Hi again, I have two questions using the similarity matrix in single_snp: 1) Which format do I have to provide if I use the npz format? My npz matrix throws the error below. 2) If I don't provide K0, how is the similarity matrix calculated and is it possible to store the matrix for other runs? Thanks a lot Stefanie Error: Traceback (most recent call last): File "C:/Users//PycharmProjects/BCC_Experiments/lmm/lmm01.py", line 27, in <module> results_df = single_snp(bed_fn, pheno_fn, K0=k) File "C:\Users\\AppData\Local\Continuum\anaconda3\envs\gwas_flow\lib\site-packages\fastlmm\association\single_snp.py", line 246, in single_snp runner = runner) File "C:\Users\\AppData\Local\Continuum\anaconda3\envs\gwas_flow\lib\site-packages\pysnptools\util\mapreduce1\mapreduce.py", line 202, in map_reduce result = runner.run(dist) File "C:\Users\\AppData\Local\Continuum\anaconda3\envs\gwas_flow\lib\site-packages\pysnptools\util\mapreduce1\runner\local.py", line 48, in run result = _run_all_in_memory(distributable) File "C:\Users\\AppData\Local\Continuum\anaconda3\envs\gwas_flow\lib\site-packages\pysnptools\util\mapreduce1\runner\__init__.py", line 30, in _run_all_in_memory return work.reduce(result_sequence) File "C:\Users\\AppData\Local\Continuum\anaconda3\envs\gwas_flow\lib\site-packages\pysnptools\util\mapreduce1\mapreduce.py", line 77, in reduce return self.reducer(output_seq) File "C:\Users\\AppData\Local\Continuum\anaconda3\envs\gwas_flow\lib\site-packages\fastlmm\association\single_snp.py", line 228, in reducer_closure frame = pd.concat(frame_sequence) File "C:\Users\\AppData\Local\Continuum\anaconda3\envs\gwas_flow\lib\site-packages\pandas\core\reshape\concat.py", line 295, in concat sort=sort, File "C:\Users\\AppData\Local\Continuum\anaconda3\envs\gwas_flow\lib\site-packages\pandas\core\reshape\concat.py", line 339, in __init__ objs = list(objs) File "C:\Users\\AppData\Local\Continuum\anaconda3\envs\gwas_flow\lib\site-packages\pysnptools\util\mapreduce1\runner\__init__.py", line 14, in work_sequence_to_result_sequence result = work() File "C:\Users\\AppData\Local\Continuum\anaconda3\envs\gwas_flow\lib\site-packages\pysnptools\util\mapreduce1\mapreduce.py", line 65, in <lambda> yield lambda i=i, input_arg=input_arg: self.dowork(i, input_arg) # the 'i=i',etc is need to get around a strangeness in Python File "C:\Users\\AppData\Local\Continuum\anaconda3\envs\gwas_flow\lib\site-packages\pysnptools\util\mapreduce1\mapreduce.py", line 92, in dowork result = _run_all_in_memory(work) File "C:\Users\\AppData\Local\Continuum\anaconda3\envs\gwas_flow\lib\site-packages\pysnptools\util\mapreduce1\runner\__init__.py", line 25, in _run_all_in_memory return work() File "C:\Users\\AppData\Local\Continuum\anaconda3\envs\gwas_flow\lib\site-packages\pysnptools\util\mapreduce1\mapreduce.py", line 91, in <lambda> work = lambda : self.mapper(input_arg) File "C:\Users\\AppData\Local\Continuum\anaconda3\envs\gwas_flow\lib\site-packages\fastlmm\association\single_snp.py", line 211, in nested_closure K0_chrom = _K_per_chrom(K0 or G0 or test_snps, chrom, test_snps.iid) File "C:\Users\\AppData\Local\Continuum\anaconda3\envs\gwas_flow\lib\site-packages\fastlmm\association\single_snp.py", line 301, in _K_per_chrom return SnpKernel(K_all.snpreader[:,K_all.pos[:,0] != chrom],K_all.standardizer) File "C:\Users\\AppData\Local\Continuum\anaconda3\envs\gwas_flow\lib\site-packages\pysnptools\kernelreader\snpkernel.py", line 150, in pos return self.snpreader.pos File "C:\Users\\AppData\Local\Continuum\anaconda3\envs\gwas_flow\lib\site-packages\pysnptools\snpreader\snpreader.py", line 404, in pos return self.col_property File "C:\Users\\AppData\Local\Continuum\anaconda3\envs\gwas_flow\lib\site-packages\pysnptools\pstreader\pstnpz.py", line 67, in col_property self._run_once() File "C:\Users\\AppData\Local\Continuum\anaconda3\envs\gwas_flow\lib\site-packages\pysnptools\pstreader\pstnpz.py", line 82, in _run_once self._row = data['row'] File "C:\Users\\AppData\Local\Continuum\anaconda3\envs\gwas_flow\lib\site-packages\numpy\lib\npyio.py", line 259, in __getitem__ raise KeyError("%s is not a file in the archive" % key) KeyError: 'row is not a file in the archive' Process finished with exit code 1