problem running the example tfrec conversion on Windows Subsystem for Linux WSL and likewise on docker about deepmicrobes HOT 7 OPEN

Hi,
It was "parallel" that did not work properly. Could you please check whether parallel has been properly installed? If not, try install parallel by yourself (instead of using the executable file in the bin directory).

(wget -O - pi.dk/3 || curl pi.dk/3/) | bash

Thanks

from deepmicrobes.

Hi,
Did you specify the path to the vocabulary file?

from deepmicrobes.

Thanks for the reply. Correct, it was related to parallel. I still get error running the same code but now a different one that seems to be related to something else. It doesn't find the vocabulary file which is in the directory (and the path)!

parallel successfully detected... seqtk successfully detected... Starting converting SRR5935743_clean_1.fastq and SRR5935743_clean_2.fastq to TFRecord (mode=prediction), output will be saved in SRR5935743.tfrec Parameters: kmer=12, vocab_file=tokens_merged_12mers.txt, split_size=4000000, sequence_type=fastq ====================================== 1. Interleaving R1 and R2... ====================================== 2. Splitting the merged file to 4000000 sequences per file... ====================================== 3. Converting to TFRecord... Academic tradition requires you to cite works you base your article on. If you use programs that use GNU Parallel to process data for an article in a scientific publication, please cite: Tange, O. (2021, September 22). GNU Parallel 20210922 ('Vindelev'). Zenodo. https://doi.org/10.5281/zenodo.5523272 This helps funding further development; AND IT WON'T COST YOU A CENT. If you pay 10000 EUR you should feel free to use GNU Parallel without citing. More about funding GNU Parallel and the citation notice: https://www.gnu.org/software/parallel/parallel_design.html#Citation-notice To silence this citation notice: run 'parallel --citation' once. Traceback (most recent call last): File "/mnt/c/Users/XYZ/Desktop/DeepMicrobes/scripts/seq2tfrec_kmer.py", line 243, in main() File "/mnt/c/Users/XYZ/Desktop/DeepMicrobes/scripts/seq2tfrec_kmer.py", line 224, in main 'Please provide the vocabulary file.') AssertionError: Please provide the vocabulary file. cat: 'subset*.tfrec': No such file or directory rm: cannot remove 'subset*.tfrec': No such file or directory Finished.

from deepmicrobes.

Hi, it worked by specifying the absolute path to the vocab file. Thanks a lot for quick reply.
Do you have any plan to make a docker image of DeepMicrobes? It would be really helpful for reproducibility of the results.

from deepmicrobes.

The server I am working on does not have a docker installed, so that currently I do not have a plan to make a docker image. Sorry about that.

from deepmicrobes.

Hi, I'm working with ramtinz on getting this to work on our current server. We are having some issues getting the install.yml to create a working environment with gpu support. We havn't exactly located the error yet and it may very well be something we are doing wrong. Would it be possible for someone to provide the output from conda list and pip freeze for an environment that works?

from deepmicrobes.

Hi, here is the output from conda list:

Name Version Build Channel
_libgcc_mutex 0.1 main conda-forge
_tflow_select 2.1.0 gpu defaults
absl-py 0.3.0 py_0 conda-forge
astor 0.7.1 py_0 conda-forge
biopython 1.70 py36_2 conda-forge
blas 1.1 openblas conda-forge
c-ares 1.15.0 h516909a_1001 conda-forge
ca-certificates 2019.11.28 hecc5488_0 conda-forge
certifi 2019.11.28 py36_0 conda-forge
cudatoolkit 9.0 h13b8566_0 defaults
cudnn 7.1.2 cuda9.0_0 defaults
cupti 9.0.176 0 defaults
gast 0.3.2 py_0 conda-forge
grpcio 1.23.0 py36he9ae1f9_0 conda-forge
h5py 2.7.1 py36_1 conda-forge
hdf5 1.8.18 3 conda-forge
libffi 3.2.1 he1b5a44_1006 conda-forge
libgcc-ng 9.2.0 hdf63c60_0 conda-forge
libgfortran 3.0.0 1 conda-forge
libgfortran-ng 7.3.0 hdf63c60_2 conda-forge
libprotobuf 3.11.1 h8b12597_0 conda-forge
libstdcxx-ng 9.2.0 hdf63c60_0 conda-forge
markdown 3.1.1 py_0 conda-forge
ncurses 6.1 hf484d3e_1002 conda-forge
numpy 1.13.3 py36_blas_openblash1522bff_1201 [blas_openblas] conda-forge
openblas 0.3.3 h9ac9557_1001 conda-forge
openssl 1.1.1d h516909a_0 conda-forge
pip 19.3.1 py36_0 conda-forge
protobuf 3.11.1 py36he1b5a44_0 conda-forge
python 3.6.7 h357f687_1006 conda-forge
readline 8.0 hf8c457e_0 conda-forge
seqtk 1.3 hed695b0_2 bioconda
setuptools 42.0.2 py36_0 conda-forge
six 1.13.0 py36_0 conda-forge
sqlite 3.30.1 hcee41ef_0 conda-forge
tensorboard 1.9.0 py36_0 conda-forge
tensorflow 1.9.0 py36_0 conda-forge
tensorflow-base 1.9.0 gpu_py36h6ecc378_0 defaults
tensorflow-gpu 1.9.0 hf154084_0 defaults
termcolor 1.1.0 py_2 conda-forge
tk 8.6.10 hed695b0_0 conda-forge
werkzeug 0.16.0 py_0 conda-forge
wheel 0.33.6 py36_0 conda-forge
xz 5.2.4 h14c3975_1001 conda-forge
zlib 1.2.11 h516909a_1006 conda-forge

from deepmicrobes.