'funannotate predict' status unclear

[ARW-UBT]

Hello, I started a annotation project of an existing genaome assembly. Funannotate clean / sort / mask / train completed successfully. Howwever funannotate predict is running since 2 days without 'visible' progress. These the corrent messsage status on the command line:

[Jan 21 10:53 AM]: OS: AlmaLinux 9.1, 40 cores, ~ 396 GB RAM. Python: 3.8.15 [Jan 21 10:53 AM]: Running funannotate v1.8.13

I have looked in the output folders, and the last modifocation is 2 days old now. It seems that funannotate got stuck somewhere. Is there any possibility to find out more about the status of funannotate? I have provided a chekc output below, it indicates some issues, unfortunately. May be you can advise me how to proceed. Best regards,

What command did you issue? funannotate predict -i ASM104565v1_genomic.cleaned.sorted.masked.fa -o fun-v1 -s "Lasius niger" --strain ASM104565v1 --cpus 40

Logfiles no logfiles available for this command

OS/Install Information funannotate has been installed using mamba for output of 'funannotate check --show-versions' see attached file funannotate-check.txt

[nextgenusfs]

Logfile is in the output directory, should tell you where it is stuck.

[ARW-UBT]

Unfortunately not! This is the entire content of the predict log file created two days ago...

$ more fun-v1/logfiles/funannotate-predict.log [01/21/23 10:53:50]: /home/bt140047/miniconda3/envs/funannotate/bin/funannotate predict -i ASM104565v1_genomic.cleaned.sorted.masked.fa -o fun-v1 -s Lasius nige r --strain ASM104565v1 --cpus 40

[01/21/23 10:53:50]: OS: AlmaLinux 9.1, 40 cores, ~ 396 GB RAM. Python: 3.8.15 [01/21/23 10:53:50]: Running funannotate v1.8.13

[nextgenusfs]

Did you run funannotate test successfully?

[ARW-UBT]

I tried it, but as soon it get to the 'funannotate predict' test, it stops. There are two places in the funannotate check output (provided as txt above, and shown here again), where some problems exist.

ERROR: local::lib not installed, install with cpanm local::lib and Checking external dependencies... tblastn: error while loading shared libraries: libnsl.so.1: cannot open shared object file: No such file or directory makeblastdb: error while loading shared libraries: libnsl.so.1: cannot open shared object file: No such file or directory

Actually, I could start a job via 'singularity', and it seems to run (until now and without GeneMark) without any errors. I will have to wait, it is at the SNAP gene prediction right now.

[nextgenusfs]

It is probably dying/stuck early on when checking dependencies, 90% if the time the problem is Augustus installation.

[ARW-UBT]

Hi @nextgenusfs Since I had some problems with perl-FindBin using GeneMark-ES/EP, I used a recently GeneMark-ETP+ instead, and a 'funannotate test -t all' test run via singularity container completed with no errors.

Is there a possibility to 'update' existing genomic annotations (at NCBI, see above) with extrinsic evidence such as RNA-Seq data to get UTRs annotated? Or would you NOT recommend to use existing annotations?

[hyphaltip]

you definitely can run 'update' on an existing annotation - that's the idea - it can import from the NCBI gbk file. This will also predict alt splicing with PASA and add UTRs if RNAseq supports evidence for that.

[ARW-UBT]

Hi @hyphaltip Thank you for that great tip. I have seen the 'update' step in the tutorials after the 'predict' step, but I was not aware that I can provide gbff anf gff from NCBI's geneomes directly to funannotate. Since 'update' uses gbff, gff and RNAseq data, is the '--busco_db' option relevant for the update script (I could not see it in the available option)? Great help! Thanks again!

[nextgenusfs]

--busco_db is not an option for funannotate update. All commands/modules have help menus, just run with -h flag.