WARNING An augustus species is mentioned in the config file, dataset default species (fly) will be ignored INFO ****************** Start a BUSCO 3.0.2 analysis, current time: 03/01/2019 15:16:53 ****************** INFO Configuration loaded from /gscratch/scrubbed/samwhite/outputs/20190301_pgen_busco_metazoa_fly_augustus/config.ini INFO Init tools... INFO Check dependencies... INFO Check input file... INFO To reproduce this run: python /gscratch/srlab/programs/busco-v3/scripts/run_BUSCO.py -i /gscratch/srlab/sam/data/P_generosa/genomes/Pgenerosa_v071_genome_snap02.all.renamed.fasta -o Pgenerosa_v071_genome_snap02.all.maker -l /gscratch/srlab/sam/data/databases/BUSCO/metazoa_odb9/ -m genome -c 28 --long -z -sp fly --augustus_parameters '--progress=true' INFO Mode is: genome INFO The lineage dataset is: metazoa_odb9 (eukaryota) INFO Temp directory is ./tmp/ INFO ****** Phase 1 of 2, initial predictions ****** INFO ****** Step 1/3, current time: 03/01/2019 15:17:09 ****** INFO Create blast database... INFO [makeblastdb] Building a new DB, current time: 03/01/2019 15:17:09 INFO [makeblastdb] New DB name: /gscratch/scrubbed/samwhite/outputs/20190301_pgen_busco_metazoa_fly_augustus/tmp/Pgenerosa_v071_genome_snap02.all.maker_842918302 INFO [makeblastdb] New DB title: /gscratch/srlab/sam/data/P_generosa/genomes/Pgenerosa_v071_genome_snap02.all.renamed.fasta INFO [makeblastdb] Sequence type: Nucleotide INFO [makeblastdb] Keep MBits: T INFO [makeblastdb] Maximum file size: 1000000000B INFO [makeblastdb] Adding sequences from FASTA; added 13988 sequences in 15.5635 seconds. INFO [makeblastdb] 1 of 1 task(s) completed at 03/01/2019 15:17:25 INFO Running tblastn, writing output to /gscratch/scrubbed/samwhite/outputs/20190301_pgen_busco_metazoa_fly_augustus/run_Pgenerosa_v071_genome_snap02.all.maker/blast_output/tblastn_Pgenerosa_v071_genome_snap02.all.maker.tsv... INFO [tblastn] 1 of 1 task(s) completed at 03/01/2019 15:22:08 INFO ****** Step 2/3, current time: 03/01/2019 15:22:08 ****** INFO Maximum number of candidate contig per BUSCO limited to: 3 INFO Getting coordinates for candidate regions... INFO Pre-Augustus scaffold extraction... INFO Running Augustus prediction using fly as species: INFO Additional parameters for Augustus are --progress=true: INFO [augustus] Please find all logs related to Augustus errors here: /gscratch/scrubbed/samwhite/outputs/20190301_pgen_busco_metazoa_fly_augustus/run_Pgenerosa_v071_genome_snap02.all.maker/augustus_output/augustus.log INFO [augustus] 90 of 894 task(s) completed at 03/01/2019 15:23:33 INFO [augustus] 179 of 894 task(s) completed at 03/01/2019 15:24:39 INFO [augustus] 269 of 894 task(s) completed at 03/01/2019 15:26:02 INFO [augustus] 358 of 894 task(s) completed at 03/01/2019 15:27:10 INFO [augustus] 448 of 894 task(s) completed at 03/01/2019 15:28:28 INFO [augustus] 537 of 894 task(s) completed at 03/01/2019 15:29:34 INFO [augustus] 626 of 894 task(s) completed at 03/01/2019 15:30:44 INFO [augustus] 716 of 894 task(s) completed at 03/01/2019 15:31:41 INFO [augustus] 805 of 894 task(s) completed at 03/01/2019 15:32:44 INFO [augustus] 894 of 894 task(s) completed at 03/01/2019 15:34:45 INFO Extracting predicted proteins... INFO ****** Step 3/3, current time: 03/01/2019 15:35:03 ****** INFO Running HMMER to confirm orthology of predicted proteins: INFO [hmmsearch] 813 of 813 task(s) completed at 03/01/2019 15:35:06 INFO Results: INFO C:61.8%[S:59.7%,D:2.1%],F:5.3%,M:32.9%,n:978 INFO 605 Complete BUSCOs (C) INFO 584 Complete and single-copy BUSCOs (S) INFO 21 Complete and duplicated BUSCOs (D) INFO 52 Fragmented BUSCOs (F) INFO 321 Missing BUSCOs (M) INFO 978 Total BUSCO groups searched INFO ****** Phase 2 of 2, predictions using species specific training ****** INFO ****** Step 1/3, current time: 03/01/2019 15:35:06 ****** INFO Extracting missing and fragmented buscos from the ancestral_variants file... INFO Running tblastn, writing output to /gscratch/scrubbed/samwhite/outputs/20190301_pgen_busco_metazoa_fly_augustus/run_Pgenerosa_v071_genome_snap02.all.maker/blast_output/tblastn_Pgenerosa_v071_genome_snap02.all.maker_missing_and_frag_rerun.tsv... INFO [tblastn] 1 of 1 task(s) completed at 03/01/2019 15:51:29 INFO Maximum number of candidate contig per BUSCO limited to: 3 INFO Getting coordinates for candidate regions... INFO ****** Step 2/3, current time: 03/01/2019 15:51:29 ****** INFO Training Augustus using Single-Copy Complete BUSCOs: INFO Converting predicted genes to short genbank files at 03/01/2019 15:51:29... INFO All files converted to short genbank files, now running the training scripts at 03/01/2019 15:55:03... WARNING Optimizing augustus metaparameters, this may take a very long time, started at 03/01/2019 15:55:08 INFO Pre-Augustus scaffold extraction... INFO Re-running Augustus with the new metaparameters, number of target BUSCOs: 373 INFO [augustus] 28 of 280 task(s) completed at 03/02/2019 03:59:46 INFO [augustus] 56 of 280 task(s) completed at 03/02/2019 04:00:03 INFO [augustus] 84 of 280 task(s) completed at 03/02/2019 04:00:25 INFO [augustus] 112 of 280 task(s) completed at 03/02/2019 04:00:44 INFO [augustus] 140 of 280 task(s) completed at 03/02/2019 04:01:02 INFO [augustus] 168 of 280 task(s) completed at 03/02/2019 04:01:24 INFO [augustus] 196 of 280 task(s) completed at 03/02/2019 04:01:40 INFO [augustus] 224 of 280 task(s) completed at 03/02/2019 04:02:00 INFO [augustus] 252 of 280 task(s) completed at 03/02/2019 04:02:24 INFO [augustus] 280 of 280 task(s) completed at 03/02/2019 04:04:24 INFO Extracting predicted proteins... INFO ****** Step 3/3, current time: 03/02/2019 04:04:32 ****** INFO Running HMMER to confirm orthology of predicted proteins: INFO [hmmsearch] 84 of 277 task(s) completed at 03/02/2019 04:04:33 INFO [hmmsearch] 277 of 277 task(s) completed at 03/02/2019 04:04:33 INFO Results: INFO C:76.6%[S:73.3%,D:3.3%],F:5.2%,M:18.2%,n:978 INFO 749 Complete BUSCOs (C) INFO 717 Complete and single-copy BUSCOs (S) INFO 32 Complete and duplicated BUSCOs (D) INFO 51 Fragmented BUSCOs (F) INFO 178 Missing BUSCOs (M) INFO 978 Total BUSCO groups searched INFO BUSCO analysis done with WARNING(s). Total running time: 46108.386420726776 seconds INFO Results written in /gscratch/scrubbed/samwhite/outputs/20190301_pgen_busco_metazoa_fly_augustus/run_Pgenerosa_v071_genome_snap02.all.maker/