Many thanks for your very prompt response — I am slow to reply as we were camping all weekend. I have followed the tutorial at (Genome annotation with Funannotate) as close as possible, the only differences being due to using my own genome assembly.
I can share my history if it would help, but in short:
I have used the 2023-05 version of Funannotate predict annotation to produce a structural annotation and this work fined, i.e. at least all the output files were produced and everything seemed in order.
I then took the protein output file of Funannotate predict annotation and ran EggNog and InterProScan for functional annotation.
Next I used the output from the 2023-05 version of Funannotate predict annotation (I have tried both the GenBank annotation file and the GFF file) in the 2023-05 version of Funannotate functional annotation, I get the error described below, where it seems the entire run is completed, but when it reaches the output of the NCBI tbl annotation file, the run is aborted with the statement “mv: target ‘out.tbl’ is not a directory” and none of the subsequent files are produced.
(I also tried the with the 2022-02 version and this resulted in the same error)
cheers and thanks
Dataset Error Report
An error occurred while running the tool toolshed.g2.bx.psu.edu/repos/iuc/funannotate_annotate/funannotate_annotate/1.8.15+galaxy2.
Execution resulted in the following messages:
Fatal error: Exit code 1 ()
Tool generated the following standard error:
[Nov 21 07:44 PM]: OS: Ubuntu 22.04, 32 cores, ~ 132 GB RAM. Python: 3.8.15
[Nov 21 07:44 PM]: Running 1.8.15
[Nov 21 07:44 PM]: Checking GenBank file for annotation
[Nov 21 07:47 PM]: Adding Functional Annotation to Marchantia foliacea, NCBI accession: None
[Nov 21 07:47 PM]: Annotation consists of: 22,317 gene models
[Nov 21 07:47 PM]: 21,991 protein records loaded
[Nov 21 07:47 PM]: Running HMMer search of PFAM version 35.0
[Nov 21 07:55 PM]: 18,666 annotations added
[Nov 21 07:55 PM]: Running Diamond blastp search of UniProt DB version 2023_02
[Nov 21 07:57 PM]: 1,485 valid gene/product annotations from 2,259 total
[Nov 21 07:57 PM]: Existing Eggnog-mapper results found: output/annotate_misc/eggnog.emapper.annotations
[Nov 21 07:57 PM]: Parsing EggNog Annotations
[Nov 21 07:57 PM]: EggNog version parsed as 2.1.8
[Nov 21 07:57 PM]: 29,070 COG and EggNog annotations added
[Nov 21 07:57 PM]: Combining UniProt/EggNog gene and product names using Gene2Product version 1.88
[Nov 21 07:57 PM]: 2,130 gene name and product description annotations added
[Nov 21 07:57 PM]: Running Diamond blastp search of MEROPS version 12.0
[Nov 21 07:57 PM]: 611 annotations added
[Nov 21 07:57 PM]: Annotating CAZYmes using HMMer search of dbCAN version 11.0
[Nov 21 07:59 PM]: 632 annotations added
[Nov 21 07:59 PM]: Annotating proteins with BUSCO embryophyta models
[Nov 21 08:21 PM]: 1,008 annotations added
[Nov 21 08:21 PM]: Skipping phobius predictions, try funannotate remote -m phobius
[Nov 21 08:21 PM]: Skipping secretome: neither SignalP nor Phobius searches were run
[Nov 21 08:21 PM]: 0 secretome and 0 transmembane annotations added
[Nov 21 08:25 PM]: Parsing InterProScan5 XML file
[Nov 21 08:31 PM]: Found 0 duplicated annotations, adding 308,140 valid annotations
[Nov 21 08:31 PM]: Converting to final Genbank format, good luck!
[Nov 21 08:36 PM]: Creating AGP file and corresponding contigs file
[Nov 21 08:37 PM]: Writing genome annotation table.
[Nov 21 08:44 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
10 gene/product names need to be curated, see output/annotate_results/Gene2Products.need-curating.txt
627 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