ValueError: Processing failed on GEMINI chunk load

[Jenn Chin]

Hey all,

I'm running gemini 20.2 and ran into an issue while loading the database. This has worked successfully on other files (even the same set of samples), the only difference is this VCF was run on grc38 instead of grc37. 

This is the command:

gemini load -v $VCF_VT_VEP -t VEP --skip-pls --cores 4 /output/path/$GEMINI_DB 

It seems to be chugging along well and then throws the following error:

...

pid 40405: 1159646 variants processed.

pid 40403: 1159646 variants processed.

pid 40411: 1139999 variants processed.

pid 40411: 1149999 variants processed.

[W::vcf_parse] INFO 'Bas' is not defined in the header, assuming Type=String

/bin/sh: line 1: 40410 Done                    grabix grab /net/grc/vol6/mendelian_projects/janecke_uwcmg_cd_macrogen_1/ngs_analysis/janecke_uwcmg_cd_macrogen_1.

HF.final.vcf.gz.VT.vep.vcf.gz 3478939 4638587

     40411 Segmentation fault      (core dumped) | gemini load_chunk -v - -t VEP --skip-pls --skip-info-string --tempdir /tmp/40406554.1.hm.q -o 3478939 /tmp/404

06554.1.hm.q/janecke_uwcmg_cd_macrogen_1.HF.final.vcf.gz.VT.vep.vcf.chunk3.db

Traceback (most recent call last):

  File "/net/gs/vol3/software/modules-sw/gemini/0.20.2/Linux/RHEL6/x86_64/bin/gemini", line 4, in <module>

    __import__('pkg_resources').run_script('gemini==0.20.2.dev0', 'gemini')

  File "/net/gs/vol3/software/modules-sw/python/2.7.3/Linux/RHEL6/x86_64/lib/python2.7/site-packages/pkg_resources/__init__.py", line 739, in run_script

    self.require(requires)[0].run_script(script_name, ns)

  File "/net/gs/vol3/software/modules-sw/python/2.7.3/Linux/RHEL6/x86_64/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1494, in run_script

    exec(code, namespace, namespace)

  File "/net/gs/vol3/software/modules-sw/gemini/0.20.2/Linux/RHEL6/x86_64/lib/python2.7/site-packages/gemini-0.20.2.dev0-py2.7.egg/EGG-INFO/scripts/gemini", line

 7, in <module>

    gemini_main.main()

  File "/net/gs/vol3/software/modules-sw/gemini/0.20.2/Linux/RHEL6/x86_64/lib/python2.7/site-packages/gemini-0.20.2.dev0-py2.7.egg/gemini/gemini_main.py", line 1

249, in main

    args.func(parser, args)

  File "/net/gs/vol3/software/modules-sw/gemini/0.20.2/Linux/RHEL6/x86_64/lib/python2.7/site-packages/gemini-0.20.2.dev0-py2.7.egg/gemini/gemini_main.py", line 2

04, in load_fn

    gemini_load.load(parser, args)

  File "/net/gs/vol3/software/modules-sw/gemini/0.20.2/Linux/RHEL6/x86_64/lib/python2.7/site-packages/gemini-0.20.2.dev0-py2.7.egg/gemini/gemini_load.py", line 4

9, in load

    load_multicore(args)

  File "/net/gs/vol3/software/modules-sw/gemini/0.20.2/Linux/RHEL6/x86_64/lib/python2.7/site-packages/gemini-0.20.2.dev0-py2.7.egg/gemini/gemini_load.py", line 9

3, in load_multicore

    chunks = load_chunks_multicore(grabix_file, args)

  File "/net/gs/vol3/software/modules-sw/gemini/0.20.2/Linux/RHEL6/x86_64/lib/python2.7/site-packages/gemini-0.20.2.dev0-py2.7.egg/gemini/gemini_load.py", line 2

64, in load_chunks_multicore

    wait_until_finished(procs)

  File "/net/gs/vol3/software/modules-sw/gemini/0.20.2/Linux/RHEL6/x86_64/lib/python2.7/site-packages/gemini-0.20.2.dev0-py2.7.egg/gemini/gemini_load.py", line 3

59, in wait_until_finished

    raise ValueError("Processing failed on GEMINI chunk load")

ValueError: Processing failed on GEMINI chunk load

Any input is appreciated, thanks!
Jenn

[Brent Pedersen]

Hi Jenn,
I'm not sure why this error is occuring, but, the default gemini
loader is only compatible with GRCh37. You can use GRCh38 data
with the new loader here: https://github.com/quinlan-lab/vcf2db/
and described some here:
http://quinlanlab.org/blog/2016/05/02/gemini-2-progress.html

briefly, you'll annotate your VCF with other files of interest and
vcf2db will load them into a gemini-compatible database.
hope that helps,
-Brent