I am trying to use the "annotate" function with the latest version I got from git clone by using only a gff3 and genome fasta file. I had to revert to use some old reference genomes due to some conflicts so I have to work with these two files and I wanted to try and perform the same annotation functions on these references as I did on my other Funannotate annotations to make it easier for down stream analysis.
Genome - Clfusi_contigs.fasta.gz
Gff3 - Clfusi_sort.gff3.txt
This is the error I am getting:
stephenwyka@bspmgenomics:/data/wyka/final_comparative_analysis/references/Clfusi$ /data/wyka/FUNANNOTATE/funannotate/funannotate.py annotate --gff gff3sort/Clfusi_sort.gff3 --fasta Clfusi_contigs.fasta -s "Claviceps fusiformis" -o Clfusi_fun_output --antismash Clfusi_antismash.gbk --iprscan Clfusi_og_ipr.xml --phobius Clfusi_og_phobius.txt --busco_db sordariomycetes --cpus 16
[03:58 PM]: OS: linux2, 24 cores, ~ 264 GB RAM. Python: 2.7.16
[03:58 PM]: Running funannotate v1.6.0-df4262f
[03:58 PM]: No NCBI SBT file given, will use default, however if you plan to submit to NCBI, create one and pass it here '--sbt'
[03:58 PM]: Output directory Clfusi_fun_output already exists, will use any existing data. If this is not what you want, exit, and provide a unique name for output folder
[03:58 PM]: Parsing annotation and preparing annotation files.
Traceback (most recent call last):
File "/data/wyka/FUNANNOTATE/funannotate/bin/funannotate-functional.py", line 469, in <module>
GeneCounts = lib.convertgff2tbl(GFF, prefix, Scaffolds, Proteins, Transcripts, annotTBL)
File "/data/wyka/FUNANNOTATE/funannotate/lib/library.py", line 1672, in convertgff2tbl
Genes = gff2dict(gff, fasta, Genes)
File "/data/wyka/FUNANNOTATE/funannotate/lib/library.py", line 3489, in gff2dict
codon_start = int(v['phase'][i][indexStart[0]]) + 1
IndexError: list index out of range
It seems to be a problem with the Gff3 file, which I did try to alter from the original one which wasn't in any particular order (not ordered by contigs or by start positions). I tried dissecting your code to try and determine how else I could alter the Gff3 to work with Funannotate, but so far I have not succeeded. Can you take a look to see if you can identify the problem?
I am trying to use the "annotate" function with the latest version I got from git clone by using only a gff3 and genome fasta file. I had to revert to use some old reference genomes due to some conflicts so I have to work with these two files and I wanted to try and perform the same annotation functions on these references as I did on my other Funannotate annotations to make it easier for down stream analysis.
Genome - Clfusi_contigs.fasta.gz
Gff3 - Clfusi_sort.gff3.txt
This is the error I am getting:
It seems to be a problem with the Gff3 file, which I did try to alter from the original one which wasn't in any particular order (not ordered by contigs or by start positions). I tried dissecting your code to try and determine how else I could alter the Gff3 to work with Funannotate, but so far I have not succeeded. Can you take a look to see if you can identify the problem?