## 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_TA_1.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/star/GRCh38.p13-D12_supernatant_TA_1.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_TA_1.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 03:19:21 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	597	19463792	15846329	0	453	3187532	0	0.163776	52742754

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	14513390	14513390
2.0	1.691403	1384744	1384744
3.0	2.169441	201533	201533
4.0	2.499958	63726	63726
5.0	2.728478	31560	31560
6.0	2.886478	19319	19319
7.0	2.995719	12864	12864
8.0	3.071249	8885	8885
9.0	3.12347	6609	6609
10.0	3.159577	4967	4967
11.0	3.18454	3857	3857
12.0	3.201801	2971	2971
13.0	3.213734	2441	2441
14.0	3.221985	2015	2015
15.0	3.22769	1818	1818
16.0	3.231634	1554	1554
17.0	3.234361	1225	1225
18.0	3.236247	1078	1078
19.0	3.237551	903	903
20.0	3.238452	792	792
21.0	3.239075	694	694
22.0	3.239506	655	655
23.0	3.239804	552	552
24.0	3.24001	568	568
25.0	3.240152	457	457
26.0	3.240251	414	414
27.0	3.240319	422	422
28.0	3.240366	318	318
29.0	3.240398	312	312
30.0	3.240421	282	282
31.0	3.240436	268	268
32.0	3.240447	255	255
33.0	3.240455	230	230
34.0	3.24046	215	215
35.0	3.240463	198	198
36.0	3.240466	178	178
37.0	3.240468	173	173
38.0	3.240469	156	156
39.0	3.24047	150	150
40.0	3.24047	153	153
41.0	3.24047	103	103
42.0	3.240471	133	133
43.0	3.240471	120	120
44.0	3.240471	86	86
45.0	3.240471	87	87
46.0	3.240471	88	88
47.0	3.240471	83	83
48.0	3.240471	86	86
49.0	3.240471	78	78
50.0	3.240471	82	82
51.0	3.240471	86	86
52.0	3.240471	67	67
53.0	3.240471	50	50
54.0	3.240471	61	61
55.0	3.240471	62	62
56.0	3.240471	61	61
57.0	3.240471	56	56
58.0	3.240471	44	44
59.0	3.240471	44	44
60.0	3.240471	49	49
61.0	3.240471	53	53
62.0	3.240471	37	37
63.0	3.240471	43	43
64.0	3.240471	46	46
65.0	3.240471	50	50
66.0	3.240471	27	27
67.0	3.240471	37	37
68.0	3.240471	28	28
69.0	3.240471	32	32
70.0	3.240471	30	30
71.0	3.240471	27	27
72.0	3.240471	32	32
73.0	3.240471	31	31
74.0	3.240471	27	27
75.0	3.240471	19	19
76.0	3.240471	24	24
77.0	3.240471	26	26
78.0	3.240471	26	26
79.0	3.240471	26	26
80.0	3.240471	26	26
81.0	3.240471	28	28
82.0	3.240471	21	21
83.0	3.240471	20	20
84.0	3.240471	17	17
85.0	3.240471	19	19
86.0	3.240471	18	18
87.0	3.240471	21	21
88.0	3.240471	16	16
89.0	3.240471	16	16
90.0	3.240471	10	10
91.0	3.240471	14	14
92.0	3.240471	19	19
93.0	3.240471	24	24
94.0	3.240471	25	25
95.0	3.240471	17	17
96.0	3.240471	17	17
97.0	3.240471	13	13
98.0	3.240471	19	19
99.0	3.240471	11	11
100.0	3.240471	19	19
101.0	0	12	12
102.0	0	14	14
103.0	0	13	13
104.0	0	8	8
105.0	0	10	10
106.0	0	12	12
107.0	0	9	9
108.0	0	12	12
109.0	0	12	12
110.0	0	14	14
111.0	0	13	13
112.0	0	7	7
113.0	0	11	11
114.0	0	10	10
115.0	0	6	6
116.0	0	6	6
117.0	0	17	17
118.0	0	10	10
119.0	0	10	10
120.0	0	12	12
121.0	0	9	9
122.0	0	9	9
123.0	0	11	11
124.0	0	6	6
125.0	0	10	10
126.0	0	5	5
127.0	0	7	7
128.0	0	8	8
129.0	0	12	12
130.0	0	10	10
131.0	0	4	4
132.0	0	5	5
133.0	0	5	5
134.0	0	8	8
135.0	0	6	6
136.0	0	8	8
137.0	0	5	5
138.0	0	3	3
139.0	0	5	5
140.0	0	2	2
141.0	0	7	7
142.0	0	9	9
143.0	0	9	9
144.0	0	3	3
145.0	0	8	8
146.0	0	3	3
147.0	0	6	6
148.0	0	8	8
149.0	0	5	5
150.0	0	4	4
151.0	0	2	2
152.0	0	3	3
153.0	0	7	7
154.0	0	3	3
155.0	0	5	5
156.0	0	3	3
157.0	0	4	4
158.0	0	2	2
159.0	0	6	6
160.0	0	4	4
161.0	0	2	2
162.0	0	3	3
163.0	0	5	5
164.0	0	1	1
165.0	0	3	3
166.0	0	10	10
167.0	0	1	1
168.0	0	4	4
169.0	0	3	3
170.0	0	5	5
171.0	0	2	2
172.0	0	5	5
173.0	0	2	2
174.0	0	2	2
175.0	0	4	4
176.0	0	4	4
177.0	0	4	4
178.0	0	2	2
179.0	0	2	2
180.0	0	2	2
181.0	0	2	2
182.0	0	3	3
183.0	0	7	7
184.0	0	2	2
185.0	0	2	2
186.0	0	2	2
187.0	0	1	1
188.0	0	2	2
189.0	0	2	2
191.0	0	3	3
192.0	0	5	5
193.0	0	4	4
194.0	0	2	2
195.0	0	5	5
197.0	0	5	5
199.0	0	3	3
200.0	0	1	1
202.0	0	2	2
203.0	0	6	6
204.0	0	1	1
206.0	0	4	4
207.0	0	3	3
208.0	0	1	1
210.0	0	3	3
211.0	0	3	3
212.0	0	2	2
213.0	0	1	1
215.0	0	1	1
216.0	0	4	4
218.0	0	3	3
219.0	0	2	2
220.0	0	1	1
221.0	0	2	2
222.0	0	3	3
223.0	0	1	1
224.0	0	3	3
225.0	0	3	3
226.0	0	2	2
227.0	0	1	1
228.0	0	1	1
229.0	0	4	4
231.0	0	2	2
232.0	0	3	3
233.0	0	3	3
234.0	0	1	1
235.0	0	2	2
237.0	0	1	1
240.0	0	2	2
242.0	0	2	2
243.0	0	3	3
245.0	0	3	3
248.0	0	1	1
249.0	0	1	1
250.0	0	1	1
251.0	0	1	1
253.0	0	5	5
255.0	0	3	3
257.0	0	2	2
258.0	0	1	1
263.0	0	1	1
264.0	0	2	2
266.0	0	2	2
270.0	0	1	1
273.0	0	2	2
275.0	0	1	1
277.0	0	1	1
278.0	0	1	1
279.0	0	1	1
283.0	0	1	1
284.0	0	1	1
286.0	0	2	2
289.0	0	2	2
290.0	0	2	2
291.0	0	1	1
292.0	0	1	1
294.0	0	3	3
298.0	0	1	1
299.0	0	1	1
304.0	0	1	1
305.0	0	1	1
306.0	0	1	1
307.0	0	1	1
309.0	0	1	1
314.0	0	2	2
315.0	0	1	1
317.0	0	1	1
320.0	0	1	1
321.0	0	1	1
322.0	0	1	1
323.0	0	1	1
324.0	0	1	1
329.0	0	1	1
332.0	0	2	2
336.0	0	1	1
338.0	0	1	1
343.0	0	1	1
344.0	0	1	1
345.0	0	2	2
349.0	0	1	1
351.0	0	1	1
355.0	0	1	1
357.0	0	3	3
358.0	0	2	2
359.0	0	1	1
362.0	0	1	1
363.0	0	1	1
364.0	0	2	2
365.0	0	1	1
366.0	0	2	2
368.0	0	1	1
375.0	0	2	2
378.0	0	1	1
387.0	0	1	1
391.0	0	1	1
393.0	0	1	1
396.0	0	1	1
397.0	0	1	1
405.0	0	1	1
408.0	0	4	4
421.0	0	1	1
422.0	0	1	1
424.0	0	1	1
426.0	0	1	1
428.0	0	1	1
435.0	0	1	1
436.0	0	1	1
437.0	0	1	1
440.0	0	1	1
442.0	0	1	1
453.0	0	1	1
454.0	0	1	1
456.0	0	1	1
458.0	0	1	1
469.0	0	1	1
474.0	0	1	1
478.0	0	1	1
479.0	0	1	1
483.0	0	1	1
484.0	0	2	2
489.0	0	1	1
494.0	0	1	1
500.0	0	1	1
508.0	0	1	1
522.0	0	2	2
533.0	0	1	1
536.0	0	1	1
538.0	0	1	1
548.0	0	1	1
549.0	0	1	1
555.0	0	1	1
562.0	0	1	1
568.0	0	1	1
580.0	0	1	1
583.0	0	1	1
585.0	0	1	1
588.0	0	1	1
597.0	0	1	1
612.0	0	1	1
636.0	0	1	1
640.0	0	1	1
641.0	0	1	1
712.0	0	1	1
733.0	0	1	1
772.0	0	1	1
781.0	0	1	1
782.0	0	1	1
801.0	0	1	1
805.0	0	1	1
821.0	0	1	1
825.0	0	1	1
840.0	0	1	1
844.0	0	1	1
850.0	0	1	1
907.0	0	1	1
934.0	0	1	1
1026.0	0	1	1
1028.0	0	1	1
1044.0	0	1	1
1046.0	0	1	1
1053.0	0	1	1
1065.0	0	1	1
1071.0	0	1	1
1101.0	0	1	1
1124.0	0	1	1
1129.0	0	1	1
1145.0	0	1	1
1155.0	0	1	1
1331.0	0	1	1
1344.0	0	1	1
1356.0	0	1	1
1357.0	0	1	1