Detecting error in Ubuntu environment

Question

[ArusjakGevorgyan]

Hi everyone,

I have a script(Blast_helper.sh) that tries to create blast database of the reference Fasta files(ALLSeqs.faa) in UBUNTU. I do this with help of this command: "Blast_helper.sh -i ALLSeqs.faa", but I get this error: Error in tempfile() using template /tmp/parXXXXX.par: Parent directory (/tmp/) does not exist at /usr/bin/parallel line 3280. Do someone know the reason for this error? I will be very grateful for your help.

[Michael]

What is the output of

ls -ld /tmp

?

[ArusjakGevorgyan]

Hello :) This is the output:

ls: cannot access '/tmp': No such file or directory

[Michael]

looks like someone removed your /tmp directory. /tmp is the standard UNIX directory for putting temporary files, it should always be there. Ask your system administrator to fix it or see https://askubuntu.com/questions/178751/accidentally-deleted-tmp-folder. You might experience other problems on that system. I agree that is not really a bioinformatics problem.

[ArusjakGevorgyan]

Thank you so much for your help. I'm really grateful.

[Ram]

FYI: Script source is https://github.com/ballesterus/UPhO/blob/master/Blast_helper.sh

Answer 1

[Ram]

This is more of an Ubuntu question than a bioinformatics question. Try running a sudo apt-get update followed by a sudo apt-get install parallel

[GenoMax]

If OP does not have sudo privileges this would not work.

[ArusjakGevorgyan]

Thank you for your help sir, but I have already tried that it doesn't work, I get the same error.

[noorpratap.singh]

Could you share the script. It seems it is trying to create a temp directory which you cannot excess or does not exist. Possibly changing that directory where it stores might help.

[ArusjakGevorgyan]

#!/bin/bash
############################
#Usage:
#
# Blast_helper.sh <input.fasta> <query.fasta>
# Note: To produce comaparable results the effective  database size set to 34355436272, the number 
#aminoacids in uniprot release  2017_12 of 20-Dec-201
#Requires:
#
#    -gnu-parallel
#    -blast+ (tested with versions 2.2.30)
# 
############################

#Global variable definitions

ldb_path='local_db'
db_type='prot'
type='blastp'
input=''
query=''


#echo $query



#functions

CreateBlastDB ()
{
    if ! [ -d $ldb_path ]
    then mkdir $ldb_path;
    echo 'Creating local blast database at ' ldb_path  
    fi
    makeblastdb -dbtype $db_type -in $input -input_type 'fasta' -out local_db/localDB
}

AllvsAll ()
{
    find . -empty -delete
    echo 'Starting BLAST search' $query 'vs.' $input 'using' $type.
    if [ ! -e BLAST_results_${query%.*}.csv ]
    then
    cat $query | parallel --block 100k --pipe --recstart '>' $type -evalue 0.001 -outfmt 10 -db local_db/localDB -dbsize 34355436272 -query - > BLAST_results_${query%.*}.csv
    else
    echo 'A BLAST output file matching the query name exist in the wd.'
    #Lets try to restart the BLAST search from where it was left.
    # Firts lets see what is the last record written  to the output file
    last=`tail -n1 BLAST_results_${query%.*}.csv | cut -f 1 -d ','`
    qline=`grep -n  $last $query | cut -f 1 -d ':'`
    #remove last query from the output
    sed -i -e "/^"$last"/d" BLAST_results_${query%.*}.csv
    #start from previous last query
    echo "Re-starting from line:" $qline "=" $last 
    tail -n +$qline $query | parallel  --block 100k --pipe --recstart '>' $type -evalue 0.001 -outfmt 10 -db local_db/localDB -dbsize 34355436272  -query - >> BLAST_results_${query%.*}.csv
    fi
}


usage() {
cat <<EOF
usage: $0 <options>
This script helps the user to perform local BLAST searches for protein
homology assesment. It takes as input a file with sequences in FASTA format 
from which a local BLAST database is created. This same file is use as the
query unless otherwise specified trough -q.  GNU parallel and BLAST+
should be in installed and properly cited when using this script.
-h   |  Print this help
-i   |  The input FASTA file to build a BLASTDB   
-q   |  Specify a query file, otherwise all vs. all will be performed using the "-i" file.
-p   |  Use psiblast instead of blastp
EOF
}

### Main
OPTIND=1
while getopts "hepq:i:" opt; do

    case "$opt" in
    h)
        usage
        exit 0
        ;;

    i)
        input=$OPTARG
        ;;

    q) 
        query=$OPTARG
        ;;

    p)
        type='psiblast'
        ;;

    '?')
        usage 
        exit 1
        ;;
    :)
        usage
        exit 1
        ;;
    esac

done

shift $((OPTIND-1))
if [ "$query" = "" ]
then
    query=$input
fi

echo $query vs $input
echo $type

if [ "$input" != "" ]
then
    if ls local_db/localDB* 1> /dev/null 2>&1;
    then
    echo "A local BLAST database exist, proceeding to the search step";
    AllvsAll;
    else
    echo "Creating local BLAST database."
    CreateBlastDB && AllvsAll;
    fi
else
    echo "ERROR: Input file needed [-i]"
    exit 1

fi
exit $?

[Ram]

Run mkdir ~/tmp and then run the script after changing each parallel (I see them in lines 45 and 56) to parallel --tmpdir ~/tmp