Creating specified working directory /gscratch/scrubbed/samwhite/outputs/20210712_pgen_blobtools_Panopea-generosa-v1.0/cov_stats.
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 4
Rules claiming more threads will be scaled down.
Job counts:
	count	jobs
	1	add_cov_to_tsv
	1	all
	1	run_mosdepth
	3
Select jobs to execute...

[Wed Jul 28 17:58:34 2021]
rule run_mosdepth:
    input: ../minimap/Panopea_generosa_v1.reads.bam, ../minimap/Panopea_generosa_v1.reads.bam.csi, ../chunk_stats/Panopea_generosa_v1.chunk_stats.mask.bed
    output: Panopea_generosa_v1.reads.regions.bed.gz
    log: logs/Panopea_generosa_v1/run_mosdepth/reads.log
    jobid: 2
    benchmark: logs/Panopea_generosa_v1/run_mosdepth/reads.benchmark.txt
    wildcards: assembly=Panopea_generosa_v1, sra=reads
    threads: 4

mosdepth -n -x -b ../chunk_stats/Panopea_generosa_v1.chunk_stats.mask.bed                  -t 4 Panopea_generosa_v1.reads ../minimap/Panopea_generosa_v1.reads.bam 2> logs/Panopea_generosa_v1/run_mosdepth/reads.log
[Wed Jul 28 18:12:04 2021]
Finished job 2.
1 of 3 steps (33%) done
Select jobs to execute...

[Wed Jul 28 18:12:04 2021]
rule add_cov_to_tsv:
    input: Panopea_generosa_v1.reads.regions.bed.gz, ../busco/Panopea_generosa_v1.chunk_stats.tsv
    output: Panopea_generosa_v1.chunk_stats.tsv
    log: logs/Panopea_generosa_v1/add_cov_to_tsv.log
    jobid: 1
    benchmark: logs/Panopea_generosa_v1/add_cov_to_tsv.benchmark.txt
    wildcards: assembly=Panopea_generosa_v1
    threads: 4

(paste ../busco/Panopea_generosa_v1.chunk_stats.tsv <(echo reads_cov && gunzip -c Panopea_generosa_v1.reads.regions.bed.gz | cut -f 4) > Panopea_generosa_v1.chunk_stats.tsv) 2> logs/Panopea_generosa_v1/add_cov_to_tsv.log
[Wed Jul 28 18:12:05 2021]
Finished job 1.
2 of 3 steps (67%) done
Select jobs to execute...

[Wed Jul 28 18:12:05 2021]
localrule all:
    input: Panopea_generosa_v1.chunk_stats.tsv
    jobid: 0

[Wed Jul 28 18:12:05 2021]
Finished job 0.
3 of 3 steps (100%) done
Complete log: /gscratch/scrubbed/samwhite/outputs/20210712_pgen_blobtools_Panopea-generosa-v1.0/cov_stats/.snakemake/log/2021-07-28T175826.517412.snakemake.log