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: 07/10/2019 14:20:17 ****************** INFO Configuration loaded from /gscratch/scrubbed/samwhite/outputs/20190710_busco_pgen_v074_unannotated/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_v074.fa -o Pgenerosa_v074 -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: 07/10/2019 14:20:30 ****** INFO Create blast database... INFO [makeblastdb] Building a new DB, current time: 07/10/2019 14:20:30 INFO [makeblastdb] New DB name: /gscratch/scrubbed/samwhite/outputs/20190710_busco_pgen_v074_unannotated/tmp/Pgenerosa_v074_4076027899 INFO [makeblastdb] New DB title: /gscratch/srlab/sam/data/P_generosa/genomes/Pgenerosa_v074.fa INFO [makeblastdb] Sequence type: Nucleotide INFO [makeblastdb] Keep MBits: T INFO [makeblastdb] Maximum file size: 1000000000B INFO [makeblastdb] Adding sequences from FASTA; added 18 sequences in 11.4399 seconds. INFO [makeblastdb] 1 of 1 task(s) completed at 07/10/2019 14:20:42 INFO Running tblastn, writing output to /gscratch/scrubbed/samwhite/outputs/20190710_busco_pgen_v074_unannotated/run_Pgenerosa_v074/blast_output/tblastn_Pgenerosa_v074.tsv... INFO [tblastn] 1 of 1 task(s) completed at 07/10/2019 14:25:21 INFO ****** Step 2/3, current time: 07/10/2019 14:25:21 ****** 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/20190710_busco_pgen_v074_unannotated/run_Pgenerosa_v074/augustus_output/augustus.log INFO [augustus] 77 of 769 task(s) completed at 07/10/2019 14:26:40 INFO [augustus] 154 of 769 task(s) completed at 07/10/2019 14:27:54 INFO [augustus] 231 of 769 task(s) completed at 07/10/2019 14:28:56 INFO [augustus] 308 of 769 task(s) completed at 07/10/2019 14:29:56 INFO [augustus] 385 of 769 task(s) completed at 07/10/2019 14:30:58 INFO [augustus] 462 of 769 task(s) completed at 07/10/2019 14:32:02 INFO [augustus] 539 of 769 task(s) completed at 07/10/2019 14:33:08 INFO [augustus] 616 of 769 task(s) completed at 07/10/2019 14:34:15 INFO [augustus] 693 of 769 task(s) completed at 07/10/2019 14:35:25 INFO [augustus] 769 of 769 task(s) completed at 07/10/2019 14:36:53 INFO Extracting predicted proteins... INFO ****** Step 3/3, current time: 07/10/2019 14:37:08 ****** INFO Running HMMER to confirm orthology of predicted proteins: INFO [hmmsearch] 73 of 730 task(s) completed at 07/10/2019 14:37:09 INFO [hmmsearch] 146 of 730 task(s) completed at 07/10/2019 14:37:09 INFO [hmmsearch] 584 of 730 task(s) completed at 07/10/2019 14:37:10 INFO [hmmsearch] 730 of 730 task(s) completed at 07/10/2019 14:37:11 INFO Results: INFO C:59.7%[S:59.1%,D:0.6%],F:3.9%,M:36.4%,n:978 INFO 584 Complete BUSCOs (C) INFO 578 Complete and single-copy BUSCOs (S) INFO 6 Complete and duplicated BUSCOs (D) INFO 38 Fragmented BUSCOs (F) INFO 356 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: 07/10/2019 14:37:11 ****** INFO Extracting missing and fragmented buscos from the ancestral_variants file... INFO Running tblastn, writing output to /gscratch/scrubbed/samwhite/outputs/20190710_busco_pgen_v074_unannotated/run_Pgenerosa_v074/blast_output/tblastn_Pgenerosa_v074_missing_and_frag_rerun.tsv... INFO [tblastn] 1 of 1 task(s) completed at 07/10/2019 14:54:31 INFO Maximum number of candidate contig per BUSCO limited to: 3 INFO Getting coordinates for candidate regions... INFO ****** Step 2/3, current time: 07/10/2019 14:54:31 ****** INFO Training Augustus using Single-Copy Complete BUSCOs: INFO Converting predicted genes to short genbank files at 07/10/2019 14:54:31... INFO All files converted to short genbank files, now running the training scripts at 07/10/2019 14:57:15... WARNING Optimizing augustus metaparameters, this may take a very long time, started at 07/10/2019 14:57:20 INFO Pre-Augustus scaffold extraction... INFO Re-running Augustus with the new metaparameters, number of target BUSCOs: 394 INFO [augustus] 22 of 211 task(s) completed at 07/11/2019 01:56:21 INFO [augustus] 43 of 211 task(s) completed at 07/11/2019 01:56:39 INFO [augustus] 64 of 211 task(s) completed at 07/11/2019 01:57:03 INFO [augustus] 85 of 211 task(s) completed at 07/11/2019 01:57:22 INFO [augustus] 106 of 211 task(s) completed at 07/11/2019 01:57:37 INFO [augustus] 127 of 211 task(s) completed at 07/11/2019 01:57:56 INFO [augustus] 148 of 211 task(s) completed at 07/11/2019 01:58:10 INFO [augustus] 169 of 211 task(s) completed at 07/11/2019 01:58:36 INFO [augustus] 190 of 211 task(s) completed at 07/11/2019 01:58:55 INFO [augustus] 211 of 211 task(s) completed at 07/11/2019 02:01:09 INFO Extracting predicted proteins... INFO ****** Step 3/3, current time: 07/11/2019 02:01:15 ****** INFO Running HMMER to confirm orthology of predicted proteins: INFO [hmmsearch] 63 of 209 task(s) completed at 07/11/2019 02:01:15 INFO [hmmsearch] 147 of 209 task(s) completed at 07/11/2019 02:01:15 INFO [hmmsearch] 209 of 209 task(s) completed at 07/11/2019 02:01:16 INFO Results: INFO C:71.6%[S:70.7%,D:0.9%],F:4.7%,M:23.7%,n:978 INFO 700 Complete BUSCOs (C) INFO 691 Complete and single-copy BUSCOs (S) INFO 9 Complete and duplicated BUSCOs (D) INFO 46 Fragmented BUSCOs (F) INFO 232 Missing BUSCOs (M) INFO 978 Total BUSCO groups searched INFO BUSCO analysis done with WARNING(s). Total running time: 42093.80747580528 seconds INFO Results written in /gscratch/scrubbed/samwhite/outputs/20190710_busco_pgen_v074_unannotated/run_Pgenerosa_v074/