jaswindersingh2/spot-rna2

Improved RNA Secondary Secondary Structure Prediction using Evolutionary Profile, Mutational Coupling and Two-dimensional Transfer Learning

spot-rna2's Issues

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Always Error at "nt database doesn't exists"

Hi developers,
I have installed SPOT-RNA2 in my computer according to install guide. However, after set inferal and BLASTN binary path and the nt_database path, run ./run_spotrna2.sh sample_run/6ufj.fasta always error at "nt database doesn't exist."

# conda virutal environment
$ /home/zjl/anaconda3/bin/blastn -h
USAGE
  blastn [-h] [-help] [-import_search_strategy filename]
    [-export_search_strategy filename] [-task task_name]...

$ /home/zjl/anaconda3/bin/cmscan -h
# cmscan :: search sequence(s) against a CM database
# INFERNAL 1.1.4 (Dec 2020)
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 


#run_spotrna2.sh 
path_blastn=/home/zjl/anaconda3/bin                                             # set path to the folder contains executable binary files of Blast package
path_blastn_database=/data/amax83t/Databases/ncbi_nt                            # set path to the formatted NCBI's database file without extension 
path_infernal=/home/zjl/anaconda3/bin
path_infernal_database=$path_blastn_database                            # set path to the NCBI's database database file


# nt_database
$ pwd
/data/amax83t/Databases/ncbi_nt
$ ls
nt         nt.08.nhr   nt.106.nin  nt.113.nsq  nt.121.nhr  nt.129.nin  nt.19.nsq  nt.28.nhr  nt.36.nin  nt.44.nsq  nt.53.nhr  nt.61.nin  nt.69.nsq  nt.78.nhr  nt.86.nin  nt.94.nsq
nt.00.nhr  nt.08.nin   nt.106.nsq  nt.114.nhr  nt.121.nin  nt.129.nsq  nt.20.nhr  nt.28.nin  nt.36.nsq  nt.45.nhr  nt.53.nin  nt.61.nsq  nt.70.nhr  nt.78.nin  nt.86.nsq  nt.95.nhr
nt.00.nin  nt.08.nsq   nt.107.nhr  nt.114.nin  nt.121.nsq  nt.12.nhr   nt.20.nin  nt.28.nsq  nt.37.nhr  nt.45.nin  nt.53.nsq  nt.62.nhr  nt.70.nin  nt.78.nsq  nt.87.nhr  nt.95.nin
nt.00.nsq  nt.09.nhr   nt.107.nin  nt.114.nsq  nt.122.nhr  nt.12.nin   nt.20.nsq  nt.29.nhr  nt.37.nin  nt.45.nsq  nt.54.nhr  nt.62.nin  nt.70.nsq  nt.79.nhr  nt.87.nin  nt.95.nsq
nt.01.nhr  nt.09.nin   nt.107.nsq  nt.115.nhr  nt.122.nin  nt.12.nsq   nt.21.nhr  nt.29.nin  nt.37.nsq  nt.46.nhr  nt.54.nin  nt.62.nsq  nt.71.nhr  nt.79.nin  nt.87.nsq  nt.96.nhr
nt.01.nin  nt.09.nsq   nt.108.nhr  nt.115.nin  nt.122.nsq  nt.13.nhr   nt.21.nin  nt.29.nsq  nt.38.nhr  nt.46.nin  nt.54.nsq  nt.63.nhr  nt.71.nin  nt.79.nsq  nt.88.nhr  nt.96.nin
nt.01.nsq  nt.100.nhr  nt.108.nin  nt.115.nsq  nt.123.nhr  nt.13.nin   nt.21.nsq  nt.30.nhr  nt.38.nin  nt.46.nsq  nt.55.nhr  nt.63.nin  nt.71.nsq  nt.80.nhr  nt.88.nin  nt.96.nsq
nt.02.nhr  nt.100.nin  nt.108.nsq  nt.116.nhr  nt.123.nin  nt.13.nsq   nt.22.nhr  nt.30.nin  nt.38.nsq  nt.47.nhr  nt.55.nin  nt.63.nsq  nt.72.nhr  nt.80.nin  nt.88.nsq  nt.97.nhr
nt.02.nin  nt.100.nsq  nt.109.nhr  nt.116.nin  nt.123.nsq  nt.14.nhr   nt.22.nin  nt.30.nsq  nt.39.nhr  nt.47.nin  nt.55.nsq  nt.64.nhr  nt.72.nin  nt.80.nsq  nt.89.nhr  nt.97.nin
nt.02.nsq  nt.101.nhr  nt.109.nin  nt.116.nsq  nt.124.nhr  nt.14.nin   nt.22.nsq  nt.31.nhr  nt.39.nin  nt.47.nsq  nt.56.nhr  nt.64.nin  nt.72.nsq  nt.81.nhr  nt.89.nin  nt.97.nsq
nt.03.nhr  nt.101.nin  nt.109.nsq  nt.117.nhr  nt.124.nin  nt.14.nsq   nt.23.nhr  nt.31.nin  nt.39.nsq  nt.48.nhr  nt.56.nin  nt.64.nsq  nt.73.nhr  nt.81.nin  nt.89.nsq  nt.98.nhr
nt.03.nin  nt.101.nsq  nt.10.nhr   nt.117.nin  nt.124.nsq  nt.15.nhr   nt.23.nin  nt.31.nsq  nt.40.nhr  nt.48.nin  nt.56.nsq  nt.65.nhr  nt.73.nin  nt.81.nsq  nt.90.nhr  nt.98.nin
nt.03.nsq  nt.102.nhr  nt.10.nin   nt.117.nsq  nt.125.nhr  nt.15.nin   nt.23.nsq  nt.32.nhr  nt.40.nin  nt.48.nsq  nt.57.nhr  nt.65.nin  nt.73.nsq  nt.82.nhr  nt.90.nin  nt.98.nsq
nt.04.nhr  nt.102.nin  nt.10.nsq   nt.118.nhr  nt.125.nin  nt.15.nsq   nt.24.nhr  nt.32.nin  nt.40.nsq  nt.49.nhr  nt.57.nin  nt.65.nsq  nt.74.nhr  nt.82.nin  nt.90.nsq  nt.99.nhr
nt.04.nin  nt.102.nsq  nt.110.nhr  nt.118.nin  nt.125.nsq  nt.16.nhr   nt.24.nin  nt.32.nsq  nt.41.nhr  nt.49.nin  nt.57.nsq  nt.66.nhr  nt.74.nin  nt.82.nsq  nt.91.nhr  nt.99.nin
nt.04.nsq  nt.103.nhr  nt.110.nin  nt.118.nsq  nt.126.nhr  nt.16.nin   nt.24.nsq  nt.33.nhr  nt.41.nin  nt.49.nsq  nt.58.nhr  nt.66.nin  nt.74.nsq  nt.83.nhr  nt.91.nin  nt.99.nsq
nt.05.nhr  nt.103.nin  nt.110.nsq  nt.119.nhr  nt.126.nin  nt.16.nsq   nt.25.nhr  nt.33.nin  nt.41.nsq  nt.50.nhr  nt.58.nin  nt.66.nsq  nt.75.nhr  nt.83.nin  nt.91.nsq  nt.gz.md5
nt.05.nin  nt.103.nsq  nt.111.nhr  nt.119.nin  nt.126.nsq  nt.17.nhr   nt.25.nin  nt.33.nsq  nt.42.nhr  nt.50.nin  nt.58.nsq  nt.67.nhr  nt.75.nin  nt.83.nsq  nt.92.nhr  nt.nal
nt.05.nsq  nt.104.nhr  nt.111.nin  nt.119.nsq  nt.127.nhr  nt.17.nin   nt.25.nsq  nt.34.nhr  nt.42.nin  nt.50.nsq  nt.59.nhr  nt.67.nin  nt.75.nsq  nt.84.nhr  nt.92.nin
nt.06.nhr  nt.104.nin  nt.111.nsq  nt.11.nhr   nt.127.nin  nt.17.nsq   nt.26.nhr  nt.34.nin  nt.42.nsq  nt.51.nhr  nt.59.nin  nt.67.nsq  nt.76.nhr  nt.84.nin  nt.92.nsq
nt.06.nin  nt.104.nsq  nt.112.nhr  nt.11.nin   nt.127.nsq  nt.18.nhr   nt.26.nin  nt.34.nsq  nt.43.nhr  nt.51.nin  nt.59.nsq  nt.68.nhr  nt.76.nin  nt.84.nsq  nt.93.nhr
nt.06.nsq  nt.105.nhr  nt.112.nin  nt.11.nsq   nt.128.nhr  nt.18.nin   nt.26.nsq  nt.35.nhr  nt.43.nin  nt.51.nsq  nt.60.nhr  nt.68.nin  nt.76.nsq  nt.85.nhr  nt.93.nin
nt.07.nhr  nt.105.nin  nt.112.nsq  nt.120.nhr  nt.128.nin  nt.18.nsq   nt.27.nhr  nt.35.nin  nt.43.nsq  nt.52.nhr  nt.60.nin  nt.68.nsq  nt.77.nhr  nt.85.nin  nt.93.nsq
nt.07.nin  nt.105.nsq  nt.113.nhr  nt.120.nin  nt.128.nsq  nt.19.nhr   nt.27.nin  nt.35.nsq  nt.44.nhr  nt.52.nin  nt.60.nsq  nt.69.nhr  nt.77.nin  nt.85.nsq  nt.94.nhr
nt.07.nsq  nt.106.nhr  nt.113.nin  nt.120.nsq  nt.129.nhr  nt.19.nin   nt.27.nsq  nt.36.nhr  nt.44.nin  nt.52.nsq  nt.61.nhr  nt.69.nin  nt.77.nsq  nt.86.nhr  nt.94.nin

./run_spotrna2.sh sample_run/6ufj.fasta


========================================================================================
            Looks like nt database doesn't exists in the path /data/amax83t/Databases/ncbi_nt.    
            If you want to download the database now, please make sure you have enough  
            space in mounted directory and internet connection have enough bandwidth as 
            file is of size 270 GBs after unzip. It may take forever to download if     
                                internet is slow!                                       
========================================================================================

Type 'y' for download or any other key to exit: n

===========================================================
      Exiting the program because nt database is missing! 
===========================================================

I have tried many times, could please help me figure it out? thank you .

Error infernal.

I installed Infernal according to the manual. But there is an error message saying that error occured while building Covariance Model (CM) from it.

Make SPOT-RNA2 available as Bioconda package

Hi @jaswindersingh2,

I'd like to try SPOT-RNA2 for the prediction of internal transcribed spacer 2 (ITS2) rRNA sequences on my local machine.

I know that you provide a Docker Image for installing SPOT-RNA2. Yet, I was wondering if it would be possible for you to also make SPOT-RNA2 available as a Bioconda package for linux-64 and osx-64, too?

Many thanks in advance for any feedback!

When I execute “docker image build -t spot_rna2 .”，there have an error "ERROR: failed to solve: process "/bin/sh -c cpanm Graph" did not complete successfully: exit code: 1"

=> ERROR [ 4/13] RUN cpanm Graph 26.2s

[ 4/13] RUN cpanm Graph:
#0 14.35 --> Working on Graph
#0 14.35 Fetching http://www.cpan.org/authors/id/E/ET/ETJ/Graph-0.9726.tar.gz ... OK
#0 26.23
#0 26.23 gzip: stdin: unexpected end of file
#0 26.23 /bin/tar: Child returned status 1
#0 26.23 /bin/tar: Error is not recoverable: exiting now
#0 26.23 ! Failed to unpack Graph-0.9726.tar.gz: no directory
#0 26.23 ! Failed to fetch distribution Graph-0.9726

---

Dockerfile:6

4 | RUN rm /bin/sh && ln -s /bin/bash /bin/sh
5 | RUN apt-get update && apt-get install -y build-essential wget virtualenv git python-minimal cpanminus gawk
6 | >>> RUN cpanm Graph
7 |
8 | RUN wget 'https://www.dropbox.com/s/h6j53u7wjyj6uir/SPOT-RNA2.tar.xz' || wget 'https://app.nihaocloud.com/f/3e826caf8efc43adaaa0/?dl=1' && tar -xvf SPOT-RNA2.tar.xz && rm SPOT-RNA2.tar.xz

ERROR: failed to solve: process "/bin/sh -c cpanm Graph" did not complete successfully: exit code: 1

How can I check out whether it is working on GPU?

Hi,

I have a question.
I just wonder If there is an way to ensure this code is working on GPU.

I installed tensorflow-gpu 1.14.0 by Anaconda.
The problem is it took much time to process a sequence than I expected.

Any tips for this?

Sincerely
Dek

unzip failed

Failed to unzip the compressed package(nt.gz)
When the compression finishes, the size of the resulting file is smaller than expected