New stack trace that exits instead of the main thread getting stuck:
Warning: 'rfunc' cannot be imported. R with the 'qvalue' library and the 'rpy2' Python package are needed to compute q-values.
[Jun 18 11:54:09] Running TensorQTL v1.0.9: cis-QTL mapping
* WARNING: using CPU!
* using seed 777
* reading phenotypes (single_uniform_expression.phenotype.bed)
* cis-window detected as position ± 1,000,000
* loading genotypes
cis-QTL mapping: nominal associations for all variant-phenotype pairs
* 3 samples
* 1 phenotypes
* 1 variants
* cis-window: ±1,000,000
** dropping 1 constant phenotypes
* Computing associations
Mapping chromosome chr1
Traceback (most recent call last):
File "/Users/kshakir/miniconda3/envs/tensorqtl/lib/python3.9/runpy.py", line 197, in _run_module_as_main
return _run_code(code, main_globals, None,
File "/Users/kshakir/miniconda3/envs/tensorqtl/lib/python3.9/runpy.py", line 87, in _run_code
exec(code, run_globals)
File "/Users/kshakir/src/tensorqtl/tensorqtl/__main__.py", line 2, in <module>
tensorqtl.main()
File "/Users/kshakir/src/tensorqtl/tensorqtl/tensorqtl.py", line 180, in main
cis.map_nominal(genotype_df, variant_df, phenotype_df, phenotype_pos_df, args.prefix, covariates_df=covariates_df,
File "/Users/kshakir/src/tensorqtl/tensorqtl/cis.py", line 256, in map_nominal
for k, (phenotype, genotypes, genotype_range, phenotype_id) in enumerate(igc.generate_data(chrom=chrom, verbose=verbose), k+1):
File "/Users/kshakir/src/tensorqtl/tensorqtl/genotypeio.py", line 68, in __next__
return self.next()
File "/Users/kshakir/src/tensorqtl/tensorqtl/genotypeio.py", line 64, in next
raise next_item
File "/Users/kshakir/src/tensorqtl/tensorqtl/genotypeio.py", line 51, in run
for item in self.generator:
File "/Users/kshakir/src/tensorqtl/tensorqtl/genotypeio.py", line 496, in generate_data
chr_offset = offset_dict[chrom]
KeyError: 'chr1'
Process finished with exit code 1
Resolves #139.
New stack trace that exits instead of the main thread getting stuck: