Lacking VEP cache file Homo_sapiens.GRCh38.dna.toplevel.fa.gz

[wwoskie]

VEP cache has been (successfuly?) pulled during installation process and spawned a bunch of files. However, on the next start pipeline throws: ERROR: Resource file does not exist: /media/alex/_data_ext/nextNEOpi/resources/databases/vep_cache/homo_sapiens/110_GRCh38/Homo_sapiens.GRCh38.dna.toplevel.fa.gz Please check the references resource file settings in conf/resources.config

vep_cache/Plugins/ and vep_cache/homo_sapiens/110_GRCh38 seem to be populated too

Thanks!

[riederd]

The file in question should exist:

$ ls -l 110_GRCh38/*.gz
-rw-r--r-- 1 rieder bioinf 950947839 Jul 21 15:56 110_GRCh38/Homo_sapiens.GRCh38.dna.toplevel.fa.gz

can you check if it is there?

ls -l /media/alex/_data_ext/nextNEOpi/resources/databases/vep_cache/homo_sapiens/110_GRCh38/Homo_sapiens.GRCh38.dna.toplevel.fa.gz

if it is, can you check if there is the installation check file?

ls -la /media/alex/_data_ext/nextNEOpi/resources/databases/vep_cache/.homo_sapiens_GRCh38_110_cache_ok.chck

[wwoskie]

Actually, I've just downloaded it manually from http://ftp.ensembl.org/pub/current_fasta/homo_sapiens/dna/ However, check file exists and was created way earlier (Sep 3rd)

`╰─➤ ls -la /media/alex/_data_ext/nextNEOpi/resources/databases/vep_cache/.homo_sapiens_GRCh38_110_cache_ok.chck

-rw-rw-r-- 1 alex alex 3 Sep 19 23:56 /media/alex/_data_ext/nextNEOpi/resources/databases/vep_cache/.homo_sapiens_GRCh38_110_cache_ok.chck`

[riederd]

Can you check your .nextflow.log* file(s) and find the workdir for the process called installVEPcache and post the vep_errors.txt file therein?

[wwoskie]

WARNING: No download found for homo_sapiens

[riederd]

Do you have any VEP_* variable in your environment set? If yes, try to unset VEP_[your_vars] and then enter the workdir for the installVEPcache and run the process manually again using bash .command.run

[wwoskie]

Manual download actually helped, thx!