****************** Start a BUSCO 3.0.2 analysis, current time: 01/21/2021 15:36:17 ****************** Configuration loaded from /DATB/markop/CPB/CPB_rcf_DNAseq/quast/Lactococcus/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/Lactococcus/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/Lactococcus/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/Lactococcus/busco_stats/tmp/ ****** Phase 1 of 2, initial predictions ****** ****** Step 1/3, current time: 01/21/2021 15:36:18 ****** Create blast database... [makeblastdb] Building a new DB, current time: 01/21/2021 15:36:18 [makeblastdb] New DB name: /DATB/markop/CPB/CPB_rcf_DNAseq/quast/Lactococcus/busco_stats/tmp/spades_1023268921 [makeblastdb] New DB title: /DATB/markop/CPB/CPB_rcf_DNAseq/quast/Lactococcus/quast_corrected_input/spades.fasta [makeblastdb] Sequence type: Nucleotide [makeblastdb] Keep MBits: T [makeblastdb] Maximum file size: 1000000000B [makeblastdb] Adding sequences from FASTA; added 242 sequences in 0.0442681 seconds. [makeblastdb] 1 of 1 task(s) completed at 01/21/2021 15:36:18 Running tblastn, writing output to /DATB/markop/CPB/CPB_rcf_DNAseq/quast/Lactococcus/busco_stats/run_spades/blast_output/tblastn_spades.tsv... [tblastn] 1 of 1 task(s) completed at 01/21/2021 15:36:19 ****** Step 2/3, current time: 01/21/2021 15:36:19 ****** 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/Lactococcus/busco_stats/run_spades/augustus_output/augustus.log [augustus] 15 of 145 task(s) completed at 01/21/2021 15:36:24 [augustus] 29 of 145 task(s) completed at 01/21/2021 15:36:26 [augustus] 44 of 145 task(s) completed at 01/21/2021 15:36:28 [augustus] 58 of 145 task(s) completed at 01/21/2021 15:36:31 [augustus] 73 of 145 task(s) completed at 01/21/2021 15:36:33 [augustus] 87 of 145 task(s) completed at 01/21/2021 15:36:36 [augustus] 102 of 145 task(s) completed at 01/21/2021 15:36:39 [augustus] 116 of 145 task(s) completed at 01/21/2021 15:36:41 [augustus] 131 of 145 task(s) completed at 01/21/2021 15:36:44 [augustus] 145 of 145 task(s) completed at 01/21/2021 15:36:50 Extracting predicted proteins... ****** Step 3/3, current time: 01/21/2021 15:36:53 ****** Running HMMER to confirm orthology of predicted proteins: [hmmsearch] 129 of 143 task(s) completed at 01/21/2021 15:36:54 [hmmsearch] 143 of 143 task(s) completed at 01/21/2021 15:36:54 Results: C:90.6%[S:89.9%,D:0.7%],F:0.0%,M:9.4%,n:148 134 Complete BUSCOs (C) 133 Complete and single-copy BUSCOs (S) 1 Complete and duplicated BUSCOs (D) 0 Fragmented BUSCOs (F) 14 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 15:36:54 ****** Extracting missing and fragmented buscos from the ancestral_variants file... Running tblastn, writing output to /DATB/markop/CPB/CPB_rcf_DNAseq/quast/Lactococcus/busco_stats/run_spades/blast_output/tblastn_spades_missing_and_frag_rerun.tsv... [tblastn] 1 of 1 task(s) completed at 01/21/2021 15:36:55 Maximum number of candidate contig per BUSCO limited to: 3 Getting coordinates for candidate regions... ****** Step 2/3, current time: 01/21/2021 15:36:55 ****** Training Augustus using Single-Copy Complete BUSCOs: Converting predicted genes to short genbank files at 01/21/2021 15:36:55... All files converted to short genbank files, now running the training scripts at 01/21/2021 15:36:56... Pre-Augustus scaffold extraction... Re-running Augustus with the new metaparameters, number of target BUSCOs: 14 [augustus] 1 of 10 task(s) completed at 01/21/2021 15:36:57 [augustus] 2 of 10 task(s) completed at 01/21/2021 15:36:57 [augustus] 3 of 10 task(s) completed at 01/21/2021 15:36:57 [augustus] 4 of 10 task(s) completed at 01/21/2021 15:36:57 [augustus] 5 of 10 task(s) completed at 01/21/2021 15:36:57 [augustus] 6 of 10 task(s) completed at 01/21/2021 15:36:57 [augustus] 7 of 10 task(s) completed at 01/21/2021 15:36:57 [augustus] 8 of 10 task(s) completed at 01/21/2021 15:36:57 [augustus] 9 of 10 task(s) completed at 01/21/2021 15:36:57 [augustus] 10 of 10 task(s) completed at 01/21/2021 15:36:57 Extracting predicted proteins... ****** Step 3/3, current time: 01/21/2021 15:36:57 ****** Running HMMER to confirm orthology of predicted proteins: [hmmsearch] 2 of 10 task(s) completed at 01/21/2021 15:36:57 [hmmsearch] 3 of 10 task(s) completed at 01/21/2021 15:36:57 [hmmsearch] 4 of 10 task(s) completed at 01/21/2021 15:36:57 [hmmsearch] 5 of 10 task(s) completed at 01/21/2021 15:36:57 [hmmsearch] 6 of 10 task(s) completed at 01/21/2021 15:36:57 [hmmsearch] 7 of 10 task(s) completed at 01/21/2021 15:36:57 [hmmsearch] 8 of 10 task(s) completed at 01/21/2021 15:36:57 [hmmsearch] 9 of 10 task(s) completed at 01/21/2021 15:36:57 [hmmsearch] 10 of 10 task(s) completed at 01/21/2021 15:36:58 Results: C:97.3%[S:96.6%,D:0.7%],F:0.0%,M:2.7%,n:148 144 Complete BUSCOs (C) 143 Complete and single-copy BUSCOs (S) 1 Complete and duplicated BUSCOs (D) 0 Fragmented BUSCOs (F) 4 Missing BUSCOs (M) 148 Total BUSCO groups searched BUSCO analysis done. Total running time: 40.276991844177246 seconds Results written in /DATB/markop/CPB/CPB_rcf_DNAseq/quast/Lactococcus/busco_stats/run_spades/