Always Error at "nt database doesn't exists"

[Zjianglin]

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 .

[jaswindersingh2]

Hi,

If you change path_blastn_database=/data/amax83t/Databases/ncbi_nt to path_blastn_database=/data/amax83t/Databases/ncbi_nt/nt, then it should fix this problem.

Jaswinder

[Zjianglin]

Hi， @jaswindersingh2 I have changed path_blastn_database as you suggestted, and the program now runs normally.

However, It seems the original nt file from NCBI should be kept in the path_blastn_database directory. I'm wonder why the file should be kept ? The original sequences data have been split into pieces, didn't it?

[jaswindersingh2]

Yeah, both formatted database files (*.nhr, *.nin *.nsq) and the original database file (nt) should be in the /data/amax83t/Databases/ncbi_nt/ directory. Formatted database files (*.nhr, *.nin *.nsq) are used by BLAST-N and the original database file (nt) is used by the INFERNAL for MSA search.

Jaswinder

[Zjianglin]

Okay, got it.

one more thing ,would you please tell me the best RNA sequence length range that SPOT-RNA2 could accurately predict their secondary structures? I'm not familiar with machine learning and/or deep learning and I don't see any options for SPOT-RNA2 . Hence, if you could point that and/or give me some guidelines ,it will be more helpful.

[B3zm4n]

Hi, I see the solution for this, but how do I this on my terminal?