galaxyproject / usegalaxy-playbook

Ansible Playbook for usegalaxy.org

Geek Repo:Geek Repo

Github PK Tool:Github PK Tool

annovar reference data missing [was ANNOVAR Annotate VCF producing 0 lines]

ewaugh1 opened this issue · comments

ANNOVAR Annotate VCF produces 0 lines
ANNOVAR was being used to annotate a VCF file of exome data however, whenever ran produces 0 lines. I get this information after ANNOVAR has finished running:

0 lines
format tabular database hg19
NOTICE: Finished reading 41350 lines from VCF file
NOTICE: A total of 41195 locus in VCF file passed QC threshold, representing 37258 SNPs (26400 transitions and 10858 transversions) and 4033 indels/substitutions
NOTICE: Finished writting 37258 SNPs (264

I also get this error, which is found under the i icon:

Error: the required database file /galaxy-repl/localdata/annovar/hg19/hg19_refGene.txt does not exist.
cat: output.hg19_multianno.txt: No such file or directory
python: can't open file '/galaxy/main/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/table_annovar/08b003ee9db7/table_annovar/replace_NA.py': [Errno 2] No such file or directory

I experienced the issue first 12-01-2022 at 00:23am.

link to history of workflow:
https://usegalaxy.org/u/m2108729/h/assignment

Galaxy Version and/or server at which you observed the bug
Galaxy Version: {"version_major": "21.09", "version_minor": "1.dev0"}