ValueError: Processing failed on GEMINI chunk load

[tanayb001]

I want to use gemini to annotate my variants generated from GATK pipeline using hg38 genome. Below is the gemini version I'm using: iit@iit:~$ /home/iit/bin/gemini -v gemini 0.30.2

Installation:

Gemini data files updated Finished: gemini, tools and data installed Tools installed in: ~/Toolkit/gemini NOTE: be sure to add ~/Toolkit/gemini/bin to your PATH. Data installed in: ~/Toolkit/gemini NOTE: Install data files for GERP_bp & CADD_scores (not installed by default).

Here is my full command that I used and get the following error:

$ /home/iit/bin/gemini load -v /home/iit/Documents/geminifile/sample.somatic.filtered.PASS.vep.vcf --cores 4 --skip-gerp-bp --skip-cadd -t VEP /home/iit/Documents/geminifile/sample.somatic.filtered.PASS.vep.vcf.db /media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/gemini/anaconda/lib/python2.7/site-packages/gemini/config.py:61: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details. config = yaml.load(in_handle) Bgzipping /home/iit/Documents/geminifile/sample.somatic.filtered.PASS.vep.vcf into /home/iit/Documents/geminifile/sample.somatic.filtered.PASS.vep.vcf.gz. Indexing /home/iit/Documents/geminifile/sample.somatic.filtered.PASS.vep.vcf.gz with grabix. Loading 103 variants. Breaking /home/iit/Documents/geminifile/sample.somatic.filtered.PASS.vep.vcf.gz into 4 chunks. Loading chunk 0. Loading chunk 1. /bin/sh: 1: gemini: Permission denied Loading chunk 2. /bin/sh: 1: gemini: Permission denied Loading chunk 3. /bin/sh: 1: gemini: Permission denied /bin/sh: 1: gemini: Permission denied Traceback (most recent call last): File "/home/iit/bin/gemini", line 7, in gemini_main.main() File "/media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/gemini/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 1249, in main args.func(parser, args) File "/media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/gemini/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 204, in load_fn gemini_load.load(parser, args) File "/media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/gemini/anaconda/lib/python2.7/site-packages/gemini/gemini_load.py", line 49, in load load_multicore(args) File "/media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/gemini/anaconda/lib/python2.7/site-packages/gemini/gemini_load.py", line 93, in load_multicore chunks = load_chunks_multicore(grabix_file, args) File "/media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/gemini/anaconda/lib/python2.7/site-packages/gemini/gemini_load.py", line 264, in load_chunks_multicore wait_until_finished(procs) File "/media/iit/f2bf4ae5-e0cd-4f34-9453-b6a8e1a665e21/Toolkit/gemini/anaconda/lib/python2.7/site-packages/gemini/gemini_load.py", line 359, in wait_until_finished raise ValueError("Processing failed on GEMINI chunk load") ValueError: Processing failed on GEMINI chunk load

$

Please let me know how to solve it.

Thanks.

[brentp]

Hi, it looks like your gemini is not executable:

/bin/sh: 1: gemini: Permission denied

you can do chmod +x /path/to/gemini to make it so. You should be able to run gemini without any arguments.

Also, unless you have a specific reason to use gemini, consider trying slivar

[tanayb001]

chmod +x /path/to/gemini is not working. Checked sliver but not understanding it. It gives:

Finished. evaluated 70 total variants and wrote 67 variants that passed your slivar expressions

But it looks like it just applied some filters . GEMINI brings in information from a variety of sources including: OMIM, ClinVar, GERP, PolyPhen 2, SIFT, ESP, 1000 Genomes, ExAC, ENCODE, CADD and more! which are not there in slivar. Is it correct ?

[brentp]

Hi, your gemini must be executable for gemini_load to work. If you run and show the full command and full output it will be easier to hep you.