We read every piece of feedback, and take your input very seriously.
To see all available qualifiers, see our documentation.
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
I have tried the to run SPOT-RNA with gpu and cpu, but in both cases the execution hangs at the step mentioned in the title for > 1 day.
python3 ~/.bin/SPOT-RNA/SPOT-RNA.py --inputs stat1.fa --outputs './' --gpu 0 python3 ~/.bin/SPOT-RNA/SPOT-RNA.py --inputs stat1.fa --outputs './' --cpu 16
I am running Ubuntu 20.04
pip list:
Package Version -------------------- ------------------- absl-py 0.13.0 astor 0.8.1 certifi 2021.5.30 coverage 5.5 Cython 0.29.24 gast 0.5.1 google-pasta 0.2.0 grpcio 1.36.1 h5py 2.10.0 importlib-metadata 3.10.0 Keras-Applications 1.0.8 Keras-Preprocessing 1.1.2 Markdown 3.3.4 mkl-fft 1.2.0 mkl-random 1.1.1 mkl-service 2.3.0 numpy 1.16.4 pandas 1.1.5 pip 21.0.1 protobuf 3.17.2 python-dateutil 2.8.2 pytz 2021.1 scipy 1.5.2 setuptools 52.0.0.post20210125 six 1.16.0 tensorboard 1.14.0 tensorflow 1.14.0 tensorflow-estimator 1.14.0 termcolor 1.1.0 tqdm 4.62.0 typing-extensions 3.10.0.0 Werkzeug 1.0.1 wheel 0.37.0 wrapt 1.12.1 zipp 3.5.0
conda list:
# packages in environment at /home/david/.bin/miniconda3/envs/spotrna: # # Name Version Build Channel _libgcc_mutex 0.1 main _openmp_mutex 4.5 1_gnu _tflow_select 2.1.0 gpu absl-py 0.13.0 py36h06a4308_0 astor 0.8.1 py36h06a4308_0 blas 1.0 mkl c-ares 1.17.1 h27cfd23_0 ca-certificates 2021.7.5 h06a4308_1 certifi 2021.5.30 py36h06a4308_0 coverage 5.5 py36h27cfd23_2 cudatoolkit 10.1.243 h6bb024c_0 cudnn 7.6.5 cuda10.1_0 cupti 10.1.168 0 cython 0.29.24 py36h295c915_0 gast 0.5.1 pyhd3eb1b0_0 google-pasta 0.2.0 py_0 grpcio 1.36.1 py36h2157cd5_1 h5py 2.10.0 py36hd6299e0_1 hdf5 1.10.6 hb1b8bf9_0 importlib-metadata 3.10.0 py36h06a4308_0 intel-openmp 2021.3.0 h06a4308_3350 keras-applications 1.0.8 py_1 keras-preprocessing 1.1.2 pyhd3eb1b0_0 ld_impl_linux-64 2.35.1 h7274673_9 libffi 3.3 he6710b0_2 libgcc-ng 9.3.0 h5101ec6_17 libgfortran-ng 7.5.0 ha8ba4b0_17 libgfortran4 7.5.0 ha8ba4b0_17 libgomp 9.3.0 h5101ec6_17 libprotobuf 3.17.2 h4ff587b_1 libstdcxx-ng 9.3.0 hd4cf53a_17 markdown 3.3.4 py36h06a4308_0 mkl 2020.2 256 mkl-service 2.3.0 py36he8ac12f_0 mkl_fft 1.2.0 py36h23d657b_0 mkl_random 1.1.1 py36h0573a6f_0 ncurses 6.2 he6710b0_1 numpy 1.16.4 py36h7e9f1db_0 numpy-base 1.16.4 py36hde5b4d6_0 openssl 1.1.1k h27cfd23_0 pandas 1.1.5 py36h2531618_0 pip 21.0.1 py36h06a4308_0 protobuf 3.17.2 py36h295c915_0 python 3.6.13 h12debd9_1 python-dateutil 2.8.2 pyhd3eb1b0_0 pytz 2021.1 pyhd3eb1b0_0 readline 8.1 h27cfd23_0 scipy 1.5.2 py36h0b6359f_0 setuptools 52.0.0 py36h06a4308_0 six 1.16.0 pyhd3eb1b0_0 sqlite 3.36.0 hc218d9a_0 tensorboard 1.14.0 py36hf484d3e_0 tensorflow 1.14.0 gpu_py36h3fb9ad6_0 tensorflow-base 1.14.0 gpu_py36he45bfe2_0 tensorflow-estimator 1.14.0 py_0 tensorflow-gpu 1.14.0 h0d30ee6_0 termcolor 1.1.0 py36h06a4308_1 tk 8.6.10 hbc83047_0 tqdm 4.62.0 pyhd3eb1b0_1 typing_extensions 3.10.0.0 pyh06a4308_0 werkzeug 1.0.1 pyhd3eb1b0_0 wheel 0.37.0 pyhd3eb1b0_0 wrapt 1.12.1 py36h7b6447c_1 xz 5.2.5 h7b6447c_0 zipp 3.5.0 pyhd3eb1b0_0 zlib 1.2.11 h7b6447c_3
rna fasta:
>stat AGCGCUGCCUUUUCUCCUGCCGGGUAGUUUCGCUUUCCUGCGCAGAGUCUGCGGAGGGGCUCGGCUGCACCGGGGGGAUCGCGCCUGGCAGACCCCAGACCGAGCAGAGGCGACCCAGCGCGCUCGGGAGAGGCUGCACCGCCGCGCCCCCGCCUAGCCCUUCCGGAUCCUGCGCGCAGAAAAGUUUCAUUUGCUGUAUGCCAUCCUCGAGAGCUGUCUAGGUUAACGUUCGCACUCUGUGUAUAUAACCUCGACAGUCUUGGCACCUAACGUGCUGUGCGUAGCUGCUCCUUUGGUUGAAUCCCCAGGCCCUUGUUGGGGCACAAGGUGGCAGGAUGUCUCAGUGGUACGAACUUCAGCAGCUUGACUCAAAAUUCCUGGAGCAGGUUCACCAGCUUUAUGAUGACAGUUUUCCCAUGGAAAUCAGACAGUACCUGGCACAGUGGUUAGAAAAGCAAGACUGGGAGCACGCUGCCAAUGAUGUUUCAUUUGCCACCAUCCGUUUUCAUGACCUCCUGUCACAGCUGGAUGAUCAAUAUAGUCGCUUUUCUUUGGAGAAUAACUUCUUGCUACAGCAUAACAUAAGGAAAAGCAAGCGUAAUCUUCAGGAUAAUUUUCAGGAAGACCCAAUCCAGAUGUCUAUGAUCAUUUACAGCUGUCUGAAGGAAGAAAGGAAAAUUCUGGAAAACGCCCAGAGAUUUAAUCAGGCUCAGUCGGGGAAUAUUCAGAGCACAGUGAUGUUAGACAAACAGAAAGAGCUUGACAGUAAAGUCAGAAAUGUGAAGGACAAGGUUAUGUGUAUAGAGCAUGAAAUCAAGAGCCUGGAAGAUUUACAAGAUGAAUAUGACUUCAAAUGCAAAACCUUGCAGAACAGAGAACACGAGACCAAUGGUGUGGCAAAGAGUGAUCAGAAACAAGAACAGCUGUUACUCAAGAAGAUGUAUUUAAUGCUUGACAAUAAGAGAAAGGAAGUAGUUCACAAAAUAAUAGAGUUGCUGAAUGUCACUGAACUUACCCAGAAUGCCCUGAUUAAUGAUGAACUAGUGGAGUGGAAGCGGAGACAGCAGAGCGCCUGUAUUGGGGGGCCGCCCAAUGCUUGCUUGGAUCAGCUGCAGAACUGGUUCACUAUAGUUGCGGAGAGUCUGCAGCAAGUUCGGCAGCAGCUUAAAAAGUUGGAGGAAUUGGAACAGAAAUACACCUACGAACAUGACCCUAUCACAAAAAACAAACAAGUGUUAUGGGACCGCACCUUCAGUCUUUUCCAGCAGCUCAUUCAGAGCUCGUUUGUGGUGGAAAGACAGCCCUGCAUGCCAACGCACCCUCAGAGGCCGCUGGUCUUGAAGACAGGGGUCCAGUUCACUGUGAAGUUGAGACUGUUGGUGAAAUUGCAAGAGCUGAAUUAUAAUUUGAAAGUCAAAGUCUUAUUUGAUAAAGAUGUGAAUGAGAGAAAUACAGUAAAAGGAUUUAGGAAGUUCAACAUUUUGGGCACGCACACAAAAGUGAUGAACAUGGAGGAGUCCACCAAUGGCAGUCUGGCGGCUGAAUUUCGGCACCUGCAAUUGAAAGAACAGAAAAAUGCUGGCACCAGAACGAAUGAGGGUCCUCUCAUCGUUACUGAAGAGCUUCACUCCCUUAGUUUUGAAACCCAAUUGUGCCAGCCUGGUUUGGUAAUUGACCUCGAGACGACCUCUCUGCCCGUUGUGGUGAUCUCCAACGUCAGCCAGCUCCCGAGCGGUUGGGCCUCCAUCCUUUGGUACAACAUGCUGGUGGCGGAACCCAGGAAUCUGUCCUUCUUCCUGACUCCACCAUGUGCACGAUGGGCUCAGCUUUCAGAAGUGCUGAGUUGGCAGUUUUCUUCUGUCACCAAAAGAGGUCUCAAUGUGGACCAGCUGAACAUGUUGGGAGAGAAGCUUCUUGGUCCUAACGCCAGCCCCGAUGGUCUCAUUCCGUGGACGAGGUUUUGUAAGGAAAAUAUAAAUGAUAAAAAUUUUCCCUUCUGGCUUUGGAUUGAAAGCAUCCUAGAACUCAUUAAAAAACACCUGCUCCCUCUCUGGAAUGAUGGGUGCAUCAUGGGCUUCAUCAGCAAGGAGCGAGAGCGUGCCCUGUUGAAGGACCAGCAGCCGGGGACCUUCCUGCUGCGGUUCAGUGAGAGCUCCCGGGAAGGGGCCAUCACAUUCACAUGGGUGGAGCGGUCCCAGAACGGAGGCGAACCUGACUUCCAUGCGGUUGAACCCUACACGAAGAAAGAACUUUCUGCUGUUACUUUCCCUGACAUCAUUCGCAAUUACAAAGUCAUGGCUGCUGAGAAUAUUCCUGAGAAUCCCCUGAAGUAUCUGUAUCCAAAUAUUGACAAAGACCAUGCCUUUGGAAAGUAUUACUCCAGGCCAAAGGAAGCACCAGAGCCAAUGGAACUUGAUGGCCCUAAAGGAACUGGAUAUAUCAAGACUGAGUUGAUUUCUGUGUCUGAAGUGUAAGUGAACACAGAAGAGUGACAUGUUUACAAACCUCAAGCCAGCCUUGCUCCUGGCUGGGGCCUGUUGAAGAUGCUUGUAUUUUACUUUUCCAUUGUAAUUGCUAUCGCCAUCACAGCUGAACUUGUUGAGAUCCCCGUGUUACUGCCUAUCAGCAUUUUACUACUUUAAAAAAAAAAAAAAAGCCAAAAACCAAAUUUGUAUUUAAGGUAUAUAAAUUUUCCCAAAACUGAUACCCUUUGAAAAAGUAUAAAUAAAAUGAGCAAAAGUUGAUCAGAGUGGGAAAGUAGUUCUUUUCAAUCUAGAAAAGGCCAAAGUAAUGAUUGAGAUACACUGUCUCCACUUGCUUUGAUUUUGUUGUUUCAUUUUAUAAAAGGUAGAAAAAAUUUUGGAAAUGUCAUUGUCAGUUAUUUGGCCUGCAGCACUGUCUUGGGGUGAAUGGAUGUAGCCUUCAUGUAAAAACACUGUGUGGAGCAGCUUUAUCUGCAUUCAAACCUCAAGUCACCCUUCUAGACUUCAGACCACAGACAACCUGCUCCCCAUGUCUCCUGAGGAGUUUGACGAGGUGUCUCGGAUAGUGGGCUCUGUAGAAUUCGACAGUAUGAUGAACACAGUAUAGAGCAUGAAUUUUUUUCAUCUUCUCUGGCGACAGUUUUCCUUCUCAUCUGUGAUUCCCUCCUGCUACUCUGUUCCUUCACAUCCUGUGUUUCUAGGGAAAUGAAAGAAAGGCCAGCAAAUUCGCUGCAACCUGUUGAUAGCAAGUGAAUUUUUCUCUAACUCAGAAACAUCAGUUACUCUGAAGGGCAUCAUGCAUCUUACUGAAGGUAAAAUUGAAAGGCAUUCUCUGAAGAGUGGGUUUCACAAGUGAAAAACAUCCAGAUACACCCAAAGUAUCAGGACGAGAAUGAGGGUCCUUUGGGAAAGGAGAAGUUAAGCAACAUCUAGCAAAUGUUAUGCAUAAAGUCAGUGCCCAACUGUUAUAGGUUGUUGGAUAAAUCAGUGGUUAUUUAGGGAACUGCUUGACGUAGGAACGGUAAAUUUCUGUGGGAGAAUUCUUACAUGUUUUCUUUGCUUUAAGUGUAACUGGCAGUUUUCCAUUGGUUUACCUGUGAAAUAGUUCAAAGCCAAGUUUAUAUACAAUUAUAUCAGUCCUCUUUCAAAGGUAGCCAUCAUGGAUCUGGUAGGGGGAAAAUGUGUAUUUUAUUACAUCUUUCACAUUGGCUAUUUAAAGACAAAGACAAAUUCUGUUUCUUGAGAAGAGAAUAUUAGCUUUACUGUUUGUUAUGGCUUAAUGACACUAGCUAAUAUCAAUAGAAGGAUGUACAUUUCCAAAUUCACAAGUUGUGUUUGAUAUCCAAAGCUGAAUACAUUCUGCUUUCAUCUUGGUCACAUACAAUUAUUUUUACAGUUCUCCCAAGGGAGUUAGGCUAUUCACAACCACUCAUUCAAAAGUUGAAAUUAACCAUAGAUGUAGAUAAACUCAGAAAUUUAAUUCAUGUUUCUUAAAUGGGCUACUUUGUCCUUUUUGUUAUUAGGGUGGUAUUUAGUCUAUUAGCCACAAAAUUGGGAAAGGAGUAGAAAAAGCAGUAACUGACAACUUGAAUAAUACACCAGAGAUAAUAUGAGAAUCAGAUCAUUUCAAAACUCAUUUCCUAUGUAACUGCAUUGAGAACUGCAUAUGUUUCGCUGAUAUAUGUGUUUUUCACAUUUGCGAAUGGUUCCAUUCUCUCUCCUGUACUUUUUCCAGACACUUUUUUGAGUGGAUGAUGUUUCGUGAAGUAUACUGUAUUUUUACCUUUUUCCUUCCUUAUCACUGACACAAAAAGUAGAUUAAGAGAUGGGUUUGACAAGGUUCUUCCCUUUUACAUACUGCUGUCUAUGUGGCUGUAUCUUGUUUUUCCACUACUGCUACCACAACUAUAUUAUCAUGCAAAUGCUGUAUUCUUCUUUGGUGGAGAUAAAGAUUUCUUGAGUUUUGUUUUAAAAUUAAAGCUAAAGUAUCUGUAUUGCAUUAAAUAUAAUAUGCACACAGUGCUUUCCGUGGCACUGCAUACAAUCUGAGGCCUCCUCUCUCAGUUUUUAUAUAGAUGGCGAGAACCUAAGUUUCAGUUGAUUUUACAAUUGAAAUGACUAAAAAACAAAGAAGACAACAUUAAAACAAUAUUGUUUCUAAUUGCUGAGGUUUAGCUGUCAGUUCUUUUUGCCCUUUGGGAAUUCGGCAUGGUUUCAUUUUACUGCACUAGCCAAGAGACUUUACUUUUAAGAAGUAUUAAAAUUCUAAAAUUCUAUUAAUCUCUCAUUAAUAGUAUUUAAUAUAAAGAUUCUUAAAAUUA
The text was updated successfully, but these errors were encountered:
No branches or pull requests
I have tried the to run SPOT-RNA with gpu and cpu, but in both cases the execution hangs at the step mentioned in the title for > 1 day.
python3 ~/.bin/SPOT-RNA/SPOT-RNA.py --inputs stat1.fa --outputs './' --gpu 0
python3 ~/.bin/SPOT-RNA/SPOT-RNA.py --inputs stat1.fa --outputs './' --cpu 16
I am running Ubuntu 20.04
pip list:
conda list:
rna fasta:
The text was updated successfully, but these errors were encountered: