search

haotianteng / Chiron

A basecaller for Oxford Nanopore Technologies' sequencers
Other
122 stars 53 forks source link

TensorFlow Version #52

Closed qianlou closed 6 years ago

qianlou commented 6 years ago

Hi, Haotianteng.

Can you tell me the version of tensorflow you used to run Chiron? Or is it no matter about the versions of tensorflow? Based on my previous experience, the version of tensorflow is very important because different versions of tensorflow have different APIs. If the version of my tensorflow does not match yours, maybe I can't install your Chiron program.

qianlou commented 6 years ago

Sorry. I have found that you have answered this question. Thanks.

qianlou commented 6 years ago

Does this program support Python 3.6?

haotianteng commented 6 years ago

Hi I test with tf 1.3 1.4 1.6 and they all work. So I think tf>1.30 will do the job, older version will not work as they change the definition of model protobuf since tf1.3.

Thanks Teng

On Wed, May 16, 2018, 8:57 AM qianlou notifications@github.com wrote:

Hi, Haotianteng.

Can you tell me the version of tensorflow you used to run Chiron? Or is it no matter about the versions of tensorflow? Based on my previous experience, the version of tensorflow is very important because different versions of tensorflow have different APIs. If the version of my tensorflow does not match yours, maybe I can't install your Chiron program.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/haotianteng/Chiron/issues/52, or mute the thread https://github.com/notifications/unsubscribe-auth/AKo3X4XxEvk91kcGpjamMBwx1L7x0kayks5ty11IgaJpZM4UAZZg .

haotianteng commented 6 years ago

Yes, the current version is py2/3 compatible.

On Wed, May 16, 2018, 9:04 AM qianlou notifications@github.com wrote:

Does this program support Python 3.6?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/haotianteng/Chiron/issues/52#issuecomment-389341674, or mute the thread https://github.com/notifications/unsubscribe-auth/AKo3X4H2w6FfAWiVQCt7ui7fZ0VHayCjks5ty179gaJpZM4UAZZg .

qianlou commented 6 years ago

Hi teng,

Thanks for your reply. I just tested the example data under the CPU version. But I met NotFound errors. I found others met this error previously. Do I must use Version 0.3? Thanks. Qian

On May 15, 2018, at 8:59 PM, Haotian Teng notifications@github.com wrote:

Hi I test with tf 1.3 1.4 1.6 and they all work. So I think tf>1.30 will do the job, older version will not work as they change the definition of model protobuf since tf1.3.

Thanks Teng

On Wed, May 16, 2018, 8:57 AM qianlou notifications@github.com wrote:

Hi, Haotianteng.

Can you tell me the version of tensorflow you used to run Chiron? Or is it no matter about the versions of tensorflow? Based on my previous experience, the version of tensorflow is very important because different versions of tensorflow have different APIs. If the version of my tensorflow does not match yours, maybe I can't install your Chiron program.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/haotianteng/Chiron/issues/52, or mute the thread https://github.com/notifications/unsubscribe-auth/AKo3X4XxEvk91kcGpjamMBwx1L7x0kayks5ty11IgaJpZM4UAZZg .

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

haotianteng commented 6 years ago

Please give me the command you used and the detail of the error.

On Wed, May 16, 2018, 1:50 PM qianlou notifications@github.com wrote:

Hi teng,

Thanks for your reply. I just tested the example data under the CPU version. But I met NotFound errors. I found others met this error previously. Do I must use Version 0.3? Thanks. Qian

On May 15, 2018, at 8:59 PM, Haotian Teng notifications@github.com wrote:

Hi I test with tf 1.3 1.4 1.6 and they all work. So I think tf>1.30 will do the job, older version will not work as they change the definition of model protobuf since tf1.3.

Thanks Teng

On Wed, May 16, 2018, 8:57 AM qianlou notifications@github.com wrote:

Hi, Haotianteng.

Can you tell me the version of tensorflow you used to run Chiron? Or is it no matter about the versions of tensorflow? Based on my previous experience, the version of tensorflow is very important because different versions of tensorflow have different APIs. If the version of my tensorflow does not match yours, maybe I can't install your Chiron program.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/haotianteng/Chiron/issues/52, or mute the thread < https://github.com/notifications/unsubscribe-auth/AKo3X4XxEvk91kcGpjamMBwx1L7x0kayks5ty11IgaJpZM4UAZZg

.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/haotianteng/Chiron/issues/52#issuecomment-389386059, or mute the thread https://github.com/notifications/unsubscribe-auth/AKo3X3fzP5Vqe4_iaih9oTt4WVktKrNuks5ty6IJgaJpZM4UAZZg .

qianlou commented 6 years ago

Hi Teng, I used a command like this : python chiron/entry.py call -i chiron/example_data/ -o ./ >> test.txt Then I got the following outputs attached on the test.txt test.txt

haotianteng commented 6 years ago

Hi Qianlou, Yes, I can reproduce the problem, it's because the missing of the configuration file, I will fix it hopefully today.

Thanks Teng

On Wed, May 16, 2018, 2:06 PM qianlou notifications@github.com wrote:

Hi Teng, I used a command like this : python chiron/entry.py call -i chiron/example_data/ -o ./ >> test.txt Then I got the following outputs attached on the test.txt test.txt https://github.com/haotianteng/Chiron/files/2007480/test.txt

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/haotianteng/Chiron/issues/52#issuecomment-389387960, or mute the thread https://github.com/notifications/unsubscribe-auth/AKo3Xzl6blfIKppaWYZ0IbAvsDmacaeqks5ty6WtgaJpZM4UAZZg .

haotianteng commented 6 years ago

I have uploaded the configuration file, can you update and try again?

On Wed, May 16, 2018, 3:17 PM 昊天滕 havens.teng@gmail.com wrote:

Hi Qianlou, Yes, I can reproduce the problem, it's because the missing of the configuration file, I will fix it hopefully today.

Thanks Teng

On Wed, May 16, 2018, 2:06 PM qianlou notifications@github.com wrote:

Hi Teng, I used a command like this : python chiron/entry.py call -i chiron/example_data/ -o ./ >> test.txt Then I got the following outputs attached on the test.txt test.txt https://github.com/haotianteng/Chiron/files/2007480/test.txt

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/haotianteng/Chiron/issues/52#issuecomment-389387960, or mute the thread https://github.com/notifications/unsubscribe-auth/AKo3Xzl6blfIKppaWYZ0IbAvsDmacaeqks5ty6WtgaJpZM4UAZZg .

qianlou commented 6 years ago

Thanks again, Teng. Now I run "python chiron/entry.py call .." this command successfully. I will try to run Chiron on my GPU and train a new model. During the future process, maybe I also need to discuss with you. So please let me say thank you in advance.

Best regards, Qian