Mummerplot running errors and solutions

Mummerplot is a excellent program and it has been a long time since last version 3.23

Here are some trouble-shooting:

1. For large reference genome (>536,870,908 bp) 

Error: mummer: suffix tree construction failed: textlen=ddddddd larger than maximal textlen=536870908

1.1 compile

Explanation: default compiled x86 version only support small genome (less than 536,870,908bp). If you have a larger one, you need to enable x64 version. So compile mummerplot again using

        $ make CPPFLAGS=” -O3 -DSIXTYFOURBITS”

1.2 modify nucmer

And if you still get that error, you need to modify nucmer program, here is how-to

    1. open ‘nucmer’ file using text editor like ‘gedit’

    2. jump to line 336-343

open(ALGO_PIPE, “$algo_path $algo $mdir -l $size -n $pfx.ntref $qry_file |”)

                or $tigr->bail (“ERROR: could not open $algo_path output pipe $!”);

open(CLUS_PIPE, “| $mgaps_path -l $clus -s $gap -d $ddiff -f $dfrac > $pfx.mgaps”)

                or $tigr->bail (“ERROR: could not open $mgaps_path input pipe $!”);

while ( <ALGO_PIPE> ) {

                print CLUS_PIPE

                or $tigr->bail (“ERROR: could not write to $mgaps_path pipe $!”);

}

$err[0] = close(ALGO_FILE);

$err[1] = close(CLUS_PIPE);

    3. replace them with

    $err[0] = $tigr->runCommand (“$algo_path $algo $mdir -l $size -n $pfx.ntref $qry_file > $pfx.mummmer”);

    if ( $err[0] != 0 ) {

        $tigr->bail(“ERROR: Error: mummer output error\n”);

    }

    unless (-s “$pfx.mummmer”) {

        die “Error: mummer output error\n”;

    }

    open(ALGO_FILE, “< $pfx.mummmer”)

                or $tigr->bail (“ERROR: could not open $algo_path output file: $pfx.mummmer”);

    open(CLUS_PIPE, “| $mgaps_path -l $clus -s $gap -d $ddiff -f $dfrac > $pfx.mgaps”)

                or $tigr->bail (“ERROR: could not open $mgaps_path input pipe $!”);

    while ( <ALGO_FILE> ) {

                print CLUS_PIPE

                or $tigr->bail (“ERROR: could not write to $mgaps_path pipe $!”);

    }

    $err[0] = close(ALGO_FILE);

    $err[1] = close(CLUS_PIPE);

    4.So use nucmer2 instead of nucmer

     Explanation: nucmer use pipe to tranfer mummer output to feed mgaps as input. some times that is problematic. better to separate them. In this case there will be another output file: $prefix.mummer

1.3 replace mummer with e-mem [[[ OPTIONAL with care ]]]

    IF IF IF IF you still have some problem, trying to use multi-thread version of mummer: E-MEM. But do it carefully.

    5. install e-mem, E-mem was reported to use multithreads and run in low memory requirements

    6. create a file ’emem’ in the same path as nucmer2/nucmer/mummerplot, and this is the content

#!/bin/bash

numthreads=1

### edit this number to use multithreads

/path/to/e-mem -t $numthreads “$@”

### edit /path/to/e-mem to where to find e-mem program

if [ $? -ne 0 ]; then

    echo “Error: E-mem running failed” >&2

    exit 100

else

    echo “E-mem running succeeded”

    exit 0

fi

    7. make ’emem’ to be an excutable

  $ chmod +x /path/to/emem

    8. text editor open ‘nucmer2‘ and save as ‘nucmer_emem‘

                 Go to line 99, and 247, find ‘$BIN_DIR/mummer‘ and replace them with ‘$BIN_DIR/emem‘

    9.So use nucmer_emem instead of nucmer

 

2. modify mummerplot

    1. text editor open ‘mummerplot’

   2. go to line 565 and 575, change first + to *

replace :

if ( /^\s+(\d+)\s+(\d+)\s+(\d+)$/ ) {

by :

if ( /^\s*(\d+)\s+(\d+)\s+(\d+)$/ ) {

    Quick explanation : it search for a line that begin with one or more space, but when you have a start superior to 9999999, this space do not exist anymore.

    So if you change ‘+’ by ‘*’ it search for 0 or more spaces.

    3. Go line: line 884, 894, 981, 991, 1034, 1044, remove ‘defined’ and the corresponding bracket pairs'()’

           replace if (defined(%hash)) { … }

           by if (%hash) { … }

    Quick explanation : OLD perl grammar may report error in latest perl

 

3. TO BE CONTUED

 

Leave some comments please if you think it’s useful for you. ^_^