Paired end solexa (goat/gerald) pipeline

[bioinfosm]

Hi,

I am unable to go beyond the Solexa pipeline on paired end data. The data is 72 cycles of images in a single folder (36 x 2). I am not really sure of what the config.txt file should be!
Any ideas?

$ cat config.txt
ANALYSIS sequence_pair
USE_BASES Y35n,Y35n
SEQUENCE_FORMAT --fastq
ELAND_MULTIPLE_INSTANCES 6

This one says:
Found 1 reads.
Read 1: length 72.
Overriding lengths using option 72.
Error: Too many reads specified in USE_BASES=Y35n,Y35n.
Removing temporary file /tmp/tmp-GERALD-4440-4807.txt
Error: ../Gerald/GERALD.pl (/data3/Solexa2/Vasatzis/111408_30J7KAAXX_300164_20/Data/config.txt) returned error code 2
Error: Failed to process Gerald configuration.

[dvh]

Try just:
ANALYSIS sequence_pair
SEQUENCE_FORMAT --fastq
nothing else.

[webbrewer]

There should be a file called PairedEndInfo.xml in the run folder that the pipeline looks for to know the sequences length. Is this file present and you are using GAPipeline 1.0?

[bioinfosm]

PairedEndInfo.xml it was!

Although mine read like this-
$ cat ../../PairedEndInfo.xml
<?xml version="1.0"?>
<FirstRead Length="36" />

I added the line
<SecondRead Length="36" />

[bioinfosm]

___________________________