Functional annotation output: mv: target 'out.tbl' is not a directory

[mmotoc]

Hello,

I am not sure what this error output means, as I am not sure what/where the out.tbl file is, and am not aware of how to fix this.

If it helps, this code was run through Galaxy.

[mmotoc]

Full output:

[Sep 07 04:16 PM]: OS: Rocky Linux 8.6, 125 cores, ~ 438 GB RAM. Python: 3.8.10 [Sep 07 04:16 PM]: Running 1.8.9 [Sep 07 04:16 PM]: Checking GenBank file for annotation [Sep 07 04:18 PM]: Adding Functional Annotation to Braula coeca, NCBI accession: None [Sep 07 04:18 PM]: Annotation consists of: 25,344 gene models [Sep 07 04:18 PM]: 20,861 protein records loaded [Sep 07 04:18 PM]: Running HMMer search of PFAM version 35.0 [Sep 07 05:01 PM]: 17,715 annotations added [Sep 07 05:01 PM]: Running Diamond blastp search of UniProt DB version 2021_04 [Sep 07 05:09 PM]: 1,484 valid gene/product annotations from 3,300 total [Sep 07 05:09 PM]: Existing Eggnog-mapper results found: output/annotate_misc/eggnog.emapper.annotations [Sep 07 05:09 PM]: Parsing EggNog Annotations [Sep 07 05:09 PM]: EggNog version parsed as 2.1.8 [Sep 07 05:09 PM]: 30,895 COG and EggNog annotations added [Sep 07 05:09 PM]: Combining UniProt/EggNog gene and product names using Gene2Product version 1.73 [Sep 07 05:09 PM]: 7,200 gene name and product description annotations added [Sep 07 05:09 PM]: Running Diamond blastp search of MEROPS version 12.0 [Sep 07 05:10 PM]: 650 annotations added [Sep 07 05:10 PM]: Annotating CAZYmes using HMMer search of dbCAN version 10.0 [Sep 07 05:20 PM]: 211 annotations added [Sep 07 05:20 PM]: Annotating proteins with BUSCO diptera models [Sep 07 05:45 PM]: 2,464 annotations added [Sep 07 05:45 PM]: Skipping phobius predictions, try funannotate remote -m phobius [Sep 07 05:45 PM]: Skipping secretome: neither SignalP nor Phobius searches were run [Sep 07 05:45 PM]: 0 secretome and 0 transmembane annotations added [Sep 07 05:45 PM]: Parsing InterProScan5 XML file [Sep 07 05:45 PM]: Found 0 duplicated annotations, adding 130,818 valid annotations [Sep 07 05:46 PM]: Converting to final Genbank format, good luck! [Sep 07 05:54 PM]: Creating AGP file and corresponding contigs file [Sep 07 05:54 PM]: Writing genome annotation table. [Sep 07 05:55 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
       128 gene/product names need to be curated, see output/annotate_results/Gene2Products.need-curating.txt
       848 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]

Not sure. "mv" is not called by funannotate so must be something with the galaxy wrapper.

[TomHarrop]

Hi @nextgenusfs

I’m trying to troubleshoot this in the Galaxy wrapper. The wrapper has a mv command that only expects one *.tbl file.

Are there situations when funannotate would produce more than one *.tbl file in the output folder?

@mmotoc did you find a way to run it on Galaxy that avoids the issue?

thanks both!

[TomHarrop]

It's because there are sometimes multiple tbl and sqn *part_n files in the output.

$ ls -lh full_run_output/annotate_results/*.tbl
-rw-rw-r-- 1 tom tom 2.4M Oct 19 15:20 full_run_output/annotate_results/funannotate_subject.part_10.tbl
-rw-rw-r-- 1 tom tom 2.5M Oct 19 15:20 full_run_output/annotate_results/funannotate_subject.part_11.tbl
-rw-rw-r-- 1 tom tom 2.4M Oct 19 15:20 full_run_output/annotate_results/funannotate_subject.part_12.tbl
-rw-rw-r-- 1 tom tom 5.5M Oct 19 15:20 full_run_output/annotate_results/funannotate_subject.part_1.tbl
-rw-rw-r-- 1 tom tom 2.9M Oct 19 15:20 full_run_output/annotate_results/funannotate_subject.part_2.tbl
-rw-rw-r-- 1 tom tom 2.6M Oct 19 15:20 full_run_output/annotate_results/funannotate_subject.part_3.tbl
-rw-rw-r-- 1 tom tom 2.5M Oct 19 15:20 full_run_output/annotate_results/funannotate_subject.part_4.tbl
-rw-rw-r-- 1 tom tom 2.4M Oct 19 15:20 full_run_output/annotate_results/funannotate_subject.part_5.tbl
-rw-rw-r-- 1 tom tom 2.5M Oct 19 15:20 full_run_output/annotate_results/funannotate_subject.part_6.tbl
-rw-rw-r-- 1 tom tom 2.5M Oct 19 15:20 full_run_output/annotate_results/funannotate_subject.part_7.tbl
-rw-rw-r-- 1 tom tom 2.5M Oct 19 15:20 full_run_output/annotate_results/funannotate_subject.part_8.tbl
-rw-rw-r-- 1 tom tom 2.5M Oct 19 15:20 full_run_output/annotate_results/funannotate_subject.part_9.tbl
-rw-rw-r-- 1 tom tom  33M Oct 19 15:20 full_run_output/annotate_results/funannotate_subject.tbl

I assume these are combined into the final .tbl and .sqn files.

I've added a workaround in the galaxy wrapper (https://github.com/galaxyproject/tools-iuc/pull/5528) but they could alternatively be deleted by funannotate if they're not needed.