paired-end run failed in pipeline v1.3.2

[ttkuaile]

During our first paired-end run in new version of pipeLine (v1.3.2), the image analysis and base call step passed, but the Gerald step failed to complete. In this run, the two reads of a pair have been stored into two separate RUN Folders. I used the Goat command to specify the two run folders. Do you have any idea or suggestion regarding this problem?

The goat command, Gerald config file and error message are shown as follows:

**********BEGIN PIPELINE COMMAN**********
/opt/GAPipeline-1.3.2/bin/goat_pipeline.py
/home/researchers/RunAnalysis/flowcell0014_1/Images
/home/researchers/RunAnalysis/flowcell0014_2/Images
--with-prb --with-sig2 --with-seq --with-qhg --with-qval --
GERALD=/home/researchers/RunAnalysis/flowcell0014_1/pair_gerald_config_rs
un.txt --control-lane=4 --make

then cd to /home/researchers/RunAnalysis/flowcell0014_1/Data/C1-
52_Firecrest1.3.2_14-04-2009_researchers/

run "make -j8 recursive"
********** END COMMAND*****************


***********BEGIN GERALD CONFIG FILE******
4:ELAND_GENOME home/researchers/RunAnalysis/eland_genomes/phiX
1235678:ELAND_GENOME
/home/researchers/RunAnalysis/eland_genomes/Plasmodium_falciparum
1235678:ANALYSIS eland_pair
USE_BASES all
ELAND_MULTIPLE_INSTANCES 8
*********End CONFIG FILE *************************


**********BEGIN ERROR MESSAGE **********
/opt/GAPipeline-1.3.2/bin/legacyMakeQseqs.pl --orig_read_lengths 26:26 --
qseq_suffix _qseq.txt.tmp --bustard_path
/home/researchers/RunAnalysis/flowcell0014_1/Data/C1-
52_Firecrest1.3.2_14-04-2009_researchers/Bustard1.3.2_14-04-
2009_researchers \
/home/researchers/RunAnalysis/flowcell0014_1/Data/C1-
52_Firecrest1.3.2_14-04-2009_researchers/Bustard1.3.2_14-04-
2009_researchers/s_3_0001_seq.txt \
/home/researchers/RunAnalysis/flowcell0014_1/Data/C1-
52_Firecrest1.3.2_14-04-2009_researchers/Bustard1.3.2_14-04-
2009_researchers/s_3_0001_qhg.txt \
/home/researchers/RunAnalysis/flowcell0014_1/Data/C1-
52_Firecrest1.3.2_14-04-2009_researchers/Bustard1.3.2_14-04-
2009_researchers/s_3_0001_1_qcal.txt
/home/researchers/RunAnalysis/flowcell0014_1/Data/C1-
52_Firecrest1.3.2_14-04-2009_researchers/Bustard1.3.2_14-04-
2009_researchers/s_3_0001_2_qcal.txt \
&& mv /home/researchers/RunAnalysis/flowcell0014_1/Data/C1-
52_Firecrest1.3.2_14-04-2009_researchers/Bustard1.3.2_14-04-
2009_researchers/s_3_1_0001_qseq.txt.tmp
/home/researchers/RunAnalysis/flowcell0014_1/Data/C1-
52_Firecrest1.3.2_14-04-2009_researchers/Bustard1.3.2_14-04-
2009_researchers/s_3_1_0001_qseq.txt && mv
/home/researchers/RunAnalysis/flowcell0014_1/Data/C1-
52_Firecrest1.3.2_14-04-2009_researchers/Bustard1.3.2_14-04-
2009_researchers/s_3_2_0001_qseq.txt.tmp
/home/researchers/RunAnalysis/flowcell0014_1/Data/C1-
52_Firecrest1.3.2_14-04-2009_researchers/Bustard1.3.2_14-04-
2009_researchers/s_3_2_0001_qseq.txt \
&& echo `date` >
/home/researchers/RunAnalysis/flowcell0014_1/Data/C1-
52_Firecrest1.3.2_14-04-2009_researchers/Bustard1.3.2_14-04-
2009_researchers/s_3_0001_qseqs.txt \
&& touch /home/researchers/RunAnalysis/flowcell0014_1/Data/C1-
52_Firecrest1.3.2_14-04-2009_researchers/Bustard1.3.2_14-04-
2009_researchers/s_3_1_0001_qseq.txt && touch
/home/researchers/RunAnalysis/flowcell0014_1/Data/C1-
52_Firecrest1.3.2_14-04-2009_researchers/Bustard1.3.2_14-04-
2009_researchers/s_3_2_0001_qseq.txt
Unexpected runfolder directory name format at /opt/GAPipeline-
1.3.2/bin/legacyMakeQseqs.pl line 73.
make: *** [/home/researchers/RunAnalysis/flowcell0014_1/Data/C1-
52_Firecrest1.3.2_14-04-2009_researchers/Bustard1.3.2_14-04-
2009_researchers/s_3_0001_qseqs.txt] Error 255

**********END ERROR MESSAGE*******************

[cbrennan]

You shouldn't give it the "Images" folder -- just the top level, like you would for a single-read

try:

/opt/GAPipeline-1.3.2/bin/goat_pipeline.py
/home/researchers/RunAnalysis/flowcell0014_1/
/home/researchers/RunAnalysis/flowcell0014_2/
--with-prb --with-sig2 --with-seq --with-qhg --with-qval --
GERALD=/home/researchers/RunAnalysis/flowcell0014_1/pair_gerald_config_rs
un.txt --control-lane=4 --make

Christine