/
provided_lineages: /home/tereiter/github/2020-ibd/outputs/genbank/gather_vita_vars_gtdb_shared_assemblies.x.genbank.lineages.csv
scaled: 1000
strict: 1
# END
[Wed Jul  7 13:41:37 2021]
Finished job 0.
1 of 1 steps (100%) done
Complete log: /home/tereiter/github/2020-ibd/.snakemake/log/2021-07-07T134134.444098.snakemake.log

I'm very hopeful that i'm being dumb...but i can't see what mistake i'm making. Including a list below of all of the different commands i tried. I know many of them are wrong, but I thought i'd give them a go any way

python -m charcoal run inputs/charcoal-conf.yml -j 1 clean -n
python -m charcoal run inputs/charcoal-conf.yml clean -j 1 -n
charcoal run inputs/charcoal-conf.yml clean
charcoal run inputs/charcoal-conf.yml -n
charcoal check inputs/charcoal-conf.yml
charcoal clean inputs/charcoal-conf.yml -n
charcoal run inputs/charcoal-conf.yml stage1 -n
charcoal run inputs/charcoal-conf.yml -n
python -m charcoal inputs/charcoal-conf.yml -n
python -m charcoal run inputs/charcoal-conf.yml -n
python -m charcoal run inputs/charcoal-conf.yml -n
python -m charcoal run inputs/charcoal-conf.yml clean -n
python -m charcoal run inputs/charcoal-conf.yml report -n