Creating specified working directory /gscratch/scrubbed/samwhite/outputs/20210712_pgen_blobtools_Panopea-generosa-v1.0/blastn.
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	chunk_nohit_fasta
	1	extract_nohit_fasta
	1	run_blastn
	1	unchunk_blastn
	5
Select jobs to execute...

[Wed Jul 28 20:33:41 2021]
rule extract_nohit_fasta:
    input: ../diamond/Panopea_generosa_v1.diamond.reference_proteomes.out, ../windowmasker/Panopea_generosa_v1.windowmasker.fasta
    output: Panopea_generosa_v1.nohit.fasta
    log: logs/Panopea_generosa_v1/extract_nohit_fasta.log
    jobid: 4
    benchmark: logs/Panopea_generosa_v1/extract_nohit_fasta.benchmark.txt
    wildcards: assembly=Panopea_generosa_v1
    threads: 4

seqtk subseq ../windowmasker/Panopea_generosa_v1.windowmasker.fasta <(grep '>' ../windowmasker/Panopea_generosa_v1.windowmasker.fasta |             grep -v -w -f <(awk '{if($14<1e-25){print $1}}' ../diamond/Panopea_generosa_v1.diamond.reference_proteomes.out |                 sort | uniq)             | cut -f1 | sed 's/>//') > Panopea_generosa_v1.nohit.fasta
[Wed Jul 28 20:33:46 2021]
Finished job 4.
1 of 5 steps (20%) done
Select jobs to execute...

[Wed Jul 28 20:33:46 2021]
rule chunk_nohit_fasta:
    input: Panopea_generosa_v1.nohit.fasta
    output: Panopea_generosa_v1.nohit.fasta.chunks
    log: logs/Panopea_generosa_v1/chunk_fasta.log
    jobid: 3
    benchmark: logs/Panopea_generosa_v1/chunk_fasta.benchmark.txt
    wildcards: assembly=Panopea_generosa_v1

/gscratch/srlab/programs/anaconda3/envs/btk_env/bin/python3.8 /gscratch/scrubbed/samwhite/outputs/20210712_pgen_blobtools_Panopea-generosa-v1.0/blastn/.snakemake/scripts/tmpz2m34dkz.chunk_fasta.py
2021-07-28 20:33:47,182 [INFO] Splitting Panopea_generosa_v1.nohit.fasta into chunks
[Wed Jul 28 20:33:47 2021]
Finished job 3.
2 of 5 steps (40%) done
Select jobs to execute...

[Wed Jul 28 20:33:47 2021]
rule run_blastn:
    input: Panopea_generosa_v1.nohit.fasta.chunks, /gscratch/srlab/blastdbs/20210401_ncbi_nt/nt.nal
    output: Panopea_generosa_v1.blastn.nt.out.raw
    log: logs/Panopea_generosa_v1/run_blastn.log
    jobid: 2
    benchmark: logs/Panopea_generosa_v1/run_blastn.benchmark.txt
    wildcards: assembly=Panopea_generosa_v1
    threads: 30

(if [ -s Panopea_generosa_v1.nohit.fasta.chunks ]; then             blastn -task megablast                 -query Panopea_generosa_v1.nohit.fasta.chunks                 -db /gscratch/srlab/blastdbs/20210401_ncbi_nt/nt                 -outfmt "6 qseqid staxids bitscore std"                 -max_target_seqs 10                 -max_hsps 1                 -evalue 1e-10                 -num_threads 30                 -negative_taxids 1049056                 -lcase_masking                 -dust "20 64 1"                 > Panopea_generosa_v1.blastn.nt.out.raw;         else             > Panopea_generosa_v1.blastn.nt.out.raw;         fi) 2> logs/Panopea_generosa_v1/run_blastn.log
[Wed Jul 28 20:33:47 2021]
Finished job 2.
3 of 5 steps (60%) done
Select jobs to execute...

[Wed Jul 28 20:33:47 2021]
rule unchunk_blastn:
    input: Panopea_generosa_v1.blastn.nt.out.raw
    output: Panopea_generosa_v1.blastn.nt.out
    log: logs/Panopea_generosa_v1/unchunk_blastn.log
    jobid: 1
    benchmark: logs/Panopea_generosa_v1/unchunk_blastn.benchmark.txt
    wildcards: assembly=Panopea_generosa_v1

/gscratch/srlab/programs/anaconda3/envs/btk_env/bin/python3.8 /gscratch/scrubbed/samwhite/outputs/20210712_pgen_blobtools_Panopea-generosa-v1.0/blastn/.snakemake/scripts/tmpbhu3y7zl.unchunk_blast.py
[Wed Jul 28 20:33:47 2021]
Finished job 1.
4 of 5 steps (80%) done
Select jobs to execute...

[Wed Jul 28 20:33:47 2021]
localrule all:
    input: Panopea_generosa_v1.blastn.nt.out
    jobid: 0

[Wed Jul 28 20:33:47 2021]
Finished job 0.
5 of 5 steps (100%) done
Complete log: /gscratch/scrubbed/samwhite/outputs/20210712_pgen_blobtools_Panopea-generosa-v1.0/blastn/.snakemake/log/2021-07-28T203341.207595.snakemake.log