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nanoporetech
A question about the text-ouput
Hi！Dear developer, Thanks for your work and share. Recently I met a question after detect modification. I got the stat file and wanna to generate the output file.But when I type：
tombo text_output browser_files --fast5-basedirs ../single_merge/ --statistics-filename tombo.RNA.5mC.model.5mC.tombo.stats --file-types coverage dampened_fraction --browser-file-basename soybean_out [13:13:57] Parsing Tombo index file(s). [13:14:13] Getting and writing coverage bedgraphs. [13:14:13] Calculating read coverage regions. [13:14:13] Calculating read coverage. [13:14:22] Loading statistics from file. Traceback (most recent call last): File "/home/ubuntu/xf/cxf/keiwen/soybean0116/tombo/tombo/tombo/tombo_stats.py", line 2680, in init self._parse_stats() File "/home/ubuntu/xf/cxf/keiwen/soybean0116/tombo/tombo/tombo/tombo_stats.py", line 2566, in _parse_stats self._fp = h5py.File(self.stats_fn, 'r') File "/home/ubuntu/.local/lib/python3.6/site-packages/h5py/_hl/files.py", line 408, in init swmr=swmr) File "/home/ubuntu/.local/lib/python3.6/site-packages/h5py/_hl/files.py", line 173, in make_fid fid = h5f.open(name, flags, fapl=fapl) File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper File "h5py/h5f.pyx", line 88, in h5py.h5f.open OSError: Unable to open file (addr overflow, addr = 6144, size = 88, eoa = 2048)
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/home/ubuntu/xf/cxf/keiwen/soybean0116/tombo/tombo/tombo/tombo_stats.py", line 3233, in TomboStats stats = ModelStats(stat_fn) File "/home/ubuntu/xf/cxf/keiwen/soybean0116/tombo/tombo/tombo/tombo_stats.py", line 2685, in init 'was created before Tombo v1.3.1') tombo.tombo_helper.TomboError: Invalid statistics file provided. Try running tombo/scripts/convert_stats.py if this stats file was created before Tombo v1.3.1
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/ubuntu/.local/bin/tombo", line 33, in
I use different environment to anlaysis, and below tombo was installed by pip
When I use tombo installed by conda I got the similar result
tombo text_output browser_files --fast5-basedirs ../single_merge/ --statistics-filename tombo.RNA.5mC.model.5mC.tombo.stats --file-types coverage dampened_fraction --browser-file-basename soybean0116_5mC [13:30:53] Parsing Tombo index file(s). [13:31:09] Getting and writing coverage bedgraphs. [13:31:09] Calculating read coverage regions. [13:31:09] Calculating read coverage. [13:31:18] Loading statistics from file. Traceback (most recent call last): File "/home/ubuntu/anaconda3/envs/cxf/lib/python3.7/site-packages/tombo/tombo_stats.py", line 2680, in init self._parse_stats() File "/home/ubuntu/anaconda3/envs/cxf/lib/python3.7/site-packages/tombo/tombo_stats.py", line 2566, in _parse_stats self._fp = h5py.File(self.stats_fn, 'r') File "/home/ubuntu/anaconda3/envs/cxf/lib/python3.7/site-packages/h5py/_hl/files.py", line 445, in init swmr=swmr) File "/home/ubuntu/anaconda3/envs/cxf/lib/python3.7/site-packages/h5py/_hl/files.py", line 195, in make_fid fid = h5f.open(name, flags, fapl=fapl) File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper File "h5py/h5f.pyx", line 96, in h5py.h5f.open OSError: Unable to open file (addr overflow, addr = 6144, size = 88, eoa = 2048)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/ubuntu/anaconda3/envs/cxf/bin/tombo", line 11, in
I try the previous document had been anlaysised by tombo well（the same pipline with the same version） with the same command.But its stats file works well and no error. I am so confused and hope for help, thanks
I have noticed something after several test. I ran the same command on my early research. When i ran modification and output, it worked well. So it seemed that the .stat file has problem. And when i test the questioned file, it showed that after the modification`s process reached 100%, i can not type any command ,seem as the command did not finish yet. The test file is far smaller than the problem one.so i do not sure if the problem is too large so it will take more time to generate stat file ,but i stop it so it is broken or it just a bug？
