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nextgenusfs / funannotate

Eukaryotic Genome Annotation Pipeline
http://funannotate.readthedocs.io
BSD 2-Clause "Simplified" License
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I tried to run Funannotate functional annotation in usegalaxy.org.au, program has got run successfully. However the files are not getting generated in history and its marked error with red colour. #945

Closed BharathBioinfo closed 8 months ago

BharathBioinfo commented 11 months ago

[Aug 02 09:55 PM]: OS: Ubuntu 20.04, 16 cores, ~ 66 GB RAM. Python: 3.8.15 [Aug 02 09:55 PM]: Running 1.8.15 [Aug 02 09:55 PM]: No NCBI SBT file given, will use default, however if you plan to submit to NCBI, create one and pass it here '--sbt' [Aug 02 09:55 PM]: Checking GenBank file for annotation [Aug 02 09:57 PM]: Adding Functional Annotation to ltgalaxy.tools.parameters.basic.ConnectedValue object at 0x7fd26c407ee0gt, NCBI accession: None [Aug 02 09:57 PM]: Annotation consists of: 31,171 gene models [Aug 02 09:57 PM]: 30,147 protein records loaded [Aug 02 09:57 PM]: Running HMMer search of PFAM version 35.0 [Aug 02 10:37 PM]: 28,245 annotations added [Aug 02 10:37 PM]: Running Diamond blastp search of UniProt DB version 2021_04 [Aug 02 10:46 PM]: 4,514 valid gene/product annotations from 6,809 total [Aug 02 10:46 PM]: Existing Eggnog-mapper results found: output/annotate_misc/eggnog.emapper.annotations [Aug 02 10:46 PM]: Parsing EggNog Annotations [Aug 02 10:46 PM]: EggNog version parsed as 2.1.8 [Aug 02 10:46 PM]: 48,391 COG and EggNog annotations added [Aug 02 10:46 PM]: Combining UniProt/EggNog gene and product names using Gene2Product version 1.74 [Aug 02 10:46 PM]: 5,301 gene name and product description annotations added [Aug 02 10:46 PM]: Running Diamond blastp search of MEROPS version 12.0 [Aug 02 10:46 PM]: 788 annotations added [Aug 02 10:46 PM]: Annotating CAZYmes using HMMer search of dbCAN version 10.0 [Aug 02 10:57 PM]: 1,039 annotations added [Aug 02 10:57 PM]: Annotating proteins with BUSCO eukaryota models [Aug 02 10:58 PM]: 340 annotations added [Aug 02 10:58 PM]: Skipping phobius predictions, try funannotate remote -m phobius [Aug 02 10:58 PM]: Skipping secretome: neither SignalP nor Phobius searches were run [Aug 02 10:58 PM]: 0 secretome and 0 transmembane annotations added [Aug 02 10:58 PM]: InterProScan error, output/annotate_misc/iprscan.xml is empty, or no XML file passed via --iprscan. Functional annotation will be lacking. [Aug 02 10:58 PM]: Found 0 duplicated annotations, adding 89,405 valid annotations [Aug 02 10:58 PM]: Converting to final Genbank format, good luck! [Aug 02 11:05 PM]: Creating AGP file and corresponding contigs file [Aug 02 11:06 PM]: Writing genome annotation table. [Aug 02 11:07 PM]: Funannotate annotate has completed successfully!

    We need YOUR help to improve gene names/product descriptions:
       0 gene/products names MUST be fixed, see output/annotate_results/Gene2Products.must-fix.txt
       19 gene/product names need to be curated, see output/annotate_results/Gene2Products.need-curating.txt
       1,941 gene/product names passed but are not in Database, see output/annotate_results/Gene2Products.new-names-passed.txt

    Please consider contributing a PR at https://github.com/nextgenusfs/gene2product

mv: target 'out.tbl' is not a directory

nextgenusfs commented 8 months ago

duplicate #777