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zheminzhou / PEPPAN

Phylogeny Enhanded Prediction of PAN-genome
https://doi.org/10.1101/2020.01.03.894154
GNU General Public License v3.0
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ValueError: setting an array element with a sequence #1

Closed marade closed 4 years ago

marade commented 4 years ago

After running for a few hours without issues I get this:

Traceback (most recent call last): File "/home/ubuntu/PEPPA/PEPPA.py", line 1809, in ortho(sys.argv[1:]) File "/home/ubuntu/PEPPA/PEPPA.py", line 1804, in ortho write_output(params['prefix'], params['prediction'], genomes, genes, encodes, old_predictions, params['pseudogene'], params['untrusted'], params['gtable'], params.get('clust', None), params.get('self_bsn', None)) File "/home/ubuntu/PEPPA/PEPPA.py", line 1317, in write_output prediction = pd.DataFrame(np.vstack([prediction, np.array(list(old_to_add))])).sort_values(by=[5,9]).values ValueError: setting an array element with a sequence

Any ideas?

zheminzhou commented 4 years ago

I have updated the code to solve this error. Please pull down the latest code and have a try. Many thanks for the report.