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: 02/28/2019 15:47:12 ****************** INFO Configuration loaded from /gscratch/scrubbed/samwhite/outputs/20190228_pgen_busco_metazoa_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 human --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: 02/28/2019 15:47:30 ****** INFO Create blast database... INFO [makeblastdb] Building a new DB, current time: 02/28/2019 15:47:30 INFO [makeblastdb] New DB name: /gscratch/scrubbed/samwhite/outputs/20190228_pgen_busco_metazoa_augustus/tmp/Pgenerosa_v071_genome_snap02.all.maker_1223389482 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 15.245 seconds. INFO [makeblastdb] 1 of 1 task(s) completed at 02/28/2019 15:47:45 INFO Running tblastn, writing output to /gscratch/scrubbed/samwhite/outputs/20190228_pgen_busco_metazoa_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 02/28/2019 15:52:26 INFO ****** Step 2/3, current time: 02/28/2019 15:52:26 ****** 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 human 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/20190228_pgen_busco_metazoa_augustus/run_Pgenerosa_v071_genome_snap02.all.maker/augustus_output/augustus.log INFO [augustus] 90 of 897 task(s) completed at 02/28/2019 15:53:18 INFO [augustus] 180 of 897 task(s) completed at 02/28/2019 15:54:00 INFO [augustus] 270 of 897 task(s) completed at 02/28/2019 15:54:50 INFO [augustus] 359 of 897 task(s) completed at 02/28/2019 15:55:42 INFO [augustus] 449 of 897 task(s) completed at 02/28/2019 15:56:27 INFO [augustus] 539 of 897 task(s) completed at 02/28/2019 15:57:11 INFO [augustus] 628 of 897 task(s) completed at 02/28/2019 15:57:58 INFO [augustus] 718 of 897 task(s) completed at 02/28/2019 15:58:29 INFO [augustus] 808 of 897 task(s) completed at 02/28/2019 15:59:14 INFO [augustus] 897 of 897 task(s) completed at 02/28/2019 16:00:57 INFO Extracting predicted proteins... INFO ****** Step 3/3, current time: 02/28/2019 16:01:15 ****** INFO Running HMMER to confirm orthology of predicted proteins: INFO [hmmsearch] 89 of 890 task(s) completed at 02/28/2019 16:01:16 INFO [hmmsearch] 356 of 890 task(s) completed at 02/28/2019 16:01:16 INFO [hmmsearch] 623 of 890 task(s) completed at 02/28/2019 16:01:17 INFO [hmmsearch] 890 of 890 task(s) completed at 02/28/2019 16:01:18 INFO Results: INFO C:68.0%[S:65.4%,D:2.6%],F:7.0%,M:25.0%,n:978 INFO 665 Complete BUSCOs (C) INFO 640 Complete and single-copy BUSCOs (S) INFO 25 Complete and duplicated BUSCOs (D) INFO 68 Fragmented BUSCOs (F) INFO 245 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: 02/28/2019 16:01:18 ****** INFO Extracting missing and fragmented buscos from the ancestral_variants file... INFO Running tblastn, writing output to /gscratch/scrubbed/samwhite/outputs/20190228_pgen_busco_metazoa_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 02/28/2019 16:14:04 INFO Maximum number of candidate contig per BUSCO limited to: 3 INFO Getting coordinates for candidate regions... INFO ****** Step 2/3, current time: 02/28/2019 16:14:04 ****** INFO Training Augustus using Single-Copy Complete BUSCOs: INFO Converting predicted genes to short genbank files at 02/28/2019 16:14:04... INFO All files converted to short genbank files, now running the training scripts at 02/28/2019 16:18:01... WARNING Optimizing augustus metaparameters, this may take a very long time, started at 02/28/2019 16:18:05 INFO Pre-Augustus scaffold extraction... INFO Re-running Augustus with the new metaparameters, number of target BUSCOs: 313 INFO [augustus] 21 of 209 task(s) completed at 03/01/2019 08:53:32 INFO [augustus] 42 of 209 task(s) completed at 03/01/2019 08:53:42 INFO [augustus] 63 of 209 task(s) completed at 03/01/2019 08:53:53 INFO [augustus] 84 of 209 task(s) completed at 03/01/2019 08:54:08 INFO [augustus] 105 of 209 task(s) completed at 03/01/2019 08:54:20 INFO [augustus] 126 of 209 task(s) completed at 03/01/2019 08:54:33 INFO [augustus] 147 of 209 task(s) completed at 03/01/2019 08:54:51 INFO [augustus] 168 of 209 task(s) completed at 03/01/2019 08:55:08 INFO [augustus] 189 of 209 task(s) completed at 03/01/2019 08:55:25 INFO [augustus] 209 of 209 task(s) completed at 03/01/2019 08:56:27 INFO Extracting predicted proteins... INFO ****** Step 3/3, current time: 03/01/2019 08:56:33 ****** INFO Running HMMER to confirm orthology of predicted proteins: INFO [hmmsearch] 21 of 206 task(s) completed at 03/01/2019 08:56:33 INFO [hmmsearch] 42 of 206 task(s) completed at 03/01/2019 08:56:33 INFO [hmmsearch] 83 of 206 task(s) completed at 03/01/2019 08:56:34 INFO [hmmsearch] 104 of 206 task(s) completed at 03/01/2019 08:56:34 INFO [hmmsearch] 145 of 206 task(s) completed at 03/01/2019 08:56:34 INFO [hmmsearch] 186 of 206 task(s) completed at 03/01/2019 08:56:34 INFO [hmmsearch] 206 of 206 task(s) completed at 03/01/2019 08:56:34 INFO Results: INFO C:76.3%[S:73.3%,D:3.0%],F:5.2%,M:18.5%,n:978 INFO 746 Complete BUSCOs (C) INFO 717 Complete and single-copy BUSCOs (S) INFO 29 Complete and duplicated BUSCOs (D) INFO 51 Fragmented BUSCOs (F) INFO 181 Missing BUSCOs (M) INFO 978 Total BUSCO groups searched INFO BUSCO analysis done with WARNING(s). Total running time: 61803.18575048447 seconds INFO Results written in /gscratch/scrubbed/samwhite/outputs/20190228_pgen_busco_metazoa_augustus/run_Pgenerosa_v071_genome_snap02.all.maker/