--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/out_dir/configuration.cfg	Fri Sep 08 10:14:40 2017 -0400
@@ -0,0 +1,57 @@
+[pipeline]
+basecall_type = linear
+log_summaries = false
+log_all_intermodule_messages = false
+desc_file = /home/jeremy/.local/lib/python3.5/site-packages/albacore/data_versioned/layout_basecall_barcode_1d.jsn
+
+[data_trimmer]
+ev_window = 20
+ev_threshold = 5
+min_events = 3
+delta = 2
+
+[event_detector]
+window1 = 4
+window2 = 8
+threshold1 = 1.5
+threshold2 = 9.0
+peak_height = 0.2
+min_events = 1000
+trim_front = 0
+
+[basecaller]
+model = template_r9.5_450bps_5mer.jsn
+min_events = 100
+max_events = 1000
+overlap = 50
+min_quality = -100.0
+min_prob = 1e-5
+simple_decoding = 1
+model_path = /home/jeremy/.local/lib/python3.5/site-packages/albacore/data_versioned
+
+[call_handler]
+record_base = read
+qscore_adjuster_intercept = -4.5
+qscore_adjuster_slope = 3.0
+
+[barcode_detector]
+arrangements_files = barcode_arrs_pcr96.cfg barcode_arrs_nb.cfg barcode_arrs_rbk.cfg barcode_arrs_lwb.cfg barcode_arrs_rlb.cfg barcode_arrs_rab.cfg
+score_matrix = 4x4_mismatch_matrix.txt
+start_gap1 = 40
+end_gap1 = 40
+open_gap1 = 40
+extend_gap1 = 40
+start_gap2 = 40
+end_gap2 = 40
+open_gap2 = 160
+extend_gap2 = 160
+min_score = 60.0
+front_window_size = 150
+rear_window_size = 150
+
+[fastq]
+header = {read_id} runid={run_id} read={read_number} ch={channel_id} start_time={start_time_utc}
+header_with_barcoding = {read_id} runid={run_id} read={read_number} ch={channel_id} start_time={start_time_utc} barcode={barcode_id}
+batch_file_name = fastq_runid_{run_id}_{batch_counter}.fastq
+single_file_name = {read_id}.fastq
+