Customer support archive contents

Report.pdf

A PDF file of the analysis report and plugin results (similar to the output of the Download as PDF button on a run report).

DefaultTFs.conf

Contains a list of known test fragment sequences and their bases.

drmaa_stderr_block.txt

The analysis pipeline error log for the block being executed by Oracle™ Grid Engine.

drmaa_stdout.txt

The log of events after primary analysis.

drmaa_stdout_block.txt

The analysis pipeline output log for the block being executed by Oracle™ Grid Engine.

explog.txt

The initial run settings needed for Torrent Suite™ Software analysis when being exported from an instrument.

explog_final.txt

The final run settings needed for Torrent Suite™ Software analysis when being exported from an instrument.

InitLog.txt

The instrument auto pH log.

InitValsW2.txt

The pH log of the W2 solution.

InitValsW3.txt

The pH log of the W3 solution.

ion_params_00.json

A JSON-format file that contains the Planned Run related metadata.

<barcode>_rawlib.ionstats_alignment.json

A JSON-format file with Quality Control metrics.

ionstats_alignment.json

A JSON-format file with Quality Control metrics.

iontrace_Test_Fragment.png

Graphic that shows the peak signal per well in the first key flow.

RawInit.txt

Contains initialization data output.

sysinfo.txt

Contains Torrent Suite™ Software system settings.

uploadStatus

The log of metrics being uploaded to the Torrent Suite™ Software.

version.txt

Lists the Torrent Suite™ Software versions used for the analysis report.

basecaller.log

A log file for the BaseCaller analysis module.

BaseCaller.json

A JSON-format file with Quality Control metrics.

datasets_basecaller.json

A JSON-format file of the settings needed for the BaseCaller module to analyze the sample data.

datasets_pipeline.json

A JSON-format file of the settings needed by the pipeline to run the BaseCaller module.

datasets_tf.json

A JSON-format file of the settings needed for the BaseCaller module to analyze the Test Fragments.

<barcode>_rawlib.ionstats_basecaller.json

A JSON-format file with Quality Control metrics for the barcode.

<barcode>_rawlib.sparkline.png

A graphics file with the thumbnail histogram that shows the read lengths for the barcode.

ionstats_basecaller.json

A JSON-format file with Quality Control metrics.

ionstats_tf.json

A JSON-format file with Quality Control metrics.

nomatch_rawlib.ionstats_ basecaller.json

A JSON-format file with Quality Control metrics for the reads that cannot be classified as into one of the barcodes (the no-match group).

nomatch_rawlib.sparkline.png

A graphics file with the thumbnail histogram that shows the read lengths for the no match group.

TFStats.json

A JSON-format file of test fragments results statistics.

BaseCaller.json

A log file for the BaseCaller analysis module during base recalibration.

basecaller.log

A JSON-format file with Quality Control metrics for base recalibration.

datasets_basecaller.json

A JSON-format file of the settings needed for the BaseCaller module to analyze the sample data for base recalibration.

datasets_pipeline.json

A JSON-format file of the settings needed by the pipeline to run the BaseCaller module for base recalibration.

datasets_basecaller.json

A JSON-format file of the settings needed for the BaseCaller module to analyze the sample data, when generating the raw BAM file.

datasets_basecaller.json

A JSON-format file of the settings needed for the BaseCaller module to analyze the sample data, when generating the raw BAM file.

analysis.bfmask.stats

Contains analysis statistics of wells in the bead find stage (the bfmask is a set of bit flags for each well, indicating the contents of each well).

avgNukeTrace_ATCG.txt

Contains ATCG key signal measurements.

avgNukeTrace_TCAG.txt

Contains TCAG key signal measurements.

bfmask.stats

Contains summary statistics of wells in the bead find stage.

BkgModelFilterData.h5

Contains debug information for the polyclonal filter. In particular, this file contains PPF (percent positive flows) and SSQ (residual) values for each read.

pinsPerFlow.txt

Contains the number of pixels that are detected as pinned in each flow. Pinned pixels either contain zero or a very high signal (above the threshold) in the flow.

processParameters.txt

Contains parameter settings for analysis signal processing.

sigproc.log

A log file for the analysis module.

dcOffset.txt

The background model parameter values of dcOffset.