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_cg_genes_comp 6 MOSGA_get_proteins_nuc_seq 1 all 1 blastdb 1 blastn 6 busco 1 busco_comparator 1 busco_visual 1 fastani 1 fastani_visual 1 mafft 1 phylogenetic_tree 1 prepare_msa 1 raxml 1 raxml_bootstrapping 1 raxml_maximum_likelihood 1 trimal 27 [Tue Jul 6 16:13:02 2021] rule fastani: input: /opt/mosga/snakemake/../gui/uploads/195325c3/a5559a11b76e89eb5e819001, /opt/mosga/snakemake/../gui/uploads/195325c3/9108fb9b755248880b5bfdc3, /opt/mosga/snakemake/../gui/uploads/195325c3/5b6fc498bc099b5bf794aca1, /opt/mosga/snakemake/../gui/uploads/195325c3/8804969e79f23866f2fc15e3, /opt/mosga/snakemake/../gui/uploads/195325c3/18c62eb443972a0e6c96bf5d, /opt/mosga/snakemake/../gui/uploads/195325c3/b0a0c70ba9787ec737a33233 output: /opt/mosga/snakemake/../gui/uploads/195325c3/ani/ani.out log: /opt/mosga/snakemake/../gui/uploads/195325c3/logs/fastani.log jobid: 5 threads: 14 Job counts: count jobs 1 fastani 1  FILES=(/opt/mosga/snakemake/../gui/uploads/195325c3/a5559a11b76e89eb5e819001 /opt/mosga/snakemake/../gui/uploads/195325c3/9108fb9b755248880b5bfdc3 /opt/mosga/snakemake/../gui/uploads/195325c3/5b6fc498bc099b5bf794aca1 /opt/mosga/snakemake/../gui/uploads/195325c3/8804969e79f23866f2fc15e3 /opt/mosga/snakemake/../gui/uploads/195325c3/18c62eb443972a0e6c96bf5d /opt/mosga/snakemake/../gui/uploads/195325c3/b0a0c70ba9787ec737a33233) NAMES=("Saccharomyces paradoxus" "Y12" "SK1" "sake001" "S288C" "HLJ167") for (( query=0 ; query<${#FILES[@]} ; query++ )) ; do for (( ref=0 ; ref<${#FILES[@]} ; ref++ )) ; do if [[ "$query" == "$ref" ]]; then continue; fi /opt/mosga/tools/FastANI/fastANI -q ${FILES[query]} -r ${FILES[ref]} -o /opt/mosga/snakemake/../gui/uploads/195325c3/ani/temp.ani --kmer 16 --fragLen 3000 --minFraction 0.2 --visualize --threads 14 >>/opt/mosga/snakemake/../gui/uploads/195325c3/logs/fastani.log 2>&1 sed -e "s/\s/,/g" -e "s#${FILES[query]}#${NAMES[query]}#" -e "s#${FILES[ref]}#${NAMES[ref]}#" /opt/mosga/snakemake/../gui/uploads/195325c3/ani/temp.ani >> /opt/mosga/snakemake/../gui/uploads/195325c3/ani/ani.out sed -e "s#${FILES[query]}#${NAMES[query]}#" -e "s#${FILES[ref]}#${NAMES[ref]}#" /opt/mosga/snakemake/../gui/uploads/195325c3/ani/temp.ani.visual >> /opt/mosga/snakemake/../gui/uploads/195325c3/ani/ani.out.visual rm /opt/mosga/snakemake/../gui/uploads/195325c3/ani/temp.* done done  [Tue Jul 6 16:15:24 2021] Finished job 5. 1 of 27 steps (4%) done [Tue Jul 6 16:15:24 2021] rule busco: input: /opt/mosga/snakemake/../gui/uploads/195325c3/18c62eb443972a0e6c96bf5d output: /opt/mosga/snakemake/../gui/uploads/195325c3/busco/18c62eb443972a0e6c96bf5d/run_saccharomycetes_odb10/full_table.tsv log: /opt/mosga/snakemake/../gui/uploads/195325c3/logs/busco_18c62eb443972a0e6c96bf5d.log jobid: 24 wildcards: file=18c62eb443972a0e6c96bf5d threads: 14 cd /opt/mosga/snakemake/../gui/uploads/195325c3/busco/ AUGUSTUS_CONFIG_PATH=/opt/mosga/tools/augustus/config python3 /opt/mosga/tools/BUSCO/bin/busco -i /opt/mosga/snakemake/../gui/uploads/195325c3/18c62eb443972a0e6c96bf5d -o 18c62eb443972a0e6c96bf5d --out_path /opt/mosga/snakemake/../gui/uploads/195325c3/busco/ -l saccharomycetes_odb10 --cpu 14 --force --config /opt/mosga/scripts/busco_config.ini >/opt/mosga/snakemake/../gui/uploads/195325c3/logs/busco_18c62eb443972a0e6c96bf5d.log 2>&1 cd /opt/mosga/snakemake/../gui/uploads/195325c3/busco//18c62eb443972a0e6c96bf5d tar cpf - blast_db/ logs/ run_saccharomycetes_odb10/ short_summary.* | pbzip2 -c > busco_18c62eb443972a0e6c96bf5d.tar.bz2 2>/dev/null rm -rf blast_db/ logs/ run_eukaryota_odb10/augustus_output/ run_eukaryota_odb10/blast_output/ run_eukaryota_odb10/hmmer_output/ run_eukaryota_odb10/busco_sequences/fragmented_busco_sequences/ 2>/dev/null [Tue Jul 6 16:31:20 2021] Finished job 24. 2 of 27 steps (7%) done [Tue Jul 6 16:31:20 2021] rule MOSGA_get_proteins_nuc_seq: input: /opt/mosga/gui/uploads/ebe13994/a5559a11b76e89eb5e819001_n output: /opt/mosga/snakemake/../gui/uploads/195325c3/gene_comparison/sequences/ebe13994_gene_sequences.fna jobid: 11 wildcards: uid=ebe13994 threads: 3 python3 /opt/mosga/accumulator/mosga.py get_proteins_nuc_seq ebe13994 /opt/mosga/gui/uploads/ebe13994/a5559a11b76e89eb5e819001_n -dir /opt/mosga/gui/uploads --prefix_genome --no_transcripts > /opt/mosga/snakemake/../gui/uploads/195325c3/gene_comparison/sequences/ebe13994_gene_sequences.fna [Tue Jul 6 16:31:20 2021] rule MOSGA_get_proteins_nuc_seq: input: /opt/mosga/gui/uploads/ec00695e/5b6fc498bc099b5bf794aca1_n output: /opt/mosga/snakemake/../gui/uploads/195325c3/gene_comparison/sequences/ec00695e_gene_sequences.fna jobid: 13 wildcards: uid=ec00695e threads: 3 python3 /opt/mosga/accumulator/mosga.py get_proteins_nuc_seq ec00695e /opt/mosga/gui/uploads/ec00695e/5b6fc498bc099b5bf794aca1_n -dir /opt/mosga/gui/uploads --prefix_genome --no_transcripts > /opt/mosga/snakemake/../gui/uploads/195325c3/gene_comparison/sequences/ec00695e_gene_sequences.fna [Tue Jul 6 16:31:20 2021] rule MOSGA_get_proteins_nuc_seq: input: /opt/mosga/gui/uploads/bf90f1fe/18c62eb443972a0e6c96bf5d_n output: /opt/mosga/snakemake/../gui/uploads/195325c3/gene_comparison/sequences/bf90f1fe_gene_sequences.fna jobid: 15 wildcards: uid=bf90f1fe threads: 3 python3 /opt/mosga/accumulator/mosga.py get_proteins_nuc_seq bf90f1fe /opt/mosga/gui/uploads/bf90f1fe/18c62eb443972a0e6c96bf5d_n -dir /opt/mosga/gui/uploads --prefix_genome --no_transcripts > /opt/mosga/snakemake/../gui/uploads/195325c3/gene_comparison/sequences/bf90f1fe_gene_sequences.fna [Tue Jul 6 16:31:20 2021] rule fastani_visual: input: /opt/mosga/snakemake/../gui/uploads/195325c3/ani/ani.out output: /opt/mosga/snakemake/../gui/uploads/195325c3/ani/heatmap.html jobid: 2 python3 /opt/mosga/scripts/ani_visual.py -i /opt/mosga/snakemake/../gui/uploads/195325c3/ani/ani.out -o /opt/mosga/snakemake/../gui/uploads/195325c3/ani/ --text [Tue Jul 6 16:31:20 2021] rule MOSGA_get_proteins_nuc_seq: input: /opt/mosga/gui/uploads/43cb4a18/8804969e79f23866f2fc15e3_n output: /opt/mosga/snakemake/../gui/uploads/195325c3/gene_comparison/sequences/43cb4a18_gene_sequences.fna jobid: 14 wildcards: uid=43cb4a18 threads: 3 python3 /opt/mosga/accumulator/mosga.py get_proteins_nuc_seq 43cb4a18 /opt/mosga/gui/uploads/43cb4a18/8804969e79f23866f2fc15e3_n -dir /opt/mosga/gui/uploads --prefix_genome --no_transcripts > /opt/mosga/snakemake/../gui/uploads/195325c3/gene_comparison/sequences/43cb4a18_gene_sequences.fna [Tue Jul 6 16:31:21 2021] Finished job 2. 3 of 27 steps (11%) done [Tue Jul 6 16:31:31 2021] Finished job 14. 4 of 27 steps (15%) done [Tue Jul 6 16:31:31 2021] rule MOSGA_get_proteins_nuc_seq: input: /opt/mosga/gui/uploads/021b80bb/b0a0c70ba9787ec737a33233_n output: /opt/mosga/snakemake/../gui/uploads/195325c3/gene_comparison/sequences/021b80bb_gene_sequences.fna jobid: 16 wildcards: uid=021b80bb threads: 3 python3 /opt/mosga/accumulator/mosga.py get_proteins_nuc_seq 021b80bb /opt/mosga/gui/uploads/021b80bb/b0a0c70ba9787ec737a33233_n -dir /opt/mosga/gui/uploads --prefix_genome --no_transcripts > /opt/mosga/snakemake/../gui/uploads/195325c3/gene_comparison/sequences/021b80bb_gene_sequences.fna [Tue Jul 6 16:31:31 2021] Finished job 13. 5 of 27 steps (19%) done [Tue Jul 6 16:31:31 2021] rule MOSGA_get_proteins_nuc_seq: input: /opt/mosga/gui/uploads/133adcd4/9108fb9b755248880b5bfdc3_n output: /opt/mosga/snakemake/../gui/uploads/195325c3/gene_comparison/sequences/133adcd4_gene_sequences.fna jobid: 12 wildcards: uid=133adcd4 threads: 3 python3 /opt/mosga/accumulator/mosga.py get_proteins_nuc_seq 133adcd4 /opt/mosga/gui/uploads/133adcd4/9108fb9b755248880b5bfdc3_n -dir /opt/mosga/gui/uploads --prefix_genome --no_transcripts > /opt/mosga/snakemake/../gui/uploads/195325c3/gene_comparison/sequences/133adcd4_gene_sequences.fna [Tue Jul 6 16:31:31 2021] Finished job 15. 6 of 27 steps (22%) done [Tue Jul 6 16:31:31 2021] Finished job 11. 7 of 27 steps (26%) done [Tue Jul 6 16:31:42 2021] Finished job 16. 8 of 27 steps (30%) done [Tue Jul 6 16:31:42 2021] Finished job 12. 9 of 27 steps (33%) done [Tue Jul 6 16:31:42 2021] rule blastdb: input: /opt/mosga/snakemake/../gui/uploads/195325c3/gene_comparison/sequences/ebe13994_gene_sequences.fna, /opt/mosga/snakemake/../gui/uploads/195325c3/gene_comparison/sequences/133adcd4_gene_sequences.fna, /opt/mosga/snakemake/../gui/uploads/195325c3/gene_comparison/sequences/ec00695e_gene_sequences.fna, /opt/mosga/snakemake/../gui/uploads/195325c3/gene_comparison/sequences/43cb4a18_gene_sequences.fna, /opt/mosga/snakemake/../gui/uploads/195325c3/gene_comparison/sequences/bf90f1fe_gene_sequences.fna, /opt/mosga/snakemake/../gui/uploads/195325c3/gene_comparison/sequences/021b80bb_gene_sequences.fna output: /opt/mosga/snakemake/../gui/uploads/195325c3/gene_comparison/blast/blastGenes jobid: 9 threads: 3 cat /opt/mosga/snakemake/../gui/uploads/195325c3/gene_comparison/sequences/*_gene_sequences.fna > /opt/mosga/snakemake/../gui/uploads/195325c3/gene_comparison/genes.fna makeblastdb -dbtype nucl -in /opt/mosga/snakemake/../gui/uploads/195325c3/gene_comparison/genes.fna -input_type fasta -title Genes -out /opt/mosga/snakemake/../gui/uploads/195325c3/gene_comparison/blast/blastGenes -parse_seqids if [ $(find /opt/mosga/snakemake/../gui/uploads/195325c3/gene_comparison/blast/ -name 'blastGenes.*' | wc -l) -gt 1 ]; then touch /opt/mosga/snakemake/../gui/uploads/195325c3/gene_comparison/blast/blastGenes; fi Building a new DB, current time: 07/06/2021 16:31:42 New DB name: /opt/mosga/gui/uploads/195325c3/gene_comparison/blast/blastGenes New DB title: Genes Sequence type: Nucleotide Keep MBits: T Maximum file size: 1000000000B Adding sequences from FASTA; added 28621 sequences in 0.713027 seconds. [Tue Jul 6 16:31:43 2021] Finished job 9. 10 of 27 steps (37%) done [Tue Jul 6 16:31:43 2021] rule busco: input: /opt/mosga/snakemake/../gui/uploads/195325c3/5b6fc498bc099b5bf794aca1 output: /opt/mosga/snakemake/../gui/uploads/195325c3/busco/5b6fc498bc099b5bf794aca1/run_saccharomycetes_odb10/full_table.tsv log: /opt/mosga/snakemake/../gui/uploads/195325c3/logs/busco_5b6fc498bc099b5bf794aca1.log jobid: 22 wildcards: file=5b6fc498bc099b5bf794aca1 threads: 14 cd /opt/mosga/snakemake/../gui/uploads/195325c3/busco/ AUGUSTUS_CONFIG_PATH=/opt/mosga/tools/augustus/config python3 /opt/mosga/tools/BUSCO/bin/busco -i /opt/mosga/snakemake/../gui/uploads/195325c3/5b6fc498bc099b5bf794aca1 -o 5b6fc498bc099b5bf794aca1 --out_path /opt/mosga/snakemake/../gui/uploads/195325c3/busco/ -l saccharomycetes_odb10 --cpu 14 --force --config /opt/mosga/scripts/busco_config.ini >/opt/mosga/snakemake/../gui/uploads/195325c3/logs/busco_5b6fc498bc099b5bf794aca1.log 2>&1 cd /opt/mosga/snakemake/../gui/uploads/195325c3/busco//5b6fc498bc099b5bf794aca1 tar cpf - blast_db/ logs/ run_saccharomycetes_odb10/ short_summary.* | pbzip2 -c > busco_5b6fc498bc099b5bf794aca1.tar.bz2 2>/dev/null rm -rf blast_db/ logs/ run_eukaryota_odb10/augustus_output/ run_eukaryota_odb10/blast_output/ run_eukaryota_odb10/hmmer_output/ run_eukaryota_odb10/busco_sequences/fragmented_busco_sequences/ 2>/dev/null [Tue Jul 6 16:47:39 2021] Finished job 22. 11 of 27 steps (41%) done [Tue Jul 6 16:47:39 2021] rule busco: input: /opt/mosga/snakemake/../gui/uploads/195325c3/a5559a11b76e89eb5e819001 output: /opt/mosga/snakemake/../gui/uploads/195325c3/busco/a5559a11b76e89eb5e819001/run_saccharomycetes_odb10/full_table.tsv log: /opt/mosga/snakemake/../gui/uploads/195325c3/logs/busco_a5559a11b76e89eb5e819001.log jobid: 20 wildcards: file=a5559a11b76e89eb5e819001 threads: 14 cd /opt/mosga/snakemake/../gui/uploads/195325c3/busco/ AUGUSTUS_CONFIG_PATH=/opt/mosga/tools/augustus/config python3 /opt/mosga/tools/BUSCO/bin/busco -i /opt/mosga/snakemake/../gui/uploads/195325c3/a5559a11b76e89eb5e819001 -o a5559a11b76e89eb5e819001 --out_path /opt/mosga/snakemake/../gui/uploads/195325c3/busco/ -l saccharomycetes_odb10 --cpu 14 --force --config /opt/mosga/scripts/busco_config.ini >/opt/mosga/snakemake/../gui/uploads/195325c3/logs/busco_a5559a11b76e89eb5e819001.log 2>&1 cd /opt/mosga/snakemake/../gui/uploads/195325c3/busco//a5559a11b76e89eb5e819001 tar cpf - blast_db/ logs/ run_saccharomycetes_odb10/ short_summary.* | pbzip2 -c > busco_a5559a11b76e89eb5e819001.tar.bz2 2>/dev/null rm -rf blast_db/ logs/ run_eukaryota_odb10/augustus_output/ run_eukaryota_odb10/blast_output/ run_eukaryota_odb10/hmmer_output/ run_eukaryota_odb10/busco_sequences/fragmented_busco_sequences/ 2>/dev/null [Tue Jul 6 17:03:52 2021] Finished job 20. 12 of 27 steps (44%) done [Tue Jul 6 17:03:52 2021] rule busco: input: /opt/mosga/snakemake/../gui/uploads/195325c3/8804969e79f23866f2fc15e3 output: /opt/mosga/snakemake/../gui/uploads/195325c3/busco/8804969e79f23866f2fc15e3/run_saccharomycetes_odb10/full_table.tsv log: /opt/mosga/snakemake/../gui/uploads/195325c3/logs/busco_8804969e79f23866f2fc15e3.log jobid: 23 wildcards: file=8804969e79f23866f2fc15e3 threads: 14 cd /opt/mosga/snakemake/../gui/uploads/195325c3/busco/ AUGUSTUS_CONFIG_PATH=/opt/mosga/tools/augustus/config python3 /opt/mosga/tools/BUSCO/bin/busco -i /opt/mosga/snakemake/../gui/uploads/195325c3/8804969e79f23866f2fc15e3 -o 8804969e79f23866f2fc15e3 --out_path /opt/mosga/snakemake/../gui/uploads/195325c3/busco/ -l saccharomycetes_odb10 --cpu 14 --force --config /opt/mosga/scripts/busco_config.ini >/opt/mosga/snakemake/../gui/uploads/195325c3/logs/busco_8804969e79f23866f2fc15e3.log 2>&1 cd /opt/mosga/snakemake/../gui/uploads/195325c3/busco//8804969e79f23866f2fc15e3 tar cpf - blast_db/ logs/ run_saccharomycetes_odb10/ short_summary.* | pbzip2 -c > busco_8804969e79f23866f2fc15e3.tar.bz2 2>/dev/null rm -rf blast_db/ logs/ run_eukaryota_odb10/augustus_output/ run_eukaryota_odb10/blast_output/ run_eukaryota_odb10/hmmer_output/ run_eukaryota_odb10/busco_sequences/fragmented_busco_sequences/ 2>/dev/null [Tue Jul 6 17:19:27 2021] Finished job 23. 13 of 27 steps (48%) done [Tue Jul 6 17:19:27 2021] rule busco: input: /opt/mosga/snakemake/../gui/uploads/195325c3/b0a0c70ba9787ec737a33233 output: /opt/mosga/snakemake/../gui/uploads/195325c3/busco/b0a0c70ba9787ec737a33233/run_saccharomycetes_odb10/full_table.tsv log: /opt/mosga/snakemake/../gui/uploads/195325c3/logs/busco_b0a0c70ba9787ec737a33233.log jobid: 25 wildcards: file=b0a0c70ba9787ec737a33233 threads: 14 cd /opt/mosga/snakemake/../gui/uploads/195325c3/busco/ AUGUSTUS_CONFIG_PATH=/opt/mosga/tools/augustus/config python3 /opt/mosga/tools/BUSCO/bin/busco -i /opt/mosga/snakemake/../gui/uploads/195325c3/b0a0c70ba9787ec737a33233 -o b0a0c70ba9787ec737a33233 --out_path /opt/mosga/snakemake/../gui/uploads/195325c3/busco/ -l saccharomycetes_odb10 --cpu 14 --force --config /opt/mosga/scripts/busco_config.ini >/opt/mosga/snakemake/../gui/uploads/195325c3/logs/busco_b0a0c70ba9787ec737a33233.log 2>&1 cd /opt/mosga/snakemake/../gui/uploads/195325c3/busco//b0a0c70ba9787ec737a33233 tar cpf - blast_db/ logs/ run_saccharomycetes_odb10/ short_summary.* | pbzip2 -c > busco_b0a0c70ba9787ec737a33233.tar.bz2 2>/dev/null rm -rf blast_db/ logs/ run_eukaryota_odb10/augustus_output/ run_eukaryota_odb10/blast_output/ run_eukaryota_odb10/hmmer_output/ run_eukaryota_odb10/busco_sequences/fragmented_busco_sequences/ 2>/dev/null [Tue Jul 6 17:35:25 2021] Finished job 25. 14 of 27 steps (52%) done [Tue Jul 6 17:35:25 2021] rule busco: input: /opt/mosga/snakemake/../gui/uploads/195325c3/9108fb9b755248880b5bfdc3 output: /opt/mosga/snakemake/../gui/uploads/195325c3/busco/9108fb9b755248880b5bfdc3/run_saccharomycetes_odb10/full_table.tsv log: /opt/mosga/snakemake/../gui/uploads/195325c3/logs/busco_9108fb9b755248880b5bfdc3.log jobid: 21 wildcards: file=9108fb9b755248880b5bfdc3 threads: 14 cd /opt/mosga/snakemake/../gui/uploads/195325c3/busco/ AUGUSTUS_CONFIG_PATH=/opt/mosga/tools/augustus/config python3 /opt/mosga/tools/BUSCO/bin/busco -i /opt/mosga/snakemake/../gui/uploads/195325c3/9108fb9b755248880b5bfdc3 -o 9108fb9b755248880b5bfdc3 --out_path /opt/mosga/snakemake/../gui/uploads/195325c3/busco/ -l saccharomycetes_odb10 --cpu 14 --force --config /opt/mosga/scripts/busco_config.ini >/opt/mosga/snakemake/../gui/uploads/195325c3/logs/busco_9108fb9b755248880b5bfdc3.log 2>&1 cd /opt/mosga/snakemake/../gui/uploads/195325c3/busco//9108fb9b755248880b5bfdc3 tar cpf - blast_db/ logs/ run_saccharomycetes_odb10/ short_summary.* | pbzip2 -c > busco_9108fb9b755248880b5bfdc3.tar.bz2 2>/dev/null rm -rf blast_db/ logs/ run_eukaryota_odb10/augustus_output/ run_eukaryota_odb10/blast_output/ run_eukaryota_odb10/hmmer_output/ run_eukaryota_odb10/busco_sequences/fragmented_busco_sequences/ 2>/dev/null [Tue Jul 6 17:50:12 2021] Finished job 21. 15 of 27 steps (56%) done [Tue Jul 6 17:50:12 2021] rule busco_visual: input: /opt/mosga/snakemake/../gui/uploads/195325c3/busco/a5559a11b76e89eb5e819001/run_saccharomycetes_odb10/full_table.tsv, /opt/mosga/snakemake/../gui/uploads/195325c3/busco/9108fb9b755248880b5bfdc3/run_saccharomycetes_odb10/full_table.tsv, /opt/mosga/snakemake/../gui/uploads/195325c3/busco/5b6fc498bc099b5bf794aca1/run_saccharomycetes_odb10/full_table.tsv, /opt/mosga/snakemake/../gui/uploads/195325c3/busco/8804969e79f23866f2fc15e3/run_saccharomycetes_odb10/full_table.tsv, /opt/mosga/snakemake/../gui/uploads/195325c3/busco/18c62eb443972a0e6c96bf5d/run_saccharomycetes_odb10/full_table.tsv, /opt/mosga/snakemake/../gui/uploads/195325c3/busco/b0a0c70ba9787ec737a33233/run_saccharomycetes_odb10/full_table.tsv output: /opt/mosga/snakemake/../gui/uploads/195325c3/busco/bar_chart.html, /opt/mosga/snakemake/../gui/uploads/195325c3/busco/strip_chart.html jobid: 26 threads: 3 python3 /opt/mosga/scripts/busco_visual.py -i /opt/mosga/snakemake/../gui/uploads/195325c3/busco/a5559a11b76e89eb5e819001/run_saccharomycetes_odb10/ /opt/mosga/snakemake/../gui/uploads/195325c3/busco/9108fb9b755248880b5bfdc3/run_saccharomycetes_odb10/ /opt/mosga/snakemake/../gui/uploads/195325c3/busco/5b6fc498bc099b5bf794aca1/run_saccharomycetes_odb10/ /opt/mosga/snakemake/../gui/uploads/195325c3/busco/8804969e79f23866f2fc15e3/run_saccharomycetes_odb10/ /opt/mosga/snakemake/../gui/uploads/195325c3/busco/18c62eb443972a0e6c96bf5d/run_saccharomycetes_odb10/ /opt/mosga/snakemake/../gui/uploads/195325c3/busco/b0a0c70ba9787ec737a33233/run_saccharomycetes_odb10/ -o /opt/mosga/snakemake/../gui/uploads/195325c3/busco/ -n "Saccharomyces paradoxus" "Y12" "SK1" "sake001" "S288C" "HLJ167" --title saccharomycetes_odb10 [Tue Jul 6 17:50:14 2021] Finished job 26. 16 of 27 steps (59%) done [Tue Jul 6 17:50:14 2021] rule busco_comparator: input: /opt/mosga/snakemake/../gui/uploads/195325c3/busco/a5559a11b76e89eb5e819001/run_saccharomycetes_odb10/full_table.tsv, /opt/mosga/snakemake/../gui/uploads/195325c3/busco/9108fb9b755248880b5bfdc3/run_saccharomycetes_odb10/full_table.tsv, /opt/mosga/snakemake/../gui/uploads/195325c3/busco/5b6fc498bc099b5bf794aca1/run_saccharomycetes_odb10/full_table.tsv, /opt/mosga/snakemake/../gui/uploads/195325c3/busco/8804969e79f23866f2fc15e3/run_saccharomycetes_odb10/full_table.tsv, /opt/mosga/snakemake/../gui/uploads/195325c3/busco/18c62eb443972a0e6c96bf5d/run_saccharomycetes_odb10/full_table.tsv, /opt/mosga/snakemake/../gui/uploads/195325c3/busco/b0a0c70ba9787ec737a33233/run_saccharomycetes_odb10/full_table.tsv, /opt/mosga/snakemake/../gui/uploads/195325c3/busco/bar_chart.html, /opt/mosga/snakemake/../gui/uploads/195325c3/busco/strip_chart.html output: /opt/mosga/snakemake/../gui/uploads/195325c3/busco/genes.fa log: /opt/mosga/snakemake/../gui/uploads/195325c3/logs/busco_comparator.log jobid: 19 threads: 3 python3 /opt/mosga/scripts/busco_comparator.py -i /opt/mosga/snakemake/../gui/uploads/195325c3/busco/a5559a11b76e89eb5e819001/run_saccharomycetes_odb10/ /opt/mosga/snakemake/../gui/uploads/195325c3/busco/9108fb9b755248880b5bfdc3/run_saccharomycetes_odb10/ /opt/mosga/snakemake/../gui/uploads/195325c3/busco/5b6fc498bc099b5bf794aca1/run_saccharomycetes_odb10/ /opt/mosga/snakemake/../gui/uploads/195325c3/busco/8804969e79f23866f2fc15e3/run_saccharomycetes_odb10/ /opt/mosga/snakemake/../gui/uploads/195325c3/busco/18c62eb443972a0e6c96bf5d/run_saccharomycetes_odb10/ /opt/mosga/snakemake/../gui/uploads/195325c3/busco/b0a0c70ba9787ec737a33233/run_saccharomycetes_odb10/ -o /opt/mosga/snakemake/../gui/uploads/195325c3/busco/genes.fa -n "a5559a11b76e89eb5e819001" "9108fb9b755248880b5bfdc3" "5b6fc498bc099b5bf794aca1" "8804969e79f23866f2fc15e3" "18c62eb443972a0e6c96bf5d" "b0a0c70ba9787ec737a33233" -ms 150 -ml 100 -md -1 >/opt/mosga/snakemake/../gui/uploads/195325c3/logs/busco_comparator.log 2>&1 [Tue Jul 6 17:50:14 2021] Finished job 19. 17 of 27 steps (63%) done [Tue Jul 6 17:50:14 2021] rule prepare_msa: input: /opt/mosga/snakemake/../gui/uploads/195325c3/busco/genes.fa output: /opt/mosga/snakemake/../gui/uploads/195325c3/phylogenetic/genes.fa jobid: 18 Job counts: count jobs 1 prepare_msa 1 cp /opt/mosga/snakemake/../gui/uploads/195325c3/busco/genes.fa /opt/mosga/snakemake/../gui/uploads/195325c3/phylogenetic/genes.fa [Tue Jul 6 17:50:14 2021] Finished job 18. 18 of 27 steps (67%) done [Tue Jul 6 17:50:14 2021] rule mafft: input: /opt/mosga/snakemake/../gui/uploads/195325c3/phylogenetic/genes.fa output: /opt/mosga/snakemake/../gui/uploads/195325c3/phylogenetic/mafft/genes.ph jobid: 17 threads: 14 mafft --thread 14 --amino --phylipout --op 1.53 --ep 0 --quiet /opt/mosga/snakemake/../gui/uploads/195325c3/phylogenetic/genes.fa > /opt/mosga/snakemake/../gui/uploads/195325c3/phylogenetic/mafft/genes.ph [Tue Jul 6 18:01:17 2021] Finished job 17. 19 of 27 steps (70%) done [Tue Jul 6 18:01:17 2021] rule trimal: input: /opt/mosga/snakemake/../gui/uploads/195325c3/phylogenetic/mafft/genes.ph output: /opt/mosga/snakemake/../gui/uploads/195325c3/phylogenetic/trimal/genes.clean.ph jobid: 10 threads: 3 /opt/mosga/tools/trimAl/source/trimal -in /opt/mosga/snakemake/../gui/uploads/195325c3/phylogenetic/mafft/genes.ph -out /opt/mosga/snakemake/../gui/uploads/195325c3/phylogenetic/trimal/genes.clean.ph -strictplus -automated1 [Tue Jul 6 18:01:18 2021] Finished job 10. 20 of 27 steps (74%) done [Tue Jul 6 18:01:18 2021] rule raxml_maximum_likelihood: input: /opt/mosga/snakemake/../gui/uploads/195325c3/phylogenetic/trimal/genes.clean.ph output: /opt/mosga/snakemake/../gui/uploads/195325c3/phylogenetic/raxml/maximum_likelihood/RAxML_bestTree.tree-ml log: /opt/mosga/snakemake/../gui/uploads/195325c3/logs/raxml_likelyhood.log jobid: 7 threads: 7 /opt/mosga/tools/RAxML/raxmlHPC-PTHREADS-AVX -T 7 -m PROTGAMMAAUTO -s /opt/mosga/snakemake/../gui/uploads/195325c3/phylogenetic/trimal/genes.clean.ph -o a5559a11b7 -n tree-ml -w /opt/mosga/snakemake/../gui/uploads/195325c3/phylogenetic/raxml/maximum_likelihood/ -p 31415926535 >/opt/mosga/snakemake/../gui/uploads/195325c3/logs/raxml_likelyhood.log 2>&1 [Tue Jul 6 18:01:18 2021] rule raxml_bootstrapping: input: /opt/mosga/snakemake/../gui/uploads/195325c3/phylogenetic/trimal/genes.clean.ph output: /opt/mosga/snakemake/../gui/uploads/195325c3/phylogenetic/raxml/bootstrapping/RAxML_bootstrap.tree-bo log: /opt/mosga/snakemake/../gui/uploads/195325c3/logs/raxml_bootstrapping.log jobid: 8 threads: 7 /opt/mosga/tools/RAxML/raxmlHPC-PTHREADS-AVX -f d -T 7 -m PROTGAMMAAUTO -s /opt/mosga/snakemake/../gui/uploads/195325c3/phylogenetic/trimal/genes.clean.ph -o a5559a11b7 -n tree-bo -w /opt/mosga/snakemake/../gui/uploads/195325c3/phylogenetic/raxml/bootstrapping/ -# 25 -p 31415926535 -b 31415926535 >/opt/mosga/snakemake/../gui/uploads/195325c3/logs/raxml_bootstrapping.log 2>&1 [Tue Jul 6 18:01:36 2021] Finished job 7. 21 of 27 steps (78%) done [Tue Jul 6 18:04:09 2021] Finished job 8. 22 of 27 steps (81%) done [Tue Jul 6 18:04:09 2021] rule raxml: input: /opt/mosga/snakemake/../gui/uploads/195325c3/phylogenetic/raxml/maximum_likelihood/RAxML_bestTree.tree-ml, /opt/mosga/snakemake/../gui/uploads/195325c3/phylogenetic/raxml/bootstrapping/RAxML_bootstrap.tree-bo output: /opt/mosga/snakemake/../gui/uploads/195325c3/phylogenetic/raxml/RAxML_bipartitions.tree log: /opt/mosga/snakemake/../gui/uploads/195325c3/logs/raxml.log jobid: 4 threads: 14 /opt/mosga/tools/RAxML/raxmlHPC-PTHREADS-AVX -f b -T 14 -m GTRCAT -z /opt/mosga/snakemake/../gui/uploads/195325c3/phylogenetic/raxml/bootstrapping/RAxML_bootstrap.tree-bo -t /opt/mosga/snakemake/../gui/uploads/195325c3/phylogenetic/raxml/maximum_likelihood/RAxML_bestTree.tree-ml -n tree -o a5559a11b7 -w /opt/mosga/snakemake/../gui/uploads/195325c3/phylogenetic/raxml/ >/opt/mosga/snakemake/../gui/uploads/195325c3/logs/raxml.log 2>&1 [Tue Jul 6 18:04:09 2021] Finished job 4. 23 of 27 steps (85%) done [Tue Jul 6 18:04:09 2021] rule phylogenetic_tree: input: /opt/mosga/snakemake/../gui/uploads/195325c3/phylogenetic/raxml/RAxML_bipartitions.tree output: /opt/mosga/snakemake/../gui/uploads/195325c3/phylogenetic/phy_tree.svg log: /opt/mosga/snakemake/../gui/uploads/195325c3/logs/phylogenetic_tree.log jobid: 1 threads: 3 cp /opt/mosga/snakemake/../gui/uploads/195325c3/phylogenetic/raxml/RAxML_bipartitions.tree /opt/mosga/snakemake/../gui/uploads/195325c3/phylogenetic/phy_tree.nwk Rscript /opt/mosga/scripts/PhyTree.R /opt/mosga/snakemake/../gui/uploads/195325c3/phylogenetic/raxml/RAxML_bipartitions.tree /opt/mosga/snakemake/../gui/uploads/195325c3/phylogenetic/phy_tree.svg static line "a5559a11b76e89eb5e819001=Saccharomyces paradoxus,9108fb9b755248880b5bfdc3=Y12,5b6fc498bc099b5bf794aca1=SK1,8804969e79f23866f2fc15e3=sake001,18c62eb443972a0e6c96bf5d=S288C,b0a0c70ba9787ec737a33233=HLJ167" >/opt/mosga/snakemake/../gui/uploads/195325c3/logs/phylogenetic_tree.log 2>&1 [Tue Jul 6 18:04:10 2021] Finished job 1. 24 of 27 steps (89%) done [Tue Jul 6 18:04:10 2021] rule blastn: input: /opt/mosga/snakemake/../gui/uploads/195325c3/gene_comparison/blast/blastGenes output: /opt/mosga/snakemake/../gui/uploads/195325c3/gene_comparison/blast/genes_filtered.csv.gz jobid: 6 threads: 14 blastn -num_threads 14 -db /opt/mosga/snakemake/../gui/uploads/195325c3/gene_comparison/blast/blastGenes -query /opt/mosga/snakemake/../gui/uploads/195325c3/gene_comparison/genes.fna -outfmt "6 qseqid sseqid nident pident evalue bitscore score mismatch gapopen gaps qcovs qcovhsp" | gzip -c > /opt/mosga/snakemake/../gui/uploads/195325c3/gene_comparison/blast/blast_result.csv.gz zcat /opt/mosga/snakemake/../gui/uploads/195325c3/gene_comparison/blast/blast_result.csv.gz | awk '($4+0) >= 90.0' | sort --version-sort -k1,1 -k4,4 -k5,5r | sort --version-sort -u -k1,1 -k2,2 | gzip -c > /opt/mosga/snakemake/../gui/uploads/195325c3/gene_comparison/blast/genes_filtered.csv.gz [Tue Jul 6 18:04:35 2021] Finished job 6. 25 of 27 steps (93%) done [Tue Jul 6 18:04:35 2021] rule MOSGA_cg_genes_comp: input: /opt/mosga/snakemake/../gui/uploads/195325c3/gene_comparison/blast/genes_filtered.csv.gz output: /opt/mosga/snakemake/../gui/uploads/195325c3/gene_comparison/cg_genome_similarity.svg jobid: 3 threads: 3 python3 /opt/mosga/accumulator/mosga.py cg_genes_comp "/opt/mosga/snakemake/../gui/uploads/195325c3/gene_comparison/genes.fna" "/opt/mosga/snakemake/../gui/uploads/195325c3/gene_comparison/blast/genes_filtered.csv.gz" --chart "/opt/mosga/snakemake/../gui/uploads/195325c3/gene_comparison/" --heatmap -v --labels "ebe13994=Saccharomyces paradoxus,133adcd4=Y12,ec00695e=SK1,43cb4a18=sake001,bf90f1fe=S288C,021b80bb=HLJ167" [Tue Jul 6 18:04:39 2021] Finished job 3. 26 of 27 steps (96%) done [Tue Jul 6 18:04:39 2021] localrule all: input: /opt/mosga/snakemake/../gui/uploads/195325c3/phylogenetic/phy_tree.svg, /opt/mosga/snakemake/../gui/uploads/195325c3/ani/heatmap.html, /opt/mosga/snakemake/../gui/uploads/195325c3/gene_comparison/cg_genome_similarity.svg jobid: 0 [Tue Jul 6 18:04:39 2021] Finished job 0. 27 of 27 steps (100%) done Complete log: /opt/mosga/snakemake/.snakemake/log/2021-07-06T161302.002184.snakemake.log