Running GERALD.pl on RTA PE data - wrong Summary.htm

[JakobHedegaard]

Hi,

I have just analyzed the first PE dataset produced after upgrading to SCS2.5/RTA Version 1.5.35.0 and pipeline 1.5.1 and found that the Summary.htm produced by GERALD.pl was lacking the "Lane Result Summary" and "Expanded Lane Summary" information for both read 1 and 2? Looks like the Summary.htm file for a single read analysis...
Otherwise, the analysis performed apparently well producing the expected s_X_1_sequence.txt and s_X_2_sequence.txt files.

Anyone else experinecd this issue with the Summary.htm file from GERALD.pl?

Jakob

[seq_GA]

Hi,
I just happened to see the same today for one of the GA run analysis output. I did find no errors in the pipeline log. I have started the reanalysis to see whther this problem is solved.
I could see s_*_*_sequence.txt till respective sorted.txt.
But summary page didn't have any read1 and read2 summary as well as alignment was showing 0%. No idea why this happened.

Did you manage to find the cause Jakob?

[JakobHedegaard]

We (and Illumina tech support...) have not identified the cause yet but I have been informed that a few other users have experienced the same problem. I suggest that you contact Illumina tech support as well and provides them with log and config files etc. to clarify the issue.

I have just completed the analysis of a new run from the same GA that caused problems - this run was identical to the "problematic" one (same sample, same recipe) - and this time GERALD.pl completed without problems producing a Summary.htm looking as expected with information for both read1 and 2!

The problems are perhaps caused by the fact that the run was the first after upgrading to SCS2.5
Was your problematic run also the first after upgrading?

[seq_GA]

Hi Jacob,
Thanks for your response. It is is not one of the latest upgraded instrument. But I see the sorted.txt etc.. as per the normal run under Gerald directory but the summary page is problematic.
What do I do with this run? Thanks.

[JakobHedegaard]

Hi, I have just received the workaround below from Illumina and I am going to try it today...

a. Copy tiles.txt from the affected GERALD folder to the BaseCalls folder. Also copy score.txt and rescore.txt from GERALD/Temp directory back into the GERALD directory
b. Change directory to the BaseCalls folder.
c. Run “/path/to/pipeline/GAPipeline-1.5.1/bin/produceIntensityStats.pl .” this results in a warning regarding samples.xml but that can be ignored.
d. Change directory to the affected GERALD folder.
e. Run “/path/to/pipeline/GAPipeline-1.5.1/bin/jerboa.pl ”
f. You should now have a correct Summary.xml/htm file.