I use CASAVA 1.8.2 for paired-end seq alignment. I trimmed certain low quality data from both directions, the resulting seq length is dynamic for both files. I am using eland_standalone v1.8.2 for alignment. seq length is 101 bases. However, it always showed the error mesg.
/opt/rocks/bin/perl /opt/CASAVA_v1.8.2/bin/ELAND_standalone.pl \
-if mm/R1.fastq -if pp/R2.fastq -ref genome/hg18/ \
-it FASTQ -bq 30 -cr -rt -ub Y*n -ub Y*n \
-l tmp.log
Command line options:
$VAR1 = {
'ref-sequences' => '/genome/hg18',
'input-file' => [
'/Users/seq/mm/R1.fastq',
'/Users/seq/pp/R2.fastq'
],
'base-quality' => 30,
'remove-temps' => 1,
'index' => 'NoIndex',
'input-type' => 'FASTQ',
'copy-references' => 1,
'use-bases' => [
'Y*n',
'Y*n'
],
'log' => '/Users/seq/tmp.log',
'lane' => 1
};
Dynamic exception type: boost::exception_detail::clone_impl<casava::common::InvalidParameterException>
std::exception::what: Tried to apply a 65-cycle UseBases mask to data actually containing 99 bases.
: Tried to apply a 65-cycle UseBases mask to data actually containing 99 bases.
Thanks!
/opt/rocks/bin/perl /opt/CASAVA_v1.8.2/bin/ELAND_standalone.pl \
-if mm/R1.fastq -if pp/R2.fastq -ref genome/hg18/ \
-it FASTQ -bq 30 -cr -rt -ub Y*n -ub Y*n \
-l tmp.log
Command line options:
$VAR1 = {
'ref-sequences' => '/genome/hg18',
'input-file' => [
'/Users/seq/mm/R1.fastq',
'/Users/seq/pp/R2.fastq'
],
'base-quality' => 30,
'remove-temps' => 1,
'index' => 'NoIndex',
'input-type' => 'FASTQ',
'copy-references' => 1,
'use-bases' => [
'Y*n',
'Y*n'
],
'log' => '/Users/seq/tmp.log',
'lane' => 1
};
Dynamic exception type: boost::exception_detail::clone_impl<casava::common::InvalidParameterException>
std::exception::what: Tried to apply a 65-cycle UseBases mask to data actually containing 99 bases.
: Tried to apply a 65-cycle UseBases mask to data actually containing 99 bases.
Thanks!