INFO ****************** Start a BUSCO 3.0.2 analysis, current time: 09/11/2018 15:34:21 ****************** INFO Configuration loaded from /busco/scripts/../config/config.ini INFO Init tools... INFO Check dependencies... INFO Check input file... INFO To reproduce this run: python /busco/scripts/run_BUSCO.py -i Olurida_v081.fa -o 20180911_busco -l eukaryota_odb9/ -m genome -c 1 -sp fly INFO Mode is: genome INFO The lineage dataset is: eukaryota_odb9 (eukaryota) INFO Temp directory is ./tmp/ INFO ****** Phase 1 of 2, initial predictions ****** INFO ****** Step 1/3, current time: 09/11/2018 15:34:25 ****** INFO Create blast database... INFO [makeblastdb] Building a new DB, current time: 09/11/2018 15:34:27 INFO [makeblastdb] New DB name: /data/tmp/20180911_busco_2432604931 INFO [makeblastdb] New DB title: Olurida_v081.fa INFO [makeblastdb] Sequence type: Nucleotide INFO [makeblastdb] Keep MBits: T INFO [makeblastdb] Maximum file size: 1000000000B INFO [makeblastdb] Adding sequences from FASTA; added 159429 sequences in 27.8002 seconds. INFO [makeblastdb] 1 of 1 task(s) completed at 09/11/2018 15:34:55 INFO Running tblastn, writing output to /data/run_20180911_busco/blast_output/tblastn_20180911_busco.tsv... INFO [tblastn] 1 of 1 task(s) completed at 09/11/2018 15:50:15 INFO ****** Step 2/3, current time: 09/11/2018 15:50:15 ****** 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 [augustus] Please find all logs related to Augustus errors here: /data/run_20180911_busco/augustus_output/augustus.log INFO [augustus] 36 of 352 task(s) completed at 09/11/2018 15:52:40 INFO [augustus] 71 of 352 task(s) completed at 09/11/2018 15:55:58 INFO [augustus] 106 of 352 task(s) completed at 09/11/2018 15:59:09 INFO [augustus] 141 of 352 task(s) completed at 09/11/2018 16:01:46 INFO [augustus] 177 of 352 task(s) completed at 09/11/2018 16:04:26 INFO [augustus] 212 of 352 task(s) completed at 09/11/2018 16:07:46 INFO [augustus] 247 of 352 task(s) completed at 09/11/2018 16:10:18 INFO [augustus] 282 of 352 task(s) completed at 09/11/2018 16:13:48 INFO [augustus] 317 of 352 task(s) completed at 09/11/2018 16:17:23 INFO [augustus] 352 of 352 task(s) completed at 09/11/2018 16:19:59 INFO Extracting predicted proteins... INFO ****** Step 3/3, current time: 09/11/2018 16:20:02 ****** INFO Running HMMER to confirm orthology of predicted proteins: INFO [hmmsearch] 21 of 208 task(s) completed at 09/11/2018 16:20:03 INFO [hmmsearch] 42 of 208 task(s) completed at 09/11/2018 16:20:04 INFO [hmmsearch] 63 of 208 task(s) completed at 09/11/2018 16:20:05 INFO [hmmsearch] 84 of 208 task(s) completed at 09/11/2018 16:20:05 INFO [hmmsearch] 105 of 208 task(s) completed at 09/11/2018 16:20:06 INFO [hmmsearch] 125 of 208 task(s) completed at 09/11/2018 16:20:06 INFO [hmmsearch] 146 of 208 task(s) completed at 09/11/2018 16:20:07 INFO [hmmsearch] 167 of 208 task(s) completed at 09/11/2018 16:20:07 INFO [hmmsearch] 188 of 208 task(s) completed at 09/11/2018 16:20:08 INFO [hmmsearch] 208 of 208 task(s) completed at 09/11/2018 16:20:08 INFO Results: INFO C:34.6%[S:34.3%,D:0.3%],F:14.9%,M:50.5%,n:303 INFO 105 Complete BUSCOs (C) INFO 104 Complete and single-copy BUSCOs (S) INFO 1 Complete and duplicated BUSCOs (D) INFO 45 Fragmented BUSCOs (F) INFO 153 Missing BUSCOs (M) INFO 303 Total BUSCO groups searched INFO ****** Phase 2 of 2, predictions using species specific training ****** INFO ****** Step 1/3, current time: 09/11/2018 16:20:08 ****** INFO Extracting missing and fragmented buscos from the ancestral_variants file... INFO Running tblastn, writing output to /data/run_20180911_busco/blast_output/tblastn_20180911_busco_missing_and_frag_rerun.tsv... INFO [tblastn] 1 of 1 task(s) completed at 09/11/2018 17:52:44 INFO Maximum number of candidate contig per BUSCO limited to: 3 INFO Getting coordinates for candidate regions... INFO ****** Step 2/3, current time: 09/11/2018 17:52:45 ****** INFO Training Augustus using Single-Copy Complete BUSCOs: INFO Converting predicted genes to short genbank files at 09/11/2018 17:52:45... INFO All files converted to short genbank files, now running the training scripts at 09/11/2018 18:00:57... INFO Pre-Augustus scaffold extraction... INFO Re-running Augustus with the new metaparameters, number of target BUSCOs: 198 INFO [augustus] 26 of 253 task(s) completed at 09/11/2018 18:02:32 INFO [augustus] 51 of 253 task(s) completed at 09/11/2018 18:03:37 INFO [augustus] 76 of 253 task(s) completed at 09/11/2018 18:04:26 INFO [augustus] 102 of 253 task(s) completed at 09/11/2018 18:05:21 INFO [augustus] 127 of 253 task(s) completed at 09/11/2018 18:06:09 INFO [augustus] 152 of 253 task(s) completed at 09/11/2018 18:07:29 INFO [augustus] 178 of 253 task(s) completed at 09/11/2018 18:08:42 INFO [augustus] 203 of 253 task(s) completed at 09/11/2018 18:10:10 INFO [augustus] 228 of 253 task(s) completed at 09/11/2018 18:12:26 INFO [augustus] 253 of 253 task(s) completed at 09/11/2018 18:14:01 INFO Extracting predicted proteins... INFO ****** Step 3/3, current time: 09/11/2018 18:14:03 ****** INFO Running HMMER to confirm orthology of predicted proteins: INFO [hmmsearch] 22 of 218 task(s) completed at 09/11/2018 18:14:04 INFO [hmmsearch] 44 of 218 task(s) completed at 09/11/2018 18:14:04 INFO [hmmsearch] Error: Failed to open sequence file /data/run_20180911_busco/augustus_output/extracted_proteins/EOG09370O51.faa.1 for reading INFO [hmmsearch] Error: Failed to open sequence file /data/run_20180911_busco/augustus_output/extracted_proteins/EOG09370T6W.faa.1 for reading INFO [hmmsearch] 66 of 218 task(s) completed at 09/11/2018 18:14:05 INFO [hmmsearch] Error: Failed to open sequence file /data/run_20180911_busco/augustus_output/extracted_proteins/EOG09370JZ3.faa.2 for reading INFO [hmmsearch] 88 of 218 task(s) completed at 09/11/2018 18:14:06 INFO [hmmsearch] Error: Failed to open sequence file /data/run_20180911_busco/augustus_output/extracted_proteins/EOG09370SON.faa.1 for reading INFO [hmmsearch] Error: Failed to open sequence file /data/run_20180911_busco/augustus_output/extracted_proteins/EOG09370TH4.faa.1 for reading INFO [hmmsearch] 110 of 218 task(s) completed at 09/11/2018 18:14:06 INFO [hmmsearch] Error: Failed to open sequence file /data/run_20180911_busco/augustus_output/extracted_proteins/EOG093707LO.faa.3 for reading INFO [hmmsearch] Error: Failed to open sequence file /data/run_20180911_busco/augustus_output/extracted_proteins/EOG09370QFD.faa.1 for reading INFO [hmmsearch] 131 of 218 task(s) completed at 09/11/2018 18:14:07 INFO [hmmsearch] 153 of 218 task(s) completed at 09/11/2018 18:14:07 INFO [hmmsearch] 175 of 218 task(s) completed at 09/11/2018 18:14:08 INFO [hmmsearch] 197 of 218 task(s) completed at 09/11/2018 18:14:09 INFO [hmmsearch] 218 of 218 task(s) completed at 09/11/2018 18:14:09 INFO Results: INFO C:43.9%[S:43.6%,D:0.3%],F:31.7%,M:24.4%,n:303 INFO 133 Complete BUSCOs (C) INFO 132 Complete and single-copy BUSCOs (S) INFO 1 Complete and duplicated BUSCOs (D) INFO 96 Fragmented BUSCOs (F) INFO 74 Missing BUSCOs (M) INFO 303 Total BUSCO groups searched INFO BUSCO analysis done. Total running time: 9588.91876077652 seconds INFO Results written in /data/run_20180911_busco/