Preprocessing Tool: Fatal error on some files

emro commented 5 years ago

I tried to process the following three files using the file converter tool and each of them resulted in a fatal error:

Human GRCh38 GENCODE v29 GFF3: ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_29/gencode.v29.annotation.gff3.gz
Human hg19 GENCODE v29 GFF3: ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_29/GRCh37_mapping/gencode.v29lift37.annotation.gff3.gz
Mouse mm10 GENCODE M21 GFF3: ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M21/gencode.vM21.annotation.gff3.gz

I'm not sure exactly what the issue is, because I have been able to process other large GFF3 files from GENCODE successfully.

haxiomic commented 5 years ago

Thanks for the report @emro!

The crash was due to the converter's memory running out of space – I can tweak things so that it process large files incrementally rather than all in one go

haxiomic commented 5 years ago

This should be fixed now :) – I've tested all 3 files and they all look healthy in the viewer

VALIS-software / valis-hpgv

Preprocessing Tool: Fatal error on some files #22