## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Pen_Lin_1_2009-11-16/US_Pen_Lin_1_2009-11-16.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Pen_Lin_1_2009-11-16/US_Pen_Lin_1_2009-11-16.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Pen_Lin_1_2009-11-16/US_Pen_Lin_1_2009-11-16.mark_duplicates_report.txt REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=SILENT    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Fri Jan 20 18:45:39 UTC 2023

## METRICS CLASS	picard.sam.DuplicationMetrics
LIBRARY	UNPAIRED_READS_EXAMINED	READ_PAIRS_EXAMINED	SECONDARY_OR_SUPPLEMENTARY_RDS	UNMAPPED_READS	UNPAIRED_READ_DUPLICATES	READ_PAIR_DUPLICATES	READ_PAIR_OPTICAL_DUPLICATES	PERCENT_DUPLICATION	ESTIMATED_LIBRARY_SIZE
lib1	1016745	42572128	0	0	344768	985518	0	0.026878	905263229

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	39630327	39630327
2.0	1.954061	338367	338367
3.0	2.864294	28889	28889
4.0	3.732712	5779	5779
5.0	4.561236	2340	2340
6.0	5.351699	1324	1324
7.0	6.105849	890	890
8.0	6.825354	596	596
9.0	7.511807	421	421
10.0	8.166724	347	347
11.0	8.791555	290	290
12.0	9.387683	231	231
13.0	9.956425	190	190
14.0	10.49904	148	148
15.0	11.016728	133	133
16.0	11.510633	117	117
17.0	11.98185	101	101
18.0	12.431419	90	90
19.0	12.860336	102	102
20.0	13.269549	87	87
21.0	13.659964	81	81
22.0	14.032443	84	84
23.0	14.387811	57	57
24.0	14.726853	79	79
25.0	15.050321	47	47
26.0	15.358929	44	44
27.0	15.65336	53	53
28.0	15.934265	55	55
29.0	16.202266	38	38
30.0	16.457955	29	29
31.0	16.701898	37	37
32.0	16.934634	33	33
33.0	17.156679	26	26
34.0	17.368524	25	25
35.0	17.570637	27	27
36.0	17.763465	23	23
37.0	17.947434	33	33
38.0	18.122952	24	24
39.0	18.290408	18	18
40.0	18.45017	20	20
41.0	18.602594	21	21
42.0	18.748015	17	17
43.0	18.886755	13	13
44.0	19.019123	19	19
45.0	19.145409	9	9
46.0	19.265894	14	14
47.0	19.380844	12	12
48.0	19.490513	14	14
49.0	19.595145	14	14
50.0	19.694969	18	18
51.0	19.790208	11	11
52.0	19.881072	12	12
53.0	19.967761	8	8
54.0	20.050468	9	9
55.0	20.129376	12	12
56.0	20.204659	5	5
57.0	20.276483	10	10
58.0	20.345008	10	10
59.0	20.410385	13	13
60.0	20.472759	7	7
61.0	20.532267	12	12
62.0	20.589041	8	8
63.0	20.643208	7	7
64.0	20.694886	9	9
65.0	20.74419	10	10
66.0	20.791229	5	5
67.0	20.836107	6	6
68.0	20.878923	9	9
69.0	20.919773	6	6
70.0	20.958746	8	8
71.0	20.995928	7	7
72.0	21.031403	9	9
73.0	21.065248	5	5
74.0	21.097538	7	7
75.0	21.128344	7	7
76.0	21.157736	6	6
77.0	21.185777	4	4
78.0	21.21253	3	3
79.0	21.238054	10	10
80.0	21.262406	7	7
81.0	21.285639	3	3
82.0	21.307804	6	6
83.0	21.328952	9	9
84.0	21.349127	6	6
85.0	21.368376	4	4
86.0	21.386741	5	5
87.0	21.404262	3	3
88.0	21.420978	9	9
89.0	21.436927	7	7
90.0	21.452142	6	6
91.0	21.466659	1	1
92.0	21.480508	7	7
93.0	21.493722	4	4
94.0	21.506328	2	2
95.0	21.518356	5	5
96.0	21.529831	3	3
97.0	21.540778	2	2
98.0	21.551223	2	2
99.0	21.561188	1	1
100.0	21.570695	2	2
101.0	0	1	1
102.0	0	6	6
103.0	0	3	3
104.0	0	4	4
105.0	0	4	4
106.0	0	3	3
107.0	0	2	2
108.0	0	3	3
109.0	0	1	1
110.0	0	1	1
111.0	0	5	5
112.0	0	3	3
113.0	0	5	5
114.0	0	1	1
115.0	0	2	2
116.0	0	3	3
117.0	0	2	2
118.0	0	3	3
119.0	0	4	4
121.0	0	1	1
122.0	0	4	4
123.0	0	2	2
124.0	0	4	4
125.0	0	3	3
126.0	0	2	2
127.0	0	1	1
128.0	0	4	4
129.0	0	1	1
131.0	0	3	3
132.0	0	1	1
133.0	0	1	1
134.0	0	3	3
135.0	0	1	1
136.0	0	1	1
137.0	0	2	2
139.0	0	3	3
141.0	0	3	3
142.0	0	4	4
145.0	0	1	1
146.0	0	1	1
148.0	0	4	4
149.0	0	4	4
150.0	0	4	4
151.0	0	1	1
154.0	0	2	2
157.0	0	1	1
159.0	0	1	1
162.0	0	1	1
164.0	0	2	2
165.0	0	1	1
166.0	0	3	3
167.0	0	1	1
170.0	0	1	1
171.0	0	1	1
173.0	0	1	1
174.0	0	3	3
175.0	0	1	1
176.0	0	1	1
178.0	0	1	1
179.0	0	2	2
184.0	0	1	1
187.0	0	2	2
189.0	0	2	2
191.0	0	1	1
192.0	0	1	1
193.0	0	1	1
196.0	0	1	1
197.0	0	1	1
199.0	0	2	2
200.0	0	3	3
203.0	0	3	3
208.0	0	1	1
209.0	0	2	2
210.0	0	2	2
211.0	0	3	3
214.0	0	1	1
215.0	0	1	1
218.0	0	2	2
220.0	0	2	2
225.0	0	1	1
227.0	0	2	2
229.0	0	1	1
231.0	0	1	1
235.0	0	2	2
236.0	0	3	3
237.0	0	1	1
238.0	0	2	2
239.0	0	3	3
240.0	0	3	3
241.0	0	1	1
244.0	0	1	1
245.0	0	3	3
248.0	0	1	1
249.0	0	1	1
253.0	0	1	1
254.0	0	1	1
256.0	0	1	1
257.0	0	1	1
258.0	0	1	1
262.0	0	1	1
263.0	0	2	2
265.0	0	1	1
267.0	0	3	3
271.0	0	1	1
272.0	0	2	2
275.0	0	1	1
277.0	0	1	1
282.0	0	1	1
283.0	0	1	1
284.0	0	1	1
287.0	0	1	1
289.0	0	1	1
290.0	0	2	2
291.0	0	2	2
293.0	0	1	1
295.0	0	1	1
297.0	0	2	2
298.0	0	1	1
299.0	0	1	1
302.0	0	1	1
303.0	0	1	1
308.0	0	1	1
314.0	0	1	1
315.0	0	1	1
316.0	0	1	1
319.0	0	2	2
320.0	0	1	1
321.0	0	1	1
330.0	0	1	1
331.0	0	1	1
332.0	0	1	1
333.0	0	2	2
334.0	0	2	2
337.0	0	1	1
338.0	0	2	2
347.0	0	1	1
348.0	0	1	1
349.0	0	1	1
350.0	0	1	1
352.0	0	1	1
354.0	0	1	1
355.0	0	2	2
356.0	0	1	1
357.0	0	1	1
358.0	0	1	1
360.0	0	1	1
362.0	0	1	1
363.0	0	2	2
366.0	0	1	1
367.0	0	1	1
372.0	0	1	1
374.0	0	1	1
375.0	0	1	1
376.0	0	1	1
378.0	0	1	1
382.0	0	3	3
386.0	0	1	1
390.0	0	1	1
391.0	0	2	2
394.0	0	1	1
399.0	0	2	2
401.0	0	1	1
403.0	0	1	1
406.0	0	1	1
407.0	0	1	1
408.0	0	1	1
409.0	0	1	1
414.0	0	1	1
415.0	0	1	1
418.0	0	2	2
421.0	0	1	1
422.0	0	1	1
425.0	0	1	1
429.0	0	1	1
432.0	0	1	1
433.0	0	1	1
434.0	0	1	1
435.0	0	3	3
436.0	0	1	1
437.0	0	1	1
438.0	0	1	1
443.0	0	1	1
447.0	0	1	1
448.0	0	3	3
451.0	0	1	1
457.0	0	1	1
459.0	0	3	3
460.0	0	1	1
461.0	0	1	1
463.0	0	1	1
466.0	0	1	1
467.0	0	1	1
469.0	0	1	1
470.0	0	2	2
471.0	0	1	1
477.0	0	1	1
479.0	0	3	3
485.0	0	1	1
486.0	0	2	2
492.0	0	3	3
497.0	0	1	1
508.0	0	1	1
510.0	0	2	2
512.0	0	1	1
513.0	0	1	1
515.0	0	1	1
518.0	0	2	2
519.0	0	1	1
520.0	0	1	1
523.0	0	1	1
524.0	0	1	1
525.0	0	1	1
526.0	0	1	1
527.0	0	1	1
540.0	0	1	1
541.0	0	1	1
543.0	0	1	1
544.0	0	2	2
545.0	0	1	1
547.0	0	1	1
550.0	0	1	1
553.0	0	1	1
558.0	0	1	1
559.0	0	1	1
562.0	0	1	1
564.0	0	1	1
565.0	0	2	2
568.0	0	1	1
573.0	0	1	1
577.0	0	1	1
578.0	0	1	1
579.0	0	2	2
581.0	0	1	1
588.0	0	1	1
589.0	0	1	1
590.0	0	2	2
591.0	0	1	1
597.0	0	1	1
598.0	0	1	1
602.0	0	1	1
613.0	0	1	1
614.0	0	1	1
617.0	0	1	1
630.0	0	1	1
632.0	0	2	2
637.0	0	1	1
640.0	0	1	1
643.0	0	1	1
644.0	0	1	1
658.0	0	1	1
663.0	0	1	1
665.0	0	1	1
678.0	0	1	1
682.0	0	1	1
687.0	0	1	1
697.0	0	1	1
698.0	0	1	1
703.0	0	1	1
708.0	0	1	1
712.0	0	1	1
718.0	0	1	1
720.0	0	1	1
743.0	0	1	1
753.0	0	1	1
754.0	0	1	1
758.0	0	1	1
761.0	0	1	1
763.0	0	2	2
772.0	0	1	1
774.0	0	1	1
784.0	0	1	1
795.0	0	2	2
797.0	0	1	1
805.0	0	1	1
809.0	0	1	1
817.0	0	1	1
819.0	0	1	1
826.0	0	1	1
833.0	0	1	1
837.0	0	1	1
848.0	0	1	1
864.0	0	1	1
872.0	0	1	1
873.0	0	1	1
878.0	0	2	2
883.0	0	1	1
899.0	0	1	1
901.0	0	1	1
902.0	0	1	1
911.0	0	1	1
927.0	0	1	1
956.0	0	1	1
964.0	0	1	1
965.0	0	1	1
967.0	0	1	1
972.0	0	1	1
978.0	0	1	1
988.0	0	1	1
995.0	0	1	1
998.0	0	1	1
1004.0	0	1	1
1015.0	0	1	1
1020.0	0	1	1
1035.0	0	1	1
1055.0	0	1	1
1066.0	0	1	1
1071.0	0	1	1
1084.0	0	1	1
1087.0	0	1	1
1102.0	0	1	1
1114.0	0	1	1
1115.0	0	1	1
1127.0	0	1	1
1134.0	0	1	1
1137.0	0	1	1
1147.0	0	1	1
1148.0	0	1	1
1149.0	0	1	1
1153.0	0	1	1
1171.0	0	1	1
1181.0	0	1	1
1189.0	0	1	1
1196.0	0	1	1
1210.0	0	1	1
1218.0	0	1	1
1235.0	0	1	1
1237.0	0	1	1
1238.0	0	1	1
1249.0	0	1	1
1254.0	0	1	1
1288.0	0	1	1
1290.0	0	2	2
1295.0	0	1	1
1314.0	0	1	1
1333.0	0	1	1
1336.0	0	2	2
1344.0	0	1	1
1351.0	0	1	1
1352.0	0	1	1
1395.0	0	1	1
1428.0	0	1	1
1434.0	0	1	1
1458.0	0	1	1
1469.0	0	1	1
1530.0	0	1	1
1588.0	0	1	1
1592.0	0	1	1
1596.0	0	1	1
1613.0	0	1	1
1684.0	0	1	1
1722.0	0	1	1
1738.0	0	1	1
1762.0	0	1	1
1772.0	0	1	1
1777.0	0	1	1
1788.0	0	1	1
1829.0	0	1	1
1837.0	0	1	1
1907.0	0	1	1
1944.0	0	1	1
2016.0	0	1	1
2017.0	0	1	1
2039.0	0	1	1
2090.0	0	1	1
2165.0	0	1	1
2182.0	0	1	1
2346.0	0	1	1
2349.0	0	1	1
2444.0	0	1	1
2550.0	0	1	1
2585.0	0	1	1
2598.0	0	1	1
2619.0	0	1	1
2650.0	0	1	1
2667.0	0	1	1
2791.0	0	1	1
2806.0	0	1	1
2843.0	0	1	1
3044.0	0	1	1
3110.0	0	1	1
3153.0	0	1	1
3331.0	0	1	1
3401.0	0	1	1
3409.0	0	1	1
3491.0	0	1	1
3504.0	0	1	1
3804.0	0	1	1
4163.0	0	1	1
4193.0	0	1	1
4314.0	0	1	1
4431.0	0	1	1
4482.0	0	1	1
4670.0	0	1	1
5178.0	0	1	1
5184.0	0	1	1
5415.0	0	1	1
5751.0	0	1	1
5940.0	0	1	1
6182.0	0	1	1
6485.0	0	1	1
6490.0	0	1	1
6539.0	0	1	1
7382.0	0	1	1
8382.0	0	1	1
8696.0	0	1	1
11457.0	0	1	1
12857.0	0	1	1
25987.0	0	1	1