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arq5x / gemini

a lightweight db framework for exploring genetic variation.
http://gemini.readthedocs.org
MIT License
317 stars 119 forks source link

Error installing #950

Open Phillip-a-richmond opened 3 years ago

Phillip-a-richmond commented 3 years ago

Hello,

I keep running into this error while trying to run GEMINI, and I'm wondering if anyone has come across this before:

Error.  nthreads cannot be larger than environment variable "NUMEXPR_MAX_THREADS" (64)Traceback (most recent call last):
  File "/usr/local/bin/gemini", line 7, in <module>
    gemini_main.main()
  File "/usr/local/lib/python2.7/site-packages/gemini/gemini_main.py", line 1249, in main
    args.func(parser, args)
  File "/usr/local/lib/python2.7/site-packages/gemini/gemini_main.py", line 935, in de_novo_fn
    DeNovo(args).run()
  File "/usr/local/lib/python2.7/site-packages/gemini/gim.py", line 307, in run
    for i, s in enumerate(self.report_candidates()):
  File "/usr/local/lib/python2.7/site-packages/gemini/gim.py", line 213, in report_candidates
    for gene, li in self.candidates():
  File "/usr/local/lib/python2.7/site-packages/gemini/gim.py", line 357, in candidates
    for g, li in self.gen_candidates('gene' if kins is not None else None):
  File "/usr/local/lib/python2.7/site-packages/gemini/gim.py", line 120, in gen_candidates
    for grp_key, grp in it.groupby(self.gq, group_key):
  File "/usr/local/lib/python2.7/site-packages/gemini/GeminiQuery.py", line 782, in next
    if row[col] is not None:
  File "/usr/local/lib/python2.7/site-packages/gemini/GeminiQuery.py", line 449, in __getitem__
    self.cache[key] = self.unpack(self.row[key])
  File "/usr/local/lib/python2.7/site-packages/gemini/compression.py", line 99, in snappy_unpack_blob
    arr.setflags(write=True)
ValueError: cannot set WRITEABLE flag to True of this array

The database is created with vcf2db.py, and is compatible with a gemini which is installed on a separate system. It is unclear why the install for gemini is not working on my newer system. I continually get this error after trying the docker image for v30.2:

module load singularity
singularity pull docker://quay.io/biocontainers/gemini:0.30.2--py27h6395249_3

DATA_DIR=/mnt/scratch/Public/TESTING/GenomicsPipelineTest/Case4/

singularity run \
        -B $DATA_DIR:"/data/" \
        gemini_0.30.2--py27h6395249_3.sif \
        gemini de_novo "/data/Case4_Gemini.db"

Or trying with a fresh install using the gemini_install script:

wget https://github.com/arq5x/gemini/raw/master/gemini/scripts/gemini_install.py
python gemini_install.py $PWD/gemini_tools $PWD/gemini_data/

I think the issue comes up with the versions>0.20.0 for me, because when I tried dropping to 0.20.0 (the last version I had working with the VCF2DB-created database), the docker image ended up working:

module load singularity
singularity pull docker://quay.io/biocontainers/gemini:0.20.0--py27_0

DATA_DIR=/mnt/scratch/Public/TESTING/GenomicsPipelineTest/Case4/

singularity run \
        -B /usr/lib/locale/:/usr/lib/locale/ \
        -B $DATA_DIR:"/data/" \
        gemini_0.20.0--py27_0.sif \
        gemini de_novo "/data/Case4_Gemini.db"

Which ends up producing the de novo results I'm looking for.

Any ideas how to overcome this? I can share the db I'm working with but it's ~371Mb.

Thanks, Phil