H5 file not found error message

[Yangzyangjin]

Dear CoCoNet developer,

I am really interested in your tool and installed the tool by following your documents. I tried to run it on your test dataset but it failed because of some errors. I don't really understand what the error message means. I wonder if you can help me with the issue.

Thanks!

Best wishes, Herina Yang

My code is: coconet run --fasta tests/sim_data/assembly.fasta --coverage tests/sim_data/*.bam --output output_test

Traceback (most recent call last): File "/root/miniconda3/envs/vamb/bin/coconet", line 8, in sys.exit(main()) File "/root/miniconda3/envs/vamb/lib/python3.7/site-packages/coconet/coconet.py", line 62, in main learn(cfg) File "/root/miniconda3/envs/vamb/lib/python3.7/site-packages/coconet/coconet.py", line 197, in learn model = load_model(cfg) File "/root/miniconda3/envs/vamb/lib/python3.7/site-packages/coconet/dl.py", line 67, in load_model input_shapes = config.get_input_shapes() File "/root/miniconda3/envs/vamb/lib/python3.7/site-packages/coconet/core/config.py", line 200, in get_input_shapes with h5py.File(self.io['h5'], 'r') as handle: File "/root/miniconda3/envs/vamb/lib/python3.7/site-packages/h5py/_hl/files.py", line 507, in init fid = make_fid(name, mode, userblock_size, fapl, fcpl, swmr=swmr) File "/root/miniconda3/envs/vamb/lib/python3.7/site-packages/h5py/_hl/files.py", line 220, 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 106, in h5py.h5f.open FileNotFoundError: [Errno 2] Unable to open file (unable to open file: name = '/workspace/coconet/CoCoNet/output_test/coverage.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

[Puumanamana]

Hello Yangzyangjin,

What version of coconet did you install? The --coverage argument was used in a previous version, and now it's --bam

Since coconet might not throw an error if you have an incorrect argument name, maybe you can also try your same comment by fixing the flag.

[Puumanamana]

Hi Yuxuan,

Which command did you use?

Cedric

On Jan 3, 2022, at 11:41 AM, Yuxuan Du @.***> wrote:

Hello,

I use the coconut v1.1.0 and meet the same problem that the H5 file can not be found. I downloaded the software through pip.

Best

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[dyxstat]

Thanks for your reply. I find that my problem has been solved in the previous issue.

Best, Yuxuan