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: 08/14/2020 16:04:33 ****************** INFO Configuration loaded from /gscratch/scrubbed/samwhite/outputs/20200814_hemat_busco_transcriptomes_v1.6_v1.7_v2.1_v.3.1/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: 08/14/2020 16:04:34 ****** INFO Create blast database... INFO [makeblastdb] Building a new DB, current time: 08/14/2020 16:04:34 INFO [makeblastdb] New DB name: /gscratch/scrubbed/samwhite/outputs/20200814_hemat_busco_transcriptomes_v1.6_v1.7_v2.1_v.3.1/tmp/hemat_transcriptome_v1.6.fasta_4036006891 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 40247 sequences in 1.52288 seconds. INFO [makeblastdb] 1 of 1 task(s) completed at 08/14/2020 16:04:36 INFO Running tblastn, writing output to /gscratch/scrubbed/samwhite/outputs/20200814_hemat_busco_transcriptomes_v1.6_v1.7_v2.1_v.3.1/run_hemat_transcriptome_v1.6.fasta/blast_output/tblastn_hemat_transcriptome_v1.6.fasta.tsv... INFO [tblastn] 1 of 1 task(s) completed at 08/14/2020 16:05:50 INFO ****** Step 2/2, current time: 08/14/2020 16:05:50 ****** 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] 175 of 1745 task(s) completed at 08/14/2020 16:06:01 INFO [hmmsearch] 524 of 1745 task(s) completed at 08/14/2020 16:06:01 INFO [hmmsearch] 1745 of 1745 task(s) completed at 08/14/2020 16:06:04 INFO Results: INFO C:91.8%[S:64.9%,D:26.9%],F:6.0%,M:2.2%,n:978 INFO 898 Complete BUSCOs (C) INFO 635 Complete and single-copy BUSCOs (S) INFO 263 Complete and duplicated BUSCOs (D) INFO 59 Fragmented BUSCOs (F) INFO 21 Missing BUSCOs (M) INFO 978 Total BUSCO groups searched INFO BUSCO analysis done with WARNING(s). Total running time: 96.05740904808044 seconds INFO Results written in /gscratch/scrubbed/samwhite/outputs/20200814_hemat_busco_transcriptomes_v1.6_v1.7_v2.1_v.3.1/run_hemat_transcriptome_v1.6.fasta/ /var/spool/slurm/d/job186355/slurm_script: line 136: 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: 08/14/2020 16:06:11 ****************** INFO Configuration loaded from /gscratch/scrubbed/samwhite/outputs/20200814_hemat_busco_transcriptomes_v1.6_v1.7_v2.1_v.3.1/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: 08/14/2020 16:06:11 ****** INFO Create blast database... INFO [makeblastdb] Building a new DB, current time: 08/14/2020 16:06:12 INFO [makeblastdb] New DB name: /gscratch/scrubbed/samwhite/outputs/20200814_hemat_busco_transcriptomes_v1.6_v1.7_v2.1_v.3.1/tmp/hemat_transcriptome_v1.7.fasta_693130180 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 20543 sequences in 0.927057 seconds. INFO [makeblastdb] 1 of 1 task(s) completed at 08/14/2020 16:06:13 INFO Running tblastn, writing output to /gscratch/scrubbed/samwhite/outputs/20200814_hemat_busco_transcriptomes_v1.6_v1.7_v2.1_v.3.1/run_hemat_transcriptome_v1.7.fasta/blast_output/tblastn_hemat_transcriptome_v1.7.fasta.tsv... INFO [tblastn] 1 of 1 task(s) completed at 08/14/2020 16:07:07 INFO ****** Step 2/2, current time: 08/14/2020 16:07:07 ****** 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] 320 of 1599 task(s) completed at 08/14/2020 16:07:14 INFO [hmmsearch] 1280 of 1599 task(s) completed at 08/14/2020 16:07:16 INFO [hmmsearch] 1599 of 1599 task(s) completed at 08/14/2020 16:07:17 INFO Results: INFO C:86.5%[S:65.5%,D:21.0%],F:8.3%,M:5.2%,n:978 INFO 846 Complete BUSCOs (C) INFO 641 Complete and single-copy BUSCOs (S) INFO 205 Complete and duplicated BUSCOs (D) INFO 81 Fragmented BUSCOs (F) INFO 51 Missing BUSCOs (M) INFO 978 Total BUSCO groups searched INFO BUSCO analysis done with WARNING(s). Total running time: 68.74763369560242 seconds INFO Results written in /gscratch/scrubbed/samwhite/outputs/20200814_hemat_busco_transcriptomes_v1.6_v1.7_v2.1_v.3.1/run_hemat_transcriptome_v1.7.fasta/ /var/spool/slurm/d/job186355/slurm_script: line 136: cho: command not found Generating checksum for hemat_transcriptome_v1.7.fasta Finished generating checksum for hemat_transcriptome_v1.7.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: 08/14/2020 16:07:22 ****************** INFO Configuration loaded from /gscratch/scrubbed/samwhite/outputs/20200814_hemat_busco_transcriptomes_v1.6_v1.7_v2.1_v.3.1/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_v2.1.fasta -o hemat_transcriptome_v2.1.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: 08/14/2020 16:07:22 ****** INFO Create blast database... INFO [makeblastdb] Building a new DB, current time: 08/14/2020 16:07:23 INFO [makeblastdb] New DB name: /gscratch/scrubbed/samwhite/outputs/20200814_hemat_busco_transcriptomes_v1.6_v1.7_v2.1_v.3.1/tmp/hemat_transcriptome_v2.1.fasta_1392625469 INFO [makeblastdb] New DB title: /gscratch/srlab/sam/data/Hematodinium/transcriptomes/hemat_transcriptome_v2.1.fasta INFO [makeblastdb] Sequence type: Nucleotide INFO [makeblastdb] Keep MBits: T INFO [makeblastdb] Maximum file size: 1000000000B INFO [makeblastdb] Adding sequences from FASTA; added 30612 sequences in 1.51489 seconds. INFO [makeblastdb] 1 of 1 task(s) completed at 08/14/2020 16:07:24 INFO Running tblastn, writing output to /gscratch/scrubbed/samwhite/outputs/20200814_hemat_busco_transcriptomes_v1.6_v1.7_v2.1_v.3.1/run_hemat_transcriptome_v2.1.fasta/blast_output/tblastn_hemat_transcriptome_v2.1.fasta.tsv... INFO [tblastn] 1 of 1 task(s) completed at 08/14/2020 16:09:10 INFO ****** Step 2/2, current time: 08/14/2020 16:09:10 ****** 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] 1105 of 1227 task(s) completed at 08/14/2020 16:09:19 INFO [hmmsearch] 1227 of 1227 task(s) completed at 08/14/2020 16:09:20 INFO Results: INFO C:33.7%[S:6.2%,D:27.5%],F:2.9%,M:63.4%,n:978 INFO 330 Complete BUSCOs (C) INFO 61 Complete and single-copy BUSCOs (S) INFO 269 Complete and duplicated BUSCOs (D) INFO 28 Fragmented BUSCOs (F) INFO 620 Missing BUSCOs (M) INFO 978 Total BUSCO groups searched INFO BUSCO analysis done with WARNING(s). Total running time: 119.29840755462646 seconds INFO Results written in /gscratch/scrubbed/samwhite/outputs/20200814_hemat_busco_transcriptomes_v1.6_v1.7_v2.1_v.3.1/run_hemat_transcriptome_v2.1.fasta/ /var/spool/slurm/d/job186355/slurm_script: line 136: cho: command not found Generating checksum for hemat_transcriptome_v2.1.fasta Finished generating checksum for hemat_transcriptome_v2.1.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: 08/14/2020 16:09:23 ****************** INFO Configuration loaded from /gscratch/scrubbed/samwhite/outputs/20200814_hemat_busco_transcriptomes_v1.6_v1.7_v2.1_v.3.1/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_v3.1.fasta -o hemat_transcriptome_v3.1.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: 08/14/2020 16:09:24 ****** INFO Create blast database... INFO [makeblastdb] Building a new DB, current time: 08/14/2020 16:09:24 INFO [makeblastdb] New DB name: /gscratch/scrubbed/samwhite/outputs/20200814_hemat_busco_transcriptomes_v1.6_v1.7_v2.1_v.3.1/tmp/hemat_transcriptome_v3.1.fasta_2388333594 INFO [makeblastdb] New DB title: /gscratch/srlab/sam/data/Hematodinium/transcriptomes/hemat_transcriptome_v3.1.fasta INFO [makeblastdb] Sequence type: Nucleotide INFO [makeblastdb] Keep MBits: T INFO [makeblastdb] Maximum file size: 1000000000B INFO [makeblastdb] Adding sequences from FASTA; added 29863 sequences in 1.7712 seconds. INFO [makeblastdb] 1 of 1 task(s) completed at 08/14/2020 16:09:26 INFO Running tblastn, writing output to /gscratch/scrubbed/samwhite/outputs/20200814_hemat_busco_transcriptomes_v1.6_v1.7_v2.1_v.3.1/run_hemat_transcriptome_v3.1.fasta/blast_output/tblastn_hemat_transcriptome_v3.1.fasta.tsv... INFO [tblastn] 1 of 1 task(s) completed at 08/14/2020 16:11:11 INFO ****** Step 2/2, current time: 08/14/2020 16:11:11 ****** 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] 1228 of 1228 task(s) completed at 08/14/2020 16:11:21 INFO Results: INFO C:34.3%[S:6.3%,D:28.0%],F:3.2%,M:62.5%,n:978 INFO 336 Complete BUSCOs (C) INFO 62 Complete and single-copy BUSCOs (S) INFO 274 Complete and duplicated BUSCOs (D) INFO 31 Fragmented BUSCOs (F) INFO 611 Missing BUSCOs (M) INFO 978 Total BUSCO groups searched INFO BUSCO analysis done with WARNING(s). Total running time: 118.98100137710571 seconds INFO Results written in /gscratch/scrubbed/samwhite/outputs/20200814_hemat_busco_transcriptomes_v1.6_v1.7_v2.1_v.3.1/run_hemat_transcriptome_v3.1.fasta/ /var/spool/slurm/d/job186355/slurm_script: line 136: cho: command not found Generating checksum for hemat_transcriptome_v3.1.fasta Finished generating checksum for hemat_transcriptome_v3.1.fasta