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 count_busco_genes 5 run_busco_v5 7 Select jobs to execute... [Wed Jul 28 11:32:54 2021] rule run_busco_v5: input: Panopea_generosa_v1.fasta output: Panopea_generosa_v1.busco.arthropoda_odb10/full_table.tsv.gz log: logs/Panopea_generosa_v1/run_busco/arthropoda_odb10.log jobid: 3 benchmark: logs/Panopea_generosa_v1/run_busco/arthropoda_odb10.benchmark.txt wildcards: assembly=Panopea_generosa_v1, lineage=arthropoda_odb10 threads: 30 mkdir -p Panopea_generosa_v1.busco.arthropoda_odb10 && busco -f -i Panopea_generosa_v1.fasta -o Panopea_generosa_v1_arthropoda_odb10 --download_path /gscratch/srlab/sam/data/databases/BUSCO -l arthropoda_odb10 --offline -m geno -c 30 > logs/Panopea_generosa_v1/run_busco/arthropoda_odb10.log 2>&1 && gzip -c Panopea_generosa_v1_arthropoda_odb10/run_arthropoda_odb10/full_table.tsv > Panopea_generosa_v1.busco.arthropoda_odb10/full_table.tsv.gz && gzip -c Panopea_generosa_v1_arthropoda_odb10/run_arthropoda_odb10/short_summary.txt > Panopea_generosa_v1.busco.arthropoda_odb10/short_summary.txt.gz && gzip -c Panopea_generosa_v1_arthropoda_odb10/run_arthropoda_odb10/missing_busco_list.tsv > Panopea_generosa_v1.busco.arthropoda_odb10/missing_busco_list.tsv.gz && tar czf Panopea_generosa_v1.busco.arthropoda_odb10/busco_sequences.tar.gz -C Panopea_generosa_v1_arthropoda_odb10/run_arthropoda_odb10 busco_sequences && rm -rf Panopea_generosa_v1_arthropoda_odb10 && exit 0 || if grep -q "Prodigal did not recognize any genes" logs/Panopea_generosa_v1/run_busco/arthropoda_odb10.log; then touch Panopea_generosa_v1.busco.arthropoda_odb10/full_table.tsv.gz && rm -rf Panopea_generosa_v1_arthropoda_odb10 && exit 0; fi; rm -rf Panopea_generosa_v1_arthropoda_odb10 && exit 1 [Wed Jul 28 13:22:41 2021] Finished job 3. 1 of 7 steps (14%) done Select jobs to execute... [Wed Jul 28 13:22:42 2021] rule run_busco_v5: input: Panopea_generosa_v1.fasta output: Panopea_generosa_v1.busco.bacteria_odb10/full_table.tsv.gz log: logs/Panopea_generosa_v1/run_busco/bacteria_odb10.log jobid: 4 benchmark: logs/Panopea_generosa_v1/run_busco/bacteria_odb10.benchmark.txt wildcards: assembly=Panopea_generosa_v1, lineage=bacteria_odb10 threads: 30 mkdir -p Panopea_generosa_v1.busco.bacteria_odb10 && busco -f -i Panopea_generosa_v1.fasta -o Panopea_generosa_v1_bacteria_odb10 --download_path /gscratch/srlab/sam/data/databases/BUSCO -l bacteria_odb10 --offline -m geno -c 30 > logs/Panopea_generosa_v1/run_busco/bacteria_odb10.log 2>&1 && gzip -c Panopea_generosa_v1_bacteria_odb10/run_bacteria_odb10/full_table.tsv > Panopea_generosa_v1.busco.bacteria_odb10/full_table.tsv.gz && gzip -c Panopea_generosa_v1_bacteria_odb10/run_bacteria_odb10/short_summary.txt > Panopea_generosa_v1.busco.bacteria_odb10/short_summary.txt.gz && gzip -c Panopea_generosa_v1_bacteria_odb10/run_bacteria_odb10/missing_busco_list.tsv > Panopea_generosa_v1.busco.bacteria_odb10/missing_busco_list.tsv.gz && tar czf Panopea_generosa_v1.busco.bacteria_odb10/busco_sequences.tar.gz -C Panopea_generosa_v1_bacteria_odb10/run_bacteria_odb10 busco_sequences && rm -rf Panopea_generosa_v1_bacteria_odb10 && exit 0 || if grep -q "Prodigal did not recognize any genes" logs/Panopea_generosa_v1/run_busco/bacteria_odb10.log; then touch Panopea_generosa_v1.busco.bacteria_odb10/full_table.tsv.gz && rm -rf Panopea_generosa_v1_bacteria_odb10 && exit 0; fi; rm -rf Panopea_generosa_v1_bacteria_odb10 && exit 1 [Wed Jul 28 13:25:31 2021] Finished job 4. 2 of 7 steps (29%) done Select jobs to execute... [Wed Jul 28 13:25:31 2021] rule run_busco_v5: input: Panopea_generosa_v1.fasta output: Panopea_generosa_v1.busco.eukaryota_odb10/full_table.tsv.gz log: logs/Panopea_generosa_v1/run_busco/eukaryota_odb10.log jobid: 5 benchmark: logs/Panopea_generosa_v1/run_busco/eukaryota_odb10.benchmark.txt wildcards: assembly=Panopea_generosa_v1, lineage=eukaryota_odb10 threads: 30 mkdir -p Panopea_generosa_v1.busco.eukaryota_odb10 && busco -f -i Panopea_generosa_v1.fasta -o Panopea_generosa_v1_eukaryota_odb10 --download_path /gscratch/srlab/sam/data/databases/BUSCO -l eukaryota_odb10 --offline -m geno -c 30 > logs/Panopea_generosa_v1/run_busco/eukaryota_odb10.log 2>&1 && gzip -c Panopea_generosa_v1_eukaryota_odb10/run_eukaryota_odb10/full_table.tsv > Panopea_generosa_v1.busco.eukaryota_odb10/full_table.tsv.gz && gzip -c Panopea_generosa_v1_eukaryota_odb10/run_eukaryota_odb10/short_summary.txt > Panopea_generosa_v1.busco.eukaryota_odb10/short_summary.txt.gz && gzip -c Panopea_generosa_v1_eukaryota_odb10/run_eukaryota_odb10/missing_busco_list.tsv > Panopea_generosa_v1.busco.eukaryota_odb10/missing_busco_list.tsv.gz && tar czf Panopea_generosa_v1.busco.eukaryota_odb10/busco_sequences.tar.gz -C Panopea_generosa_v1_eukaryota_odb10/run_eukaryota_odb10 busco_sequences && rm -rf Panopea_generosa_v1_eukaryota_odb10 && exit 0 || if grep -q "Prodigal did not recognize any genes" logs/Panopea_generosa_v1/run_busco/eukaryota_odb10.log; then touch Panopea_generosa_v1.busco.eukaryota_odb10/full_table.tsv.gz && rm -rf Panopea_generosa_v1_eukaryota_odb10 && exit 0; fi; rm -rf Panopea_generosa_v1_eukaryota_odb10 && exit 1 [Wed Jul 28 15:18:57 2021] Finished job 5. 3 of 7 steps (43%) done Select jobs to execute... [Wed Jul 28 15:18:58 2021] rule run_busco_v5: input: Panopea_generosa_v1.fasta output: Panopea_generosa_v1.busco.archaea_odb10/full_table.tsv.gz log: logs/Panopea_generosa_v1/run_busco/archaea_odb10.log jobid: 1 benchmark: logs/Panopea_generosa_v1/run_busco/archaea_odb10.benchmark.txt wildcards: assembly=Panopea_generosa_v1, lineage=archaea_odb10 threads: 30 mkdir -p Panopea_generosa_v1.busco.archaea_odb10 && busco -f -i Panopea_generosa_v1.fasta -o Panopea_generosa_v1_archaea_odb10 --download_path /gscratch/srlab/sam/data/databases/BUSCO -l archaea_odb10 --offline -m geno -c 30 > logs/Panopea_generosa_v1/run_busco/archaea_odb10.log 2>&1 && gzip -c Panopea_generosa_v1_archaea_odb10/run_archaea_odb10/full_table.tsv > Panopea_generosa_v1.busco.archaea_odb10/full_table.tsv.gz && gzip -c Panopea_generosa_v1_archaea_odb10/run_archaea_odb10/short_summary.txt > Panopea_generosa_v1.busco.archaea_odb10/short_summary.txt.gz && gzip -c Panopea_generosa_v1_archaea_odb10/run_archaea_odb10/missing_busco_list.tsv > Panopea_generosa_v1.busco.archaea_odb10/missing_busco_list.tsv.gz && tar czf Panopea_generosa_v1.busco.archaea_odb10/busco_sequences.tar.gz -C Panopea_generosa_v1_archaea_odb10/run_archaea_odb10 busco_sequences && rm -rf Panopea_generosa_v1_archaea_odb10 && exit 0 || if grep -q "Prodigal did not recognize any genes" logs/Panopea_generosa_v1/run_busco/archaea_odb10.log; then touch Panopea_generosa_v1.busco.archaea_odb10/full_table.tsv.gz && rm -rf Panopea_generosa_v1_archaea_odb10 && exit 0; fi; rm -rf Panopea_generosa_v1_archaea_odb10 && exit 1 [Wed Jul 28 15:20:10 2021] Finished job 1. 4 of 7 steps (57%) done Select jobs to execute... [Wed Jul 28 15:20:11 2021] rule run_busco_v5: input: Panopea_generosa_v1.fasta output: Panopea_generosa_v1.busco.metazoa_odb10/full_table.tsv.gz log: logs/Panopea_generosa_v1/run_busco/metazoa_odb10.log jobid: 6 benchmark: logs/Panopea_generosa_v1/run_busco/metazoa_odb10.benchmark.txt wildcards: assembly=Panopea_generosa_v1, lineage=metazoa_odb10 threads: 30 mkdir -p Panopea_generosa_v1.busco.metazoa_odb10 && busco -f -i Panopea_generosa_v1.fasta -o Panopea_generosa_v1_metazoa_odb10 --download_path /gscratch/srlab/sam/data/databases/BUSCO -l metazoa_odb10 --offline -m geno -c 30 > logs/Panopea_generosa_v1/run_busco/metazoa_odb10.log 2>&1 && gzip -c Panopea_generosa_v1_metazoa_odb10/run_metazoa_odb10/full_table.tsv > Panopea_generosa_v1.busco.metazoa_odb10/full_table.tsv.gz && gzip -c Panopea_generosa_v1_metazoa_odb10/run_metazoa_odb10/short_summary.txt > Panopea_generosa_v1.busco.metazoa_odb10/short_summary.txt.gz && gzip -c Panopea_generosa_v1_metazoa_odb10/run_metazoa_odb10/missing_busco_list.tsv > Panopea_generosa_v1.busco.metazoa_odb10/missing_busco_list.tsv.gz && tar czf Panopea_generosa_v1.busco.metazoa_odb10/busco_sequences.tar.gz -C Panopea_generosa_v1_metazoa_odb10/run_metazoa_odb10 busco_sequences && rm -rf Panopea_generosa_v1_metazoa_odb10 && exit 0 || if grep -q "Prodigal did not recognize any genes" logs/Panopea_generosa_v1/run_busco/metazoa_odb10.log; then touch Panopea_generosa_v1.busco.metazoa_odb10/full_table.tsv.gz && rm -rf Panopea_generosa_v1_metazoa_odb10 && exit 0; fi; rm -rf Panopea_generosa_v1_metazoa_odb10 && exit 1 Removing temporary output file Panopea_generosa_v1.fasta. [Wed Jul 28 17:57:56 2021] Finished job 6. 5 of 7 steps (71%) done Select jobs to execute... [Wed Jul 28 17:57:57 2021] rule count_busco_genes: input: Panopea_generosa_v1.busco.archaea_odb10/full_table.tsv.gz, Panopea_generosa_v1.busco.arthropoda_odb10/full_table.tsv.gz, Panopea_generosa_v1.busco.bacteria_odb10/full_table.tsv.gz, Panopea_generosa_v1.busco.eukaryota_odb10/full_table.tsv.gz, Panopea_generosa_v1.busco.metazoa_odb10/full_table.tsv.gz, ../chunk_stats/Panopea_generosa_v1.chunk_stats.tsv output: Panopea_generosa_v1.chunk_stats.tsv log: logs/Panopea_generosa_v1/count_busco_genes.log jobid: 7 benchmark: logs/Panopea_generosa_v1/count_busco_genes.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/busco/.snakemake/scripts/tmp_dpg4xcj.count_busco_genes.py [Wed Jul 28 17:58:23 2021] Finished job 7. 6 of 7 steps (86%) done Select jobs to execute... [Wed Jul 28 17:58:23 2021] localrule all: input: Panopea_generosa_v1.busco.archaea_odb10/full_table.tsv.gz, Panopea_generosa_v1.busco.arthropoda_odb10/full_table.tsv.gz, Panopea_generosa_v1.busco.bacteria_odb10/full_table.tsv.gz, Panopea_generosa_v1.busco.eukaryota_odb10/full_table.tsv.gz, Panopea_generosa_v1.busco.metazoa_odb10/full_table.tsv.gz, Panopea_generosa_v1.chunk_stats.tsv jobid: 0 [Wed Jul 28 17:58:23 2021] Finished job 0. 7 of 7 steps (100%) done Complete log: /gscratch/scrubbed/samwhite/outputs/20210712_pgen_blobtools_Panopea-generosa-v1.0/busco/.snakemake/log/2021-07-28T113249.333802.snakemake.log