gemini dont work with several cores

[aurelBZH]

I have a problem of multicore loading with gemini 0.20.1, grabix 0.1.8 and python 2.7. With 4 cores the gemini load command don't work : ./tools/bin/gemini load --cores 4 -t VEP -v result.vcf.gz test_db.db

the error message :

Indexing /home/aurelien.beliard/varapp/result.vcf.gz with grabix. Loading 286164 variants. Breaking /home/aurelien.beliard/varapp/result.vcf.gz into 4 chunks. Loading chunk 0. Loading chunk 1. /bin/sh: 1: gemini: not found Loading chunk 2. /bin/sh: 1: gemini: not found Loading chunk 3. /bin/sh: 1: gemini: not found /bin/sh: 1: gemini: not found Traceback (most recent call last): File "./tools/bin/gemini", line 7, in <module> gemini_main.main() File "/home/aurelien.beliard/varapp/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 1248, in main args.func(parser, args) File "/home/aurelien.beliard/varapp/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 204, in load_fn gemini_load.load(parser, args) File "/home/aurelien.beliard/varapp/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load.py", line 49, in load load_multicore(args) File "/home/aurelien.beliard/varapp/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load.py", line 93, in load_multicore chunks = load_chunks_multicore(grabix_file, args) File "/home/aurelien.beliard/varapp/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load.py", line 264, in load_chunks_multicore wait_until_finished(procs) File "/home/aurelien.beliard/varapp/data/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 while with one core : ./tools/bin/gemini load --cores 1 -t VEP -v result.vcf.gz test_db.db

it work perfectly

[brentp]

Make sure that gemini is on your $PATH it looks like that is not the case since you are using /tools/bin/gemini

[aurelBZH]

oh ok i didn't add it to the the path. I don't understand why i can't use it without add it to the path but it work now.

thanks for your help