Program hangs at "Preparing tfr records file for SPOT-RNA:" #17
Description
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