nextgenusfs
lacks elements in /scratch/mdegenna/slin023/funannotate/dikarya/prfl
Hi, I used funannotate 1.8.3 to run the genome annotation. But I ran into these errors while running funannotate predict :
`WARNING The dataset you provided does not contain the file dataset.cfg, likely because it is an old version. Some parameters will be deduced from the dataset folder name
INFO The lineage dataset is: dikarya (eukaryota)
INFO Mode is: genome
INFO Maximum number of regions limited to: 3
INFO To reproduce this run: python /funannotate/lib/python2.7/site-packages/funannotate/aux_scripts/funannotate-BUSCO2-py2.py -i /home/slin023/funannotate/funannotateout/predict_misc/genome.softmasked.fa -o phormia_regina -l /scratch/mdegenna/slin023/funannotate/dikarya/ -m genome -c 2 -sp anidulans
INFO Check dependencies...
INFO Check input file...
ERROR The dataset you provided lacks elements in /scratch/mdegenna/slin023/funannotate/dikarya/prfl
ERROR BUSCO analysis failed !
INFO Check the logs, read the user guide, if you still need technical support, then please contact mailto:[email protected]`
Here is the command I used to run funannotate predict:
`module load singularity-3.8.2
pwd; hostname; date
echo "Running program on $SLURM_CPUS_ON_NODE CPU cores"
singularity exec --env-file /home/slin023/funannotate.txt /home/slurmsample/singularity/funannotate_1.8.3.sif funannotate predict -i /home/slin023/funannotate/masked.fasta --species "Phormia regina" --transcript_evidence /scratch/mdegenna/slin023/Transannotation/Trinity-GG.fasta --rna_bam /home/data/FLAG/PhormiaMaggotAging/aging/TrimMapping/trimSorted.out.bam -o funannotateout`
I referred to this thread, and used funannotate setup -b dikarya , but still got the same issue. Is there anyway to manual install the missing dataset, or it indicates the dataset.cf is missing. If there is any suggestion, please let me know.
This appears to be an incomplete download of the BUSCO dataset, ie here is what should be in the dikarya folder
$ ls -l $FUNANNOTATE_DB/dikarya
total 10624
-rw-r--r--@ 1 jon admin 472K Feb 13 2017 ancestral
-rw-r--r--@ 1 jon admin 4.6M Feb 13 2017 ancestral_variants
-rw-r--r--@ 1 jon admin 132B Feb 13 2017 dataset.cfg
drwxr-xr-x 1314 jon admin 41K Feb 13 2017 hmms/
drwxr-xr-x 6 jon admin 192B Feb 13 2017 info/
-rw-r--r--@ 1 jon admin 47K Feb 13 2017 lengths_cutoff
drwxr-xr-x 1314 jon admin 41K Feb 13 2017 prfl/
-rw-r--r--@ 1 jon admin 31K Feb 13 2017 scores_cutoff
Hi, thank you for the reply. I solved the problem by manually downloading the dikarya database from "busco-data.ezlab.org"!