search

Illumina / SpliceAI

A deep learning-based tool to identify splice variants
Other
399 stars 158 forks source link

No training configuration found in save file #151

Open YS-Github-bug opened 2 weeks ago

YS-Github-bug commented 2 weeks ago

i met a problem in installing this software. I first create a conda environment using python=3.6. Then I pip install packages:pandas==0.24.2 keras==2.0.5 tensorflow==1.9.0 h5py==2.10.0 Following this, pip install spliceai and also run conda install mkl-service

i try to test the install succeed, using "spliceai -I input.vcf -O output.vcf -R hg38_p14.fa -A grch38".

I get the following errors and didn't get expected output. So that i didn't get any predicted values.

UserWarning: No training configuration found in save file: the model was not compiled. Compile it manually. warnings.warn('No training configuration found in save file: ' WARNING:root:Skipping record (ref issue): 2 152389953 . T A,C,G . . .

WARNING:root:Skipping record (ref issue): 2 179446218 . ATACT A . . .

WARNING:root:Skipping record (ref issue): 2 179446218 . ATACT AT,ATA . . .

WARNING:root:Skipping record (ref issue): 2 179642185 . G A . . .

WARNING:root:Skipping record (ref issue): 19 38958362 . C T . . .

Do you have any good solutions?

kishorejaganathan commented 1 week ago

Skipping record (ref issue) happens when the reference nucleotide provided in the VCF does not match with what is inferred from the fasta file. For example, in your fasta file, 2:152389953 does not have T (I have checked this in the genome browser and it is an A). It is possible your VCF is hg19.