Creating specified working directory /gscratch/scrubbed/samwhite/outputs/20210712_pgen_blobtools_Panopea-generosa-v1.0/windowmasker.
Building DAG of jobs...
Using shell: /usr/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	run_windowmasker
	1	unzip_assembly_fasta
	3
Select jobs to execute...

[Fri Jul 16 05:46:48 2021]
rule unzip_assembly_fasta:
    input: /gscratch/scrubbed/samwhite/outputs/20210712_pgen_blobtools_Panopea-generosa-v1.0/Panopea_generosa_v1.fasta.gz
    output: Panopea_generosa_v1.fasta
    log: logs/Panopea_generosa_v1/unzip_assembly_fasta.log
    jobid: 2
    benchmark: logs/Panopea_generosa_v1/unzip_assembly_fasta.benchmark.txt
    wildcards: assembly=Panopea_generosa_v1

(gunzip -c /gscratch/scrubbed/samwhite/outputs/20210712_pgen_blobtools_Panopea-generosa-v1.0/Panopea_generosa_v1.fasta.gz > Panopea_generosa_v1.fasta) &> logs/Panopea_generosa_v1/unzip_assembly_fasta.log
[Fri Jul 16 05:46:54 2021]
Finished job 2.
1 of 3 steps (33%) done
Select jobs to execute...

[Fri Jul 16 05:46:54 2021]
rule run_windowmasker:
    input: Panopea_generosa_v1.fasta
    output: Panopea_generosa_v1.windowmasker.counts, Panopea_generosa_v1.windowmasker.fasta
    log: logs/Panopea_generosa_v1/run_windowmasker.log
    jobid: 1
    benchmark: logs/Panopea_generosa_v1/run_windowmasker.benchmark.txt

windowmasker -in Panopea_generosa_v1.fasta                      -infmt fasta                      -mk_counts                      -sformat obinary                      -out Panopea_generosa_v1.windowmasker.counts 2> logs/Panopea_generosa_v1/run_windowmasker.log &&         windowmasker -in Panopea_generosa_v1.fasta                      -infmt fasta                      -ustat Panopea_generosa_v1.windowmasker.counts                      -dust T                      -outfmt fasta                      -out Panopea_generosa_v1.windowmasker.fasta 2>> logs/Panopea_generosa_v1/run_windowmasker.log
Removing temporary output file Panopea_generosa_v1.fasta.
[Fri Jul 16 05:54:08 2021]
Finished job 1.
2 of 3 steps (67%) done
Select jobs to execute...

[Fri Jul 16 05:54:09 2021]
localrule all:
    input: Panopea_generosa_v1.windowmasker.fasta
    jobid: 0

[Fri Jul 16 05:54:09 2021]
Finished job 0.
3 of 3 steps (100%) done
Complete log: /gscratch/scrubbed/samwhite/outputs/20210712_pgen_blobtools_Panopea-generosa-v1.0/windowmasker/.snakemake/log/2021-07-16T054647.993836.snakemake.log