running `casc` for CRISPR analyses

• running casc via the workflows/analysis.smk, after commitID #14b1bfc5 giving the following error.

Activating conda environment: /mnt/lscratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/.snakemake/conda/1645784e
[Fri May 29 18:00:37 2020]
Error in rule casc:
    jobid: 4
    output: results/analysis/crispr/casc/metaspades_hybrid_casc_output/metaspades_hybrid.results.txt, results/analysis/crispr/casc/metaspades_hybrid_casc_output/casc_CRISPR_output.txt
    log: results/analysis/crispr/casc/metaspades_hybrid_casc_output/casc.log (check log file(s) for error message)
    conda-env: /mnt/lscratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/.snakemake/conda/1645784e
    shell:

        (date &&        export PATH=$PATH:/mnt/lscratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/crispr/bin &&\
        export PERL5LIB=/mnt/lscratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/crispr/lib/site_perl
        casc -i results/assembly/metaspades_hybrid.fa -o $(dirname results/analysis/crispr/casc/metaspades_hybrid_casc_output/metaspades_hybrid.results.txt) -n 12 --conservative &&        echo $(basename -s ".results.txt" results/analysis/crispr/casc/metaspades_hybrid_casc_output/metaspades_hybrid.results.txt) >> results/analysis/crispr/casc/metaspades_hybrid_casc_output/casc_CRISPR_output.txt &&        awk '$8 == "true" {sum += $2} END {print sum}' results/analysis/crispr/casc/metaspades_hybrid_casc_output/metaspades_hybrid.results.txt >> results/analysis/crispr/casc/metaspades_hybrid_casc_output/casc_CRISPR_output.txt &&        date) &> >(tee results/analysis/crispr/casc/metaspades_hybrid_casc_output/casc.log)

        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Fri May 29 18:00:37 CEST 2020
/usr/bin/bash:  : command not found
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /mnt/lscratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/.snakemake/log/2020-05-29T175815.238274.snakemake.log

• /usr/bin/bash: : command not found Does it have to do with the grep and awk commands?
• Help please!!

changed milestone to %Done: To-do

added To Do label

changed the description

• Maybe I fixed it, let's see.
• See commitID # 51c5727f

Notes-to-future-self:

1. snakemake does not seem to like commented out lines within the shell directive, if using &&\
2. If using awk within the "shell", better cat the file first, and then pipe into awk

• I was too optimistic
• casc was activated but now for some reason, it doesn't want to find it either. possibly the way it is installed

• Think it finally worked with this commit - 88ef1d4d

• Actually, it's this commit - e98663ed, which also includes fixes for the minced_CRISPR_output.txt file path
• Maybe 'hacky' but it works and that's all folks..

changed milestone to %Greatness achieved

closed

added Figure label