## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=999 INPUT=[/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/star/GRCh38.p13-D12_supernatant_TA1uM_2.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/star/GRCh38.p13-D12_supernatant_TA1uM_2.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/markdup/GRCh38.p13-D12_supernatant_TA1uM_2.samtools-coordinate.metrics.txt TMP_DIR=[/scratch/slrinzema/tmp]    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false FLOW_MODE=false FLOW_QUALITY_SUM_STRATEGY=false USE_END_IN_UNPAIRED_READS=false USE_UNPAIRED_CLIPPED_END=false UNPAIRED_END_UNCERTAINTY=0 FLOW_SKIP_FIRST_N_FLOWS=0 FLOW_Q_IS_KNOWN_END=false FLOW_EFFECTIVE_QUALITY_THRESHOLD=15 ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false 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 VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Fri Oct 06 03:32:52 CEST 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
Unknown Library	1181	18158126	19141692	0	1073	2600534	0	0.143241	57184801

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	14472007	14472007
2.0	1.727942	758267	758267
3.0	2.257841	141659	141659
4.0	2.643577	59999	59999
5.0	2.92437	33137	33137
6.0	3.128771	20484	20484
7.0	3.277564	14141	14141
8.0	3.385876	9951	9951
9.0	3.464721	7292	7292
10.0	3.522115	5636	5636
11.0	3.563895	4416	4416
12.0	3.594308	3672	3672
13.0	3.616447	3057	3057
14.0	3.632563	2466	2466
15.0	3.644295	2089	2089
16.0	3.652835	1771	1771
17.0	3.659051	1494	1494
18.0	3.663576	1300	1300
19.0	3.666871	1206	1206
20.0	3.669268	1060	1060
21.0	3.671014	931	931
22.0	3.672285	850	850
23.0	3.67321	724	724
24.0	3.673883	670	670
25.0	3.674373	577	577
26.0	3.67473	515	515
27.0	3.67499	448	448
28.0	3.675179	462	462
29.0	3.675316	426	426
30.0	3.675417	346	346
31.0	3.675489	350	350
32.0	3.675543	310	310
33.0	3.675581	297	297
34.0	3.675609	272	272
35.0	3.67563	220	220
36.0	3.675645	219	219
37.0	3.675656	193	193
38.0	3.675663	193	193
39.0	3.675669	187	187
40.0	3.675673	176	176
41.0	3.675676	170	170
42.0	3.675679	173	173
43.0	3.67568	123	123
44.0	3.675681	158	158
45.0	3.675682	108	108
46.0	3.675683	104	104
47.0	3.675683	116	116
48.0	3.675684	104	104
49.0	3.675684	101	101
50.0	3.675684	101	101
51.0	3.675684	92	92
52.0	3.675684	85	85
53.0	3.675684	85	85
54.0	3.675684	79	79
55.0	3.675684	69	69
56.0	3.675685	92	92
57.0	3.675685	48	48
58.0	3.675685	64	64
59.0	3.675685	53	53
60.0	3.675685	65	65
61.0	3.675685	52	52
62.0	3.675685	68	68
63.0	3.675685	61	61
64.0	3.675685	58	58
65.0	3.675685	54	54
66.0	3.675685	41	41
67.0	3.675685	43	43
68.0	3.675685	51	51
69.0	3.675685	30	30
70.0	3.675685	37	37
71.0	3.675685	44	44
72.0	3.675685	33	33
73.0	3.675685	32	32
74.0	3.675685	42	42
75.0	3.675685	26	26
76.0	3.675685	29	29
77.0	3.675685	33	33
78.0	3.675685	40	40
79.0	3.675685	30	30
80.0	3.675685	25	25
81.0	3.675685	33	33
82.0	3.675685	21	21
83.0	3.675685	33	33
84.0	3.675685	23	23
85.0	3.675685	23	23
86.0	3.675685	22	22
87.0	3.675685	29	29
88.0	3.675685	23	23
89.0	3.675685	16	16
90.0	3.675685	24	24
91.0	3.675685	21	21
92.0	3.675685	22	22
93.0	3.675685	19	19
94.0	3.675685	21	21
95.0	3.675685	15	15
96.0	3.675685	23	23
97.0	3.675685	14	14
98.0	3.675685	15	15
99.0	3.675685	18	18
100.0	3.675685	16	16
101.0	0	11	11
102.0	0	8	8
103.0	0	13	13
104.0	0	16	16
105.0	0	17	17
106.0	0	16	16
107.0	0	16	16
108.0	0	14	14
109.0	0	18	18
110.0	0	15	15
111.0	0	17	17
112.0	0	15	15
113.0	0	17	17
114.0	0	11	11
115.0	0	3	3
116.0	0	14	14
117.0	0	9	9
118.0	0	7	7
119.0	0	12	12
120.0	0	15	15
121.0	0	9	9
122.0	0	6	6
123.0	0	15	15
124.0	0	9	9
125.0	0	7	7
126.0	0	5	5
127.0	0	9	9
128.0	0	6	6
129.0	0	16	16
130.0	0	7	7
131.0	0	4	4
132.0	0	7	7
133.0	0	6	6
134.0	0	9	9
135.0	0	8	8
136.0	0	5	5
137.0	0	5	5
138.0	0	6	6
139.0	0	3	3
140.0	0	7	7
141.0	0	5	5
142.0	0	4	4
143.0	0	7	7
144.0	0	5	5
145.0	0	6	6
146.0	0	3	3
147.0	0	10	10
148.0	0	7	7
149.0	0	10	10
150.0	0	5	5
151.0	0	8	8
152.0	0	3	3
153.0	0	5	5
154.0	0	6	6
155.0	0	7	7
156.0	0	7	7
157.0	0	1	1
158.0	0	4	4
159.0	0	6	6
160.0	0	6	6
161.0	0	3	3
162.0	0	2	2
163.0	0	3	3
164.0	0	6	6
165.0	0	5	5
166.0	0	2	2
167.0	0	1	1
168.0	0	7	7
170.0	0	3	3
171.0	0	5	5
172.0	0	1	1
173.0	0	1	1
174.0	0	3	3
175.0	0	4	4
176.0	0	5	5
177.0	0	1	1
178.0	0	2	2
179.0	0	5	5
180.0	0	4	4
182.0	0	1	1
183.0	0	3	3
184.0	0	1	1
185.0	0	5	5
186.0	0	4	4
187.0	0	1	1
188.0	0	3	3
189.0	0	1	1
190.0	0	3	3
191.0	0	1	1
192.0	0	3	3
193.0	0	4	4
194.0	0	4	4
195.0	0	3	3
196.0	0	1	1
197.0	0	2	2
198.0	0	2	2
199.0	0	3	3
200.0	0	1	1
201.0	0	1	1
202.0	0	1	1
203.0	0	4	4
204.0	0	5	5
205.0	0	1	1
206.0	0	1	1
207.0	0	1	1
208.0	0	1	1
209.0	0	4	4
210.0	0	1	1
211.0	0	1	1
212.0	0	3	3
213.0	0	4	4
214.0	0	1	1
215.0	0	2	2
216.0	0	1	1
217.0	0	2	2
218.0	0	1	1
220.0	0	2	2
221.0	0	3	3
222.0	0	1	1
223.0	0	1	1
224.0	0	1	1
225.0	0	2	2
226.0	0	5	5
228.0	0	3	3
229.0	0	1	1
230.0	0	1	1
231.0	0	2	2
232.0	0	1	1
233.0	0	1	1
234.0	0	4	4
235.0	0	1	1
236.0	0	2	2
238.0	0	1	1
240.0	0	1	1
241.0	0	2	2
244.0	0	1	1
245.0	0	7	7
246.0	0	1	1
248.0	0	1	1
249.0	0	2	2
250.0	0	1	1
251.0	0	3	3
252.0	0	1	1
253.0	0	1	1
256.0	0	2	2
258.0	0	1	1
259.0	0	2	2
260.0	0	3	3
261.0	0	1	1
262.0	0	2	2
266.0	0	3	3
267.0	0	1	1
268.0	0	1	1
269.0	0	1	1
271.0	0	2	2
273.0	0	2	2
274.0	0	1	1
275.0	0	1	1
276.0	0	3	3
278.0	0	1	1
282.0	0	2	2
283.0	0	1	1
284.0	0	2	2
286.0	0	3	3
287.0	0	2	2
288.0	0	1	1
290.0	0	1	1
292.0	0	2	2
295.0	0	1	1
296.0	0	1	1
297.0	0	1	1
301.0	0	2	2
305.0	0	1	1
311.0	0	1	1
312.0	0	2	2
313.0	0	2	2
315.0	0	1	1
316.0	0	1	1
319.0	0	1	1
320.0	0	2	2
323.0	0	1	1
327.0	0	2	2
328.0	0	1	1
332.0	0	1	1
333.0	0	1	1
334.0	0	1	1
336.0	0	1	1
337.0	0	1	1
339.0	0	1	1
342.0	0	1	1
348.0	0	1	1
350.0	0	3	3
351.0	0	1	1
358.0	0	1	1
363.0	0	1	1
364.0	0	1	1
367.0	0	2	2
369.0	0	1	1
370.0	0	1	1
371.0	0	1	1
376.0	0	2	2
379.0	0	1	1
381.0	0	1	1
387.0	0	2	2
394.0	0	1	1
398.0	0	1	1
400.0	0	1	1
404.0	0	1	1
405.0	0	1	1
410.0	0	1	1
414.0	0	1	1
415.0	0	1	1
416.0	0	1	1
418.0	0	1	1
420.0	0	1	1
431.0	0	1	1
444.0	0	1	1
448.0	0	2	2
486.0	0	2	2
487.0	0	1	1
491.0	0	1	1
507.0	0	1	1
519.0	0	1	1
528.0	0	1	1
546.0	0	1	1
559.0	0	1	1
569.0	0	1	1
583.0	0	1	1
587.0	0	1	1
591.0	0	1	1
599.0	0	1	1
600.0	0	1	1
611.0	0	1	1
613.0	0	1	1
619.0	0	1	1
622.0	0	1	1
623.0	0	1	1
626.0	0	2	2
657.0	0	1	1
659.0	0	1	1
674.0	0	1	1
711.0	0	1	1
731.0	0	1	1
735.0	0	1	1
768.0	0	1	1
802.0	0	2	2
804.0	0	1	1
828.0	0	1	1
829.0	0	1	1
853.0	0	1	1
867.0	0	1	1
870.0	0	1	1
906.0	0	1	1
916.0	0	1	1
986.0	0	1	1
1058.0	0	1	1
1167.0	0	1	1
1309.0	0	1	1
1333.0	0	1	1
2706.0	0	1	1