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spacegraphcats / spacegraphcats-twofoo-example

A small-but-real-ish example of spacegraphcats on a mock metagenome.
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Snakefile is out of date #3

Closed taylorreiter closed 3 years ago

taylorreiter commented 3 years ago

I'm pretty sure the snakefile is out of date for the 2.X changes to spacegraphcats

ctb commented 3 years ago

it works for me with latest dev version of sgc, so I'll close this issue ;)

taylorreiter commented 3 years ago

I get 

Error: No such command 'config.yaml'.
snakemake -j 1 -p
/home/tereiter/github/spacegraphcats/spacegraphcats/snakemake.py:30: YAMLLoadWarning: calling yaml.load() without Loader=... is
 deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
  jj = yaml.load(fp)
/home/tereiter/github/spacegraphcats/spacegraphcats/snakemake.py:60: YAMLLoadWarning: calling yaml.load() without Loader=... is
 deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
  jj = yaml.load(fp)
/home/tereiter/github/spacegraphcats/spacegraphcats/snakemake.py:8: YAMLLoadWarning: calling yaml.load() without Loader=... is
deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
  jj = yaml.load(fp)
/home/tereiter/github/spacegraphcats/spacegraphcats/snakemake.py:86: YAMLLoadWarning: calling yaml.load() without Loader=... is
 deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
  jj = yaml.load(fp)
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       all
        1       build
        1       extract
        1       search
        4

[Thu Apr 15 16:46:53 2021]
rule build:
    input: data/twofoo.fq.gz
    output: twofoo/bcalm.twofoo.k31.unitigs.fa, twofoo_k31_r1/catlas.csv, twofoo_k31_r1/cdbg.gxt, twofoo_k31_r1/contigs.fa.gz.indices, twofoo_k31_r1/contigs.fa.gz.info.csv, twofoo_k31_r1/contigs.fa.gz.mphf, twofoo_k31_r1/first_doms.txt
    jobid: 2

/home/tereiter/miniconda3/envs/sgc_latest/bin/python3.8 -m spacegraphcats config.yaml build --nolock
Usage: __main__.py [OPTIONS] COMMAND [ARGS]...
Try '__main__.py --help' for help.

Error: No such command 'config.yaml'.
[Thu Apr 15 16:46:53 2021]
Error in rule build:
    jobid: 2
    output: twofoo/bcalm.twofoo.k31.unitigs.fa, twofoo_k31_r1/catlas.csv, twofoo_k31_r1/cdbg.gxt, twofoo_k31_r1/contigs.fa.gz.indices, twofoo_k31_r1/contigs.fa.gz.info.csv, twofoo_k31_r1/contigs.fa.gz.mphf, twofoo_k31_r1/first_doms.txt
    shell:
        /home/tereiter/miniconda3/envs/sgc_latest/bin/python3.8 -m spacegraphcats config.yaml build --nolock
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
$ spacegraphcats info

This is spacegraphcats version v2.0b12.dev5+ga8ed324

Package install path: /home/tereiter/github/spacegraphcats/spacegraphcats
snakemake Snakefile: /home/tereiter/github/spacegraphcats/spacegraphcats/conf/Snakefile