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: 09/24/2020 04:51:37 ****************** INFO Configuration loaded from /gscratch/scrubbed/samwhite/outputs/20200924_cbai_genome_v1.01_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_v1.01.fasta -o cbai_genome_v1.01.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: 09/24/2020 04:51:38 ****** INFO Create blast database... INFO [makeblastdb] Building a new DB, current time: 09/24/2020 04:51:38 INFO [makeblastdb] New DB name: /gscratch/scrubbed/samwhite/outputs/20200924_cbai_genome_v1.01_busco/tmp/cbai_genome_v1.01.fasta_145855183 INFO [makeblastdb] New DB title: /gscratch/srlab/sam/data/C_bairdi/genomes/cbai_genome_v1.01.fasta INFO [makeblastdb] Sequence type: Nucleotide INFO [makeblastdb] Keep MBits: T INFO [makeblastdb] Maximum file size: 1000000000B INFO [makeblastdb] Adding sequences from FASTA; added 2431 sequences in 0.554962 seconds. INFO [makeblastdb] 1 of 1 task(s) completed at 09/24/2020 04:51:39 INFO Running tblastn, writing output to /gscratch/scrubbed/samwhite/outputs/20200924_cbai_genome_v1.01_busco/run_cbai_genome_v1.01.fasta/blast_output/tblastn_cbai_genome_v1.01.fasta.tsv... INFO [tblastn] 1 of 1 task(s) completed at 09/24/2020 04:51:45 INFO ****** Step 2/3, current time: 09/24/2020 04:51:45 ****** 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/20200924_cbai_genome_v1.01_busco/run_cbai_genome_v1.01.fasta/augustus_output/augustus.log INFO [augustus] 3 of 28 task(s) completed at 09/24/2020 04:51:46 INFO [augustus] 6 of 28 task(s) completed at 09/24/2020 04:51:47 INFO [augustus] 9 of 28 task(s) completed at 09/24/2020 04:51:47 INFO [augustus] 12 of 28 task(s) completed at 09/24/2020 04:51:47 INFO [augustus] 14 of 28 task(s) completed at 09/24/2020 04:51:47 INFO [augustus] 17 of 28 task(s) completed at 09/24/2020 04:51:47 INFO [augustus] 20 of 28 task(s) completed at 09/24/2020 04:51:48 INFO [augustus] 23 of 28 task(s) completed at 09/24/2020 04:51:48 INFO [augustus] 26 of 28 task(s) completed at 09/24/2020 04:51:51 INFO [augustus] 28 of 28 task(s) completed at 09/24/2020 04:51:55 INFO Extracting predicted proteins... INFO ****** Step 3/3, current time: 09/24/2020 04:51:56 ****** INFO Running HMMER to confirm orthology of predicted proteins: INFO [hmmsearch] 3 of 22 task(s) completed at 09/24/2020 04:51:56 INFO [hmmsearch] 7 of 22 task(s) completed at 09/24/2020 04:51:56 INFO [hmmsearch] 9 of 22 task(s) completed at 09/24/2020 04:51:56 INFO [hmmsearch] 14 of 22 task(s) completed at 09/24/2020 04:51:56 INFO [hmmsearch] 16 of 22 task(s) completed at 09/24/2020 04:51:56 INFO [hmmsearch] 18 of 22 task(s) completed at 09/24/2020 04:51:56 INFO [hmmsearch] 20 of 22 task(s) completed at 09/24/2020 04:51:56 INFO [hmmsearch] 22 of 22 task(s) completed at 09/24/2020 04:51:56 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: 09/24/2020 04:51:56 ****** INFO Extracting missing and fragmented buscos from the ancestral_variants file... INFO Running tblastn, writing output to /gscratch/scrubbed/samwhite/outputs/20200924_cbai_genome_v1.01_busco/run_cbai_genome_v1.01.fasta/blast_output/tblastn_cbai_genome_v1.01.fasta_missing_and_frag_rerun.tsv... INFO [tblastn] 1 of 1 task(s) completed at 09/24/2020 04:52:40 ERROR tblastn has ended prematurely (the result file lacks the expected final line), which will produce incomplete results in the next steps ! This problem likely appeared in blast+ 2.4 and seems not fully fixed in 2.6. It happens only when using multiple cores. You can use a single core (-c 1) or downgrade to blast+ 2.2.x, a safe choice regarding this issue. See blast+ documentation for more information. ERROR BUSCO analysis failed ! ERROR Check the logs, read the user guide, if you still need technical support, then please contact mailto:support@orthodb.org Generating checksum for cbai_genome_v1.01.fasta Finished generating checksum for cbai_genome_v1.01.fasta