hyphaltip
commented
2 years ago Is your gff structured gff3 with gene / mRNA /CDS features?
On Tue, Jun 28, 2022 at 5:59 AM JC-therea @.***> wrote:
Hello,
Describe the bug
I am using the lastest version of Funannotate and I am having problems with funannotate update. I think the problem is related with the function gff2pasa and my annotation but I don't know how to fix it. The locus tags looks like: gene-YPR204W
command
funannotate update -f $GENOMEFIX -g $GFF -o Scer --nanopore_mrna $dRNA --no_trimmomatic --pasa_db mysql --stranded F --jaccard_clip --species "Saccharomyces cerevisiae" --cpus 8 --no-progress Logfiles [Jun 18 10:20 AM]: OS: CentOS Linux 7, 48 cores, ~ 528 GB RAM. Python: 3.7.12 [Jun 18 10:20 AM]: Running 1.8.9 [Jun 18 10:20 AM]: No NCBI SBT file given, will use default, for NCBI submissions pass one here '--sbt' ERROR: ID=gene-YIL175W has no CDS features, removing gene model ERROR: ID=gene-YIL174W has no CDS features, removing gene model ERROR: ID=gene-YIL171W has no CDS features, removing gene model ERROR: ID=gene-YIL170W has no CDS features, removing gene model ERROR: ID=gene-YFL056C has no CDS features, removing gene model ERROR: ID=gene-YAR061W has no CDS features, removing gene model ERROR: ID=gene-YPL276W has no CDS features, removing gene model ERROR: ID=gene-YPL275W has no CDS features, removing gene model ERROR: ID=gene-YLL017W has no CDS features, removing gene model ERROR: ID=gene-YLL016W has no CDS features, removing gene model ERROR: ID=gene-YLR110C has no CDS features, removing gene model ERROR: ID=gene-YCL075W has no CDS features, removing gene model ERROR: ID=gene-YCL074W has no CDS features, removing gene model [Jun 18 10:21 AM]: Previous annotation consists of: 5,948 protein coding gene models and 310 non-coding gene models [Jun 18 10:21 AM]: Trimmomatic will be skipped [Jun 18 10:21 AM]: Existing BAM alignments found: Scer/update_misc/transcript.alignments.bam [Jun 18 10:21 AM]: Running PASA alignment step using 499,999 transcripts [Jun 23 11:22 PM]: Running PASA annotation comparison step 1 [Jun 23 11:48 PM]: Running PASA annotation comparison step 2 [Jun 24 12:17 AM]: Generating relative expression values to PASA transcripts [Jun 24 12:19 AM]: Parsing Kallisto results. Keeping alt-splicing transcripts if expressed at least 10.0% of highest transcript per locus. [Jun 24 12:19 AM]: Wrote 6,140 transcripts derived from 5,961 protein coding loci.
Traceback (most recent call last): File "/soft/EB_repo/devel/programs/noarch/miniconda3/2022-05/envs/funannotate/bin/funannotate", line 10, in sys.exit(main()) File "/soft/EB_repo/devel/programs/noarch/miniconda3/2022-05/envs/funannotate/lib/python3.7/site-packages/funannotate/funannotate.py", line 705, in main mod.main(arguments) File "/soft/EB_repo/devel/programs/noarch/miniconda3/2022-05/envs/funannotate/lib/python3.7/site-packages/funannotate/update.py", line 2324, in main alt_transcripts=args.alt_transcripts) File "/soft/EB_repo/devel/programs/noarch/miniconda3/2022-05/envs/funannotate/lib/python3.7/site-packages/funannotate/update.py", line 1149, in GFF2tblCombinedNEW genenumber = int(genenumber) ValueError: invalid literal for int() with base 10: '204W'
Is there some way to modify my annotation to solve this?
Thank you very much.
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Jason Stajich - @.***
JC-therea
nextgenusfs
Hello,
Describe the bug
I am using the lastest version of Funannotate and I am having problems with funannotate update. I think the problem is related with the function gff2pasa and my annotation but I don't know how to fix it. My last locus tags is: gene-YPR204W
command
Logfiles
Is there some way to modify my annotation to solve this?
Thank you very much.