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KeyboardInterrupt Traceback (most recent call last)
<ipython-input-15-0a5f194e9019> in <module>()
1 #select the 2nd kernel and run GWAS
2 results_df = single_snp_all_plus_select(test_snps=test_snps,G=snp_reader,
----> 3 pheno=pheno,GB_goal=2,do_plot=True,runner=runner)
4
5 import fastlmm.util.util as flutil
/home/diogro/bin/anaconda3/envs/limmbo/lib/python2.7/site-packages/fastlmm/association/single_snp_all_plus_select.pyc in single_snp_all_plus_select(test_snps, pheno, G, covar, k_list, n_folds, seed, output_file_name, GB_goal, force_full_rank, force_low_rank, mixing, h2, do_plot, runner)
405 common_input_files = [test_snps, G, pheno, covar]
406
--> 407 chrom_index_to_best_sid = _best_snps_for_each_chrom(chrom_list, common_input_files, runner, G, n_folds, seed, pheno, covar, force_full_rank, force_low_rank, mixing, h2, k_list, GB_goal)
408
409 frame = _gwas_2k_via_loo_chrom(test_snps, chrom_list, common_input_files, runner, G, chrom_index_to_best_sid, pheno, covar, force_full_rank, force_low_rank, mixing, h2, output_file_name, GB_goal)
/home/diogro/bin/anaconda3/envs/limmbo/lib/python2.7/site-packages/fastlmm/association/single_snp_all_plus_select.pyc in _best_snps_for_each_chrom(chrom_list, input_files, runner, G, n_folds, seed, pheno, covar, force_full_rank, force_low_rank, mixing, h2, k_list, GB_goal)
341 input_files=input_files,
342 name="best snps for each chrom",
--> 343 runner=runner)
344 return chrom_index_to_best_sid
345
/home/diogro/bin/anaconda3/envs/limmbo/lib/python2.7/site-packages/fastlmm/util/mapreduce.pyc in map_reduce(input_seq, mapper, reducer, input_files, output_files, name, runner, nested)
178 runner = Local()
179
--> 180 result = runner.run(dist)
181 return result
182
/home/diogro/bin/anaconda3/envs/limmbo/lib/python2.7/site-packages/fastlmm/util/runner/LocalMultiProc.pyc in run(self, distributable)
62
63 for taskindex, proc in enumerate(proc_list):
---> 64 rc = proc.wait()
65 #for line in proc.stdout.readlines():
66 # sys.stdout.write(line)
/home/diogro/bin/anaconda3/envs/limmbo/lib/python2.7/subprocess.pyc in wait(self)
1075 while self.returncode is None:
1076 try:
-> 1077 pid, sts = _eintr_retry_call(os.waitpid, self.pid, 0)
1078 except OSError as e:
1079 if e.errno != errno.ECHILD:
/home/diogro/bin/anaconda3/envs/limmbo/lib/python2.7/subprocess.pyc in _eintr_retry_call(func, *args)
119 while True:
120 try:
--> 121 return func(*args)
122 except (OSError, IOError) as e:
123 if e.errno == errno.EINTR:
KeyboardInterrupt: