Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9c/23677ccc4d2b40c8b99bdeb5215367/A549_FFPE_01_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/85/e452164a5ea24ace77320f6faee8f5/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/85/e452164a5ea24ace77320f6faee8f5/.command.run
==> STAGING COMPLETE (3 inputs)

PAIRED_END_BAM_INPUT
paired = 89435
unpaired = 21881
MERGED PAIRED END READS = 89435
MATES PROCESSED = 200751
TOTAL READS     = 111316
DISTINCT READS  = 26919
DISTINCT COUNTS = 184
MAX COUNT       = 2551
COUNTS OF 1     = 17363
MAX TERMS       = 54
OBSERVED COUNTS (2552)
1	17363
2	4120
3	1568
4	876
5	537
6	380
7	286
8	189
9	175
10	124
11	107
12	94
13	81
14	80
15	59
16	53
17	45
18	26
19	40
20	34
21	23
22	42
23	26
24	25
25	31
26	16
27	28
28	27
29	19
30	14
31	13
32	18
33	10
34	11
35	15
36	5
37	12
38	11
39	9
40	11
41	11
42	7
43	4
44	7
45	3
46	8
47	4
48	10
49	8
50	8
51	6
52	6
53	4
54	6
55	2
57	3
58	4
59	4
60	2
61	5
62	3
63	3
64	3
65	3
66	5
67	4
68	3
69	4
70	1
71	5
72	5
73	4
74	4
75	5
76	5
78	1
79	3
80	1
81	2
82	1
83	2
84	1
85	3
86	1
88	2
89	4
92	4
94	2
95	3
96	2
97	3
98	1
99	1
100	2
104	1
105	2
106	1
107	2
110	3
112	2
116	1
117	2
122	3
125	1
126	2
128	1
129	1
130	1
132	1
133	1
136	1
139	1
140	2
142	1
143	2
145	1
146	2
148	1
150	1
151	1
153	1
155	1
158	1
160	1
162	1
164	2
165	2
166	1
169	1
176	1
180	1
181	2
184	1
186	1
187	1
188	1
192	1
193	1
197	1
203	1
213	2
214	1
225	1
228	1
230	1
231	1
233	1
236	2
242	1
243	1
245	1
247	1
252	1
257	1
267	1
270	2
297	1
299	1
300	1
306	1
318	1
324	1
342	1
343	1
380	1
403	1
407	1
408	1
445	1
448	1
482	1
490	1
523	1
538	1
544	1
589	1
618	1
1094	1
1341	1
1353	1
1466	1
2008	1
2040	1
2551	1

[ESTIMATING YIELD CURVE]
[BOOTSTRAPPING HISTOGRAM]
..........._......_.....................................................
................_..............
[COMPUTING CONFIDENCE INTERVALS]
[WRITING OUTPUT]