mesihk / prost Goto Github PK

Dear Mesih Kılınç,
I hope you are well. I am writing to seek your insights on an issue I encountered while using the PROST tool to identify homologous relationships between species.

To put it simply,when I use species A to make database and use species B for search, the results I get are different from when I use species A to build a database and use species A for search.
For example，humans were used to build the database and yeast was used for search，the results were 50,756 items.But when yest were used to build the database and humans was used for search，the results were 55858 items！The difference is nearly 10%！

I appreciate your expertise as the inventor of PROST and would be grateful for any clarification you can provide on this disparity.
I earnestly request an explanation for this disparity.

Could you please explain this problem from the perspective of the working principle of the software？It would be grateful for any clarification you can provide on this disparity.

Thank you for your time.

Sincerely,
Elena

hello, i use prost makedb, error is urlib.error,URLErroe Network is unreachable . I use ubuntu . I am in china . Then I try VPN in windows,also the same error. what is the reseason? If Network is the reseason, is there altenative to overcome it ? Thanks

Dear Mesih,

I get an memory allocation error, this is because on our GPU server multiple devices are running and it seems that the code always only uses the first GPU:

torch.cuda.OutOfMemoryError: CUDA out of memory. Tried to allocate 26.00 MiB (GPU 0; 10.75 GiB total capacity; 25.19 MiB already allocated; 11.62 MiB free; 42.00 MiB reserved in total by PyTorch) If reserved memory is >> allocated memory try setting max_split_size_mb to avoid fragmentation.  See documentation for Memory Management and PYTORCH_CUDA_ALLOC_CONF

Could you please provide a @click option to select the cuda devices for pytorch, e.g. cuda:1

Since on other devices the memory is not full and I would like to be able to select the device or even cuda:all

|   0  NVIDIA GeForce ...  On   | 00000000:1A:00.0 Off |                  N/A |
|  0%   22C    P8     1W / 250W |  10421MiB / 11264MiB |      0%      Default |
|                               |                      |                  N/A |
+-------------------------------+----------------------+----------------------+
|   1  NVIDIA GeForce ...  On   | 00000000:1B:00.0 Off |                  N/A |
|  0%   22C    P8    10W / 250W |    343MiB / 11264MiB |      0%      Default |
|                               |                      |                  N/A |

Thank you in anticipation

Best regards

Kristian

Dear Mesih,

I get an RuntimeError .when i run : prost makedb XX.fasta sp.prdb , It will generate an error message like this：
Traceback (most recent call last): File "/home/shiyi/miniconda3/envs/py3_10/bin/prost", line 417, in <module> cli() File "/home/shiyi/miniconda3/envs/py3_10/lib/python3.10/site-packages/click/core.py", line 764, in __call__ return self.main(*args, **kwargs) File "/home/shiyi/miniconda3/envs/py3_10/lib/python3.10/site-packages/click/core.py", line 717, in main rv = self.invoke(ctx) File "/home/shiyi/miniconda3/envs/py3_10/lib/python3.10/site-packages/click/core.py", line 1137, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/home/shiyi/miniconda3/envs/py3_10/lib/python3.10/site-packages/click/core.py", line 956, in invoke return ctx.invoke(self.callback, **ctx.params) File "/home/shiyi/miniconda3/envs/py3_10/lib/python3.10/site-packages/click/core.py", line 555, in invoke return callback(*args, **kwargs) File "/home/shiyi/miniconda3/envs/py3_10/bin/prost", line 270, in makedb from pyprost import quantSeq File "/home/shiyi/miniconda3/envs/py3_10/lib/python3.10/site-packages/pyprost/__init__.py", line 58, in <module> from .prosttools import quantSeq,prostDistance File "/home/shiyi/miniconda3/envs/py3_10/lib/python3.10/site-packages/pyprost/prosttools.py", line 1, in <module> from .esmts25_13 import embed File "/home/shiyi/miniconda3/envs/py3_10/lib/python3.10/site-packages/pyprost/esmts25_13.py", line 16, in <module> esm1b = torch.jit.load(prostdir+'/traced_esm1b_25_13.pt').eval() File "/home/shiyi/miniconda3/envs/py3_10/lib/python3.10/site-packages/torch/jit/_serialization.py", line 162, in load cpp_module = torch._C.import_ir_module(cu, str(f), map_location, _extra_files, _restore_shapes) # type: ignore[call-arg] RuntimeError: PytorchStreamReader failed reading zip archive: failed finding central directory

it seems to be a problem with the click package ， I tried all distributions of click package，but it does not work.
What is the click package version that is compatible with PROST v0.2.15?

Or please take a look, maybe there are other problems?

Thank you so much！