08 Bin Completion with Spacegraphcats: Mamba > Snakemake?

[ccbaumler]

Got this error from spacegraphcats:

Error: mamba package manager is not available. The mamba package manager (https://github.com/mamba-org/mamba) is an extremely fast and robust conda replacement. It is the recommended way of using Snakemake's conda integration. It can be installed with `conda install -n base -c conda-forge mamba.If you still prefer to use conda, you can enforce that by setting `--conda-frontend conda`.
Error in snakemake invocation: Command '['snakemake', '-s', '/home/baumlerc/miniconda3/envs/sgc/lib/python3.8/site-packages/spacegraphcats/conf/Snakefile', '--use-conda', '-j', '1', 'extract_contigs', 'extract_reads', '--nolock', '--configfile', '/home/baumlerc/miniconda3/envs/sgc/lib/python3.8/site-packages/spacegraphcats/conf/defaults.conf', 'conf1.yml']' returned non-zero exit status 1.

Found this similar issue So I installed mamba and I think its running now(see below).

Cheers, Colton

(sgc) baumlerc@bm4:~/2020_rotation_project/sgc$ python -m spacegraphcats run conf1.yml extract_contigs extract_reads --nolock

This is spacegraphcats 2.0.

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       bcalm_catlas_prepare_input
        1       bcalm_catlas_sort
        1       bcalm_cdbg
        1       bcalm_cdbg_inpfiles
        1       build_catlas
        1       extract_contigs
        1       extract_contigs_single_file
        1       extract_reads
        1       extract_reads_single_file
        1       index_reads
        1       make_contigs_kmer_index
        1       reads_bgzf
        1       search
        13
Select jobs to execute...

[Fri Apr 15 16:39:06 2022]
rule reads_bgzf:
    input: /home/baumlerc/2020_rotation_project/sgc/SRR1976948.abundtrim.fq.gz
    output: SRR1976948/reads.bgz
    jobid: 11
    wildcards: catlas_base=SRR1976948

output file will be SRR1976948/reads.bgz
turning /home/baumlerc/2020_rotation_project/sgc/SRR1976948.abundtrim.fq.gz into a block-gzipped (BGZF) file
Exception ignored in: <_io.FileIO name='/home/baumlerc/2020_rotation_project/sgc/SRR1976948.abundtrim.fq.gz' mode='rb' closefd=True>
Traceback (most recent call last):
  File "/home/baumlerc/miniconda3/envs/sgc/lib/python3.8/site-packages/screed/openscreed.py", line 35, in __init__
    self.iter_fn = self.open_reader(filename, *args, **kwargs)
ResourceWarning: unclosed file <_io.BufferedReader name='/home/baumlerc/2020_rotation_project/sgc/SRR1976948.abundtrim.fq.gz'>
offset for 200000 is 2207965004260