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6. GS Run Processor Appendices : 6.4 GS Run Processor Log Files - gsRunProcessor.log and gsRunProcessor_err.log
6.4
GS Run Processor Log Files - gsRunProcessor.log and gsRunProcessor_err.log
These files provide log information from the GS Run Processor job. Each line has a timestamp, and message. In the gsRunProcessor_err.log a timestamp, numeric error id, error severity, error message and source of the message is conveyed.
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“Notice” or “Information” messages are generated as the data processing progresses.
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“Warning” messages are generated when an unexpected condition is encountered and should be investigated. Conditions that may result in warning messages but can be safely ignored include:
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An unloaded / empty PTP region (GS FLX+ Instrument only)
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A region without library reads (e.g. a “Control DNA Only” Run) (GS FLX+ Instrument only)
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A missing postAnalysisScript.sh script
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“Error” messages are generated when the GS Run Processor encounters conditions from which it cannot automatically recover and will produce sub-standard or unusable results.
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“Fatal” messages are generated when the GS Run Processor encounters errors that prevent the GS Run Processor from proceeding, such as missing input files or improper configurations. The GS Run Processor will exit after generating “Fatal” messages and delete any partially generated output files.
 
All messages marked as “Warning”, “Error” or “Fatal” are placed in a “gsRunProcessor_err.log” file in addition to being placed in the gsRunProcessor.log file. If no messages of this type are generated, the gsRunProcessor_err.log file will not be created.