Use Cases

Raw

/results/<Sequencer_name>/<Run_name>/

Processed

/results/analysis/output/Home/<Report_name>/

version.txt

Lists the versions of the Ion software packages that were installed at the time the report was generated and the host name of the server. This information is also displayed on the default report.

DefaultTFs.conf

Lists all of the Test Fragment Templates that were used for generating this report. If the file size is zero and there are no data in the file, either no templates areinstalled or none are flagged isofficial . Analysis only checks against the templates that are marked isofficial , which is set using the Templates tab in the browser.

uploadStatus

Lists problems uploading data to the database. If analysis results are not being displayed in the browser, check this file.

Normal results:

Updating Analysis

Adding TF Metrics

Adding Analysis Metrics

Adding Library Metrics

Adding Quality Metrics

Error examples:

Failed addAnalysisMetrics

Failed addLibMetrics

status.txt

Analysis run status. If the analysis completed successfully, the contents of this file are a 1. A value of 0 indicates a failure occurred, requiring that you check other log files to determine the cause. No specific error information is provided in this file.

processParameters.txt

Run events and duration. The command-line passed to theAnalysisprogram is also included, which is useful if you want to re-run the same analysis. These files are in subdirectories named sigproc_results/block_ *.

sigproc_results/sigproc.log

basecaller_results/basecaller.log

alignment.log

Analysis pipeline log files. Always check for errors in these files, especially the first and the last pages.

The contents of these log files ( without HTML formatting) are available in the Torrent Browser with the run report Support tab View the report log link:

drmaa_stdout.txt

Post-analysis events.

drmaa_stderr.txt

Error messages related to processes called after the primary analysis.This has a value of zero if the analysis completed successfully.

analyzeReads_err.txt

Useful troubleshooting information generated during the alignment process. This file is only created when there is a problem.

core

A memory dump listing, usually caused by a critical fault. You should see a related exception or core dump message in an analysis pipeline log file.

alignmentQC_out.txt

Errors related to TMAP. If the file is not present, it is likely that TMAP was not called. These files are in subdirectories named basecaller_results/block_ *.