****************** Start a BUSCO 3.0.2 analysis, current time: 01/21/2021 09:58:43 ****************** Configuration loaded from /DATB/markop/CPB/quast/Serratia/busco_stats/config.ini Init tools... Check dependencies... Check input file... To reproduce this run: python /home/administrator/conda2/envs/spades/bin/quast.py -i /DATB/markop/CPB/quast/Serratia/quast_corrected_input/spades.fasta -o spades -l /home/administrator/conda2/envs/spades/lib/python3.6/site-packages/quast_libs/busco/bacteria/ -m genome -c 30 -t /DATB/markop/CPB/quast/Serratia/busco_stats/tmp/ -sp fly --augustus_parameters '''' Mode is: genome The lineage dataset is: bacteria_odb9 (prokaryota) Delete the current result folder and start a new run Temp directory is /DATB/markop/CPB/quast/Serratia/busco_stats/tmp/ ****** Phase 1 of 2, initial predictions ****** ****** Step 1/3, current time: 01/21/2021 09:58:43 ****** Create blast database... [makeblastdb] Building a new DB, current time: 01/21/2021 09:58:43 [makeblastdb] New DB name: /DATB/markop/CPB/quast/Serratia/busco_stats/tmp/spades_3913507323 [makeblastdb] New DB title: /DATB/markop/CPB/quast/Serratia/quast_corrected_input/spades.fasta [makeblastdb] Sequence type: Nucleotide [makeblastdb] Keep MBits: T [makeblastdb] Maximum file size: 1000000000B [makeblastdb] Adding sequences from FASTA; added 933 sequences in 0.0768552 seconds. [makeblastdb] 1 of 1 task(s) completed at 01/21/2021 09:58:44 Running tblastn, writing output to /DATB/markop/CPB/quast/Serratia/busco_stats/run_spades/blast_output/tblastn_spades.tsv... [tblastn] 1 of 1 task(s) completed at 01/21/2021 09:58:46 ****** Step 2/3, current time: 01/21/2021 09:58:46 ****** Maximum number of candidate contig per BUSCO limited to: 3 Getting coordinates for candidate regions... Pre-Augustus scaffold extraction... Running Augustus prediction using fly as species: Additional parameters for Augustus are '': [augustus] Please find all logs related to Augustus errors here: /DATB/markop/CPB/quast/Serratia/busco_stats/run_spades/augustus_output/augustus.log [augustus] 16 of 156 task(s) completed at 01/21/2021 09:58:50 [augustus] 32 of 156 task(s) completed at 01/21/2021 09:58:52 [augustus] 47 of 156 task(s) completed at 01/21/2021 09:58:54 [augustus] 63 of 156 task(s) completed at 01/21/2021 09:58:57 [augustus] 78 of 156 task(s) completed at 01/21/2021 09:59:00 [augustus] 94 of 156 task(s) completed at 01/21/2021 09:59:02 [augustus] 110 of 156 task(s) completed at 01/21/2021 09:59:05 [augustus] 125 of 156 task(s) completed at 01/21/2021 09:59:08 [augustus] 141 of 156 task(s) completed at 01/21/2021 09:59:10 [augustus] 156 of 156 task(s) completed at 01/21/2021 09:59:17 Extracting predicted proteins... ****** Step 3/3, current time: 01/21/2021 09:59:20 ****** Running HMMER to confirm orthology of predicted proteins: [hmmsearch] 109 of 155 task(s) completed at 01/21/2021 09:59:21 [hmmsearch] 155 of 155 task(s) completed at 01/21/2021 09:59:22 Results: C:92.6%[S:91.9%,D:0.7%],F:0.0%,M:7.4%,n:148 137 Complete BUSCOs (C) 136 Complete and single-copy BUSCOs (S) 1 Complete and duplicated BUSCOs (D) 0 Fragmented BUSCOs (F) 11 Missing BUSCOs (M) 148 Total BUSCO groups searched ****** Phase 2 of 2, predictions using species specific training ****** ****** Step 1/3, current time: 01/21/2021 09:59:22 ****** Extracting missing and fragmented buscos from the ancestral_variants file... Running tblastn, writing output to /DATB/markop/CPB/quast/Serratia/busco_stats/run_spades/blast_output/tblastn_spades_missing_and_frag_rerun.tsv... [tblastn] 1 of 1 task(s) completed at 01/21/2021 09:59:22 Maximum number of candidate contig per BUSCO limited to: 3 Getting coordinates for candidate regions... ****** Step 2/3, current time: 01/21/2021 09:59:22 ****** Training Augustus using Single-Copy Complete BUSCOs: Converting predicted genes to short genbank files at 01/21/2021 09:59:22... All files converted to short genbank files, now running the training scripts at 01/21/2021 09:59:23... Pre-Augustus scaffold extraction... Re-running Augustus with the new metaparameters, number of target BUSCOs: 11 [augustus] 2 of 11 task(s) completed at 01/21/2021 09:59:24 [augustus] 3 of 11 task(s) completed at 01/21/2021 09:59:24 [augustus] 4 of 11 task(s) completed at 01/21/2021 09:59:24 [augustus] 5 of 11 task(s) completed at 01/21/2021 09:59:24 [augustus] 6 of 11 task(s) completed at 01/21/2021 09:59:24 [augustus] 7 of 11 task(s) completed at 01/21/2021 09:59:24 [augustus] 8 of 11 task(s) completed at 01/21/2021 09:59:24 [augustus] 9 of 11 task(s) completed at 01/21/2021 09:59:25 [augustus] 10 of 11 task(s) completed at 01/21/2021 09:59:25 [augustus] 11 of 11 task(s) completed at 01/21/2021 09:59:25 Extracting predicted proteins... ****** Step 3/3, current time: 01/21/2021 09:59:25 ****** Running HMMER to confirm orthology of predicted proteins: [hmmsearch] 1 of 10 task(s) completed at 01/21/2021 09:59:25 [hmmsearch] 2 of 10 task(s) completed at 01/21/2021 09:59:25 [hmmsearch] 3 of 10 task(s) completed at 01/21/2021 09:59:25 [hmmsearch] 5 of 10 task(s) completed at 01/21/2021 09:59:25 [hmmsearch] 6 of 10 task(s) completed at 01/21/2021 09:59:25 [hmmsearch] 7 of 10 task(s) completed at 01/21/2021 09:59:25 [hmmsearch] 8 of 10 task(s) completed at 01/21/2021 09:59:25 [hmmsearch] 9 of 10 task(s) completed at 01/21/2021 09:59:25 [hmmsearch] 10 of 10 task(s) completed at 01/21/2021 09:59:25 Results: C:99.3%[S:98.6%,D:0.7%],F:0.0%,M:0.7%,n:148 147 Complete BUSCOs (C) 146 Complete and single-copy BUSCOs (S) 1 Complete and duplicated BUSCOs (D) 0 Fragmented BUSCOs (F) 1 Missing BUSCOs (M) 148 Total BUSCO groups searched BUSCO analysis done. Total running time: 42.17423892021179 seconds Results written in /DATB/markop/CPB/quast/Serratia/busco_stats/run_spades/