ERROR: ID=FUN_003286 has no CDS features, removing gene model

[zhuofeih]

Hi, We are using 1.8.9 on the cluster at our university. We received errors like the above one when the pipeline ran this step:

funannotate update -i fun_z_11748973 --cpus 20

Below is the part of the log. We are new to funannotate. Could you please take a look for us and let me know what caused the issue and how to get it resolved? If there is already a communication thread on this, could you please forward it to me? Thank you very much in advance for your help!

=======================

[May 23 12:03 AM]: Funannotate predict is finished, output files are in the fun_z_11728052/predict_results folder
[May 23 12:03 AM]: Your next step to capture UTRs and update annotation using PASA:

funannotate update -i fun_z_11728052 --cpus 20

[May 23 12:03 AM]: Training parameters file saved: fun_z_11728052/predict_results/cryptococcus_neoformans_neoformans_jec21.parameters.json
[May 23 12:03 AM]: Add species parameters to database:

funannotate species -s cryptococcus_neoformans_neoformans_jec21 -a fun_z_11728052/predict_results/cryptococcus_neoformans_neoformans_jec21.parameters.json

[May 23 12:03 AM]: OS: CentOS Linux 7, 32 cores, ~ 528 GB RAM. Python: 3.7.4
[May 23 12:03 AM]: Running 1.8.9
[May 23 12:03 AM]: No NCBI SBT file given, will use default, for NCBI submissions pass one here '--sbt'
[May 23 12:03 AM]: Found relevant files in fun_z_11728052/training, will re-use them:
Forward reads: fun_z_11728052/training/left.fq.gz
Reverse reads: fun_z_11728052/training/right.fq.gz
Forward Q-trimmed reads: fun_z_11728052/training/trimmomatic/trimmed_left.fastq.gz
Reverse Q-trimmed reads: fun_z_11728052/training/trimmomatic/trimmed_right.fastq.gz
Forward normalized reads: fun_z_11728052/training/normalize/left.norm.fq
Reverse normalized reads: fun_z_11728052/training/normalize/right.norm.fq
Trinity results: fun_z_11728052/training/funannotate_train.trinity-GG.fasta
PASA config file: fun_z_11728052/training/pasa/alignAssembly.txt
BAM alignments: fun_z_11728052/training/funannotate_train.coordSorted.bam
StringTie GTF: fun_z_11728052/training/funannotate_train.stringtie.gtf
[May 23 12:03 AM]: Reannotating cryptococcus_neoformans_neoformans_JEC21, NCBI accession: None
[May 23 12:03 AM]: Previous annotation consists of: 7,059 protein coding gene models and 138 non-coding gene models
[May 23 12:03 AM]: Converting transcript alignments to GFF3 format
[May 23 12:03 AM]: Converting Trinity transcript alignments to GFF3 format
[May 23 12:03 AM]: PASA database is SQLite: /scratch/zhuofei/funannotate_job/fun_z_11728052/training/pasa/cryptococcus_neoformans_neoformans_JEC21_pasa
[May 23 12:03 AM]: Running PASA annotation comparison step 1
[May 23 12:46 AM]: Running PASA annotation comparison step 2
[May 23 02:20 AM]: Using Kallisto TPM data to determine which PASA gene models to select at each locus
[May 23 02:20 AM]: Building Kallisto index
[May 23 02:21 AM]: Mapping reads using pseudoalignment in Kallisto
[May 23 02:22 AM]: Parsing Kallisto results. Keeping alt-splicing transcripts if expressed at least 10.0% of highest transcript per locus.
[May 23 02:22 AM]: Wrote 7,936 transcripts derived from 7,098 protein coding loci.
ERROR: ID=FUN_003169 has no CDS features, removing gene model
ERROR: ID=FUN_002998 has no CDS features, removing gene model
ERROR: ID=FUN_003078 has no CDS features, removing gene model
ERROR: ID=FUN_003358 has no CDS features, removing gene model
ERROR: ID=FUN_003286 has no CDS features, removing gene model

Traceback (most recent call last):
File "/scratch/zhuofei/funannotate/bin/funannotate", line 8, in
sys.exit(main())
File "/scratch/zhuofei/funannotate/lib/python3.7/site-packages/funannotate/funannotate.py", line 705, in main
mod.main(arguments)
File "/scratch/zhuofei/funannotate/lib/python3.7/site-packages/funannotate/update.py", line 2324, in main
alt_transcripts=args.alt_transcripts)
File "/scratch/zhuofei/funannotate/lib/python3.7/site-packages/funannotate/update.py", line 1160, in GFF2tblCombinedNEW
evm, genome, gene_inter, Genes)
File "/scratch/zhuofei/funannotate/lib/python3.7/site-packages/funannotate/library.py", line 3984, in gff2interlapDict
Genes = gff2dict(input, fasta, Genes, gap_filter=True)
File "/scratch/zhuofei/funannotate/lib/python3.7/site-packages/funannotate/library.py", line 4503, in gff2dict
Genes[k]['mRNA'][i] = sortedExons
KeyError: 'FUN_003286'

[alexvasilikop]

Hi I am having the same issue (key error in funannotate update) and I tried to see if the error is fixed but I get another error. I installed the latest commit using
$ python3 -m pip install git+https://github.com/nextgenusfs/funannotate.git

Then I activate funannotate using conda (environment where i previously have installed 1.8.9) for the dependencies.
I run:
$ /home/lege/.local/bin/funannotate update -i $outdir_predict --cpus 1 --left $left --right $right --trinity $trinity_assembly --jaccard_clip --no_trimmomatic

and I get:

[Jun 21 04:36 PM]: OS: Ubuntu 18.10, 48 cores, ~ 264 GB RAM. Python: 3.6.8
[Jun 21 04:36 PM]: Running 1.8.11
[Jun 21 04:36 PM]: No NCBI SBT file given, will use default, for NCBI submissions pass one here '--sbt'
Traceback (most recent call last):
File "/home/lege/.local/bin/funannotate", line 8, in
sys.exit(main())
File "/home/lege/.local/lib/python3.6/site-packages/funannotate/funannotate.py", line 716, in main
mod.main(arguments)
File "/home/lege/.local/lib/python3.6/site-packages/funannotate/update.py", line 1909, in main
(inputDir, '\n'.join(files_used)))
UnboundLocalError: local variable 'inputDir' referenced before assignment

What is potentially the problem?

[alexvasilikop]

Problem fixed. Thanks!