Error code at end of Funannotate functional annotation

usegalaxy.org.au support
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1

G’day, I keep getting the following error (target ‘out.tbl’ is not a directory) at the end of Funnaotate functional annotation — it seems that all the analyses are completed, but that the final output cannot be made? Any help would be appreciated. cheers John

[Nov 16 12:26 PM]: Creating AGP file and corresponding contigs file
[Nov 16 12:26 PM]: Writing genome annotation table.
[Nov 16 12:32 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
       642 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

2

Welcome, @jlbowman

Certain versions of the annotation were problematic at one server, and don’t off hand know which at AU are ok, so started some tests (see below).

Meanwhile,

  • Version 2022 should be good at both EU and AU.
  • Version 2023-09 should be good at EU.
  • Version 2023-05 should be good at AU.
  • Version 2023-04 has problems anywhere, and won’t be fixed (avoid).
  • UseGalaxy.org doesn’t currently support any. Ticket

If you are unsure of the usage, this tool is included in a tutorial. Scroll to the bottom of the tool form Help section for the links.

Examples using test data to see what is working right now:

The best advice is to double check which annotation you are using. If a working index, and you are still getting an error, the problem is likely with the other inputs or parameters, and the tutorial should help. If not, you can share more details and we can look closer.

:mechanic: What information should I include when reporting a problem?

Any persistent problems can be reported in a new question for community help. Be sure to provide enough context so others can review the situation exactly and quickly offer advice.

Consider Sharing your History or posting content from the Job Information :information_source: view as described in Troubleshooting errors.

3

G’day jennaj,

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
john

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.
Details

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

4

Hi @jlbowman

These make me guess that the output was empty, so the tool didn’t have any content to move. That use-case could probably be trapped better (and we could ticket it) but I’d like to confirm.

Now, why there were no annotations could be due to a data format problem rather than actually no annotations. Cleaning up the fasta format might be enough, and the tool NormalizeFasta could be used.

You could also remove any shorter assembly results (anything that might just be a single original read). Annotation tools can be overwhelmed by being asked to process raw assembly results that haven’t been quality filtered. You could even just run a few contigs through the tool as a test. Try that now to see what happens.

If you want to share a link to your history I’ll take a closer look at the input details (exact data, params, etc). Run your “few contigs” test first in the same history as the full sized data please.