Basset

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Used in non human species

1

I am wondering if the software can be used in nonhuman species? If not, can we train a model for other species? Many thanks!

guandailu

bedtools getfasta skipping problem

1

Hi, I am trying to implement the model following the tutorials. When I try top convert the bed file to FASTA format using getfasta, I get the error "Feature xxx...

mharoun20

preprocess_features.py file is generating empty output bed files

2

Hi All, Thanks for the tool. I am a beginner in deep learning. I was trying to reproduce the tutorials with the provided datasets. I have started with this https://github.com/davek44/Basset/blob/master/tutorials/prepare_compendium.ipynb...

ranijames

ENUM error when running basset_train.lua

7

Hi Dave, When I run basset_train.lua -job pretrained_params.txt -stagnant_t 10 er.h5, I end up getting an ENUM(50331977) error. I have tried diagnosing it, but haven't had any luck. Below are...

doczmp

how to install 'convnet' module

1

/root/torch/install/bin/luajit: /root/torch/install/share/lua/5.1/trepl/init.lua:383: module 'convnet' not found:No LuaRocks module found for convnet

song984888

install_data.py requires more than 30 GiB of memory

2

It seems like install_data.py -- in particular https://github.com/davek44/Basset/blob/6ae86b88a8df8607c58590ee84a3702662ac33dc/install_data.py#L113 and https://github.com/davek44/Basset/blob/master/src/seq_hdf5.py#L73 -- requires a lot of memory. It deterministically runs OOM on a GCE instance with 30 GiB of memory. After...

ptn24

The Docker image lzamparo/basset is great, but it is missing a few things Re Lua, it needs to have ```bash export LUA_PATH="$BASSETDIR/src/?.lua;$LUA_PATH" ``` Re Python, it does not have an...

ptn24

input and target size mismatch when running test.lua

3

Hi Dave! Sorry to interrupt you. I wanted to run this impressive pipeline but was stuck in an error. I haven't tried to train a new network yet and all...

MaYB2333

Error in running basset_sat_vcf.py

1

I am trying to run the basset_sat_vcf.py, but it returns errors: Here is the cmd: `software/Basset-master/src/basset_sat_vcf.py -t 6 -o /sat model_default_1k/dnacnn_best.th Test_run/rs13336428.vcf` And errors: ``` /opt/torch/install/bin/lua: /opt/torch/install/share/lua/5.2/nn/Container.lua:67: In 13 module...

huruifeng

Not python 3 friendly

2

Hi, Love the package, I'm keen to try it out for myself. Just wanted to point out that it doesn't seem to play well with Python 3. Some errors are...

lzamparo