Torrent Suite SoftwareAdministration Guide

Torrent Suite Software space on Ion Community

Customer Support Archive

This page describes the contents of a Customer Support Archive and how you can generate one. The Customer Support Archive is a ZIP file of log files and other technical data about your Torrent Suite Software and analysis runs. This data is useful for our support team to diagnose issues with your Torrent Suite Software. A Customer Support Archive can only be generated by a request in your Torrent Browser an archive is not generated automatically or forwarded automatically to Ion Torrent.

Generate a Customer Support Archive

You can generate a Customer Support Archive from a run report in the Torrent Browser Data > Completed Runs & Reports tab. The Support tab appears in this tab ribbon (after the run metrics and before the plugin detailed output):

Click the Support tab and then the Customer Support Archive download link. Wait while the file is downloaded. The zipped archive file can be 15 or 20 MB or more.

Customer Support Archive contents

The tables in this section describe the files included in a Customer Support Archive. Files for optional modules (such as recalibration) only appear if the optional module is run.

In the top level directory:

File	Description
alignment.log	L og of the final TMAP alignment process
*< RunName* >_< AnalysisReportName >.alignment.summary**	Text format summary of sample alignment final results
alignment.summary	Text format summary of sample alignment final results (same as the file < RunName >_< AnalysisReportName >.alignment.summary, but with a predictable file name)
backupPDF.pdf	PDF file of the analysis report and plugin results (similar to the output of the Download as PDF button on a run report)
Controller	LiveView log of user activity on the sequencing instrument
debug	Log from datacollect, the background data acquisition module
DefaultTFs.conf	List of known Test Fragment sequences and their bases
drmaa_stderr_block.txt	Analysis pipeline error log for the block being executed by Sun Grid Engine
drmaa_stdout.txt	Log of events after primary analysis
drmaa_stdout_block.txt	Analysis pipeline output log for the block being executed by Sun Grid Engine
explog.txt	Initial runs settings needed for Torrent Browser analysis when being exported from instrument
explog_final.txt	Final runs settings needed for Torrent Browser analysis when being exported from instrument
InitLog.txt	Instrument auto pH log
InitValsW2.txt	pH log of the W2 solution
InitValsW3.txt	pH log of the W3 solution
RawInit.txt	Contains initialization data output
sysinfo.txt	Torrent Browser system software settings
TF.alignment.summary	Summary of test fragment alignment results in text file
uploadStatus	Log of metrics being uploaded to the Torrent Brows er
version.txt	Torrent Suite software versions used for the analysis report

In the basecaller_results directory:

File	Description
basecaller.log	Log file for the basecaller analysis module
datasets_basecaller.json	A JSON-format file of the settings needed for basecaller to analyze the sample data
datasets_pipeline.json	A JSON-format file of the settings needed by the pipeline to run the basecallermodule
datasets_tf.json	A JSON-format file of the settings needed for basecaller to analyze the Test Fragments
*< RunName* >_< AnalysisReportName >.quality.summary**	A quality summary of basecaller unaligned reads/bases after filtering and trimming
quality.summary	Same as above, but with a predictable file name
TFStats.json	A JSON-format file of Test Fragments results statistics

In the basecaller_results/recalibration directory:

File	Description
alignment.log	L og of the TMAP alignment process during base recalibration
alignmentQC_out.txt	Log file from the TMAP analysis module

In the basecaller_results/unfiltered.trimmed directory:

File	Description
alignment.log	L og of the TMAP alignment process based on unfiltered and trimmed reads
*< RunName* >_< AnalysisReportName >. alignment** .summary	Text format summary of sample alignment results for unfiltered and trimmed reads
alignment.summary	Text format summary of sample alignment results for unfiltered and trimmed reads (same as above, but with a predictable file name)
datasets_basecaller.json	A JSON-format file of the settings needed for basecaller to analyze the sample data, when generating the raw BAM file
*< RunName* >_< AnalysisReportName >.quality.summary**	The basecaller unfiltered and trimmed reads/bases quality summary
quality.summary	The basecaller unfiltered and trimmed reads/bases quality summary (same as above, but with a predictable file name)

In the basecaller_results/unfiltered.untrimmed directory:

File	Description
alignment.log	L og of the TMAP alignment process based on unfiltered and trimmed reads
*< RunName* >_< AnalysisReportName >. alignment** .summary	Text format summary of sample alignment results for unfiltered and untrimmed reads
alignment.summary	Text format summary of sample alignment results for unfiltered and untrimmed reads (same as above, but with a predictable file name)
datasets_basecaller.json	A JSON-format file of the settings needed for basecaller to analyze the sample data, when generating the raw BAM file
*< RunName* >_< AnalysisReportName >.quality.summary**	The basecaller unfiltered and untrimmed reads/bases quality summary
quality.summary	The basecaller unfiltered and untrimmed reads/bases quality summary (same as above, but with a predictable file name)

In the sigproc_results directory:

File	Description
analysis.bfmask.stats	Analysis statistics of wells in the bead find stag e (the bfmask is a set of bit flags for each well, indicating the contents of each well )
avgNukeTrace_ATCG.txt	ATCG key signal measurements
avgNukeTrace_ TCAG .txt	TCAG key signal measurements
bfmask.stats	Summary statistics of wells in the bead find stag e
processParameters.txt	Parameter settings for analysis signal processing
separator.bftraces.txt	Matrix data to separate between live wells and empty wells during bead find phase
separator.trace.txt	Matrix data to separate between live wells and empty wells
sigproc.log	Log file for the analysis module

In the sigproc_results/dcOffset directory:

File	Description
dcOffset.txt	background model parameter values of dcOffset

In the sigproc_results/NucStep directory:

The files in this folder contain background model parameter values based on the location of the well in the chip .

File
NucStep_frametime.txt
NucStep_inlet_head.txt
NucStep_inlet_empty.txt
NucStep_inlet_empty_sd.txt
NucStep_inlet_step.txt
NucStep_middle_head.txt
NucStep_ middle _empty.txt
NucStep_ middle _empty_sd.txt
NucStep_ middle _step.txt
NucStep_outlet_head.txt
NucStep_ outlet _empty.txt
NucStep_outlet_empty_sd.txt
NucStep_outlet_step.txt