[05/07/24 18:57:03]: /venv/bin/funannotate annotate -i fun --cpus 16 [05/07/24 18:57:03]: OS: Debian GNU/Linux 10, 16 cores, ~ 791 GB RAM. Python: 3.8.12 [05/07/24 18:57:03]: Running 1.8.17 [05/07/24 18:57:03]: hmmscan version=HMMER 3.4 (Aug 2023) path=/venv/bin/hmmscan [05/07/24 18:57:03]: hmmsearch version=HMMER 3.4 (Aug 2023) path=/venv/bin/hmmsearch [05/07/24 18:57:03]: diamond version=2.1.8 path=/venv/bin/diamond [05/07/24 18:57:03]: No NCBI SBT file given, will use default, however if you plan to submit to NCBI, create one and pass it here '--sbt' [05/07/24 18:57:03]: Parsing input files [05/07/24 18:57:03]: Existing tbl found: fun/update_results/Species_name.tbl [05/07/24 18:57:32]: TBL file: fun/annotate_misc/genome.tbl [05/07/24 18:57:32]: GFF3 file: fun/update_results/Species_name.gff3 [05/07/24 18:57:32]: Proteins file: fun/annotate_misc/genome.proteins.fasta [05/07/24 18:59:00]: Adding Functional Annotation to Species name, NCBI accession: None [05/07/24 18:59:00]: Annotation consists of: 46,164 gene models [05/07/24 18:59:00]: 46,970 protein records loaded [05/07/24 18:59:01]: Running HMMer search of PFAM version 36.0 [05/07/24 19:13:58]: 43,205 annotations added [05/07/24 19:13:58]: Running Diamond blastp search of UniProt DB version 2024_01 [05/07/24 19:13:58]: diamond blastp --sensitive --query /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/annotate_misc/genome.proteins.fasta --threads 16 --out fun/annotate_misc/uniprot.xml --db /opt/databases/uniprot.dmnd --evalue 1e-05 --max-target-seqs 1 --outfmt 5 [05/07/24 19:15:26]: 11,198 valid gene/product annotations from 14,466 total [05/07/24 19:15:26]: Install eggnog-mapper or use webserver to improve functional annotation: https://github.com/jhcepas/eggnog-mapper [05/07/24 19:15:26]: No Eggnog-mapper results found. [05/07/24 19:15:27]: Combining UniProt/EggNog gene and product names using Gene2Product version 1.92 [05/07/24 19:15:28]: 11,198 gene name and product description annotations added [05/07/24 19:15:28]: Running Diamond blastp search of MEROPS version 12.0 [05/07/24 19:15:28]: diamond blastp --sensitive --query /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/annotate_misc/genome.proteins.fasta --threads 16 --out fun/annotate_misc/merops.xml --db /opt/databases/merops.dmnd --evalue 1e-05 --max-target-seqs 1 --outfmt 5 [05/07/24 19:15:34]: 1,207 annotations added [05/07/24 19:15:34]: Annotating CAZYmes using HMMer search of dbCAN version 12.0 [05/07/24 19:17:46]: 355 annotations added [05/07/24 19:17:46]: Annotating proteins with BUSCO dikarya models [05/07/24 19:17:46]: /venv/lib/python3.8/site-packages/funannotate/aux_scripts/funannotate-BUSCO2.py -i /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/annotate_misc/genome.proteins.fasta -m proteins -l /opt/databases/dikarya -o busco -c 16 -f [05/07/24 19:20:56]: INFO ****************** Start a BUSCO 2.0 analysis, current time: 05/07/2024 19:17:46 ****************** INFO The lineage dataset is: dikarya_odb9 (eukaryota) INFO Mode is: proteins INFO To reproduce this run: python /venv/lib/python3.8/site-packages/funannotate/aux_scripts/funannotate-BUSCO2.py -i /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/annotate_misc/genome.proteins.fasta -o busco -l /opt/databases/dikarya/ -m proteins -c 16 -sp aspergillus_nidulans INFO Check dependencies... INFO Check input file... INFO Temp directory is ./tmp/ INFO Running HMMER on the proteins: INFO 05/07/2024 19:17:47 => 0% of predictions performed (1312 to be done) INFO 05/07/2024 19:18:11 => 10% of predictions performed (132/1312 candidate proteins) INFO 05/07/2024 19:18:29 => 20% of predictions performed (263/1312 candidate proteins) INFO 05/07/2024 19:18:46 => 30% of predictions performed (394/1312 candidate proteins) INFO 05/07/2024 19:18:56 => 40% of predictions performed (526/1312 candidate proteins) INFO 05/07/2024 19:19:07 => 50% of predictions performed (657/1312 candidate proteins) INFO 05/07/2024 19:19:15 => 60% of predictions performed (788/1312 candidate proteins) INFO 05/07/2024 19:19:21 => 70% of predictions performed (919/1312 candidate proteins) INFO 05/07/2024 19:19:28 => 80% of predictions performed (1050/1312 candidate proteins) INFO 05/07/2024 19:19:35 => 90% of predictions performed (1182/1312 candidate proteins) INFO 05/07/2024 19:20:55 => 100% of predictions performed INFO Results: INFO C:61.4%[S:44.2%,D:17.2%],F:13.8%,M:24.8%,n:1312 INFO 806 Complete BUSCOs (C) INFO 580 Complete and single-copy BUSCOs (S) INFO 226 Complete and duplicated BUSCOs (D) INFO 181 Fragmented BUSCOs (F) INFO 325 Missing BUSCOs (M) INFO 1312 Total BUSCO groups searched INFO BUSCO analysis done. Total running time: 189.36534476280212 seconds INFO Results written in /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/annotate_misc/run_busco/ [05/07/24 19:20:56]: 1,172 annotations added [05/07/24 19:20:56]: Skipping phobius predictions, try funannotate remote -m phobius [05/07/24 19:20:56]: Skipping secretome: neither SignalP nor Phobius searches were run [05/07/24 19:20:56]: 0 secretome and 0 transmembane annotations added [05/07/24 19:20:56]: InterProScan error, fun/annotate_misc/iprscan.xml is empty, or no XML file passed via --iprscan. Functional annotation will be lacking. [05/07/24 19:20:56]: Found 0 duplicated annotations, adding 68,335 valid annotations [05/07/24 19:20:57]: Parsing tbl file: /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/annotate_misc/genome.tbl [05/07/24 19:20:59]: Converting to final Genbank format, good luck! [05/07/24 19:20:59]: /venv/bin/python /venv/lib/python3.8/site-packages/funannotate/aux_scripts/tbl2asn_parallel.py -i fun/annotate_misc/tbl2asn/genome.tbl -f fun/annotate_misc/tbl2asn/genome.fsa -o fun/annotate_misc/tbl2asn --sbt /venv/lib/python3.8/site-packages/funannotate/config/test.sbt -d discrepency.report.txt -s Species name -t -l paired-ends -v 1 -c 16 [05/07/24 19:29:05]: Creating AGP file and corresponding contigs file [05/07/24 19:29:25]: Writing genome annotation table. [05/07/24 19:37:39]: Funannotate annotate has completed successfully! We need YOUR help to improve gene names/product descriptions: 0 gene/products names MUST be fixed, see fun/annotate_results/Gene2Products.must-fix.txt 0 gene/product names need to be curated, see fun/annotate_results/Gene2Products.need-curating.txt 1,020 gene/product names passed but are not in Database, see fun/annotate_results/Gene2Products.new-names-passed.txt Please consider contributing a PR at https://github.com/nextgenusfs/gene2product