runAnalysisFilter on GS Junior computer

[ganga.jeena]

Dear SABC,
I need a refernce paramter filtering for 454 Data.
Can you mail me a copy of filterTemplate.xml pre and post changes .
I will be very thankful for the same.
Regards,
Ganga Jeena

[suefo]

Our EBox went last week from the machine we got in March. Now the valve block has gone.

[SABC]

After 2 months I finally managed to convince Roche to send me some files so that I could compare them with mine and it turns out that there is an error in the XML templates exported by my system.

Of all things, it is a comment in the XML templates, "--pipe=", that breaks the XML file. When edited to read "pipe=" instead as per the file tech support sent me, the runAnalysisFilter works like a charm.

This must be a known bug, probably with a known patch, as the templates exported by the tech support computer are fine.

In case it is relevant to other peoples' systems, ours was installed in August 2010 and we had the Ebox replaced in October 2010. gsRunProcessor version is 2.5 without patch 1.

[suefo]

runAnalysisFilter on GS Junior computer

This should only take 2 steps (see attached jpg)/

[SABC]

As far as I am aware exactly as written in the 454 Sequencing System Software manual, v2.5 part B on page 20 (except that I added a space between the runAnalysisFilter and the --pipe as the manual has a typo).

Briefly, navigate to the relevant D_fullProcessing folder, open a command line and use the gsRunProcessor --template=filterOnly > filterTemplate.xml command to generate the quality filter template xml file (left it unmodified to prevent errors creeping in)

went up to the parent R folder and used
runAnalysisFilter --pipe=filterTemplate.xml D_fullProcessing

command. I also tried running the command with absolute paths specified, checking at each point that the names were typed correctly by tabbing to complete them.

gsRunProcessorManager launched gsRunProcessor and the xml file was briefly accessed (at least the time stamp was updated according to stat command) but the gsRunProcessorManager.log file in /var/log showed an error message about the pipe being unknown.

I just want to confirm that it is possible to get it to work on the GS Junior attendant PC before spending any more time on it.

[ulz_peter]

How did you use the command?

[SABC]

I have been unable to get the runAnalysisFilter command working on the computer that runs our GS Junior.

Has anybody successfully run this (pg 20 of the 454 Sequencing System Software Manual, v2.5 Part B) on a computer that is attached to a Junior with default software set-up?

(I have seen posts about Flex results and GS Junior results reanalyzed, but it isn't specified whether the runAnalysisFilter commands were carried out on an attached or stand-alone computer and whether Flex or GS Junior software was used for the reanalysis).

Thanks
SABC