Error when training model from scratch

[oshiomah1]

Hello I'm following the gnomic demo tutorial. I'm running the line below adapted from the tutorial. I am using a Conda environment through a Mac terminal

python3 /share/hennlab/progs/gnomix/gnomix.py /share/genomes/1000genomes/phase3/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz /share/hennlab/progs/gnomix/demo/data/allchrs.b37.gmap /share/hennlab/progs/gnomix/demo/data/output 22 False /share/hennlab/progs/gnomix/demo/data/reference_1000g.vcf /share/hennlab/progs/gnomix/demo/data/1000g.smap > /share/hennlab/progs/gnomix/demo/training_log.txt`

I keep getting this error:
FileNotFoundError: [Errno 2] No such file or directory: 'False'

Is gnomix interpreting False as a file? How can I troubleshoot this error?
I'm using python 3.7.4 and I downloaded all required packages from the requirements.txt file

This is the python script that I used to create the gnomic call above:

`import numpy as np
import os
import pandas as pd

data_path = "/share/hennlab/progs/gnomix/demo/data"
query_file = "/share/genomes/1000genomes/phase3/" + "ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz"
reference_file = "/share/hennlab/progs/gnomix/demo/data/" + "reference_1000g.vcf"
sample_map_file = "/share/hennlab/progs/gnomix/demo/data/" + "1000g.smap"
genetic_map_file = "/share/hennlab/progs/gnomix/demo/data/" + "chr22.b37.gmap"
chm_nr = "22"
phase = "False"
output_basename = "/share/hennlabprogs/gnomix/demo/data/output"

train_cmd = " ".join(["python3 /share/hennlab/progs/gnomix/gnomix.py",
query_file, genetic_map_file, output_basename, chm, phase, reference_file, sample_map_file]) +
" > /share/hennlab/progs/gnomix/demo/training_log.txt"
print("Running in command line: \n\t", train_cmd)
os.system(train_cmd)

[fsharifi]

@oshiomah1 I was getting the same error, but went through the gnomix.py script, and it seems that genetic_map_file should be the 5th argument, not the second one as in demo.ipynb. So, when I used the following command it worked:

train_cmd = " ".join(["python3 /share/hennlab/progs/gnomix/gnomix.py",
query_file, output_basename, chm, phase, genetic_map_file, reference_file, sample_map_file]) + " > /share/hennlab/progs/gnomix/demo/training_log.txt"  

or

python3 gnomix.py ./demo/data/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz ./demo/output 22 False ./demo/data/allchrs.b37.gmap ./demo/data/reference_1000g.vcf ./demo/data/1000g.smap > ./demo/training_log.txt 

[oshiomah1]

@fsharifi thank you so much for your suggestion! I will try this out. My colleague took over the gnomix project while I traveled for data collection. Now that i'm back i'll attempt this again