Question: missing .chk and .mtx files after using psipred script.
gravatar for shalinikaushik1293
3 months ago by
shalinikaushik12930 wrote:

Hello, I am running my python program on two systems.

  1. Ubuntu 18.04.4 LTS (62.6 GiB, 64 bit)
  2. CentOS kernel Linux 2.6.32-504.16.2.el6.x86_64 GNOME2.28.2

I am running the python code given below:

import os
import shutil
from multiprocessing import Pool as ThreadPool
import multiprocessing as mp
import time

filepath = "/media/kakarot/ppi/unmodelled_fasta_1"
args = []

for filename in os.listdir("/media/kakarot/ppi/unmodelled_fasta_1"):

def protein(filename):
    print(filename, ' started')
    start = time.time()
    current_file = filename
    print (filename)
    path = "/media/kakarot/ppi/genthreader/"+ filename
    # if not(os.path.isdir(path)):
    #     os.mkdir("/media/kakarot/ppi/genthreader/"+ filename)
    ############ for running psipred#################
        # if not (os.path.isfile ('/media/kakarot/ppi/psipred/'+filename)):
    os.system("csh /media/kakarot/ppi/psipred/runpsipred /media/kakarot/ppi/unmodelled_fasta_1/"+filename)

    end = time.time()
    print(filename, ' ended')
    print('Time taken for ', filename,' : ', end-start)

def parallel(arguments):
    pool = ThreadPool(mp.cpu_count()), arguments)


The prebuilt runpsipred script contains:


# This is a simple script which will carry out all of the basic steps
# required to make a PSIPRED prediction. Note that it assumes that the
# following programs are in the appropriate directories:
# blastpgp - PSIBLAST executable (from NCBI toolkit)
# makemat - IMPALA utility (from NCBI toolkit)
# psipred - PSIPRED V4 program
# psipass2 - PSIPRED V4 program

# NOTE: Script modified to be more cluster friendly (DTJ April 2008)

# The name of the BLAST data bank
set dbname = /media/kakarot/ppi/genthreader/uniref_test_db/uniref100.fasta

# Where the NCBI programs have been installed
# NOTE: ensure you omit any trailing / from this setting or some terminals
#       may seg fault
set ncbidir = /media/kakarot/ppi/ncbi/blast-2.2.26/bin

# Where the PSIPRED V4 programs have been installed
set execdir = /media/kakarot/ppi/psipred/bin

# Where the PSIPRED V4 data files have been installed
set datadir = /media/kakarot/ppi/psipred/data

set basename = $1:r
set rootname = $basename:t

# Generate a "unique" temporary filename root
set hostid = `hostid`
set tmproot = psitmp$$$hostid

\cp -f $1 $tmproot.fasta

echo "Running PSI-BLAST with sequence" $1 "..."

$ncbidir/blastpgp -b 0 -j 3 -h 0.001 -v 5000 -d $dbname -i $tmproot.fasta -C $tmproot.chk >& $tmproot.blast

if ($status != 0) then
    tail $tmproot.blast
    echo "FATAL: Error whilst running blastpgp - script terminated!"
    exit $status

echo "Predicting secondary structure..."

echo $tmproot.chk > $
echo $tmproot.fasta > $

$ncbidir/makemat -P $tmproot

if ($status != 0) then
    echo "FATAL: Error whilst running makemat - script terminated!"
    exit $status

echo Pass1 ...

$execdir/psipred $tmproot.mtx $datadir/weights.dat $datadir/weights.dat2 $datadir/weights.dat3 > $

if ($status != 0) then
    echo "FATAL: Error whilst running psipred - script terminated!"
    exit $status

echo Pass2 ...

$execdir/psipass2 $datadir/weights_p2.dat 1 1.0 1.0 $rootname.ss2 $ > $rootname.horiz

if ($status != 0) then
    echo "FATAL: Error whilst running psipass2 - script terminated!"
    exit $status

# Remove temporary files

echo Cleaning up ...
#\rm -f $tmproot.* error.log

echo "Final output files:" $rootname.ss2 $rootname.horiz
echo "Finished."

I am using psipred 4.0 version. The results produced in psipred folder (where runpsipred script is) in Ubuntu 18.04.4 LTS are .mtx , .chk , .fasta, .sn, .pn, . aux, .blast, .horiz, .ss2 and .ss files while in CentOS system, the files created are only .horiz, .ss and .ss2 files.

while I am required .chk and .mtx file for further process. Can anyone please help me with this? I will appreciate the help.

linux psipred .chk .mtx • 115 views
ADD COMMENTlink written 3 months ago by shalinikaushik12930
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