nextgenusfs
ERROR: ID=FUN_003286 has no CDS features, removing gene model
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!
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[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
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
What is potentially the problem?
