Gemini not found error while loading chunks from VCF

[frankMusacchia]

Hello,
I am trying to use gemini. After installing all needed dependencies I had a successful installation.
I am using a large VCF WGS file (~12GB) with ~1000 of samples
The first time I used the "load" function, gemini complained that yaml.load was deprecated and I got an error:

/home/francesco/bin/gemini_data/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)

CADD scores are not being loaded because the annotation file could not be found.
Run gemini update --dataonly --extra cadd_score to install the annotation file.

GERP per bp is not being loaded because the annotation file could not be found.
Run gemini update --dataonly --extra gerp_bp to install the annotation file.

Loading 1714760 variants.
Breaking /media/francesco/I/gemini/ppmi.july2018.chr14.vqsr.norm.vcf.gz into 12 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
Loading chunk 4.
/bin/sh: 1: gemini: not found
Loading chunk 5.
/bin/sh: 1: gemini: not found
Loading chunk 6.
/bin/sh: 1: gemini: not found
Loading chunk 7.
/bin/sh: 1: gemini: not found
Loading chunk 8.
/bin/sh: 1: gemini: not found
Loading chunk 9.
/bin/sh: 1: gemini: not found
Loading chunk 10.
/bin/sh: 1: gemini: not found
Loading chunk 11.
/bin/sh: 1: gemini: not found
/bin/sh: 1: gemini: not found
Traceback (most recent call last):
File "/home/francesco/bin/gemini_tools/bin/gemini", line 7, in
gemini_main.main()
File "/home/francesco/bin/gemini_data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 1249, in main
args.func(parser, args)
File "/home/francesco/bin/gemini_data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 204, in load_fn
gemini_load.load(parser, args)
File "/home/francesco/bin/gemini_data/anaconda/lib/python2.7/site-packages/gemini/gemini_load.py", line 49, in load
load_multicore(args)
File "/home/francesco/bin/gemini_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/francesco/bin/gemini_data/anaconda/lib/python2.7/site-packages/gemini/gemini_load.py", line 264, in load_chunks_multicore
wait_until_finished(procs)
File "/home/francesco/bin/gemini_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

I went to:
https://github.com/yaml/pyyaml/wiki/PyYAML-yaml.load(input)-Deprecation
and I chose to modify the code to safe_yaml

But I still get the same error.
Can you please tell me if there is a known solution to this?
Thanks
Francesco

[brentp]

Hi, how are you installing gemini?
What is the path of the code you modified?

You could try to install an older version of pyyaml.

[frankMusacchia]

Hi,
I have executed the instructions at:
https://gemini.readthedocs.io/en/latest/

and installed for example grabix, vt and snpeff that were required

[brentp]

well, the most critical error is that it's not finding gemini when you run the load.
what does: env | grep -i python show?

Also, let's get your gemini install working, but you might consider using slivar (https://github.com/brentp/slivar), especially for a cohort this size.

[frankMusacchia]

Yes, the cohort is large and I was thinking if gemini would work on that. I will try slivar then.. thank you