Running Buscov3: no result found
Hi,
I trying to assess my plant de novo transcriptome assembly by running buscov3. But I'm not getting any results with both lineage dataset embryophyta and eukaryota (same with defaut evalue). Is it because of my input fasta file or the bad quality of transcriptome? the job scripts is:
python ./scripts/run_BUSCO.py -i ../bilberry_sequence.fasta -o bilannotated_busco_embry_trans2 -l ../embryophyta_odb9 -m tran -c 4 -e 1e-05 WARNING You are using a custom e-value cutoff INFO ****************** Start a BUSCO 3.0.2 analysis, current time: 01/27/2018 13:15:27 ****************** INFO Configuration loaded from /homeappl/home/ngqnga89/Bilberry_Project/BLAST/BUSCO/busco-master/config/config.ini INFO Init tools... INFO Check dependencies... INFO Check input file... INFO To reproduce this run: python ./scripts/run_BUSCO.py -i ../bilberry_sequence.fasta -o bilannotated_busco_embry_trans2 -l ../embryophyta_odb9/ -m transcriptome -c 4 -e 1e-05 INFO Mode is: transcriptome INFO The lineage dataset is: embryophyta_odb9 (eukaryota) INFO Temp directory is ./tmp/ INFO ****** Step 1/2, current time: 01/27/2018 13:15:27 ****** INFO Create blast database... INFO [makeblastdb] Building a new DB, current time: 01/27/2018 13:15:27 INFO [makeblastdb] New DB name: /homeappl/home/ngqnga89/Bilberry_Project/BLAST/BUSCO/busco-master/tmp/bilannotated_busco_embry_trans2_1190945148 INFO [makeblastdb] New DB title: ../bilberry_sequence.fasta INFO [makeblastdb] Sequence type: Nucleotide INFO [makeblastdb] Keep MBits: T INFO [makeblastdb] Maximum file size: 1000000000B INFO [makeblastdb] Adding sequences from FASTA; added 57919 sequences in 2.61163 seconds. INFO [makeblastdb] 1 of 1 task(s) completed at 01/27/2018 13:15:30 INFO Running tblastn, writing output to /homeappl/home/ngqnga89/Bilberry_Project/BLAST/BUSCO/busco-master/run_bilannotated_busco_embry_trans2/blast_output/tblastn_bilannotated_busco_embry_trans2.tsv... INFO [tblastn] 1 of 1 task(s) completed at 01/27/2018 13:26:27 INFO ****** Step 2/2, current time: 01/27/2018 13:26:27 ****** 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] 310 of 3093 task(s) completed at 01/27/2018 13:26:52 INFO [hmmsearch] 619 of 3093 task(s) completed at 01/27/2018 13:26:54 INFO [hmmsearch] 928 of 3093 task(s) completed at 01/27/2018 13:26:56 INFO [hmmsearch] 1238 of 3093 task(s) completed at 01/27/2018 13:26:58 INFO [hmmsearch] 1547 of 3093 task(s) completed at 01/27/2018 13:27:00 INFO [hmmsearch] 1856 of 3093 task(s) completed at 01/27/2018 13:27:02 INFO [hmmsearch] 2166 of 3093 task(s) completed at 01/27/2018 13:27:04 INFO [hmmsearch] 2475 of 3093 task(s) completed at 01/27/2018 13:27:06 INFO [hmmsearch] 2784 of 3093 task(s) completed at 01/27/2018 13:27:08 INFO [hmmsearch] 3093 of 3093 task(s) completed at 01/27/2018 13:27:10 INFO Results: INFO C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:1440 INFO 0 Complete BUSCOs (C) INFO 0 Complete and single-copy BUSCOs (S) INFO 0 Complete and duplicated BUSCOs (D) INFO 0 Fragmented BUSCOs (F) INFO 1440 Missing BUSCOs (M) INFO 1440 Total BUSCO groups searched INFO BUSCO analysis done with WARNING(s). Total running time: 705.429183006 seconds INFO Results written in /homeappl/home/ngqnga89/Bilberry_Project/BLAST/BUSCO/busco-master/run_bilannotated_busco_embry_trans2/
Could you please have a look and tell me there is something incorrect? Thank you, Best, Nga Nguyen