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: 11/10/2020 06:55:06 ****************** INFO Configuration loaded from /gscratch/scrubbed/samwhite/outputs/20201110_crustacean-transcriptomes_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_maenas/transcriptomes/GBXE01.1.fsa_nt -o GBXE01.1.fsa_nt -l /gscratch/srlab/sam/data/databases/BUSCO/metazoa_odb9/ -m transcriptome -c 28 --long -z INFO Mode is: transcriptome INFO The lineage dataset is: metazoa_odb9 (eukaryota) INFO Temp directory is ./tmp/ INFO ****** Step 1/2, current time: 11/10/2020 06:55:09 ****** INFO Create blast database... INFO [makeblastdb] Building a new DB, current time: 11/10/2020 06:55:09 INFO [makeblastdb] New DB name: /gscratch/scrubbed/samwhite/outputs/20201110_crustacean-transcriptomes_busco/tmp/GBXE01.1.fsa_nt_153261425 INFO [makeblastdb] New DB title: /gscratch/srlab/sam/data/C_maenas/transcriptomes/GBXE01.1.fsa_nt INFO [makeblastdb] Sequence type: Nucleotide INFO [makeblastdb] Keep MBits: T INFO [makeblastdb] Maximum file size: 1000000000B INFO [makeblastdb] Adding sequences from FASTA; added 212322 sequences in 6.95565 seconds. INFO [makeblastdb] 1 of 1 task(s) completed at 11/10/2020 06:55:16 INFO Running tblastn, writing output to /gscratch/scrubbed/samwhite/outputs/20201110_crustacean-transcriptomes_busco/run_GBXE01.1.fsa_nt/blast_output/tblastn_GBXE01.1.fsa_nt.tsv... INFO [tblastn] 1 of 1 task(s) completed at 11/10/2020 06:59:08 INFO ****** Step 2/2, current time: 11/10/2020 06:59:08 ****** INFO Maximum number of candidate transcript per BUSCO limited to: 3 INFO Getting coordinates for candidate transcripts... INFO Extracting candidate transcripts... INFO Translating candidate transcripts... INFO Running HMMER to confirm transcript orthology: INFO [hmmsearch] 2105 of 2105 task(s) completed at 11/10/2020 06:59:46 INFO Results: INFO C:95.7%[S:57.0%,D:38.7%],F:3.6%,M:0.7%,n:978 INFO 935 Complete BUSCOs (C) INFO 557 Complete and single-copy BUSCOs (S) INFO 378 Complete and duplicated BUSCOs (D) INFO 35 Fragmented BUSCOs (F) INFO 8 Missing BUSCOs (M) INFO 978 Total BUSCO groups searched INFO BUSCO analysis done with WARNING(s). Total running time: 285.33324098587036 seconds INFO Results written in /gscratch/scrubbed/samwhite/outputs/20201110_crustacean-transcriptomes_busco/run_GBXE01.1.fsa_nt/ Generating checksum for GBXE01.1.fsa_nt Finished generating checksum for GBXE01.1.fsa_nt 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: 11/10/2020 06:59:53 ****************** INFO Configuration loaded from /gscratch/scrubbed/samwhite/outputs/20201110_crustacean-transcriptomes_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/L_vannamei/transcriptomes/Trinity_Trimmed_Whiteleg_Shrimp_Transcrimptome_Assmbled_Supplemental_Data_1.fasta -o Trinity_Trimmed_Whiteleg_Shrimp_Transcrimptome_Assmbled_Supplemental_Data_1.fasta -l /gscratch/srlab/sam/data/databases/BUSCO/metazoa_odb9/ -m transcriptome -c 28 --long -z INFO Mode is: transcriptome INFO The lineage dataset is: metazoa_odb9 (eukaryota) INFO Temp directory is ./tmp/ INFO ****** Step 1/2, current time: 11/10/2020 06:59:54 ****** INFO Create blast database... INFO [makeblastdb] Building a new DB, current time: 11/10/2020 06:59:55 INFO [makeblastdb] New DB name: /gscratch/scrubbed/samwhite/outputs/20201110_crustacean-transcriptomes_busco/tmp/Trinity_Trimmed_Whiteleg_Shrimp_Transcrimptome_Assmbled_Supplemental_Data_1.fasta_4113734185 INFO [makeblastdb] New DB title: /gscratch/srlab/sam/data/L_vannamei/transcriptomes/Trinity_Trimmed_Whiteleg_Shrimp_Transcrimptome_Assmbled_Supplemental_Data_1.fasta INFO [makeblastdb] Sequence type: Nucleotide INFO [makeblastdb] Keep MBits: T INFO [makeblastdb] Maximum file size: 1000000000B INFO [makeblastdb] Adding sequences from FASTA; added 110474 sequences in 6.05999 seconds. INFO [makeblastdb] 1 of 1 task(s) completed at 11/10/2020 07:00:01 INFO Running tblastn, writing output to /gscratch/scrubbed/samwhite/outputs/20201110_crustacean-transcriptomes_busco/run_Trinity_Trimmed_Whiteleg_Shrimp_Transcrimptome_Assmbled_Supplemental_Data_1.fasta/blast_output/tblastn_Trinity_Trimmed_Whiteleg_Shrimp_Transcrimptome_Assmbled_Supplemental_Data_1.fasta.tsv... INFO [tblastn] 1 of 1 task(s) completed at 11/10/2020 07:02:43 INFO ****** Step 2/2, current time: 11/10/2020 07:02:43 ****** INFO Maximum number of candidate transcript per BUSCO limited to: 3 INFO Getting coordinates for candidate transcripts... INFO Extracting candidate transcripts... INFO Translating candidate transcripts... INFO Running HMMER to confirm transcript orthology: INFO [hmmsearch] 1539 of 1710 task(s) completed at 11/10/2020 07:03:03 INFO [hmmsearch] 1710 of 1710 task(s) completed at 11/10/2020 07:03:03 INFO Results: INFO C:98.1%[S:72.7%,D:25.4%],F:0.9%,M:1.0%,n:978 INFO 959 Complete BUSCOs (C) INFO 711 Complete and single-copy BUSCOs (S) INFO 248 Complete and duplicated BUSCOs (D) INFO 9 Fragmented BUSCOs (F) INFO 10 Missing BUSCOs (M) INFO 978 Total BUSCO groups searched INFO BUSCO analysis done with WARNING(s). Total running time: 194.1596348285675 seconds INFO Results written in /gscratch/scrubbed/samwhite/outputs/20201110_crustacean-transcriptomes_busco/run_Trinity_Trimmed_Whiteleg_Shrimp_Transcrimptome_Assmbled_Supplemental_Data_1.fasta/ Generating checksum for Trinity_Trimmed_Whiteleg_Shrimp_Transcrimptome_Assmbled_Supplemental_Data_1.fasta Finished generating checksum for Trinity_Trimmed_Whiteleg_Shrimp_Transcrimptome_Assmbled_Supplemental_Data_1.fasta