perl qlxToSam.pl <qlxinput.qlx> <assembly.fasta> <samoutput.sam>
perl -p -i -e 's/>(.+?) .+/>$1/g' <filename.fa>
perl -p -i -e 's/>(.+?) .+/>$1/g' <filename.qual>
G5ZVNFF01A0ZHGTCGCGTCTCTCAGCACACA
G5ZVNFF01BAD7STGTGTGCGTGTCGCGTCTCTCAGCACACAG
G5ZVNFF01A2RT4ATCAAGGACAGCAAGGCAGTTCATGCTGACATGGGGTACGTGATAGAAGTAGAAGAACG
G5ZVNFF01A2W0FAGCTGGAAGACTAATACATAGGGCGAGATGTACAGAACTCCACTT
G5ZVNFF01AUU29TGGTAACATTCAAGACAGCTCATGCAAGAAGCAGGAAGTGGTCGTACTAGGATCACAAGA
G5ZVNFF01A0ZHG
G5ZVNFF01BAD7S
G5ZVNFF01A2RT4
G5ZVNFF01A2W0F
I will try with few more MOSAIKs run, and also see whether this is an issue prior to SAM.
It is unfortunate because I ran MOSAIK for all my samples already and not a problem.
Will keep you informed.
I will now try rc454 and check
Fabio
On 25/03/2012, at 5:44 AM, Patrick Charlebois wrote:
I sent to you the data via cludstor, can you please confirm that you received it?
Also, I am still stuck with the SamtoQlx and I am getting convinced that it is the fact that all my qual and fna files are generated with NextgenE
thanks
Fabio
On 25/03/2012, at 10:48 AM, Patrick Charlebois wrote:
#!/usr/bin/perl
open FILE, shift(@ARGV) or die $!;
my $file = join '', <FILE>;
close FILE;
while($file =~ /(@.+?)(\n.+?\n\+\n.+?\n)/g){
$title = $1; $data = $2;
$title =~ s/\W//g;
print $title,$data;
}
substr outside of string at samToQlx.pl line 198, <samFILE> line 60564.
Use of uninitialized value in concatenation (.) or string at samToQlx.pl line 198, <samFILE> line 60564.
unless ($info->{RefBase}){
print STDERR '$info->{RefBase} not defined!',"\n";
print Dumper(\%$info),"\n\n",$info->{ReadBase},"\n";
exit;
}
.............................
Summarizing reads...
.$info->{RefBase} not defined!
$VAR1 = {
'BQ' => 32,
'ID' => 'RXOA21727745',
'NQS' => '1',
'ReadEnd' => '96',
'Polarity' => '-',
'LocusInfo' => {
'ID' => [],
'Window' => [
undef,
205,
205,
205,
... lots of increasingly larger integers...
1690,
1690,
1690,
1690,
1690,
1690,
1690,
1690,
1690,
1690,
1690,
1690,
1690,
1690,
1690
]
},
'RefEnd' => 1,
'HQ' => {
'DeleteLocus' => -1,
'BQSum' => 0,
'DeletePos' => -1,
'State' => 'R',
'InsertLocus' => -1,
'LastNuc' => 'N',
'GapLength' => 0,
'InsertPos' => -1
},
'RawBase' => 'A',
'ModelCounts' => {
'HQ' => {},
'All' => {}
},
'RefBase' => undef,
'Run' => 0,
'PosEnd' => 95,
'Region' => 0,
'ReadBase' => 'T',
'ReadLength' => '169',
'NQSSeq' => [
'1',
'1',
'1',
'1',
'1',
'1',
..... lots of data....
'0',
'0',
'0',
'0',
'0',
'0'
],
'Increment' => -1,
'BQSeq' => [
32,
32,
32,
35,
.... Lots of Quality Data...
29,
22
],
'Switch' => 0,
'CurRead' => 0,
'Reads' => 60560,
'RefPos' => 97,
'EmpiricalCounts' => {
'HQ' => {},
'All' => {}
},
'RefSeq' => [],
'ReadPos' => 0,
'All' => {
'DeleteLocus' => -1,
'BQSum' => 0,
'DeletePos' => -1,
'State' => 'R',
'InsertLocus' => -1,
'LastNuc' => 'N',
'GapLength' => 0,
'InsertPos' => -1
},
'ReadSeq' => [
'T',
LOTS OF SEQUENCE...
'C'
]
};
Use of uninitialized value in print at vphaser.pl line 1834, <FFILE> line 363360.
DQ380149ZH501S2.vph_calls.txt
DQ380149ZH501S2.vph_model.txt
DQ380149ZH501S2.vph_out.txt
DQ380149ZH501S2.vph_snp.txt
jacobs$ perl vprofiler.pl -i ~/DQ380149-vprofiler-input.txt -o ~/vpro -noendvariant=10 -nt -codon
invalid VPhaser input file for RVFV ~/DQ380149ZH501S2.vph_calls.txt at vprofiler.pl line 192, <INPUT> line 11.
substr outside of string at bioinformatics/VpSoftwarePackage/vprofiler.pl line 823, <AAALIGN> line 23426.
Use of uninitialized value $newqualstr in substr at bioinformatics/VpSoftwarePackage/vprofiler.pl line 771, <AAALIGN> line 23426.
Use of uninitialized value $newqualstr in substr at bioinformatics/VpSoftwarePackage/vprofiler.pl line 823, <AAALIGN> line 23426.
Error in library(gplots) : there is no package called ‘gplots’Execution haltedError in library(gplots) : there is no package called ‘gplots’Execution haltedError in library(gplots) : there is no package called ‘gplots’Execution haltedmv: rename /Users/jjacobs/vpro_RVFV_Heatmap_All//Users/jjacobs/vpro_RVFV_Heatmap_Syn/RVFV_Full_Heatmap.pdf to /Users/jjacobs/vpro_RVFV_Heatmap_All/RVFV_Full_Heatmap_Syn.pdf: No such file or directorymv: rename /Users/jjacobs/vpro_RVFV_Heatmap_All//Users/jjacobs/vpro_RVFV_Heatmap_NonSyn/RVFV_Full_Heatmap.pdf to /Users/jjacobs/vpro_RVFV_Heatmap_All/RVFV_Full_Heatmap_NonSyn.pdf: No such file or directoryrm: /Users/jjacobs/vpro_RVFV_Heatmap_All//Users/jjacobs/vpro_RVFV_Heatmap_NonSyn: No such file or directoryrm: /Users/jjacobs/vpro_RVFV_Heatmap_All//Users/jjacobs/vpro_RVFV_Heatmap_Syn: No such file or directoryrm: /Users/jjacobs/vpro_RVFV_Heatmap_All//Users/jjacobs/vpro_RVFV_Heatmap_Textfiles_Folder: No such file or directory
I've partly solved the problem. I had renamed the fasta and qual files IDs as suggested in a post above but had not changed the sam file IDs.
I've continued despite the above error messages as my qlx file lloked good:
Are you running our latest release? We made numerous changes to samToQlx.pl earlier this month. I don't think any of them affect your problems, but I would like to start from the same base code.
Mike