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 15:41:53 ****************** INFO Configuration loaded from /gscratch/scrubbed/samwhite/outputs/20190710_busco_pgen_v070/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_v070.fa -o Pgenerosa_v070 -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 15:42:16 ****** INFO Create blast database... INFO [makeblastdb] Building a new DB, current time: 07/10/2019 15:42:16 INFO [makeblastdb] New DB name: /gscratch/scrubbed/samwhite/outputs/20190710_busco_pgen_v070/tmp/Pgenerosa_v070_445228086 INFO [makeblastdb] New DB title: /gscratch/srlab/sam/data/P_generosa/genomes/Pgenerosa_v070.fa INFO [makeblastdb] Sequence type: Nucleotide INFO [makeblastdb] Keep MBits: T INFO [makeblastdb] Maximum file size: 1000000000B INFO [makeblastdb] Adding sequences from FASTA; added 313649 sequences in 29.7676 seconds. INFO [makeblastdb] 1 of 1 task(s) completed at 07/10/2019 15:42:46 INFO Running tblastn, writing output to /gscratch/scrubbed/samwhite/outputs/20190710_busco_pgen_v070/run_Pgenerosa_v070/blast_output/tblastn_Pgenerosa_v070.tsv... INFO [tblastn] 1 of 1 task(s) completed at 07/10/2019 15:47:36 INFO ****** Step 2/3, current time: 07/10/2019 15:47:36 ****** 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_v070/run_Pgenerosa_v070/augustus_output/augustus.log INFO [augustus] 120 of 1193 task(s) completed at 07/10/2019 15:49:07 INFO [augustus] 239 of 1193 task(s) completed at 07/10/2019 15:50:36 INFO [augustus] 358 of 1193 task(s) completed at 07/10/2019 15:51:51 INFO [augustus] 478 of 1193 task(s) completed at 07/10/2019 15:53:10 INFO [augustus] 597 of 1193 task(s) completed at 07/10/2019 15:54:16 INFO [augustus] 716 of 1193 task(s) completed at 07/10/2019 15:55:28 INFO [augustus] 836 of 1193 task(s) completed at 07/10/2019 15:56:37 INFO [augustus] 955 of 1193 task(s) completed at 07/10/2019 15:57:38 INFO [augustus] 1074 of 1193 task(s) completed at 07/10/2019 15:58:53 INFO [augustus] 1193 of 1193 task(s) completed at 07/10/2019 16:01:10 INFO Extracting predicted proteins... INFO ****** Step 3/3, current time: 07/10/2019 16:01:59 ****** INFO Running HMMER to confirm orthology of predicted proteins: INFO [hmmsearch] 919 of 919 task(s) completed at 07/10/2019 16:02:13 INFO Results: INFO C:69.6%[S:65.4%,D:4.2%],F:6.4%,M:24.0%,n:978 INFO 681 Complete BUSCOs (C) INFO 640 Complete and single-copy BUSCOs (S) INFO 41 Complete and duplicated BUSCOs (D) INFO 63 Fragmented BUSCOs (F) INFO 234 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 16:02:13 ****** INFO Extracting missing and fragmented buscos from the ancestral_variants file... INFO Running tblastn, writing output to /gscratch/scrubbed/samwhite/outputs/20190710_busco_pgen_v070/run_Pgenerosa_v070/blast_output/tblastn_Pgenerosa_v070_missing_and_frag_rerun.tsv... INFO [tblastn] 1 of 1 task(s) completed at 07/10/2019 16:16:01 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 16:16:01 ****** INFO Training Augustus using Single-Copy Complete BUSCOs: INFO Converting predicted genes to short genbank files at 07/10/2019 16:16:01... INFO All files converted to short genbank files, now running the training scripts at 07/10/2019 16:22:55... WARNING Optimizing augustus metaparameters, this may take a very long time, started at 07/10/2019 16:23:00 INFO Pre-Augustus scaffold extraction... INFO Re-running Augustus with the new metaparameters, number of target BUSCOs: 297 INFO [augustus] 47 of 462 task(s) completed at 07/11/2019 06:53:09 INFO [augustus] 93 of 462 task(s) completed at 07/11/2019 06:53:22 INFO [augustus] 139 of 462 task(s) completed at 07/11/2019 06:53:37 INFO [augustus] 185 of 462 task(s) completed at 07/11/2019 06:53:57 INFO [augustus] 232 of 462 task(s) completed at 07/11/2019 06:54:08 INFO [augustus] 278 of 462 task(s) completed at 07/11/2019 06:54:25 INFO [augustus] 324 of 462 task(s) completed at 07/11/2019 06:54:41 INFO [augustus] 370 of 462 task(s) completed at 07/11/2019 06:55:15 INFO [augustus] 416 of 462 task(s) completed at 07/11/2019 06:55:41 INFO [augustus] 462 of 462 task(s) completed at 07/11/2019 06:57:51 INFO Extracting predicted proteins... INFO ****** Step 3/3, current time: 07/11/2019 06:58:06 ****** INFO Running HMMER to confirm orthology of predicted proteins: INFO [hmmsearch] Error: Failed to open sequence file /gscratch/scrubbed/samwhite/outputs/20190710_busco_pgen_v070/run_Pgenerosa_v070/augustus_output/extracted_proteins/EOG091G0SV1.faa.2 for reading INFO [hmmsearch] Error: Failed to open sequence file /gscratch/scrubbed/samwhite/outputs/20190710_busco_pgen_v070/run_Pgenerosa_v070/augustus_output/extracted_proteins/EOG091G0ARL.faa.1 for reading INFO [hmmsearch] Error: Failed to open sequence file /gscratch/scrubbed/samwhite/outputs/20190710_busco_pgen_v070/run_Pgenerosa_v070/augustus_output/extracted_proteins/EOG091G0W96.faa.2 for reading INFO [hmmsearch] Error: Failed to open sequence file /gscratch/scrubbed/samwhite/outputs/20190710_busco_pgen_v070/run_Pgenerosa_v070/augustus_output/extracted_proteins/EOG091G11IM.faa.1 for reading INFO [hmmsearch] Error: Failed to open sequence file /gscratch/scrubbed/samwhite/outputs/20190710_busco_pgen_v070/run_Pgenerosa_v070/augustus_output/extracted_proteins/EOG091G09UA.faa.2 for reading INFO [hmmsearch] Error: Failed to open sequence file /gscratch/scrubbed/samwhite/outputs/20190710_busco_pgen_v070/run_Pgenerosa_v070/augustus_output/extracted_proteins/EOG091G11IM.faa.3 for reading INFO [hmmsearch] 127 of 421 task(s) completed at 07/11/2019 06:58:07 INFO [hmmsearch] Error: Failed to open sequence file /gscratch/scrubbed/samwhite/outputs/20190710_busco_pgen_v070/run_Pgenerosa_v070/augustus_output/extracted_proteins/EOG091G0ITS.faa.3 for reading INFO [hmmsearch] Error: Failed to open sequence file /gscratch/scrubbed/samwhite/outputs/20190710_busco_pgen_v070/run_Pgenerosa_v070/augustus_output/extracted_proteins/EOG091G0J09.faa.2 for reading INFO [hmmsearch] Error: Failed to open sequence file /gscratch/scrubbed/samwhite/outputs/20190710_busco_pgen_v070/run_Pgenerosa_v070/augustus_output/extracted_proteins/EOG091G0QZ2.faa.3 for reading INFO [hmmsearch] Error: Failed to open sequence file /gscratch/scrubbed/samwhite/outputs/20190710_busco_pgen_v070/run_Pgenerosa_v070/augustus_output/extracted_proteins/EOG091G08NN.faa.2 for reading INFO [hmmsearch] Error: Failed to open sequence file /gscratch/scrubbed/samwhite/outputs/20190710_busco_pgen_v070/run_Pgenerosa_v070/augustus_output/extracted_proteins/EOG091G15HV.faa.2 for reading INFO [hmmsearch] Error: Failed to open sequence file /gscratch/scrubbed/samwhite/outputs/20190710_busco_pgen_v070/run_Pgenerosa_v070/augustus_output/extracted_proteins/EOG091G0TAU.faa.2 for reading INFO [hmmsearch] Error: Failed to open sequence file /gscratch/scrubbed/samwhite/outputs/20190710_busco_pgen_v070/run_Pgenerosa_v070/augustus_output/extracted_proteins/EOG091G0FIJ.faa.2 for reading INFO [hmmsearch] Error: Failed to open sequence file /gscratch/scrubbed/samwhite/outputs/20190710_busco_pgen_v070/run_Pgenerosa_v070/augustus_output/extracted_proteins/EOG091G0R3S.faa.2 for reading INFO [hmmsearch] Error: Failed to open sequence file /gscratch/scrubbed/samwhite/outputs/20190710_busco_pgen_v070/run_Pgenerosa_v070/augustus_output/extracted_proteins/EOG091G0QBN.faa.2 for reading INFO [hmmsearch] Error: Failed to open sequence file /gscratch/scrubbed/samwhite/outputs/20190710_busco_pgen_v070/run_Pgenerosa_v070/augustus_output/extracted_proteins/EOG091G05YC.faa.3 for reading INFO [hmmsearch] Error: Failed to open sequence file /gscratch/scrubbed/samwhite/outputs/20190710_busco_pgen_v070/run_Pgenerosa_v070/augustus_output/extracted_proteins/EOG091G0C84.faa.2 for reading INFO [hmmsearch] 421 of 421 task(s) completed at 07/11/2019 06:58:09 INFO Results: INFO C:84.2%[S:78.5%,D:5.7%],F:9.4%,M:6.4%,n:978 INFO 824 Complete BUSCOs (C) INFO 768 Complete and single-copy BUSCOs (S) INFO 56 Complete and duplicated BUSCOs (D) INFO 92 Fragmented BUSCOs (F) INFO 62 Missing BUSCOs (M) INFO 978 Total BUSCO groups searched INFO BUSCO analysis done with WARNING(s). Total running time: 55019.21382021904 seconds INFO Results written in /gscratch/scrubbed/samwhite/outputs/20190710_busco_pgen_v070/run_Pgenerosa_v070/