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: 09/18/2020 05:42:57 ****************** INFO Configuration loaded from /gscratch/scrubbed/samwhite/outputs/20200918_cbai_genome_v1.0_busco/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/C_bairdi/genomes/cbai_genome_v1.0.fasta -o cbai_genome_v1.0.fasta -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: 09/18/2020 05:42:58 ****** INFO Create blast database... INFO [makeblastdb] Building a new DB, current time: 09/18/2020 05:42:58 INFO [makeblastdb] New DB name: /gscratch/scrubbed/samwhite/outputs/20200918_cbai_genome_v1.0_busco/tmp/cbai_genome_v1.0.fasta_1620787020 INFO [makeblastdb] New DB title: /gscratch/srlab/sam/data/C_bairdi/genomes/cbai_genome_v1.0.fasta INFO [makeblastdb] Sequence type: Nucleotide INFO [makeblastdb] Keep MBits: T INFO [makeblastdb] Maximum file size: 1000000000B INFO [makeblastdb] Adding sequences from FASTA; added 3294 sequences in 0.436528 seconds. INFO [makeblastdb] 1 of 1 task(s) completed at 09/18/2020 05:42:59 INFO Running tblastn, writing output to /gscratch/scrubbed/samwhite/outputs/20200918_cbai_genome_v1.0_busco/run_cbai_genome_v1.0.fasta/blast_output/tblastn_cbai_genome_v1.0.fasta.tsv... INFO [tblastn] 1 of 1 task(s) completed at 09/18/2020 05:43:05 INFO ****** Step 2/3, current time: 09/18/2020 05:43:05 ****** 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/20200918_cbai_genome_v1.0_busco/run_cbai_genome_v1.0.fasta/augustus_output/augustus.log INFO [augustus] 3 of 27 task(s) completed at 09/18/2020 05:43:07 INFO [augustus] 6 of 27 task(s) completed at 09/18/2020 05:43:08 INFO [augustus] 9 of 27 task(s) completed at 09/18/2020 05:43:08 INFO [augustus] 11 of 27 task(s) completed at 09/18/2020 05:43:08 INFO [augustus] 14 of 27 task(s) completed at 09/18/2020 05:43:08 INFO [augustus] 17 of 27 task(s) completed at 09/18/2020 05:43:08 INFO [augustus] 19 of 27 task(s) completed at 09/18/2020 05:43:09 INFO [augustus] 22 of 27 task(s) completed at 09/18/2020 05:43:10 INFO [augustus] 25 of 27 task(s) completed at 09/18/2020 05:43:12 INFO [augustus] 27 of 27 task(s) completed at 09/18/2020 05:43:15 INFO Extracting predicted proteins... INFO ****** Step 3/3, current time: 09/18/2020 05:43:16 ****** INFO Running HMMER to confirm orthology of predicted proteins: INFO [hmmsearch] 3 of 21 task(s) completed at 09/18/2020 05:43:16 INFO [hmmsearch] 9 of 21 task(s) completed at 09/18/2020 05:43:16 INFO [hmmsearch] 13 of 21 task(s) completed at 09/18/2020 05:43:16 INFO [hmmsearch] 15 of 21 task(s) completed at 09/18/2020 05:43:16 INFO [hmmsearch] 19 of 21 task(s) completed at 09/18/2020 05:43:16 INFO [hmmsearch] 21 of 21 task(s) completed at 09/18/2020 05:43:16 INFO Results: INFO C:0.4%[S:0.3%,D:0.1%],F:0.2%,M:99.4%,n:978 INFO 4 Complete BUSCOs (C) INFO 3 Complete and single-copy BUSCOs (S) INFO 1 Complete and duplicated BUSCOs (D) INFO 2 Fragmented BUSCOs (F) INFO 972 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: 09/18/2020 05:43:16 ****** INFO Extracting missing and fragmented buscos from the ancestral_variants file... INFO Running tblastn, writing output to /gscratch/scrubbed/samwhite/outputs/20200918_cbai_genome_v1.0_busco/run_cbai_genome_v1.0.fasta/blast_output/tblastn_cbai_genome_v1.0.fasta_missing_and_frag_rerun.tsv... INFO [tblastn] 1 of 1 task(s) completed at 09/18/2020 05:44:11 INFO Maximum number of candidate contig per BUSCO limited to: 3 INFO Getting coordinates for candidate regions... INFO ****** Step 2/3, current time: 09/18/2020 05:44:11 ****** INFO Training Augustus using Single-Copy Complete BUSCOs: INFO Converting predicted genes to short genbank files at 09/18/2020 05:44:11... INFO All files converted to short genbank files, now running the training scripts at 09/18/2020 05:44:11... WARNING Optimizing augustus metaparameters, this may take a very long time, started at 09/18/2020 05:44:12 INFO Pre-Augustus scaffold extraction... INFO Re-running Augustus with the new metaparameters, number of target BUSCOs: 974 INFO [augustus] 3 of 25 task(s) completed at 09/18/2020 05:44:14 INFO [augustus] 5 of 25 task(s) completed at 09/18/2020 05:44:14 INFO [augustus] 8 of 25 task(s) completed at 09/18/2020 05:44:15 INFO [augustus] 10 of 25 task(s) completed at 09/18/2020 05:44:15 INFO [augustus] 13 of 25 task(s) completed at 09/18/2020 05:44:15 INFO [augustus] 15 of 25 task(s) completed at 09/18/2020 05:44:15 INFO [augustus] 18 of 25 task(s) completed at 09/18/2020 05:44:16 INFO [augustus] 20 of 25 task(s) completed at 09/18/2020 05:44:16 INFO [augustus] 23 of 25 task(s) completed at 09/18/2020 05:44:19 INFO [augustus] 25 of 25 task(s) completed at 09/18/2020 05:44:25 INFO Extracting predicted proteins... INFO ****** Step 3/3, current time: 09/18/2020 05:44:26 ****** INFO Running HMMER to confirm orthology of predicted proteins: INFO [hmmsearch] 8 of 25 task(s) completed at 09/18/2020 05:44:26 INFO [hmmsearch] 10 of 25 task(s) completed at 09/18/2020 05:44:26 INFO [hmmsearch] 13 of 25 task(s) completed at 09/18/2020 05:44:26 INFO [hmmsearch] 15 of 25 task(s) completed at 09/18/2020 05:44:26 INFO [hmmsearch] 18 of 25 task(s) completed at 09/18/2020 05:44:26 INFO [hmmsearch] 20 of 25 task(s) completed at 09/18/2020 05:44:26 INFO [hmmsearch] 23 of 25 task(s) completed at 09/18/2020 05:44:26 INFO [hmmsearch] 25 of 25 task(s) completed at 09/18/2020 05:44:26 INFO Results: INFO C:0.4%[S:0.3%,D:0.1%],F:0.3%,M:99.3%,n:978 INFO 4 Complete BUSCOs (C) INFO 3 Complete and single-copy BUSCOs (S) INFO 1 Complete and duplicated BUSCOs (D) INFO 3 Fragmented BUSCOs (F) INFO 971 Missing BUSCOs (M) INFO 978 Total BUSCO groups searched INFO BUSCO analysis done with WARNING(s). Total running time: 90.38169693946838 seconds INFO Results written in /gscratch/scrubbed/samwhite/outputs/20200918_cbai_genome_v1.0_busco/run_cbai_genome_v1.0.fasta/ Generating checksum for cbai_genome_v1.0.fasta Finished generating checksum for cbai_genome_v1.0.fasta