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Old 05-12-2014, 01:48 PM   #1
Junior Member
Location: New Zealand

Join Date: Feb 2014
Posts: 9
Default SureCall Software installation


I'm wondering if anyone uses this to analyse their sequences and whether anyone has issues installing this software? I've installed it and at the end of the installation it gives me a little message that some errors have occurred; however, the program still runs... sort of.

I've tried running one sample and it stops after it's converted my FastQ files to SAM files and starts doing the alignment. I've uninstalled and installed a few times and I don't know how to fix this and the IT team at work doesn't seem to know what is going on. I'm awaiting a reply from Agilent but I was wondering if anyone has this issue?
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Old 05-13-2014, 12:36 AM   #2
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Location: UK

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Posts: 390

It would help perhaps if you posted the associated errors.

Other people on the forums have had problems installing SureCall, but it has not proved to be problematic for me, and the latest release has a significant speed improvement over the initial release.
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Old 05-13-2014, 11:23 AM   #3
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I didn't post the errors because I wasn't sure if anyone else was having issues. I've extracted the installation errors and they're as follows:
Installation: Successful with errors.

7725 Successes
0 Warnings
7 NonFatalErrors
0 FatalErrors

Action Notes:


Custom Action: com.agilent.surecall.customcode.SplitUserCredentials
Status: ERROR
Additional Notes: ERROR - class com.agilent.surecall.customcode.SplitUserCredentials unavailable.

Custom Action: com.agilent.surecall.customcode.DetectSystemProxy
Status: ERROR
Additional Notes: ERROR - class com.agilent.surecall.customcode.DetectSystemProxy unavailable.

Custom Action: com.agilent.surecall.customcode.TrimVariableValues
Status: ERROR
Additional Notes: ERROR - class com.agilent.surecall.customcode.TrimVariableValues unavailable.

Custom Action: com.agilent.surecall.customcode.DataDownloadSettings
Status: ERROR
Additional Notes: ERROR - class com.agilent.surecall.customcode.DataDownloadSettings unavailable.

Custom Action: com.agilent.surecall.customcode.GetCurrentDate
Status: ERROR
Additional Notes: ERROR - class com.agilent.surecall.customcode.GetCurrentDate unavailable.

Custom Action: com.agilent.surecall.customcode.TestDataPathResolve
Status: ERROR
Additional Notes: ERROR - class com.agilent.surecall.customcode.TestDataPathResolve unavailable.

Custom Action: com.agilent.surecall.customcode.OfflineAuthSerialization
Status: ERROR
Additional Notes: ERROR - class com.agilent.surecall.customcode.OfflineAuthSerialization unavailable.

The error I get from the failed runs are as follows:

java.util.MissingResourceException: Can't find bundle for base name com.agilent.cgh.ui.NGSMessageBundle, locale en_NZ
at java.util.ResourceBundle.throwMissingResourceException(
at java.util.ResourceBundle.getBundleImpl(
at java.util.ResourceBundle.getBundle(
at com.agilent.genepanel.utility.Messages.loadMessageBundle(Unknown Source)
at com.agilent.genepanel.utility.Messages.<clinit>(Unknown Source)
at com.agilent.mutation.application.RunPipelineJob$ Source)

On SureCall the Job status summary says that it has started converting the SAM file to BAM format and then alignment has failed.

Agilent IT has replied and suggested some fixes regarding the sharing of certain folders and I've done as they said and still nothing.

If anyone has ideas I'm all ears.
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Old 05-19-2014, 05:27 AM   #4
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Location: Germany

Join Date: Jun 2012
Posts: 1

We had to activate the „full control for everyone“ settings for the folder „server/CommonStorage“ under Properties/Sharing/Advanced Sharing/ share this folder/ permissions.

Now, the analysis is running without errors.
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Old 10-05-2016, 11:06 PM   #5
Location: Madrid

Join Date: Jul 2015
Posts: 10

Thanks Cehg,

We had the same problem. Now it is working.
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