ELAND standalone problem!!! help~

[sejong]

I ran the ELAND standalone.pl

but i got an error message <just see the red color>:

perl ELAND_standalone.pl -if /raid/GAPipeline-1.4.0/DB/mouse/test/lane1.0-8.fa -it fastq -eg /raid/GAPipeline-1.4.0/DB/mouse/chromFa/
$VAR1 = {
'read-length' => [
-1
],
'pair-params' => '--circular',
'pipeline-dir' => './..',
'input-file' => [
'/raid/GAPipeline-1.4.0/DB/mouse/test/lane1.0-8.fa'
],
'seed-length' => [
-1
],
'output-prefix' => './reanalysis',
'base-quality' => 30,
'eland-genome' => '/raid/GAPipeline-1.4.0/DB/mouse/chromFa/',
'input-type' => 'fastq'
};

ELAND_standalone.pl: single input-file specified, will do single read analysis
ELAND_standalone.pl: deduced read length of 28 for data in /raid/GAPipeline-1.4.0/DB/mouse/test/lane1.0-8.fa
Could not parse >EAS41_4_1_200_725_616_963 at ELAND_standalone.pl line 192, <READ> line 3.

So... I opened this file, 'ELAND_standalone.pl'

and I found it
--> while (defined($line=<READ>))
190 {
191 chomp($line);
192 unless ($line=~s/^\@//) { die "Could not parse $line"; }

How can i solve this problem?

[mastal]

The file the program ELAND_standalone.pl is trying to read, which presumably should be in fastq format, has a line that doesn't match the perl regular expression s/^\@//.

Have a look at the file and see if you can figure out why it is causing the error.

Hope this helps.

Maria