Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 14 Rules claiming more threads will be scaled down. Job counts: count jobs 1 MOSGA_export_GFF 1 MOSGA_export_Sequin 1 MOSGA_import_barrnap 1 MOSGA_import_trnascan2 1 MOSGA_import_windowmasker 1 MOSGA_initialize_genome 1 MOSGA_vecscreen_analyse 1 all 1 barrnap 1 barrnap_tabix 1 busco 1 busco_graph 1 chop_genome 1 file_index 1 jbrowse2_add_assembly 1 jbrowse2_barrnap 1 jbrowse2_mosga_gff 1 jbrowse2_set_default_view 1 jbrowse2_trnascan_se2 1 jbrowse2_windowmasker 1 jbrowse_assembly_index 1 mitos 1 mitos_finalize 1 mosga_gff_tabix 1 normalize_fasta_header 1 plastids 1 plastids_finalize 1 prepare_vecscreen 1 search_vecscreen 1 tbl2asn 1 trnascan_se2 1 trnascan_se2_tabix 1 windowmasker_count 1 windowmasker_hardmasking 1 windowmasker_softmasking 1 windowmasker_to_gff 36 [Mon Jul 19 15:32:20 2021] rule normalize_fasta_header: input: /opt/mosga/snakemake/../gui/uploads/dd02ad62/7614fdf12303399203ee803b output: /opt/mosga/snakemake/../gui/uploads/dd02ad62/7614fdf12303399203ee803b_n jobid: 16 sum=`egrep '>' /opt/mosga/snakemake/../gui/uploads/dd02ad62/7614fdf12303399203ee803b | wc | awk 'sum=$2 {sum -= $1} END {print sum}'`; long=`egrep '>' /opt/mosga/snakemake/../gui/uploads/dd02ad62/7614fdf12303399203ee803b | wc -L`; if [ "$sum" == "0" -a "$long" -lt "50" ]; then ln -s /opt/mosga/snakemake/../gui/uploads/dd02ad62/7614fdf12303399203ee803b /opt/mosga/snakemake/../gui/uploads/dd02ad62/7614fdf12303399203ee803b_n; else python3 /opt/mosga/scripts/normalize_fasta.py /opt/mosga/snakemake/../gui/uploads/dd02ad62/7614fdf12303399203ee803b /opt/mosga/snakemake/../gui/uploads/dd02ad62/7614fdf12303399203ee803b_n; fi [Mon Jul 19 15:32:20 2021] Finished job 16. 1 of 36 steps (3%) done [Mon Jul 19 15:32:20 2021] rule MOSGA_initialize_genome: input: /opt/mosga/snakemake/../gui/uploads/dd02ad62/7614fdf12303399203ee803b_n, /opt/mosga/snakemake/../gui/uploads/dd02ad62/7614fdf12303399203ee803b output: /opt/mosga/snakemake/../gui/uploads/dd02ad62/igf.txt jobid: 23 threads: 14 python3 /opt/mosga/accumulator/mosga.py initialize_genome dd02ad62 /opt/mosga/snakemake/../gui/uploads/dd02ad62/7614fdf12303399203ee803b_n -orig /opt/mosga/snakemake/../gui/uploads/dd02ad62/7614fdf12303399203ee803b -dir /opt/mosga/gui/uploads/ touch /opt/mosga/snakemake/../gui/uploads/dd02ad62/igf.txt [Mon Jul 19 15:32:27 2021] Finished job 23. 2 of 36 steps (6%) done [Mon Jul 19 15:32:27 2021] rule windowmasker_count: input: /opt/mosga/snakemake/../gui/uploads/dd02ad62/7614fdf12303399203ee803b_n output: /opt/mosga/snakemake/../gui/uploads/dd02ad62/repeats/windowmasker/count log: /opt/mosga/snakemake/../gui/uploads/dd02ad62/logs/windowmasker.log jobid: 25 windowmasker -mk_counts -in /opt/mosga/snakemake/../gui/uploads/dd02ad62/7614fdf12303399203ee803b_n -infmt fasta -out /opt/mosga/snakemake/../gui/uploads/dd02ad62/repeats/windowmasker/count -sformat ascii -checkdup true >/opt/mosga/snakemake/../gui/uploads/dd02ad62/logs/windowmasker.log 2>&1 [Mon Jul 19 15:32:27 2021] rule chop_genome: input: /opt/mosga/snakemake/../gui/uploads/dd02ad62/7614fdf12303399203ee803b_n output: /opt/mosga/snakemake/../gui/uploads/dd02ad62/genes/chopped_genome.fna.gz log: /opt/mosga/snakemake/../gui/uploads/dd02ad62/logs/genome_chopping.log jobid: 35 /opt/mosga/tools/seq-scripts/bin/seq-chop -l 50000 -p /opt/mosga/snakemake/../gui/uploads/dd02ad62/7614fdf12303399203ee803b_n 2>/opt/mosga/snakemake/../gui/uploads/dd02ad62/logs/genome_chopping.log | gzip -c > /opt/mosga/snakemake/../gui/uploads/dd02ad62/genes/chopped_genome.fna.gz [Mon Jul 19 15:32:27 2021] rule barrnap: input: /opt/mosga/snakemake/../gui/uploads/dd02ad62/7614fdf12303399203ee803b_n output: /opt/mosga/snakemake/../gui/uploads/dd02ad62/rrnas/barrnap/output.gff log: /opt/mosga/snakemake/../gui/uploads/dd02ad62/logs/barrnap.log jobid: 20 threads: 4 /opt/mosga/tools/barrnap/bin/barrnap /opt/mosga/snakemake/../gui/uploads/dd02ad62/7614fdf12303399203ee803b_n --kingdom euk --lencutoff 0.8 --reject 0.25 --evalue 10e-6 --threads 4 --quiet > /opt/mosga/snakemake/../gui/uploads/dd02ad62/rrnas/barrnap/output.gff 2>/opt/mosga/snakemake/../gui/uploads/dd02ad62/logs/barrnap.log [Mon Jul 19 15:32:27 2021] rule trnascan_se2: input: /opt/mosga/snakemake/../gui/uploads/dd02ad62/7614fdf12303399203ee803b_n output: /opt/mosga/snakemake/../gui/uploads/dd02ad62/trnas/trnascan2/trna.txt, /opt/mosga/snakemake/../gui/uploads/dd02ad62/trnas/trnascan2/trna.bed jobid: 19 threads: 4 /opt/mosga/tools/tRNAscan/tRNAscan-SE -Q -q -E /opt/mosga/snakemake/../gui/uploads/dd02ad62/7614fdf12303399203ee803b_n -o /opt/mosga/snakemake/../gui/uploads/dd02ad62/trnas/trnascan2/trna.txt -m /opt/mosga/snakemake/../gui/uploads/dd02ad62/trnas/trnascan2/trna.stats -a /opt/mosga/snakemake/../gui/uploads/dd02ad62/trnas/trnascan2/trna.faa -b /opt/mosga/snakemake/../gui/uploads/dd02ad62/trnas/trnascan2/trna.bed --detail --thread 4 [Mon Jul 19 15:32:27 2021] rule jbrowse_assembly_index: input: /opt/mosga/snakemake/../gui/uploads/dd02ad62/7614fdf12303399203ee803b_n output: /opt/mosga/snakemake/../gui/uploads/dd02ad62/7614fdf12303399203ee803b_n.fai jobid: 17 /opt/mosga/tools/samtools/samtools faidx /opt/mosga/snakemake/../gui/uploads/dd02ad62/7614fdf12303399203ee803b_n ln -s -f /opt/mosga/snakemake/../gui/uploads/dd02ad62/jbrowse /opt/mosga/gui/jbrowse2/mosga/dd02ad62 2>/dev/null [Mon Jul 19 15:32:27 2021] Finished job 17. 3 of 36 steps (8%) done [Mon Jul 19 15:32:30 2021] Finished job 35. 4 of 36 steps (11%) done [Mon Jul 19 15:32:30 2021] rule mitos: input: /opt/mosga/snakemake/../gui/uploads/dd02ad62/genes/chopped_genome.fna.gz output: /opt/mosga/snakemake/../gui/uploads/dd02ad62/genes/mitos.chopped.txt.gz log: /opt/mosga/snakemake/../gui/uploads/dd02ad62/logs/mitos.log jobid: 32 threads: 4 /opt/mosga/tools/diamond/diamond blastx -d /opt/mosga/tools/diamond/mito -q /opt/mosga/snakemake/../gui/uploads/dd02ad62/genes/chopped_genome.fna.gz -o /opt/mosga/snakemake/../gui/uploads/dd02ad62/genes/mitos.chopped.txt.gz -b4 --compress 1 --threads 4 --evalue 0.001 -f 6 qseqid sseqid qstart qend sstart send length nident pident evalue bitscore score mismatch gapopen gaps qcovhsp stitle >/opt/mosga/snakemake/../gui/uploads/dd02ad62/logs/mitos.log 2>&1 [Mon Jul 19 15:32:36 2021] Finished job 32. 5 of 36 steps (14%) done [Mon Jul 19 15:32:36 2021] rule plastids: input: /opt/mosga/snakemake/../gui/uploads/dd02ad62/genes/chopped_genome.fna.gz output: /opt/mosga/snakemake/../gui/uploads/dd02ad62/genes/plastids.chopped.txt.gz log: /opt/mosga/snakemake/../gui/uploads/dd02ad62/logs/plastids.log jobid: 33 threads: 4 /opt/mosga/tools/diamond/diamond blastx -d /opt/mosga/tools/diamond/plastid -q /opt/mosga/snakemake/../gui/uploads/dd02ad62/genes/chopped_genome.fna.gz -o /opt/mosga/snakemake/../gui/uploads/dd02ad62/genes/plastids.chopped.txt.gz -b4 --compress 1 --threads 4 --evalue 0.001 -f 6 qseqid sseqid qstart qend sstart send length nident pident evalue bitscore score mismatch gapopen gaps qcovhsp stitle >/opt/mosga/snakemake/../gui/uploads/dd02ad62/logs/plastids.log 2>&1 [Mon Jul 19 15:32:38 2021] Finished job 20. 6 of 36 steps (17%) done [Mon Jul 19 15:32:38 2021] rule barrnap_tabix: input: /opt/mosga/snakemake/../gui/uploads/dd02ad62/rrnas/barrnap/output.gff output: /opt/mosga/snakemake/../gui/uploads/dd02ad62/rrnas/barrnap/output.gff.gz, /opt/mosga/snakemake/../gui/uploads/dd02ad62/rrnas/barrnap/output.gff.gz.tbi jobid: 11 python3 /opt/mosga/scripts/barrnap_to_gff3.py /opt/mosga/snakemake/../gui/uploads/dd02ad62/rrnas/barrnap/output.gff | gt gff3 -sortlines -tidy -retainids 2> /dev/null | bgzip > /opt/mosga/snakemake/../gui/uploads/dd02ad62/rrnas/barrnap/output.gff.gz tabix /opt/mosga/snakemake/../gui/uploads/dd02ad62/rrnas/barrnap/output.gff.gz [Mon Jul 19 15:32:38 2021] rule prepare_vecscreen: input: /opt/mosga/snakemake/../gui/uploads/dd02ad62/genes/chopped_genome.fna.gz output: /opt/mosga/snakemake/../gui/uploads/dd02ad62/genes/chopped_genome.fna jobid: 31 threads: 3 gunzip -k /opt/mosga/snakemake/../gui/uploads/dd02ad62/genes/chopped_genome.fna.gz /opt/mosga/scripts/barrnap_to_gff3.py:26: SyntaxWarning: "is" with a literal. Did you mean "=="? if line[:1] is "#": [Mon Jul 19 15:32:38 2021] Finished job 11. 7 of 36 steps (19%) done [Mon Jul 19 15:32:38 2021] Finished job 31. 8 of 36 steps (22%) done [Mon Jul 19 15:32:38 2021] rule mitos_finalize: input: /opt/mosga/snakemake/../gui/uploads/dd02ad62/genes/mitos.chopped.txt.gz output: /opt/mosga/snakemake/../gui/uploads/dd02ad62/genes/mitos.txt.gz jobid: 26 threads: 3 python3 /opt/mosga/scripts/rename_chopped_results.py /opt/mosga/snakemake/../gui/uploads/dd02ad62/genes/mitos.chopped.txt.gz /opt/mosga/snakemake/../gui/uploads/dd02ad62/genes/mitos.txt.gz [Mon Jul 19 15:32:38 2021] Finished job 26. 9 of 36 steps (25%) done [Mon Jul 19 15:32:41 2021] Finished job 33. 10 of 36 steps (28%) done [Mon Jul 19 15:32:41 2021] rule search_vecscreen: input: /opt/mosga/snakemake/../gui/uploads/dd02ad62/genes/chopped_genome.fna output: /opt/mosga/snakemake/../gui/uploads/dd02ad62/validation/vecscreen/blastn.txt.gz jobid: 22 threads: 7 blastn -db /opt/mosga/tools/vecscreen/UniVec -query /opt/mosga/snakemake/../gui/uploads/dd02ad62/genes/chopped_genome.fna -task blastn -num_threads 7 -reward 1 -penalty -5 -gapopen 3 -gapextend 3 -dust yes -soft_masking true -evalue 700 -searchsp 1750000000000 -outfmt "6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue score" | gzip -c > /opt/mosga/snakemake/../gui/uploads/dd02ad62/validation/vecscreen/blastn.txt.gz rm -f /opt/mosga/snakemake/../gui/uploads/dd02ad62/genes/chopped_genome.fna [Mon Jul 19 15:32:49 2021] Finished job 22. 11 of 36 steps (31%) done [Mon Jul 19 15:32:49 2021] rule plastids_finalize: input: /opt/mosga/snakemake/../gui/uploads/dd02ad62/genes/plastids.chopped.txt.gz output: /opt/mosga/snakemake/../gui/uploads/dd02ad62/genes/plastids.txt.gz jobid: 27 threads: 3 python3 /opt/mosga/scripts/rename_chopped_results.py /opt/mosga/snakemake/../gui/uploads/dd02ad62/genes/plastids.chopped.txt.gz /opt/mosga/snakemake/../gui/uploads/dd02ad62/genes/plastids.txt.gz [Mon Jul 19 15:32:49 2021] Finished job 27. 12 of 36 steps (33%) done [Mon Jul 19 15:32:50 2021] Finished job 25. 13 of 36 steps (36%) done [Mon Jul 19 15:32:50 2021] rule windowmasker_softmasking: input: /opt/mosga/snakemake/../gui/uploads/dd02ad62/7614fdf12303399203ee803b_n, /opt/mosga/snakemake/../gui/uploads/dd02ad62/repeats/windowmasker/count output: /opt/mosga/snakemake/../gui/uploads/dd02ad62/repeats/windowmasker/soft log: /opt/mosga/snakemake/../gui/uploads/dd02ad62/logs/windowmasker.log jobid: 18 windowmasker -in /opt/mosga/snakemake/../gui/uploads/dd02ad62/7614fdf12303399203ee803b_n -infmt fasta -ustat /opt/mosga/snakemake/../gui/uploads/dd02ad62/repeats/windowmasker/count -out /opt/mosga/snakemake/../gui/uploads/dd02ad62/repeats/windowmasker/soft -outfmt fasta >>/opt/mosga/snakemake/../gui/uploads/dd02ad62/logs/windowmasker.log 2>&1 [Mon Jul 19 15:32:55 2021] Finished job 18. 14 of 36 steps (39%) done [Mon Jul 19 15:32:55 2021] rule windowmasker_hardmasking: input: /opt/mosga/snakemake/../gui/uploads/dd02ad62/repeats/windowmasker/soft output: /opt/mosga/snakemake/../gui/uploads/dd02ad62/repeats/windowmasker/hard jobid: 34 perl -pe '/^[^>]/ and $_=~ s/[a-z]/N/g' /opt/mosga/snakemake/../gui/uploads/dd02ad62/repeats/windowmasker/soft > /opt/mosga/snakemake/../gui/uploads/dd02ad62/repeats/windowmasker/hard [Mon Jul 19 15:32:55 2021] rule windowmasker_to_gff: input: /opt/mosga/snakemake/../gui/uploads/dd02ad62/repeats/windowmasker/soft output: /opt/mosga/snakemake/../gui/uploads/dd02ad62/repeats/windowmasker/windowmasker.gff.gz jobid: 9 /opt/mosga/accumulator/mosga.py windowmasker_to_gff /opt/mosga/snakemake/../gui/uploads/dd02ad62/repeats/windowmasker/soft /opt/mosga/snakemake/../gui/uploads/dd02ad62/repeats/windowmasker/windowmasker.gff.gz -c | gt gff3 -sortlines -tidy -retainids 2>/dev/null | bgzip > /opt/mosga/snakemake/../gui/uploads/dd02ad62/repeats/windowmasker/windowmasker.gff.gz tabix /opt/mosga/snakemake/../gui/uploads/dd02ad62/repeats/windowmasker/windowmasker.gff.gz [Mon Jul 19 15:32:57 2021] Finished job 34. 15 of 36 steps (42%) done [Mon Jul 19 15:33:06 2021] Finished job 19. 16 of 36 steps (44%) done [Mon Jul 19 15:33:06 2021] rule trnascan_se2_tabix: input: /opt/mosga/snakemake/../gui/uploads/dd02ad62/trnas/trnascan2/trna.bed output: /opt/mosga/snakemake/../gui/uploads/dd02ad62/trnas/trnascan2/trna.bed.gz.tbi, /opt/mosga/snakemake/../gui/uploads/dd02ad62/trnas/trnascan2/trna.bed.gz jobid: 10 bgzip /opt/mosga/snakemake/../gui/uploads/dd02ad62/trnas/trnascan2/trna.bed -c > /opt/mosga/snakemake/../gui/uploads/dd02ad62/trnas/trnascan2/trna.bed.gz tabix /opt/mosga/snakemake/../gui/uploads/dd02ad62/trnas/trnascan2/trna.bed.gz [Mon Jul 19 15:33:06 2021] Finished job 10. 17 of 36 steps (47%) done [Mon Jul 19 15:33:07 2021] Finished job 9. 18 of 36 steps (50%) done [Mon Jul 19 15:33:07 2021] rule MOSGA_import_windowmasker: input: /opt/mosga/snakemake/../gui/uploads/dd02ad62/repeats/windowmasker/hard, /opt/mosga/snakemake/../gui/uploads/dd02ad62/repeats/windowmasker/hard, /opt/mosga/snakemake/../gui/uploads/dd02ad62/igf.txt output: /opt/mosga/snakemake/../gui/uploads/dd02ad62/repeats/windowmasker/collect.txt jobid: 28 threads: 14 python3 /opt/mosga/accumulator/mosga.py import dd02ad62 repeat -v -dir /opt/mosga/gui/uploads/ --repeat /opt/mosga/snakemake/../gui/uploads/dd02ad62/repeats/windowmasker/hard --repeat-format fasta_hard --repeat-min-length 100 --reader-repeat WindowMasker > /opt/mosga/snakemake/../gui/uploads/dd02ad62/repeats/windowmasker/collect.txt [Mon Jul 19 15:33:16 2021] Finished job 28. 19 of 36 steps (53%) done [Mon Jul 19 15:33:16 2021] rule jbrowse2_add_assembly: input: /opt/mosga/snakemake/../gui/uploads/dd02ad62/7614fdf12303399203ee803b_n, /opt/mosga/snakemake/../gui/uploads/dd02ad62/7614fdf12303399203ee803b_n.fai output: /opt/mosga/snakemake/../gui/uploads/dd02ad62/jbrowse/config.json log: /opt/mosga/snakemake/../gui/uploads/dd02ad62/logs/jbrowse.log jobid: 8 threads: 14 cd /opt/mosga/snakemake/../gui/uploads/dd02ad62/jbrowse /usr/bin/jbrowse add-assembly /opt/mosga/snakemake/../gui/uploads/dd02ad62/7614fdf12303399203ee803b_n --out /opt/mosga/snakemake/../gui/uploads/dd02ad62/jbrowse -l copy -t indexedFasta -n Genome >/opt/mosga/snakemake/../gui/uploads/dd02ad62/logs/jbrowse.log 2>&1 [Mon Jul 19 15:33:16 2021] Finished job 8. 20 of 36 steps (56%) done [Mon Jul 19 15:33:16 2021] rule busco: input: /opt/mosga/snakemake/../gui/uploads/dd02ad62/7614fdf12303399203ee803b_n output: /opt/mosga/snakemake/../gui/uploads/dd02ad62/validation/busco/summary.txt log: /opt/mosga/snakemake/../gui/uploads/dd02ad62/logs/busco.log jobid: 24 threads: 14 cd /opt/mosga/snakemake/../gui/uploads/dd02ad62/validation/ AUGUSTUS_CONFIG_PATH=/opt/mosga/tools/augustus/config python3 /opt/mosga/tools/BUSCO/bin/busco -i /opt/mosga/snakemake/../gui/uploads/dd02ad62/7614fdf12303399203ee803b_n -o busco --out_path /opt/mosga/snakemake/../gui/uploads/dd02ad62/validation/ -l eukaryota_odb10 --cpu 14 --force --config /opt/mosga/scripts/busco_config.ini >/opt/mosga/snakemake/../gui/uploads/dd02ad62/logs/busco.log 2>&1 mv busco/run_eukaryota_odb10/full_table.tsv busco/busco.tsv sed '1,/Results:/d' busco/short_summary.specific.eukaryota_odb10.busco.txt | sed -e 's/^[[:space:]]*//' | sed 1d > busco/summary.txt [Mon Jul 19 15:44:34 2021] Finished job 24. 21 of 36 steps (58%) done [Mon Jul 19 15:44:34 2021] rule MOSGA_vecscreen_analyse: input: /opt/mosga/snakemake/../gui/uploads/dd02ad62/validation/vecscreen/blastn.txt.gz, /opt/mosga/snakemake/../gui/uploads/dd02ad62/igf.txt output: /opt/mosga/snakemake/../gui/uploads/dd02ad62/validation/vecscreen/report.html log: /opt/mosga/snakemake/../gui/uploads/dd02ad62/logs/vecscreen_analyse.log jobid: 13 threads: 14 python3 /opt/mosga/accumulator/mosga.py vecscreen dd02ad62 /opt/mosga/snakemake/../gui/uploads/dd02ad62/validation/vecscreen/blastn.txt.gz /opt/mosga/snakemake/../gui/uploads/dd02ad62/validation/vecscreen/report.html -si 30 -mi 25 -wi 23 -st 24 -mt 19 -wt 16 -mh /opt/mosga/snakemake/../gui/uploads/dd02ad62/validation/vecscreen/matches.html -r /opt/mosga/snakemake/../gui/uploads/dd02ad62/validation/vecscreen/report.txt -dir /opt/mosga/gui/uploads/ >/opt/mosga/snakemake/../gui/uploads/dd02ad62/logs/vecscreen_analyse.log 2>&1 [Mon Jul 19 15:44:34 2021] Finished job 13. 22 of 36 steps (61%) done [Mon Jul 19 15:44:34 2021] rule MOSGA_import_trnascan2: input: /opt/mosga/snakemake/../gui/uploads/dd02ad62/trnas/trnascan2/trna.txt, /opt/mosga/snakemake/../gui/uploads/dd02ad62/igf.txt output: /opt/mosga/snakemake/../gui/uploads/dd02ad62/trnas/trnascan2/collect.txt jobid: 29 threads: 14 python3 /opt/mosga/accumulator/mosga.py import dd02ad62 trna -v -dir /opt/mosga/gui/uploads/ --trna /opt/mosga/snakemake/../gui/uploads/dd02ad62/trnas/trnascan2/trna.txt --trna-format CSV --trna-min-score 70 --reader-trna tRNAscan > /opt/mosga/snakemake/../gui/uploads/dd02ad62/trnas/trnascan2/collect.txt [Mon Jul 19 15:44:34 2021] Finished job 29. 23 of 36 steps (64%) done [Mon Jul 19 15:44:34 2021] rule MOSGA_import_barrnap: input: /opt/mosga/snakemake/../gui/uploads/dd02ad62/rrnas/barrnap/output.gff, /opt/mosga/snakemake/../gui/uploads/dd02ad62/igf.txt output: /opt/mosga/snakemake/../gui/uploads/dd02ad62/rrnas/barrnap/collect.txt jobid: 30 threads: 14 python3 /opt/mosga/accumulator/mosga.py import dd02ad62 rrna -v -dir /opt/mosga/gui/uploads/ --rrna /opt/mosga/snakemake/../gui/uploads/dd02ad62/rrnas/barrnap/output.gff --rrna-format GFF --reader-rrna Barrnap > /opt/mosga/snakemake/../gui/uploads/dd02ad62/rrnas/barrnap/collect.txt [Mon Jul 19 15:44:34 2021] Finished job 30. 24 of 36 steps (67%) done [Mon Jul 19 15:44:34 2021] rule jbrowse2_set_default_view: input: /opt/mosga/snakemake/../gui/uploads/dd02ad62/jbrowse/config.json output: /opt/mosga/snakemake/../gui/uploads/dd02ad62/jbrowse/setview.txt log: /opt/mosga/snakemake/../gui/uploads/dd02ad62/logs/jbrowse.log jobid: 2 /usr/bin/jbrowse set-default-session --target /opt/mosga/snakemake/../gui/uploads/dd02ad62/jbrowse/config.json --view LinearGenomeView -n "MOSGA dd02ad62" >>/opt/mosga/snakemake/../gui/uploads/dd02ad62/logs/jbrowse.log 2>&1 touch /opt/mosga/snakemake/../gui/uploads/dd02ad62/jbrowse/setview.txt [Mon Jul 19 15:44:34 2021] rule busco_graph: input: /opt/mosga/snakemake/../gui/uploads/dd02ad62/validation/busco/summary.txt output: /opt/mosga/snakemake/../gui/uploads/dd02ad62/validation/busco/busco.svg log: /opt/mosga/snakemake/../gui/uploads/dd02ad62/logs/busco.log jobid: 14 threads: 3 python3 /opt/mosga/scripts/busco_single_imager.py /opt/mosga/snakemake/../gui/uploads/dd02ad62/validation/busco/summary.txt /opt/mosga/snakemake/../gui/uploads/dd02ad62/validation/busco/busco.svg --title eukaryota_odb10 >>/opt/mosga/snakemake/../gui/uploads/dd02ad62/logs/busco.log 2>&1 [Mon Jul 19 15:44:34 2021] Finished job 2. 25 of 36 steps (69%) done [Mon Jul 19 15:44:35 2021] Finished job 14. 26 of 36 steps (72%) done [Mon Jul 19 15:44:35 2021] rule jbrowse2_windowmasker: input: /opt/mosga/snakemake/../gui/uploads/dd02ad62/repeats/windowmasker/windowmasker.gff.gz, /opt/mosga/snakemake/../gui/uploads/dd02ad62/jbrowse/setview.txt output: /opt/mosga/snakemake/../gui/uploads/dd02ad62/repeats/windowmasker/jbrowse.txt log: /opt/mosga/snakemake/../gui/uploads/dd02ad62/logs/jbrowse.log jobid: 3 threads: 14 cd /opt/mosga/snakemake/../gui/uploads/dd02ad62/jbrowse /usr/bin/jbrowse add-track /opt/mosga/snakemake/../gui/uploads/dd02ad62/repeats/windowmasker/windowmasker.gff.gz --out /opt/mosga/snakemake/../gui/uploads/dd02ad62/jbrowse --load copy --subDir=Repeats --force -n WindowMasker >>/opt/mosga/snakemake/../gui/uploads/dd02ad62/logs/jbrowse.log 2>&1 touch /opt/mosga/snakemake/../gui/uploads/dd02ad62/repeats/windowmasker/jbrowse.txt [Mon Jul 19 15:44:36 2021] Finished job 3. 27 of 36 steps (75%) done [Mon Jul 19 15:44:36 2021] rule jbrowse2_trnascan_se2: input: /opt/mosga/snakemake/../gui/uploads/dd02ad62/trnas/trnascan2/trna.bed.gz, /opt/mosga/snakemake/../gui/uploads/dd02ad62/jbrowse/setview.txt output: /opt/mosga/snakemake/../gui/uploads/dd02ad62/trnas/trnascan2/jbrowse.txt log: /opt/mosga/snakemake/../gui/uploads/dd02ad62/logs/jbrowse.log jobid: 4 threads: 14 cd /opt/mosga/snakemake/../gui/uploads/dd02ad62/jbrowse /usr/bin/jbrowse add-track /opt/mosga/snakemake/../gui/uploads/dd02ad62/trnas/trnascan2/trna.bed.gz --out /opt/mosga/snakemake/../gui/uploads/dd02ad62/jbrowse --load copy --subDir=tRNAs --force -n tRNAscan-SE >>/opt/mosga/snakemake/../gui/uploads/dd02ad62/logs/jbrowse.log 2>&1 touch /opt/mosga/snakemake/../gui/uploads/dd02ad62/trnas/trnascan2/jbrowse.txt [Mon Jul 19 15:44:36 2021] Finished job 4. 28 of 36 steps (78%) done [Mon Jul 19 15:44:36 2021] rule jbrowse2_barrnap: input: /opt/mosga/snakemake/../gui/uploads/dd02ad62/rrnas/barrnap/output.gff.gz, /opt/mosga/snakemake/../gui/uploads/dd02ad62/jbrowse/setview.txt output: /opt/mosga/snakemake/../gui/uploads/dd02ad62/rrnas/barrnap/jbrowse.txt log: /opt/mosga/snakemake/../gui/uploads/dd02ad62/logs/jbrowse.log jobid: 5 threads: 14 cd /opt/mosga/snakemake/../gui/uploads/dd02ad62/jbrowse /usr/bin/jbrowse add-track /opt/mosga/snakemake/../gui/uploads/dd02ad62/rrnas/barrnap/output.gff.gz --out /opt/mosga/snakemake/../gui/uploads/dd02ad62/jbrowse --load copy --subDir=rRNA --force -n barrnap >>/opt/mosga/snakemake/../gui/uploads/dd02ad62/logs/jbrowse.log 2>&1 touch /opt/mosga/snakemake/../gui/uploads/dd02ad62/rrnas/barrnap/jbrowse.txt [Mon Jul 19 15:44:36 2021] Finished job 5. 29 of 36 steps (81%) done [Mon Jul 19 15:44:36 2021] rule MOSGA_export_Sequin: input: /opt/mosga/snakemake/../gui/uploads/dd02ad62/genes/mitos.txt.gz, /opt/mosga/snakemake/../gui/uploads/dd02ad62/genes/plastids.txt.gz, /opt/mosga/snakemake/../gui/uploads/dd02ad62/repeats/windowmasker/collect.txt, /opt/mosga/snakemake/../gui/uploads/dd02ad62/trnas/trnascan2/collect.txt, /opt/mosga/snakemake/../gui/uploads/dd02ad62/rrnas/barrnap/collect.txt, /opt/mosga/snakemake/../gui/uploads/dd02ad62/jbrowse/setview.txt, /opt/mosga/snakemake/../gui/uploads/dd02ad62/repeats/windowmasker/jbrowse.txt, /opt/mosga/snakemake/../gui/uploads/dd02ad62/trnas/trnascan2/jbrowse.txt, /opt/mosga/snakemake/../gui/uploads/dd02ad62/rrnas/barrnap/jbrowse.txt, /opt/mosga/snakemake/../gui/uploads/dd02ad62/7614fdf12303399203ee803b_n, /opt/mosga/snakemake/../gui/uploads/dd02ad62/igf.txt output: /opt/mosga/snakemake/../gui/uploads/dd02ad62/7614fdf12303399203ee803b_n.tbl, /opt/mosga/snakemake/../gui/uploads/dd02ad62/writer.log jobid: 21 python3 /opt/mosga/accumulator/mosga.py export dd02ad62 -v -dir /opt/mosga/gui/uploads/ --organelle_indication True --organelle_file /opt/mosga/snakemake/../gui/uploads/dd02ad62/organelles.html -o /opt/mosga/snakemake/../gui/uploads/dd02ad62/7614fdf12303399203ee803b_n.tbl -w Sequin -qc True -gf /opt/mosga/snakemake/../gui/uploads/dd02ad62/7614fdf12303399203ee803b_n > /opt/mosga/snakemake/../gui/uploads/dd02ad62/writer.log [Mon Jul 19 15:44:47 2021] Finished job 21. 30 of 36 steps (83%) done [Mon Jul 19 15:44:47 2021] rule tbl2asn: input: /opt/mosga/snakemake/../gui/uploads/dd02ad62/7614fdf12303399203ee803b_n.tbl, /opt/mosga/snakemake/../gui/uploads/dd02ad62/7614fdf12303399203ee803b_n output: /opt/mosga/snakemake/../gui/uploads/dd02ad62/genome-discrepancy.txt, /opt/mosga/snakemake/../gui/uploads/dd02ad62/genome.sqn log: /opt/mosga/snakemake/../gui/uploads/dd02ad62/logs/tbl2asn.log jobid: 12 cd /opt/mosga/snakemake/../gui/uploads/dd02ad62/ /opt/mosga/tools/tbl2asn -t /opt/mosga/gui/template.sbt -i 7614fdf12303399203ee803b_n -V v -j "[organism=Nannochloropsis oceanica]" -M n -Z /opt/mosga/snakemake/../gui/uploads/dd02ad62/genome-discrepancy.txt -l map -a r10u >/opt/mosga/snakemake/../gui/uploads/dd02ad62/logs/tbl2asn.log 2>&1 mv /opt/mosga/snakemake/../gui/uploads/dd02ad62/7614fdf12303399203ee803b_n.sqn /opt/mosga/snakemake/../gui/uploads/dd02ad62/genome.sqn mv /opt/mosga/snakemake/../gui/uploads/dd02ad62/7614fdf12303399203ee803b_n.val /opt/mosga/snakemake/../gui/uploads/dd02ad62/genome-validation.txt ln -s -f /opt/mosga/snakemake/../gui/uploads/dd02ad62/7614fdf12303399203ee803b_n.tbl /opt/mosga/snakemake/../gui/uploads/dd02ad62/genome-table.txt mv /opt/mosga/snakemake/../gui/uploads/dd02ad62/errorsummary.val /opt/mosga/snakemake/../gui/uploads/dd02ad62/genome-error-summary.txt [Mon Jul 19 15:44:47 2021] rule MOSGA_export_GFF: input: /opt/mosga/snakemake/../gui/uploads/dd02ad62/7614fdf12303399203ee803b_n, /opt/mosga/snakemake/../gui/uploads/dd02ad62/7614fdf12303399203ee803b_n.tbl output: /opt/mosga/snakemake/../gui/uploads/dd02ad62/genome.gff, /opt/mosga/snakemake/../gui/uploads/dd02ad62/writer_gff.log jobid: 15 python3 /opt/mosga/accumulator/mosga.py export dd02ad62 -v -dir /opt/mosga/gui/uploads/ --organelle_indication False -o /opt/mosga/snakemake/../gui/uploads/dd02ad62/genome.gff -w GFF -qc True -gf /opt/mosga/snakemake/../gui/uploads/dd02ad62/7614fdf12303399203ee803b_n -sum /opt/mosga/snakemake/../gui/uploads/dd02ad62/summary.html -soi > /opt/mosga/snakemake/../gui/uploads/dd02ad62/writer_gff.log [Mon Jul 19 15:44:51 2021] Finished job 12. 31 of 36 steps (86%) done [Mon Jul 19 15:44:59 2021] Finished job 15. 32 of 36 steps (89%) done [Mon Jul 19 15:44:59 2021] rule file_index: input: /opt/mosga/snakemake/../gui/uploads/dd02ad62/genome.sqn, /opt/mosga/snakemake/../gui/uploads/dd02ad62/validation/vecscreen/report.html, /opt/mosga/snakemake/../gui/uploads/dd02ad62/validation/busco/busco.svg output: /opt/mosga/snakemake/../gui/uploads/dd02ad62/index.txt jobid: 6 threads: 14 cd /opt/mosga/snakemake/../gui/uploads/dd02ad62/ && find . -type f | cut -c3- | grep -v jbrowse | grep -v '^$' > /opt/mosga/snakemake/../gui/uploads/dd02ad62/index.txt [Mon Jul 19 15:44:59 2021] Finished job 6. 33 of 36 steps (92%) done [Mon Jul 19 15:44:59 2021] rule mosga_gff_tabix: input: /opt/mosga/snakemake/../gui/uploads/dd02ad62/genome.gff output: /opt/mosga/snakemake/../gui/uploads/dd02ad62/genome.gff.gz, /opt/mosga/snakemake/../gui/uploads/dd02ad62/genome.gff.gz.tbi jobid: 7 cat /opt/mosga/snakemake/../gui/uploads/dd02ad62/genome.gff | gt gff3 -sortlines -tidy -retainids 2>/dev/null | bgzip > /opt/mosga/snakemake/../gui/uploads/dd02ad62/genome.gff.gz tabix /opt/mosga/snakemake/../gui/uploads/dd02ad62/genome.gff.gz [Mon Jul 19 15:44:59 2021] Finished job 7. 34 of 36 steps (94%) done [Mon Jul 19 15:44:59 2021] rule jbrowse2_mosga_gff: input: /opt/mosga/snakemake/../gui/uploads/dd02ad62/genome.gff.gz, /opt/mosga/snakemake/../gui/uploads/dd02ad62/jbrowse/setview.txt output: /opt/mosga/snakemake/../gui/uploads/dd02ad62/jbrowse_mosga.txt log: /opt/mosga/snakemake/../gui/uploads/dd02ad62/logs/jbrowse.log jobid: 1 threads: 14 cd /opt/mosga/snakemake/../gui/uploads/dd02ad62/jbrowse /usr/bin/jbrowse add-track /opt/mosga/snakemake/../gui/uploads/dd02ad62/genome.gff.gz --out /opt/mosga/snakemake/../gui/uploads/dd02ad62/jbrowse --load copy --subDir=Genes --force -n MOSGA >>/opt/mosga/snakemake/../gui/uploads/dd02ad62/logs/jbrowse.log 2>&1 touch /opt/mosga/snakemake/../gui/uploads/dd02ad62/jbrowse_mosga.txt [Mon Jul 19 15:44:59 2021] Finished job 1. 35 of 36 steps (97%) done [Mon Jul 19 15:44:59 2021] localrule all: input: /opt/mosga/snakemake/../gui/uploads/dd02ad62/jbrowse_mosga.txt, /opt/mosga/snakemake/../gui/uploads/dd02ad62/jbrowse/setview.txt, /opt/mosga/snakemake/../gui/uploads/dd02ad62/repeats/windowmasker/jbrowse.txt, /opt/mosga/snakemake/../gui/uploads/dd02ad62/trnas/trnascan2/jbrowse.txt, /opt/mosga/snakemake/../gui/uploads/dd02ad62/rrnas/barrnap/jbrowse.txt, /opt/mosga/snakemake/../gui/uploads/dd02ad62/jbrowse_mosga.txt, /opt/mosga/snakemake/../gui/uploads/dd02ad62/index.txt jobid: 0 [Mon Jul 19 15:44:59 2021] Finished job 0. 36 of 36 steps (100%) done Complete log: /opt/mosga/snakemake/.snakemake/log/2021-07-19T153215.467032.snakemake.log