Creating specified working directory /gscratch/scrubbed/samwhite/outputs/20210712_pgen_blobtools_Panopea-generosa-v1.0/minimap.
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 30
Rules claiming more threads will be scaled down.
Job counts:
	count	jobs
	1	all
	1	run_minimap2_align
	1	run_minimap2_index
	3
Select jobs to execute...

[Fri Jul 16 05:46:48 2021]
rule run_minimap2_index:
    input: /gscratch/scrubbed/samwhite/outputs/20210712_pgen_blobtools_Panopea-generosa-v1.0/Panopea_generosa_v1.fasta.gz
    output: Panopea_generosa_v1.sr.mmi
    log: logs/Panopea_generosa_v1/run_minimap2_index/sr.log
    jobid: 2
    benchmark: logs/Panopea_generosa_v1/run_minimap2_index/sr.benchmark.txt
    wildcards: assembly=Panopea_generosa_v1, tuning=sr
    threads: 30

(minimap2 -t 30 -x sr -d Panopea_generosa_v1.sr.mmi /gscratch/scrubbed/samwhite/outputs/20210712_pgen_blobtools_Panopea-generosa-v1.0/Panopea_generosa_v1.fasta.gz) &> logs/Panopea_generosa_v1/run_minimap2_index/sr.log
[Fri Jul 16 05:47:18 2021]
Finished job 2.
1 of 3 steps (33%) done
Select jobs to execute...

[Fri Jul 16 05:47:18 2021]
rule run_minimap2_align:
    input: /gscratch/scrubbed/samwhite/outputs/20210712_pgen_blobtools_Panopea-generosa-v1.0/Panopea_generosa_v1.fasta.gz, Panopea_generosa_v1.sr.mmi, /gscratch/scrubbed/samwhite/outputs/20210712_pgen_blobtools_Panopea-generosa-v1.0/reads_1.fastq.gz, /gscratch/scrubbed/samwhite/outputs/20210712_pgen_blobtools_Panopea-generosa-v1.0/reads_2.fastq.gz
    output: Panopea_generosa_v1.reads.bam, Panopea_generosa_v1.reads.bam.csi
    log: logs/Panopea_generosa_v1/run_minimap2_align/reads.log
    jobid: 1
    benchmark: logs/Panopea_generosa_v1/run_minimap2_align/reads.benchmark.txt
    wildcards: assembly=Panopea_generosa_v1, sra=reads
    threads: 30

(minimap2 -t 30 -ax sr Panopea_generosa_v1.sr.mmi /gscratch/scrubbed/samwhite/outputs/20210712_pgen_blobtools_Panopea-generosa-v1.0/reads_1.fastq.gz /gscratch/scrubbed/samwhite/outputs/20210712_pgen_blobtools_Panopea-generosa-v1.0/reads_2.fastq.gz |         samtools view -h -T /gscratch/scrubbed/samwhite/outputs/20210712_pgen_blobtools_Panopea-generosa-v1.0/Panopea_generosa_v1.fasta.gz - |         samtools sort -@ 30 -O BAM -o Panopea_generosa_v1.reads.bam - &&
        samtools index -c Panopea_generosa_v1.reads.bam Panopea_generosa_v1.reads.bam.csi) &> logs/Panopea_generosa_v1/run_minimap2_align/reads.log
[Sun Jul 18 11:21:41 2021]
Finished job 1.
2 of 3 steps (67%) done
Select jobs to execute...

[Sun Jul 18 11:21:41 2021]
localrule all:
    input: Panopea_generosa_v1.reads.bam, Panopea_generosa_v1.reads.bam.csi
    jobid: 0

[Sun Jul 18 11:21:41 2021]
Finished job 0.
3 of 3 steps (100%) done
Complete log: /gscratch/scrubbed/samwhite/outputs/20210712_pgen_blobtools_Panopea-generosa-v1.0/minimap/.snakemake/log/2021-07-16T054647.962960.snakemake.log