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: 03/09/2021 05:33:16 ****************** INFO Configuration loaded from /gscratch/scrubbed/samwhite/outputs/20210308_hemat_busco_transcriptomes_v1.6_v1.7/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/Hematodinium/transcriptomes/hemat_transcriptome_v1.6.fasta -o hemat_transcriptome_v1.6.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: 03/09/2021 05:33:16 ****** INFO Create blast database... INFO [makeblastdb] Building a new DB, current time: 03/09/2021 05:33:17 INFO [makeblastdb] New DB name: /gscratch/scrubbed/samwhite/outputs/20210308_hemat_busco_transcriptomes_v1.6_v1.7/tmp/hemat_transcriptome_v1.6.fasta_3035315683 INFO [makeblastdb] New DB title: /gscratch/srlab/sam/data/Hematodinium/transcriptomes/hemat_transcriptome_v1.6.fasta INFO [makeblastdb] Sequence type: Nucleotide INFO [makeblastdb] Keep MBits: T INFO [makeblastdb] Maximum file size: 1000000000B INFO [makeblastdb] Adding sequences from FASTA; added 6176 sequences in 0.134228 seconds. INFO [makeblastdb] 1 of 1 task(s) completed at 03/09/2021 05:33:17 INFO Running tblastn, writing output to /gscratch/scrubbed/samwhite/outputs/20210308_hemat_busco_transcriptomes_v1.6_v1.7/run_hemat_transcriptome_v1.6.fasta/blast_output/tblastn_hemat_transcriptome_v1.6.fasta.tsv... INFO [tblastn] 1 of 1 task(s) completed at 03/09/2021 05:33:39 INFO ****** Step 2/2, current time: 03/09/2021 05:33:39 ****** 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] 79 of 788 task(s) completed at 03/09/2021 05:33:42 INFO [hmmsearch] 237 of 788 task(s) completed at 03/09/2021 05:33:43 INFO [hmmsearch] 710 of 788 task(s) completed at 03/09/2021 05:33:44 INFO [hmmsearch] 788 of 788 task(s) completed at 03/09/2021 05:33:44 INFO Results: INFO C:26.5%[S:20.7%,D:5.8%],F:11.2%,M:62.3%,n:978 INFO 259 Complete BUSCOs (C) INFO 202 Complete and single-copy BUSCOs (S) INFO 57 Complete and duplicated BUSCOs (D) INFO 110 Fragmented BUSCOs (F) INFO 609 Missing BUSCOs (M) INFO 978 Total BUSCO groups searched INFO BUSCO analysis done with WARNING(s). Total running time: 30.58730435371399 seconds INFO Results written in /gscratch/scrubbed/samwhite/outputs/20210308_hemat_busco_transcriptomes_v1.6_v1.7/run_hemat_transcriptome_v1.6.fasta/ /var/spool/slurm/d/job1661065/slurm_script: line 134: cho: command not found Generating checksum for hemat_transcriptome_v1.6.fasta Finished generating checksum for hemat_transcriptome_v1.6.fasta 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: 03/09/2021 05:33:48 ****************** INFO Configuration loaded from /gscratch/scrubbed/samwhite/outputs/20210308_hemat_busco_transcriptomes_v1.6_v1.7/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/Hematodinium/transcriptomes/hemat_transcriptome_v1.7.fasta -o hemat_transcriptome_v1.7.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: 03/09/2021 05:33:48 ****** INFO Create blast database... INFO [makeblastdb] Building a new DB, current time: 03/09/2021 05:33:48 INFO [makeblastdb] New DB name: /gscratch/scrubbed/samwhite/outputs/20210308_hemat_busco_transcriptomes_v1.6_v1.7/tmp/hemat_transcriptome_v1.7.fasta_1575583263 INFO [makeblastdb] New DB title: /gscratch/srlab/sam/data/Hematodinium/transcriptomes/hemat_transcriptome_v1.7.fasta INFO [makeblastdb] Sequence type: Nucleotide INFO [makeblastdb] Keep MBits: T INFO [makeblastdb] Maximum file size: 1000000000B INFO [makeblastdb] Adding sequences from FASTA; added 3538 sequences in 0.168631 seconds. INFO [makeblastdb] 1 of 1 task(s) completed at 03/09/2021 05:33:48 INFO Running tblastn, writing output to /gscratch/scrubbed/samwhite/outputs/20210308_hemat_busco_transcriptomes_v1.6_v1.7/run_hemat_transcriptome_v1.7.fasta/blast_output/tblastn_hemat_transcriptome_v1.7.fasta.tsv... INFO [tblastn] 1 of 1 task(s) completed at 03/09/2021 05:34:05 INFO ****** Step 2/2, current time: 03/09/2021 05:34:05 ****** 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] 586 of 586 task(s) completed at 03/09/2021 05:34:08 INFO Results: INFO C:15.0%[S:12.2%,D:2.8%],F:12.3%,M:72.7%,n:978 INFO 146 Complete BUSCOs (C) INFO 119 Complete and single-copy BUSCOs (S) INFO 27 Complete and duplicated BUSCOs (D) INFO 120 Fragmented BUSCOs (F) INFO 712 Missing BUSCOs (M) INFO 978 Total BUSCO groups searched INFO BUSCO analysis done with WARNING(s). Total running time: 20.495595455169678 seconds INFO Results written in /gscratch/scrubbed/samwhite/outputs/20210308_hemat_busco_transcriptomes_v1.6_v1.7/run_hemat_transcriptome_v1.7.fasta/ /var/spool/slurm/d/job1661065/slurm_script: line 134: cho: command not found Generating checksum for hemat_transcriptome_v1.7.fasta Finished generating checksum for hemat_transcriptome_v1.7.fasta Logging program options... Finished logging program options. Logging system PATH. Finished logging system PATH