ekirving
commented
8 months ago Hi Kritika,
Your error message indicates that the genotype file is malformed.
How did you create this file? Your messages says you "edited the SNP file" which should not be necessary.
The input files should be generated using the convertf software from the EIGENSTRAT package https://github.com/DReichLab/EIG/blob/master/CONVERTF/README
Best wishes, Evan
Hi Ervin I am running qpbrute with a new dataset. I installed qpbrute using conda. I am getting the following error
INFO: There are 5,040 possible starting orders for the given nodes. INFO: Performing an exhaustive search. INFO: Starting list ['A_magna', 'A_graeca', 'A_chukar', 'A_barbara', 'A_rufa', 'A_philbyi', 'A_melanocephala'] Traceback (most recent call last): File "/home/kritika/anaconda3/envs/qpbrute/lib/python3.8/site-packages/qpbrute/qpbrute.py", line 318, in run_qpgraph with open(log_file, "r") as fin: FileNotFoundError: [Errno 2] No such file or directory: 'alectoris_subset_1/graphs/alectoris_subset_1-96916fd2f7c6.log'
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/home/kritika/anaconda3/envs/qpbrute/bin/qpBrute", line 8, in
sys.exit(qpbrute())
File "/home/kritika/anaconda3/envs/qpbrute/lib/python3.8/site-packages/qpbrute/qpbrute.py", line 905, in qpbrute
permute_qpgraph(
File "/home/kritika/anaconda3/envs/qpbrute/lib/python3.8/site-packages/qpbrute/qpbrute.py", line 814, in permute_qpgraph
pq.find_graph()
File "/home/kritika/anaconda3/envs/qpbrute/lib/python3.8/site-packages/qpbrute/qpbrute.py", line 718, in find_graph
self.recurse_tree(root_tree, self.nodes[1], self.nodes[2:])
File "/home/kritika/anaconda3/envs/qpbrute/lib/python3.8/site-packages/qpbrute/qpbrute.py", line 120, in recurse_tree
results = self.test_trees(new_trees, depth)
File "/home/kritika/anaconda3/envs/qpbrute/lib/python3.8/site-packages/qpbrute/qpbrute.py", line 213, in test_trees
result = self.run_qpgraph((new_tree, depth))
File "/home/kritika/anaconda3/envs/qpbrute/lib/python3.8/site-packages/qpbrute/qpbrute.py", line 335, in run_qpgraph
log = run_cmd(
File "/home/kritika/anaconda3/envs/qpbrute/lib/python3.8/site-packages/qpbrute/utils.py", line 67, in run_cmd
raise RuntimeError(f"ERROR: '{err}'; RETCODE:{proc.returncode}\n" + " ".join(cmd))
RuntimeError: ERROR: 'b'fatalx:\n(genotypes) bad ID (SNP): SNP:# 1 0.0 16185 G A\n\n''; RETCODE:-6
qpGraph -p alectoris.par -g alectoris_subset_1/graphs/alectoris_subset_1-96916fd2f7c6.graph -d alectoris_subset_1/graphs/alectoris_subset_1-96916fd2f7c6.dot
The log files are not being generated. I have edited the SNP file as per the example input file and the test example file runs correctly on the system.
Please suggest a possible solution for this error. If you need any of the input files, I can email them to you.
Thank you Best regards Kritika