****************** Start a BUSCO 3.0.2 analysis, current time: 01/23/2021 12:19:13 ****************** Configuration loaded from /DATB/markop/CPB/CPB_rcf_DNAseq/quast/Enterococcus/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/CPB_rcf_DNAseq/quast/Enterococcus/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/CPB_rcf_DNAseq/quast/Enterococcus/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/CPB_rcf_DNAseq/quast/Enterococcus/busco_stats/tmp/ ****** Phase 1 of 2, initial predictions ****** ****** Step 1/3, current time: 01/23/2021 12:19:13 ****** Create blast database... [makeblastdb] Building a new DB, current time: 01/23/2021 12:19:14 [makeblastdb] New DB name: /DATB/markop/CPB/CPB_rcf_DNAseq/quast/Enterococcus/busco_stats/tmp/spades_3010562973 [makeblastdb] New DB title: /DATB/markop/CPB/CPB_rcf_DNAseq/quast/Enterococcus/quast_corrected_input/spades.fasta [makeblastdb] Sequence type: Nucleotide [makeblastdb] Keep MBits: T [makeblastdb] Maximum file size: 1000000000B [makeblastdb] Adding sequences from FASTA; added 319 sequences in 0.0267169 seconds. [makeblastdb] 1 of 1 task(s) completed at 01/23/2021 12:19:14 Running tblastn, writing output to /DATB/markop/CPB/CPB_rcf_DNAseq/quast/Enterococcus/busco_stats/run_spades/blast_output/tblastn_spades.tsv... [tblastn] 1 of 1 task(s) completed at 01/23/2021 12:19:15 ****** Step 2/3, current time: 01/23/2021 12:19:15 ****** 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/CPB_rcf_DNAseq/quast/Enterococcus/busco_stats/run_spades/augustus_output/augustus.log [augustus] 15 of 147 task(s) completed at 01/23/2021 12:19:19 [augustus] 30 of 147 task(s) completed at 01/23/2021 12:19:21 [augustus] 45 of 147 task(s) completed at 01/23/2021 12:19:23 [augustus] 74 of 147 task(s) completed at 01/23/2021 12:19:28 [augustus] 89 of 147 task(s) completed at 01/23/2021 12:19:30 [augustus] 103 of 147 task(s) completed at 01/23/2021 12:19:32 [augustus] 118 of 147 task(s) completed at 01/23/2021 12:19:34 [augustus] 133 of 147 task(s) completed at 01/23/2021 12:19:36 [augustus] 147 of 147 task(s) completed at 01/23/2021 12:19:39 Extracting predicted proteins... ****** Step 3/3, current time: 01/23/2021 12:19:43 ****** Running HMMER to confirm orthology of predicted proteins: [hmmsearch] 146 of 146 task(s) completed at 01/23/2021 12:19:44 Results: C:85.8%[S:85.8%,D:0.0%],F:2.0%,M:12.2%,n:148 127 Complete BUSCOs (C) 127 Complete and single-copy BUSCOs (S) 0 Complete and duplicated BUSCOs (D) 3 Fragmented BUSCOs (F) 18 Missing BUSCOs (M) 148 Total BUSCO groups searched ****** Phase 2 of 2, predictions using species specific training ****** ****** Step 1/3, current time: 01/23/2021 12:19:44 ****** Extracting missing and fragmented buscos from the ancestral_variants file... Running tblastn, writing output to /DATB/markop/CPB/CPB_rcf_DNAseq/quast/Enterococcus/busco_stats/run_spades/blast_output/tblastn_spades_missing_and_frag_rerun.tsv... [tblastn] 1 of 1 task(s) completed at 01/23/2021 12:19:45 Maximum number of candidate contig per BUSCO limited to: 3 Getting coordinates for candidate regions... ****** Step 2/3, current time: 01/23/2021 12:19:45 ****** Training Augustus using Single-Copy Complete BUSCOs: Converting predicted genes to short genbank files at 01/23/2021 12:19:45... All files converted to short genbank files, now running the training scripts at 01/23/2021 12:19:46... Pre-Augustus scaffold extraction... Re-running Augustus with the new metaparameters, number of target BUSCOs: 21 [augustus] 2 of 19 task(s) completed at 01/23/2021 12:19:47 [augustus] 4 of 19 task(s) completed at 01/23/2021 12:19:47 [augustus] 6 of 19 task(s) completed at 01/23/2021 12:19:47 [augustus] 8 of 19 task(s) completed at 01/23/2021 12:19:47 [augustus] 10 of 19 task(s) completed at 01/23/2021 12:19:47 [augustus] 12 of 19 task(s) completed at 01/23/2021 12:19:47 [augustus] 14 of 19 task(s) completed at 01/23/2021 12:19:47 [augustus] 16 of 19 task(s) completed at 01/23/2021 12:19:47 [augustus] 18 of 19 task(s) completed at 01/23/2021 12:19:47 [augustus] 19 of 19 task(s) completed at 01/23/2021 12:19:47 Extracting predicted proteins... ****** Step 3/3, current time: 01/23/2021 12:19:48 ****** Running HMMER to confirm orthology of predicted proteins: [hmmsearch] 4 of 19 task(s) completed at 01/23/2021 12:19:48 [hmmsearch] 14 of 19 task(s) completed at 01/23/2021 12:19:48 [hmmsearch] 16 of 19 task(s) completed at 01/23/2021 12:19:48 [hmmsearch] 18 of 19 task(s) completed at 01/23/2021 12:19:48 [hmmsearch] 19 of 19 task(s) completed at 01/23/2021 12:19:48 Results: C:93.2%[S:93.2%,D:0.0%],F:0.7%,M:6.1%,n:148 138 Complete BUSCOs (C) 138 Complete and single-copy BUSCOs (S) 0 Complete and duplicated BUSCOs (D) 1 Fragmented BUSCOs (F) 9 Missing BUSCOs (M) 148 Total BUSCO groups searched BUSCO analysis done. Total running time: 34.92380428314209 seconds Results written in /DATB/markop/CPB/CPB_rcf_DNAseq/quast/Enterococcus/busco_stats/run_spades/