MarioHsiao/autoRunTracker

Auto Run Tracker

Introduction

Auto run tracker tracks runs and output basic metrics about the run. For questions and update suggestion, please contact Leo Liu (qliu2@illumina.com) or Chen Zhao (czhao@illumina.com).

Usage

First you need to qlogin in qlogin

Command for summarizing runs

/illumina/scratch/K2-I/software/auto_run_tracker/00_parse_summary_linux_NovaSeq.R --summaryCSV=<location_of_output_csv> --runsDir=<directory_of_illumina_runs>

• --summaryCSV can be a new file or a file that has been created before using the run tracker

• --runsDir is where the runs are located. The tracker currently supports Novaseq results as well

Output

The run tracker will summarize and parse InterOp files and samplesheet to generate the following results.

The output header:

RunID	Experiment	Investigator	Experiment_Name	UniqueSampleNames	numSamples	Read1_length	Read2_length	InstrumentID	RTAVersion	FlowCellRfidTag_SerialNumber	FlowCellRfidTag_PartNumber	FlowCellRfidTag_LotNumber	FlowCellRfidTag_ExpirationDate	PR2BottleRfidTag_SerialNumber	PR2BottleRfidTag_PartNumber	PR2BottleRfidTag_LotNumber	PR2BottleRfidTag_ExpirationDate	ReagentKitRfidTag_SerialNumber	ReagentKitRfidTag_PartNumber	ReagentKitRfidTag_LotNumber	ReagentKitRfidTag_ExpirationDate	YieldTotalG	Read1_Q30Percent	Read2_Q30Percent	Q30Percent	Read1_errorRate	Read2_errorRate	Read1_Intensity	Read2_Intensity	cluster_density	cluster_percent_Pf	total_PairedReads	total_PairedReadsPf	total_PairedReadsPf_demux