OSError: Unable to open file

PMBio / pycoMeth

DNA methylation analysis downstream to Nanopolish for Oxford Nanopore DNA sequencing datasets

https://pmbio.github.io/pycoMeth/

GNU General Public License v3.0

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OSError: Unable to open file #8

Closed xiaohuli-45 closed 1 year ago

xiaohuli-45 commented 1 year ago

Hi, I'm running command "pycometh Meth_Seg" and encountering an error:

OSError: Unable to open file (unable to open file: name = '[/NAS/wg_hl/pancancer/OSCC/Methylation/f5c_meth/pycoMeth/MetH5/OSCC1/OSCC1_methylate.m5,', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0).

But my file is existing. I don't know how to solve this issue, can you help me?

xiaohuli-45 commented 1 year ago

Another issue: File "/home/wg_hl/miniconda3/envs/Methylation/lib/python3.8/site-packages/pycoMeth/meth_seg/math.py", line 86, in compute_differential_methylation good_sites = ((~np.isnan(a_nan)).sum(axis=0) > 0) & ( TypeError: ufunc 'isnan' not supported for the input types, and the inputs could not be safely coerced to any supported types according to the casting rule ''safe''

How should I do it?

PanZiwei commented 9 months ago

Hi @xiaohuli-45 I encountered the same issue for the TypeErrorufunc 'isnan', do you solve the issue later? Any hints to solve it? Thanks!