Script file	/users/dskim89/git/bds_atac/atac.bds
Program ID	atac.bds.20160622_160104_614
Start time	2016-06-22 16:01:04
Run time	03:27:52.523
Tasks executed	33
Tasks failed	0
Tasks failed names
Arguments*	[-adapter1_1, CTGTCTCTTATACACATCT, -adapter1_2, CTGTCTCTTATACACATCT, -fastq1_1, 151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.fastq.gz, -fastq1_2, 151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_2_pf.fastq.gz, -out_dir, /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA, -title, 151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA, -species, hg19, -multimapping, 4]
System*	local
Cpus*	1
Exit value	0

Thread ID	Parent	Tasks
thread_Root	None	atac.bds.20160622_160104_614/task.callpeak_etc.filt_top_peaks_rep1.line_27.id_22 atac.bds.20160622_160104_614/task.callpeak_etc.filt_top_peaks_rep1.line_27.id_23 atac.bds.20160622_160104_614/task.callpeak_etc.filt_top_peaks_rep1_pr1.line_27.id_24 atac.bds.20160622_160104_614/task.callpeak_etc.filt_top_peaks_rep1_pr2.line_27.id_25 atac.bds.20160622_160104_614/task.callpeak_etc.filt_top_peaks_rep1_pr1.line_27.id_26 atac.bds.20160622_160104_614/task.callpeak_etc.filt_top_peaks_rep1_pr2.line_27.id_27 atac.bds.20160622_160104_614/task.callpeak_etc.naive_overlap_thresh_peak.line_68.id_28 atac.bds.20160622_160104_614/task.callpeak_etc.naive_overlap_thresh_gpeak.line_68.id_29 atac.bds.20160622_160104_614/task.idr.idr2_rep1_pr.line_73.id_30 atac.bds.20160622_160104_614/task.idr.idr_final_qc.line_214.id_33 atac.bds.20160622_160104_614/task.report.peak2hammock.line_422.id_35 atac.bds.20160622_160104_614/task.report.peak2hammock.line_422.id_36 atac.bds.20160622_160104_614/task.report.peak2hammock.line_422.id_37 atac.bds.20160622_160104_614/task.report.peak2hammock.line_422.id_38 atac.bds.20160622_160104_614/task.report_graphviz.report.line_108.id_39 atac.bds.20160622_160104_614/task.report.pdf2png.line_385.id_42
thread_61	thread_Root	atac.bds.20160622_160104_614_parallel_61/task.atac.ataqc_rep1.line_951.id_34
thread_20	thread_Root	atac.bds.20160622_160104_614_parallel_20/task.align_trim_adapter.trim_adapters_PE_rep1.line_128.id_6 atac.bds.20160622_160104_614_parallel_20/task.align_bowtie2.bowtie2_PE_rep1.line_137.id_7 atac.bds.20160622_160104_614_parallel_20/task.postalign_bam.dedup_bam_PE_rep1.line_182.id_8 atac.bds.20160622_160104_614_parallel_20/task.postalign_bam.nmsrt_bam_rep1.line_297.id_9 atac.bds.20160622_160104_614_parallel_20/task.postalign_bam.bam_to_bedpe_rep1.line_406.id_10 atac.bds.20160622_160104_614_parallel_20/task.postalign_bam.bedpe_to_tag_rep1.line_445.id_11 atac.bds.20160622_160104_614_parallel_20/task.postalign_bed.spr_PE_rep1.line_275.id_12 atac.bds.20160622_160104_614_parallel_20/task.postalign_bed.shift_tag_rep1.line_163.id_13 atac.bds.20160622_160104_614_parallel_20/task.postalign_bed.shift_tag_rep1.line_163.id_14 atac.bds.20160622_160104_614_parallel_20/task.postalign_bed.shift_tag_rep1.line_163.id_15 atac.bds.20160622_160104_614_parallel_20/task.postalign_bed.subsample_bedpe2tagrep1.line_103.id_16 atac.bds.20160622_160104_614_parallel_20/task.postalign_bed.xcor_rep1.line_193.id_17 atac.bds.20160622_160104_614_parallel_20/task.callpeak_macs2.macs2_atac_rep1.line_64.id_18 atac.bds.20160622_160104_614_parallel_20/task.callpeak_macs2.macs2_atac_rep1.pval0.1.line_64.id_19 atac.bds.20160622_160104_614_parallel_20/task.callpeak_macs2.macs2_atac_rep1_pr1.pval0.1.line_64.id_20 atac.bds.20160622_160104_614_parallel_20/task.callpeak_macs2.macs2_atac_rep1_pr2.pval0.1.line_64.id_21

Task details

Task

Execution

Time

Dependencies

Task program, Errors, StdOut / StdErr

Num	1
ID	task.align_trim_adapter.trim_adapters_PE_rep1.line_128.id_6
Name	trim_adapters_PE rep1
Thread	thread_20
PID	72212

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	8
Mem

Start	2016-06-22 16:01:06
End	2016-06-22 16:10:39
Elapsed	00:09:32
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/www/kundaje/dskim89/epinomics/fastqs_2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.fastq.gz /srv/www/kundaje/dskim89/epinomics/fastqs_2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_2_pf.fastq.gz
Output files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.fastq.gz /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_2_pf.trim.fastq.gz
Dependencies

 
# SYS command. line 130

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/dskim89/git/bds_atac/.:/users/dskim89/git/bds_atac/modules:/users/dskim89/git/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 132

 cutadapt -m 5 -e 0.20 -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT -o /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.fastq -p /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_2_pf.trim.fastq /srv/www/kundaje/dskim89/epinomics/fastqs_2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.fastq.gz /srv/www/kundaje/dskim89/epinomics/fastqs_2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_2_pf.fastq.gz

# SYS command. line 134

 pigz -p 8 -f /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.fastq

# SYS command. line 135

 pigz -p 8 -f /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_2_pf.trim.fastq

# SYS command. line 137

 TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."

   
--------------------Stdout--------------------
This is cutadapt 1.9.1 with Python 2.7.11
Command line parameters: -m 5 -e 0.20 -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT -o /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.fastq -p /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_2_pf.trim.fastq /srv/www/kundaje/dskim89/epinomics/fastqs_2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.fastq.gz /srv/www/kundaje/dskim89/epinomics/fastqs_2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_2_pf.fastq.gz
Trimming 2 adapters with at most 20.0% errors in paired-end mode ...
Finished in 443.67 s (24 us/read; 2.46 M reads/minute).

=== Summary ===

Total read pairs processed:         18,199,458
  Read 1 with adapter:              10,098,096 (55.5%)
  Read 2 with adapter:              10,081,852 (55.4%)
Pairs that were too short:                 124 (0.0%)
Pairs written (passing filters):    18,199,334 (100.0%)

Total basepairs processed: 3,676,290,516 bp
  Read 1: 1,838,145,258 bp
  Read 2: 1,838,145,258 bp
Total written (filtered):  2,866,550,117 bp (78.0%)
  Read 1: 1,432,815,638 bp
  Read 2: 1,433,734,479 bp

=== First read: Adapter 1 ===

Sequence: CTGTCTCTTATACACATCT; Type: regular 3'; Length: 19; Trimmed: 10098096 times.

No. of allowed errors:
0-4 bp: 0; 5-9 bp: 1; 10-14 bp: 2; 15-19 bp: 3

Bases preceding removed adapters:
  A: 11.2%
  C: 43.1%
  G: 26.2%
  T: 19.5%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	242792	284366.5	0	242792
4	204516	71091.6	0	106863 97653
5	240862	17772.9	1	79375 161487
6	147266	4443.2	1	77129 70137
7	103564	1110.8	1	75225 28339
8	89389	277.7	1	74830 12246 2313
9	84275	69.4	1	73195 4034 7046
10	80988	17.4	2	70331 2808 7849
11	76883	4.3	2	71107 1362 4414
12	76717	1.1	2	73596 1256 1801 64
13	77379	0.3	2	74567 1656 872 284
14	83520	0.1	2	80807 1566 629 518
15	86573	0.0	3	83699 1378 452 1044
16	89934	0.0	3	87160 1586 626 562
17	91174	0.0	3	88452 1663 621 438
18	92210	0.0	3	89334 2077 443 356
19	91385	0.0	3	88858 1831 421 275
20	90389	0.0	3	88029 1743 375 242
21	86162	0.0	3	83976 1573 347 266
22	90254	0.0	3	88076 1624 330 224
23	94967	0.0	3	92602 1734 371 260
24	101066	0.0	3	98686 1739 382 259
25	104594	0.0	3	102132 1821 368 273
26	106652	0.0	3	104173 1826 387 266
27	113363	0.0	3	110669 2039 408 247
28	113913	0.0	3	111075 2128 454 256
29	113432	0.0	3	110765 1983 387 297
30	110268	0.0	3	107658 1970 373 267
31	108888	0.0	3	106184 2002 411 291
32	112759	0.0	3	110327 1813 386 233
33	117599	0.0	3	115031 1909 383 276
34	131906	0.0	3	128988 2226 398 294
35	148931	0.0	3	145445 2676 524 286
36	144676	0.0	3	141364 2580 456 276
37	144399	0.0	3	141159 2560 439 241
38	143930	0.0	3	140721 2574 389 246
39	150129	0.0	3	146852 2634 383 260
40	143969	0.0	3	140729 2625 370 245
41	138643	0.0	3	135462 2632 361 188
42	143680	0.0	3	140246 2832 349 253
43	149171	0.0	3	145772 2772 385 242
44	161736	0.0	3	158024 3056 413 243
45	178432	0.0	3	174377 3411 408 236
46	187401	0.0	3	183288 3410 431 272
47	197328	0.0	3	193060 3582 433 253
48	207842	0.0	3	203332 3762 471 277
49	244453	0.0	3	239048 4617 500 288
50	241390	0.0	3	235935 4643 541 271
51	208288	0.0	3	203653 3989 398 248
52	191435	0.0	3	187110 3761 369 195
53	194030	0.0	3	189678 3798 364 190
54	208632	0.0	3	204153 3899 393 187
55	234151	0.0	3	229412 4138 373 228
56	253498	0.0	3	248771 4144 367 216
57	257232	0.0	3	252482 4242 322 186
58	251152	0.0	3	246479 4182 331 160
59	295520	0.0	3	289910 4997 404 209
60	300718	0.0	3	295152 4942 409 215
61	264283	0.0	3	259344 4383 388 168
62	227729	0.0	3	223377 3949 277 126
63	206617	0.0	3	202632 3647 216 122
64	207423	0.0	3	203260 3757 269 137
65	187163	0.0	3	183239 3591 228 105
66	116645	0.0	3	113991 2374 181 99
67	57953	0.0	3	56576 1247 85 45
68	31459	0.0	3	30686 671 62 40
69	17272	0.0	3	16861 354 30 27
70	13007	0.0	3	12531 413 31 32
71	11450	0.0	3	11044 364 28 14
72	14195	0.0	3	13757 392 21 25
73	15379	0.0	3	14827 509 25 18
74	19985	0.0	3	19243 682 42 18
75	27167	0.0	3	25904 1179 60 24
76	2422	0.0	3	2297 115 4 6
77	432	0.0	3	390 27 0 15
78	212	0.0	3	190 11 1 10
79	96	0.0	3	76 3 1 16
80	208	0.0	3	168 17 0 23
81	87	0.0	3	78 1 0 8
82	164	0.0	3	152 3 2 7
83	54	0.0	3	43 0 0 11
84	44	0.0	3	32 2 0 10
85	22	0.0	3	9 0 1 12
86	12	0.0	3	4 1 1 6
87	13	0.0	3	2 0 0 11
88	18	0.0	3	3 0 0 15
89	14	0.0	3	0 0 2 12
90	10	0.0	3	0 0 1 9
91	15	0.0	3	2 0 1 12
92	13	0.0	3	4 1 0 8
93	44	0.0	3	1 1 1 41
94	5	0.0	3	0 0 0 5
95	6	0.0	3	0 0 0 6
96	5	0.0	3	0 0 0 5
97	8	0.0	3	0 0 0 8
98	18	0.0	3	5 0 1 12
99	8	0.0	3	0 0 0 8
100	10	0.0	3	1 0 0 9
101	24	0.0	3	20 0 0 4

=== Second read: Adapter 2 ===

Sequence: CTGTCTCTTATACACATCT; Type: regular 3'; Length: 19; Trimmed: 10081852 times.

No. of allowed errors:
0-4 bp: 0; 5-9 bp: 1; 10-14 bp: 2; 15-19 bp: 3

Bases preceding removed adapters:
  A: 11.4%
  C: 42.6%
  G: 26.4%
  T: 19.6%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	243508	284366.5	0	243508
4	205778	71091.6	0	107681 98097
5	242231	17772.9	1	79653 162578
6	147200	4443.2	1	77288 69912
7	103529	1110.8	1	75391 28138
8	89375	277.7	1	74894 12115 2366
9	84312	69.4	1	73413 3836 7063
10	80986	17.4	2	70185 2910 7891
11	76814	4.3	2	71409 1079 4326
12	76681	1.1	2	73743 1026 1849 63
13	77460	0.3	2	74767 1575 798 320
14	83432	0.1	2	80950 1233 671 578
15	86558	0.0	3	84057 1114 472 915
16	89882	0.0	3	87505 1190 603 584
17	90929	0.0	3	88803 1242 441 443
18	91978	0.0	3	89627 1594 440 317
19	91227	0.0	3	89241 1378 319 289
20	90265	0.0	3	88280 1344 381 260
21	86062	0.0	3	84219 1247 315 281
22	90087	0.0	3	88253 1252 330 252
23	94785	0.0	3	92876 1297 334 278
24	100925	0.0	3	98876 1418 338 293
25	104282	0.0	3	102201 1446 343 292
26	106447	0.0	3	104385 1389 379 294
27	113133	0.0	3	110821 1604 402 306
28	113589	0.0	3	111238 1668 387 296
29	113206	0.0	3	110831 1689 386 300
30	110003	0.0	3	107872 1521 345 265
31	108613	0.0	3	106417 1532 355 309
32	112496	0.0	3	110258 1589 356 293
33	117321	0.0	3	115137 1561 370 253
34	131604	0.0	3	129050 1820 424 310
35	148553	0.0	3	145499 2217 483 354
36	144301	0.0	3	141494 2048 451 308
37	144153	0.0	3	141604 1887 377 285
38	143632	0.0	3	140997 1964 373 298
39	149809	0.0	3	147210 1945 365 289
40	143770	0.0	3	141161 1904 392 313
41	138399	0.0	3	135859 1894 397 249
42	143430	0.0	3	140824 1960 382 264
43	148880	0.0	3	146194 1989 419 278
44	161395	0.0	3	158531 2148 407 309
45	178130	0.0	3	175000 2405 430 295
46	187112	0.0	3	183787 2562 447 316
47	197053	0.0	3	193534 2733 492 294
48	207403	0.0	3	203683 2851 509 360
49	243874	0.0	3	239324 3618 554 378
50	240822	0.0	3	236230 3594 641 357
51	207863	0.0	3	203893 3126 512 332
52	191005	0.0	3	187463 2773 446 323
53	193536	0.0	3	190078 2726 430 302
54	208079	0.0	3	204297 3037 487 258
55	233600	0.0	3	229382 3358 527 333
56	252898	0.0	3	248364 3646 553 335
57	256567	0.0	3	252089 3606 556 316
58	250581	0.0	3	246066 3593 586 336
59	294728	0.0	3	289305 4383 643 397
60	299972	0.0	3	294267 4662 653 390
61	263591	0.0	3	258650 4028 573 340
62	227014	0.0	3	222872 3356 474 312
63	206068	0.0	3	202021 3314 479 254
64	206803	0.0	3	202582 3455 508 258
65	186655	0.0	3	182779 3208 426 242
66	116299	0.0	3	113882 1985 272 160
67	57816	0.0	3	56506 1078 128 104
68	31347	0.0	3	30603 605 92 47
69	17218	0.0	3	16783 365 39 31
70	12965	0.0	3	12662 234 35 34
71	11426	0.0	3	11174 209 19 24
72	14138	0.0	3	13781 275 42 40
73	15324	0.0	3	14976 278 43 27
74	19915	0.0	3	19411 407 59 38
75	27064	0.0	3	26458 497 67 42
76	2418	0.0	3	2351 50 7 10
77	426	0.0	3	406 5 3 12
78	222	0.0	3	192 10 1 19
79	92	0.0	3	77 2 0 13
80	200	0.0	3	173 11 0 16
81	90	0.0	3	73 5 1 11
82	163	0.0	3	148 7 0 8
83	56	0.0	3	43 0 0 13
84	40	0.0	3	30 4 0 6
85	19	0.0	3	8 0 0 11
86	15	0.0	3	4 0 0 11
87	12	0.0	3	1 1 0 10
88	15	0.0	3	3 0 0 12
89	12	0.0	3	0 0 1 11
90	9	0.0	3	1 0 2 6
91	23	0.0	3	1 2 1 19
92	19	0.0	3	4 0 1 14
93	41	0.0	3	1 0 0 40
94	3	0.0	3	0 0 0 3
95	4	0.0	3	0 0 0 4
96	5	0.0	3	0 0 0 5
97	10	0.0	3	0 0 0 10
98	26	0.0	3	5 0 1 20
99	12	0.0	3	0 0 0 12
100	5	0.0	3	1 0 0 4
101	29	0.0	3	20 0 0 9

Task has finished (573 seconds).

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	2
ID	task.align_bowtie2.bowtie2_PE_rep1.line_137.id_7
Name	bowtie2_PE rep1
Thread	thread_20
PID	72500

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	8
Mem

Start	2016-06-22 16:10:41
End	2016-06-22 17:04:14
Elapsed	00:53:32
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.fastq.gz /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_2_pf.trim.fastq.gz
Output files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.bam /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/qc/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.align.log
Dependencies

 
# SYS command. line 139

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/dskim89/git/bds_atac/.:/users/dskim89/git/bds_atac/modules:/users/dskim89/git/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 141

 bowtie2 -k 4 -X2000 --mm --threads 8 -x /mnt/data/annotations/indexes/bowtie2_indexes/bowtie2/ENCODEHg19_male \
			-1 /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.fastq.gz -2 /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_2_pf.trim.fastq.gz 2>/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/qc/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.align.log | \
			samtools view -Su /dev/stdin | sambamba sort -t 1 /dev/stdin -o /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.bam

# SYS command. line 145

 TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."

   
--------------------Stdout--------------------
Task has finished (3212 seconds).

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	3
ID	task.postalign_bam.dedup_bam_PE_rep1.line_182.id_8
Name	dedup_bam_PE rep1
Thread	thread_20
PID	72861

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	8
Mem

Start	2016-06-22 17:04:16
End	2016-06-22 17:40:02
Elapsed	00:35:45
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.bam
Output files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.bam /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/qc/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.dup.qc /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/qc/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.flagstat.qc /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/qc/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pbc.qc
Dependencies

 
# SYS command. line 184

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/dskim89/git/bds_atac/.:/users/dskim89/git/bds_atac/modules:/users/dskim89/git/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 200

 if [[ 4 > 0 ]]; then \
			samtools view -F 524 -f 2 -u /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.bam | \
			sambamba sort -t 8 -n /dev/stdin -o /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.dupmark.bam; \
			samtools view -h /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.dupmark.bam | \
			$(which assign_multimappers.py) -k 4 --paired-end | \
			samtools fixmate -r /dev/stdin /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.dupmark.bam.fixmate.bam; \
		    else \
		    	samtools view -F 1804 -f 2 -q 30 -u /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.bam | \
		    	sambamba sort -t 8 -n /dev/stdin -o /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.dupmark.bam; \
		        samtools fixmate -r /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.dupmark.bam /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.dupmark.bam.fixmate.bam; \
		    fi

# SYS command. line 212

 samtools view -F 1804 -f 2 -u /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.dupmark.bam.fixmate.bam | sambamba sort -t 8 /dev/stdin -o /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.filt.bam

# SYS command. line 214

 rm -f /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.dupmark.bam.fixmate.bam

# SYS command. line 218

 export _JAVA_OPTIONS="-Xms256M -Xmx4G -XX:ParallelGCThreads=1"

# SYS command. line 219

 export MAX_JAVA_MEM="12G"

# SYS command. line 222

 if [ -f ${PICARDROOT}/MarkDuplicates.jar ]; then \
			java -Xmx4G -jar ${PICARDROOT}/MarkDuplicates.jar \
				INPUT="/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/qc/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
			else \
			java -Xmx4G -jar ${PICARDROOT}/picard.jar MarkDuplicates \
				INPUT="/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.filt.bam" OUTPUT="/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.dupmark.bam" \
				METRICS_FILE="/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/qc/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.dup.qc" VALIDATION_STRINGENCY=LENIENT \
				ASSUME_SORTED=true REMOVE_DUPLICATES=false; \
			fi

# SYS command. line 240

 mv /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.dupmark.bam /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.filt.bam

# SYS command. line 242

 samtools view -F 1804 -f 2 -b /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.filt.bam > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.bam

# SYS command. line 244

 sambamba index -t 8 /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.bam

# SYS command. line 246

 sambamba flagstat -t 8 /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.bam > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/qc/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.flagstat.qc

# SYS command. line 257

 sambamba sort -t 8 -n /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.filt.bam -o /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.filt.bam.tmp.bam

# SYS command. line 259

 bedtools bamtobed -bedpe -i /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.filt.bam.tmp.bam | \
			awk 'BEGIN{OFS="\t"}{print $1,$2,$4,$6,$9,$10}' | \
			grep -v 'chrM' | sort | uniq -c | \
			awk 'BEGIN{mt=0;m0=0;m1=0;m2=0} ($1==1){m1=m1+1} ($1==2){m2=m2+1} {m0=m0+1} {mt=mt+$1} END{printf "%d\t%d\t%d\t%d\t%f\t%f\t%f\n",mt,m0,m1,m2,m0/mt,m1/m0,m1/m2}' > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/qc/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pbc.qc

# SYS command. line 264

 rm -f /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.filt.bam.tmp.bam

# SYS command. line 266

 rm -f /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.filt.bam

# SYS command. line 267

 rm -f /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.dupmark.bam

# SYS command. line 269

 TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."

   
--------------------Stdout--------------------
Task has finished (2145 seconds).

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4G -XX:ParallelGCThreads=1
[Wed Jun 22 17:21:06 PDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.filt.bam] OUTPUT=/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.dupmark.bam METRICS_FILE=/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/qc/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.dup.qc REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Wed Jun 22 17:21:06 PDT 2016] Executing as dskim89@mitra on Linux 3.16.0-70-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_45-b14; Picard version: 1.126(4691ee611ac205d4afe2a1b7a2ea975a6f997426_1417447214) IntelDeflater
INFO	2016-06-22 17:21:06	MarkDuplicates	Start of doWork freeMemory: 254889536; totalMemory: 257425408; maxMemory: 3817865216
INFO	2016-06-22 17:21:06	MarkDuplicates	Reading input file and constructing read end information.
INFO	2016-06-22 17:21:06	MarkDuplicates	Will retain up to 14684096 data points before spilling to disk.
INFO	2016-06-22 17:21:11	MarkDuplicates	Read     1,000,000 records.  Elapsed time: 00:00:04s.  Time for last 1,000,000:    4s.  Last read position: chr10:113,131,851
INFO	2016-06-22 17:21:11	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-06-22 17:21:16	MarkDuplicates	Read     2,000,000 records.  Elapsed time: 00:00:10s.  Time for last 1,000,000:    5s.  Last read position: chr11:71,823,382
INFO	2016-06-22 17:21:16	MarkDuplicates	Tracking 50 as yet unmatched pairs. 50 records in RAM.
INFO	2016-06-22 17:21:24	MarkDuplicates	Read     3,000,000 records.  Elapsed time: 00:00:18s.  Time for last 1,000,000:    7s.  Last read position: chr12:49,882,661
INFO	2016-06-22 17:21:24	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-06-22 17:21:29	MarkDuplicates	Read     4,000,000 records.  Elapsed time: 00:00:23s.  Time for last 1,000,000:    5s.  Last read position: chr13:40,643,889
INFO	2016-06-22 17:21:29	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-06-22 17:21:36	MarkDuplicates	Read     5,000,000 records.  Elapsed time: 00:00:29s.  Time for last 1,000,000:    6s.  Last read position: chr14:74,564,166
INFO	2016-06-22 17:21:36	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-06-22 17:21:42	MarkDuplicates	Read     6,000,000 records.  Elapsed time: 00:00:36s.  Time for last 1,000,000:    6s.  Last read position: chr15:91,970,323
INFO	2016-06-22 17:21:42	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-06-22 17:21:47	MarkDuplicates	Read     7,000,000 records.  Elapsed time: 00:00:40s.  Time for last 1,000,000:    4s.  Last read position: chr16:89,788,429
INFO	2016-06-22 17:21:47	MarkDuplicates	Tracking 14 as yet unmatched pairs. 14 records in RAM.
INFO	2016-06-22 17:21:51	MarkDuplicates	Read     8,000,000 records.  Elapsed time: 00:00:45s.  Time for last 1,000,000:    4s.  Last read position: chr17:75,148,949
INFO	2016-06-22 17:21:51	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-06-22 17:21:57	MarkDuplicates	Read     9,000,000 records.  Elapsed time: 00:00:51s.  Time for last 1,000,000:    5s.  Last read position: chr19:11,319,766
INFO	2016-06-22 17:21:57	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-06-22 17:22:02	MarkDuplicates	Read    10,000,000 records.  Elapsed time: 00:00:55s.  Time for last 1,000,000:    4s.  Last read position: chr1:569,231
INFO	2016-06-22 17:22:02	MarkDuplicates	Tracking 50 as yet unmatched pairs. 50 records in RAM.
INFO	2016-06-22 17:22:07	MarkDuplicates	Read    11,000,000 records.  Elapsed time: 00:01:01s.  Time for last 1,000,000:    5s.  Last read position: chr1:76,937,737
INFO	2016-06-22 17:22:07	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-06-22 17:22:13	MarkDuplicates	Read    12,000,000 records.  Elapsed time: 00:01:07s.  Time for last 1,000,000:    6s.  Last read position: chr1:204,464,040
INFO	2016-06-22 17:22:13	MarkDuplicates	Tracking 14 as yet unmatched pairs. 14 records in RAM.
INFO	2016-06-22 17:22:18	MarkDuplicates	Read    13,000,000 records.  Elapsed time: 00:01:12s.  Time for last 1,000,000:    4s.  Last read position: chr20:60,361,050
INFO	2016-06-22 17:22:18	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-06-22 17:22:23	MarkDuplicates	Read    14,000,000 records.  Elapsed time: 00:01:16s.  Time for last 1,000,000:    4s.  Last read position: chr2:18,712,741
INFO	2016-06-22 17:22:23	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-06-22 17:22:41	MarkDuplicates	Read    15,000,000 records.  Elapsed time: 00:01:35s.  Time for last 1,000,000:   18s.  Last read position: chr2:133,039,004
INFO	2016-06-22 17:22:41	MarkDuplicates	Tracking 52 as yet unmatched pairs. 52 records in RAM.
INFO	2016-06-22 17:22:45	MarkDuplicates	Read    16,000,000 records.  Elapsed time: 00:01:39s.  Time for last 1,000,000:    4s.  Last read position: chr3:10,655,459
INFO	2016-06-22 17:22:45	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-06-22 17:22:50	MarkDuplicates	Read    17,000,000 records.  Elapsed time: 00:01:44s.  Time for last 1,000,000:    4s.  Last read position: chr3:130,514,515
INFO	2016-06-22 17:22:50	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-06-22 17:22:55	MarkDuplicates	Read    18,000,000 records.  Elapsed time: 00:01:48s.  Time for last 1,000,000:    4s.  Last read position: chr4:64,355,206
INFO	2016-06-22 17:22:55	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-06-22 17:23:01	MarkDuplicates	Read    19,000,000 records.  Elapsed time: 00:01:54s.  Time for last 1,000,000:    5s.  Last read position: chr5:22,316,529
INFO	2016-06-22 17:23:01	MarkDuplicates	Tracking 2 as yet unmatched pairs. 2 records in RAM.
INFO	2016-06-22 17:23:04	MarkDuplicates	Read    20,000,000 records.  Elapsed time: 00:01:58s.  Time for last 1,000,000:    3s.  Last read position: chr5:152,027,531
INFO	2016-06-22 17:23:04	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-06-22 17:23:08	MarkDuplicates	Read    21,000,000 records.  Elapsed time: 00:02:02s.  Time for last 1,000,000:    3s.  Last read position: chr6:77,136,136
INFO	2016-06-22 17:23:08	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-06-22 17:23:12	MarkDuplicates	Read    22,000,000 records.  Elapsed time: 00:02:06s.  Time for last 1,000,000:    3s.  Last read position: chr7:32,982,707
INFO	2016-06-22 17:23:12	MarkDuplicates	Tracking 20 as yet unmatched pairs. 20 records in RAM.
INFO	2016-06-22 17:23:18	MarkDuplicates	Read    23,000,000 records.  Elapsed time: 00:02:12s.  Time for last 1,000,000:    5s.  Last read position: chr7:157,001,128
INFO	2016-06-22 17:23:18	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-06-22 17:23:23	MarkDuplicates	Read    24,000,000 records.  Elapsed time: 00:02:16s.  Time for last 1,000,000:    4s.  Last read position: chr8:132,900,163
INFO	2016-06-22 17:23:23	MarkDuplicates	Tracking 0 as yet unmatched pairs. 0 records in RAM.
INFO	2016-06-22 17:23:28	MarkDuplicates	Read    25,000,000 records.  Elapsed time: 00:02:21s.  Time for last 1,000,000:    4s.  Last read position: chr9:127,905,815
INFO	2016-06-22 17:23:28	MarkDuplicates	Tracking 14 as yet unmatched pairs. 14 records in RAM.
INFO	2016-06-22 17:23:32	MarkDuplicates	Read    26,000,000 records.  Elapsed time: 00:02:25s.  Time for last 1,000,000:    4s.  Last read position: chrM:3,630
INFO	2016-06-22 17:23:32	MarkDuplicates	Tracking 4440 as yet unmatched pairs. 4440 records in RAM.
INFO	2016-06-22 17:23:38	MarkDuplicates	Read    27,000,000 records.  Elapsed time: 00:02:32s.  Time for last 1,000,000:    6s.  Last read position: chrM:7,701
INFO	2016-06-22 17:23:38	MarkDuplicates	Tracking 5086 as yet unmatched pairs. 5086 records in RAM.
INFO	2016-06-22 17:23:43	MarkDuplicates	Read    28,000,000 records.  Elapsed time: 00:02:36s.  Time for last 1,000,000:    4s.  Last read position: chrM:10,974
INFO	2016-06-22 17:23:43	MarkDuplicates	Tracking 3820 as yet unmatched pairs. 3820 records in RAM.
INFO	2016-06-22 17:23:47	MarkDuplicates	Read    29,000,000 records.  Elapsed time: 00:02:40s.  Time for last 1,000,000:    4s.  Last read position: chrM:14,007
INFO	2016-06-22 17:23:47	MarkDuplicates	Tracking 7726 as yet unmatched pairs. 7726 records in RAM.
INFO	2016-06-22 17:23:59	MarkDuplicates	Read    30,000,000 records.  Elapsed time: 00:02:53s.  Time for last 1,000,000:   12s.  Last read position: chrX:24,483,315
INFO	2016-06-22 17:23:59	MarkDuplicates	Tracking 12 as yet unmatched pairs. 12 records in RAM.
INFO	2016-06-22 17:24:03	MarkDuplicates	Read 30759328 records. 0 pairs never matched.
INFO	2016-06-22 17:24:04	MarkDuplicates	After buildSortedReadEndLists freeMemory: 3464872048; totalMemory: 3492806656; maxMemory: 3817865216
INFO	2016-06-22 17:24:04	MarkDuplicates	Will retain up to 119308288 duplicate indices before spilling to disk.
INFO	2016-06-22 17:24:04	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2016-06-22 17:24:09	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2016-06-22 17:24:15	MarkDuplicates	Sorting list of duplicate records.
INFO	2016-06-22 17:24:16	MarkDuplicates	After generateDuplicateIndexes freeMemory: 2506845864; totalMemory: 3488088064; maxMemory: 3817865216
INFO	2016-06-22 17:24:16	MarkDuplicates	Marking 4424326 records as duplicates.
INFO	2016-06-22 17:24:16	MarkDuplicates	Found 1426690 optical duplicate clusters.
INFO	2016-06-22 17:25:52	MarkDuplicates	Written    10,000,000 records.  Elapsed time: 00:01:36s.  Time for last 10,000,000:   96s.  Last read position: chr1:569,231
INFO	2016-06-22 17:27:30	MarkDuplicates	Written    20,000,000 records.  Elapsed time: 00:03:14s.  Time for last 10,000,000:   97s.  Last read position: chr5:152,027,531
INFO	2016-06-22 17:29:00	MarkDuplicates	Written    30,000,000 records.  Elapsed time: 00:04:43s.  Time for last 10,000,000:   89s.  Last read position: chrX:24,483,315
INFO	2016-06-22 17:29:07	MarkDuplicates	Before output close freeMemory: 3523731256; totalMemory: 3553624064; maxMemory: 3817865216
INFO	2016-06-22 17:29:08	MarkDuplicates	After output close freeMemory: 3521108760; totalMemory: 3551002624; maxMemory: 3817865216
[Wed Jun 22 17:29:08 PDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 8.03 minutes.
Runtime.totalMemory()=3551002624

Num	4
ID	task.postalign_bam.nmsrt_bam_rep1.line_297.id_9
Name	nmsrt_bam rep1
Thread	thread_20
PID	73168

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-06-22 17:40:04
End	2016-06-22 17:53:12
Elapsed	00:13:08
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.bam
Output files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.nmsrt.bam
Dependencies

 
# SYS command. line 299

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/dskim89/git/bds_atac/.:/users/dskim89/git/bds_atac/modules:/users/dskim89/git/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 302

 sambamba sort -t 1 -n /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.bam -o /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.nmsrt.bam

# SYS command. line 304

 TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."

   
--------------------Stdout--------------------
Task has finished (788 seconds).

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	5
ID	task.postalign_bam.bam_to_bedpe_rep1.line_406.id_10
Name	bam_to_bedpe rep1
Thread	thread_20
PID	73293

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-06-22 17:53:14
End	2016-06-22 17:54:34
Elapsed	00:01:20
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.nmsrt.bam
Output files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.bedpe.gz
Dependencies

 
# SYS command. line 408

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/dskim89/git/bds_atac/.:/users/dskim89/git/bds_atac/modules:/users/dskim89/git/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 411

 bedtools bamtobed -bedpe -mate1 -i /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.nmsrt.bam | gzip -c > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.bedpe.gz

# SYS command. line 413

 TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."

   
--------------------Stdout--------------------
Task has finished (80 seconds).

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	6
ID	task.postalign_bam.bedpe_to_tag_rep1.line_445.id_11
Name	bedpe_to_tag rep1
Thread	thread_20
PID	73359

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-06-22 17:54:37
End	2016-06-22 17:55:41
Elapsed	00:01:04
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tagAlign.gz
Dependencies

 
# SYS command. line 447

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/dskim89/git/bds_atac/.:/users/dskim89/git/bds_atac/modules:/users/dskim89/git/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 449

 zcat /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.bedpe.gz | awk 'BEGIN{OFS="\t"}{printf "%s\t%s\t%s\tN\t1000\t%s\n%s\t%s\t%s\tN\t1000\t%s\n",$1,$2,$3,$9,$4,$5,$6,$10}' | \
			gzip -c > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tagAlign.gz

# SYS command. line 452

 zcat /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tagAlign.gz | grep -P -v 'chrM' | gzip -c > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.rm_chr.tmp.gz; mv /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.rm_chr.tmp.gz /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tagAlign.gz

# SYS command. line 454

 TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."

   
--------------------Stdout--------------------
Task has finished (63 seconds).

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	7
ID	task.postalign_bed.spr_PE_rep1.line_275.id_12
Name	spr_PE rep1
Thread	thread_20
PID	73427

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-06-22 17:55:43
End	2016-06-22 17:56:40
Elapsed	00:00:57
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tagAlign.gz /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tagAlign.gz
Dependencies

 
# SYS command. line 277

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/dskim89/git/bds_atac/.:/users/dskim89/git/bds_atac/modules:/users/dskim89/git/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 280

 nlines=$( zcat /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.bedpe.gz | wc -l )

# SYS command. line 281

 nlines=$(( (nlines + 1) / 2 ))

# SYS command. line 285

 zcat /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.bedpe.gz | shuf | split -d -l $((nlines)) - /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.  

# SYS command. line 288

 awk 'BEGIN{OFS="\t"}{printf "%s\t%s\t%s\tN\t1000\t%s\n%s\t%s\t%s\tN\t1000\t%s\n",$1,$2,$3,$9,$4,$5,$6,$10}' "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.00" | \
			gzip -c > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tagAlign.gz

# SYS command. line 290

 rm -f /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.00

# SYS command. line 291

 awk 'BEGIN{OFS="\t"}{printf "%s\t%s\t%s\tN\t1000\t%s\n%s\t%s\t%s\tN\t1000\t%s\n",$1,$2,$3,$9,$4,$5,$6,$10}' "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.01" | \
			gzip -c > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tagAlign.gz

# SYS command. line 293

 rm -f /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.01

# SYS command. line 295

 TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."

   
--------------------Stdout--------------------
Task has finished (56 seconds).

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	8
ID	task.postalign_bed.shift_tag_rep1.line_163.id_13
Name	shift_tag rep1
Thread	thread_20
PID	73500

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-06-22 17:56:42
End	2016-06-22 17:57:18
Elapsed	00:00:36
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tagAlign.gz
Output files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.tagAlign.gz
Dependencies

 
# SYS command. line 165

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/dskim89/git/bds_atac/.:/users/dskim89/git/bds_atac/modules:/users/dskim89/git/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 167

 zcat /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tagAlign.gz | awk -F $'\t' 'BEGIN {OFS = FS}{ if ($6 == "+") {$2 = $2 + 4} else if ($6 == "-") {$3 = $3 - 5} print $0}' | gzip -c > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.tagAlign.gz

# SYS command. line 169

 TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."

   
--------------------Stdout--------------------
Task has finished (36 seconds).

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	9
ID	task.postalign_bed.shift_tag_rep1.line_163.id_14
Name	shift_tag rep1
Thread	thread_20
PID	73559

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-06-22 17:56:43
End	2016-06-22 17:57:04
Elapsed	00:00:21
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tagAlign.gz
Output files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz
Dependencies

 
# SYS command. line 165

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/dskim89/git/bds_atac/.:/users/dskim89/git/bds_atac/modules:/users/dskim89/git/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 167

 zcat /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tagAlign.gz | awk -F $'\t' 'BEGIN {OFS = FS}{ if ($6 == "+") {$2 = $2 + 4} else if ($6 == "-") {$3 = $3 - 5} print $0}' | gzip -c > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz

# SYS command. line 169

 TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."

   
--------------------Stdout--------------------
Task has finished (20 seconds).

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	10
ID	task.postalign_bed.shift_tag_rep1.line_163.id_15
Name	shift_tag rep1
Thread	thread_20
PID	73619

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-06-22 17:56:44
End	2016-06-22 17:57:05
Elapsed	00:00:21
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tagAlign.gz
Output files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz
Dependencies

 
# SYS command. line 165

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/dskim89/git/bds_atac/.:/users/dskim89/git/bds_atac/modules:/users/dskim89/git/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 167

 zcat /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tagAlign.gz | awk -F $'\t' 'BEGIN {OFS = FS}{ if ($6 == "+") {$2 = $2 + 4} else if ($6 == "-") {$3 = $3 - 5} print $0}' | gzip -c > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz

# SYS command. line 169

 TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."

   
--------------------Stdout--------------------
Task has finished (21 seconds).

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	11
ID	task.postalign_bed.subsample_bedpe2tagrep1.line_103.id_16
Name	subsample_bedpe2tagrep1
Thread	thread_20
PID	73687

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-06-22 17:57:20
End	2016-06-22 17:57:49
Elapsed	00:00:29
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.bedpe.gz
Output files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.25M.tagAlign.gz
Dependencies

 
# SYS command. line 105

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/dskim89/git/bds_atac/.:/users/dskim89/git/bds_atac/modules:/users/dskim89/git/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 109

 zcat /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.bedpe.gz | \
			grep -v "chrM" | shuf -n 25000000 | \
			awk 'BEGIN{OFS="\t"}{print $1,$2,$3,"N","1000",$9}' | gzip -c > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.25M.tagAlign.gz

# SYS command. line 113

 TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."

   
--------------------Stdout--------------------
Task has finished (29 seconds).

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	12
ID	task.postalign_bed.xcor_rep1.line_193.id_17
Name	xcor rep1
Thread	thread_20
PID	73750

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	5
Mem

Start	2016-06-22 17:57:51
End	2016-06-22 18:01:56
Elapsed	00:04:05
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.25M.tagAlign.gz
Output files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/qc/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.25M.cc.qc /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/qc/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.25M.cc.plot.pdf
Dependencies

 
# SYS command. line 195

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/dskim89/git/bds_atac/.:/users/dskim89/git/bds_atac/modules:/users/dskim89/git/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 199

 Rscript $(which run_spp_nodups.R) -rf \
			-c=/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.25M.tagAlign.gz -p=5 \
			-filtchr=chrM -savp=/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/qc/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.25M.cc.plot.pdf -out=/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/qc/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.25M.cc.qc -speak=0

# SYS command. line 202

 sed -r 's/,[^\t]+//g' /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/qc/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.25M.cc.qc > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/qc/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.25M.cc.qc.tmp

# SYS command. line 203

 mv /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/qc/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.25M.cc.qc.tmp /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/qc/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.25M.cc.qc

# SYS command. line 205

 TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."

   
--------------------Stdout--------------------
################
ChIP data: /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.25M.tagAlign.gz 
Control data: NA 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 0 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: 5 
FDR threshold: 0.01 
NumPeaks Threshold: NA 
Output Directory: /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1 
narrowPeak output file name: NA 
regionPeak output file name: NA 
Rdata filename: NA 
plot pdf filename: /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/qc/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.25M.cc.plot.pdf 
result filename: /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/qc/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.25M.cc.qc 
Overwrite files?: TRUE

Decompressing ChIP file
Reading ChIP tagAlign/BAM file /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.25M.tagAlign.gz 
opened /tmp/RtmpNmC2XE/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.25M.tagAlign1204e5061e6c7
done. read 12648909 fragments
ChIP data read length 101 
[1] TRUE
Calculating peak characteristics
Minimum cross-correlation value 0.1168226 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.274860018582327 
Top 3 estimates for fragment length 0 
Window half size 525 
Phantom peak location 95 
Phantom peak Correlation 0.2719482 
Normalized Strand cross-correlation coefficient (NSC) 2.352799 
Relative Strand Cross correlation Coefficient (RSC) 1.018771 
Phantom Peak Quality Tag 1 
null device 
          1 
Task has finished (245 seconds).

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH
Loading required package: caTools

Num	13
ID	task.callpeak_macs2.macs2_atac_rep1.line_64.id_18
Name	macs2_atac rep1
Thread	thread_20
PID	73815

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-06-22 17:57:53
End	2016-06-22 18:21:48
Elapsed	00:23:54
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.tagAlign.gz
Output files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.narrowPeak.gz /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.gappedPeak.gz /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/signal/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.fc.signal.bigwig /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/signal/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval.signal.bigwig
Dependencies

 
# SYS command. line 66

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/dskim89/git/bds_atac/.:/users/dskim89/git/bds_atac/modules:/users/dskim89/git/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 67

 export LC_COLLATE=C

# SYS command. line 69

 macs2 callpeak \
			-t /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf" -g "hs" -p 0.01 \
			--nomodel --shift -75 --extsize 150 --broad --keep-dup all

# SYS command. line 74

 sort -k 8gr,8gr "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.broadPeak.gz

# SYS command. line 75

 sort -k 14gr,14gr "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.gappedPeak.gz

# SYS command. line 76

 rm -f "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf"_peaks.broadPeak

# SYS command. line 77

 rm -f "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf"_peaks.gappedPeak

# SYS command. line 79

 macs2 callpeak \
			-t /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf" -g "hs" -p 0.01 \
			--nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits

# SYS command. line 84

 sort -k 8gr,8gr "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf"_peaks.narrowPeak

# SYS command. line 86

 rm -f "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf"_peaks.xls

# SYS command. line 87

 rm -f "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf"_summits.bed

# SYS command. line 90

 if [[ true == "true" ]]; then \
			\
			macs2 bdgcmp -t "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf" -m FE;\
			slopBed -i "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf"_FE.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.fc.signal.bedgraph; \
			rm -f "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf"_FE.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.fc.signal.bedgraph > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.fc.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/signal/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.fc.signal.bigwig"; \
			rm -f /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.fc.signal.bedgraph /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.fc.signal.srt.bedgraph; \
			\
			sval=$(wc -l <(zcat -f "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf"_treat_pileup.bdg -c "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf"_control_lambda.bdg \
				--o-prefix "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf"_ppois.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval.signal.bedgraph; \
			rm -f "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf"_ppois.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval.signal.bedgraph > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/signal/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval.signal.bigwig"; \
			rm -f /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval.signal.bedgraph /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval.signal.srt.bedgraph; \
			\
			fi

# SYS command. line 115

 rm -f "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf"_treat_pileup.bdg "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf"_control_lambda.bdg

# SYS command. line 117

 TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."

   
--------------------Stdout--------------------
Task has finished (1434 seconds).

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH
INFO  @ Wed, 22 Jun 2016 17:57:55: 
# Command line: callpeak -t /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf -g hs -p 0.01 --nomodel --shift -75 --extsize 150 --broad --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-02
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is on
 
INFO  @ Wed, 22 Jun 2016 17:57:55: #1 read tag files... 
INFO  @ Wed, 22 Jun 2016 17:57:55: #1 read treatment tags... 
INFO  @ Wed, 22 Jun 2016 17:57:57:  1000000 
INFO  @ Wed, 22 Jun 2016 17:57:58:  2000000 
INFO  @ Wed, 22 Jun 2016 17:58:00:  3000000 
INFO  @ Wed, 22 Jun 2016 17:58:01:  4000000 
INFO  @ Wed, 22 Jun 2016 17:58:03:  5000000 
INFO  @ Wed, 22 Jun 2016 17:58:05:  6000000 
INFO  @ Wed, 22 Jun 2016 17:58:06:  7000000 
INFO  @ Wed, 22 Jun 2016 17:58:08:  8000000 
INFO  @ Wed, 22 Jun 2016 17:58:09:  9000000 
INFO  @ Wed, 22 Jun 2016 17:58:11:  10000000 
INFO  @ Wed, 22 Jun 2016 17:58:12:  11000000 
INFO  @ Wed, 22 Jun 2016 17:58:14:  12000000 
INFO  @ Wed, 22 Jun 2016 17:58:15:  13000000 
INFO  @ Wed, 22 Jun 2016 17:58:17:  14000000 
INFO  @ Wed, 22 Jun 2016 17:58:18:  15000000 
INFO  @ Wed, 22 Jun 2016 17:58:20:  16000000 
INFO  @ Wed, 22 Jun 2016 17:58:21:  17000000 
INFO  @ Wed, 22 Jun 2016 17:58:23:  18000000 
INFO  @ Wed, 22 Jun 2016 17:58:24:  19000000 
INFO  @ Wed, 22 Jun 2016 17:58:26:  20000000 
INFO  @ Wed, 22 Jun 2016 17:58:27:  21000000 
INFO  @ Wed, 22 Jun 2016 17:58:29:  22000000 
INFO  @ Wed, 22 Jun 2016 17:58:31:  23000000 
INFO  @ Wed, 22 Jun 2016 17:58:32:  24000000 
INFO  @ Wed, 22 Jun 2016 17:58:34:  25000000 
INFO  @ Wed, 22 Jun 2016 17:58:36: #1 tag size is determined as 59 bps 
INFO  @ Wed, 22 Jun 2016 17:58:36: #1 tag size = 59 
INFO  @ Wed, 22 Jun 2016 17:58:36: #1  total tags in treatment: 25297818 
INFO  @ Wed, 22 Jun 2016 17:58:36: #1 finished! 
INFO  @ Wed, 22 Jun 2016 17:58:36: #2 Build Peak Model... 
INFO  @ Wed, 22 Jun 2016 17:58:36: #2 Skipped... 
INFO  @ Wed, 22 Jun 2016 17:58:36: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Wed, 22 Jun 2016 17:58:36: #2 Use 150 as fragment length 
INFO  @ Wed, 22 Jun 2016 17:58:36: #3 Call peaks... 
INFO  @ Wed, 22 Jun 2016 17:58:36: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 2.00000, 1.00000... 
INFO  @ Wed, 22 Jun 2016 17:58:36: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 22 Jun 2016 17:59:25: #3 Call peaks for each chromosome... 
INFO  @ Wed, 22 Jun 2016 18:00:33: #4 Write output xls file... /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf_peaks.xls 
INFO  @ Wed, 22 Jun 2016 18:00:36: #4 Write broad peak in broadPeak format file... /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf_peaks.broadPeak 
INFO  @ Wed, 22 Jun 2016 18:00:39: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf_peaks.gappedPeak 
INFO  @ Wed, 22 Jun 2016 18:00:42: Done! 
INFO  @ Wed, 22 Jun 2016 18:00:53: 
# Command line: callpeak -t /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf -g hs -p 0.01 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits
# ARGUMENTS LIST:
# name = /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf
# format = BED
# ChIP-seq file = ['/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-02
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is off
# Searching for subpeak summits is on
# MACS will save fragment pileup signal per million reads
 
INFO  @ Wed, 22 Jun 2016 18:00:53: #1 read tag files... 
INFO  @ Wed, 22 Jun 2016 18:00:53: #1 read treatment tags... 
INFO  @ Wed, 22 Jun 2016 18:00:54:  1000000 
INFO  @ Wed, 22 Jun 2016 18:00:56:  2000000 
INFO  @ Wed, 22 Jun 2016 18:00:58:  3000000 
INFO  @ Wed, 22 Jun 2016 18:00:59:  4000000 
INFO  @ Wed, 22 Jun 2016 18:01:01:  5000000 
INFO  @ Wed, 22 Jun 2016 18:01:02:  6000000 
INFO  @ Wed, 22 Jun 2016 18:01:04:  7000000 
INFO  @ Wed, 22 Jun 2016 18:01:06:  8000000 
INFO  @ Wed, 22 Jun 2016 18:01:07:  9000000 
INFO  @ Wed, 22 Jun 2016 18:01:09:  10000000 
INFO  @ Wed, 22 Jun 2016 18:01:10:  11000000 
INFO  @ Wed, 22 Jun 2016 18:01:12:  12000000 
INFO  @ Wed, 22 Jun 2016 18:01:14:  13000000 
INFO  @ Wed, 22 Jun 2016 18:01:15:  14000000 
INFO  @ Wed, 22 Jun 2016 18:01:17:  15000000 
INFO  @ Wed, 22 Jun 2016 18:01:19:  16000000 
INFO  @ Wed, 22 Jun 2016 18:01:20:  17000000 
INFO  @ Wed, 22 Jun 2016 18:01:22:  18000000 
INFO  @ Wed, 22 Jun 2016 18:01:23:  19000000 
INFO  @ Wed, 22 Jun 2016 18:01:25:  20000000 
INFO  @ Wed, 22 Jun 2016 18:01:26:  21000000 
INFO  @ Wed, 22 Jun 2016 18:01:28:  22000000 
INFO  @ Wed, 22 Jun 2016 18:01:30:  23000000 
INFO  @ Wed, 22 Jun 2016 18:01:31:  24000000 
INFO  @ Wed, 22 Jun 2016 18:01:33:  25000000 
INFO  @ Wed, 22 Jun 2016 18:01:35: #1 tag size is determined as 59 bps 
INFO  @ Wed, 22 Jun 2016 18:01:35: #1 tag size = 59 
INFO  @ Wed, 22 Jun 2016 18:01:35: #1  total tags in treatment: 25297818 
INFO  @ Wed, 22 Jun 2016 18:01:35: #1 finished! 
INFO  @ Wed, 22 Jun 2016 18:01:35: #2 Build Peak Model... 
INFO  @ Wed, 22 Jun 2016 18:01:35: #2 Skipped... 
INFO  @ Wed, 22 Jun 2016 18:01:35: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Wed, 22 Jun 2016 18:01:35: #2 Use 150 as fragment length 
INFO  @ Wed, 22 Jun 2016 18:01:35: #3 Call peaks... 
INFO  @ Wed, 22 Jun 2016 18:01:35: #3 Going to call summits inside each peak ... 
INFO  @ Wed, 22 Jun 2016 18:01:35: #3 Call peaks with given -log10pvalue cutoff: 2.00000 ... 
INFO  @ Wed, 22 Jun 2016 18:01:35: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 22 Jun 2016 18:02:21: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Wed, 22 Jun 2016 18:02:21: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf_treat_pileup.bdg 
INFO  @ Wed, 22 Jun 2016 18:02:21: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf_control_lambda.bdg 
INFO  @ Wed, 22 Jun 2016 18:02:21: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Wed, 22 Jun 2016 18:02:21: #3 Call peaks for each chromosome... 
INFO  @ Wed, 22 Jun 2016 18:04:59: #4 Write output xls file... /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf_peaks.xls 
INFO  @ Wed, 22 Jun 2016 18:05:00: #4 Write peak in narrowPeak format file... /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf_peaks.narrowPeak 
INFO  @ Wed, 22 Jun 2016 18:05:00: #4 Write summits bed file... /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf_summits.bed 
INFO  @ Wed, 22 Jun 2016 18:05:01: Done! 
INFO  @ Wed, 22 Jun 2016 18:05:03: Read and build treatment bedGraph... 
INFO  @ Wed, 22 Jun 2016 18:05:45: Read and build control bedGraph... 
INFO  @ Wed, 22 Jun 2016 18:06:02: Build scoreTrackII... 
INFO  @ Wed, 22 Jun 2016 18:06:20: Calculate scores comparing treatment and control by 'FE'... 
INFO  @ Wed, 22 Jun 2016 18:08:38: Write bedGraph of scores... 
INFO  @ Wed, 22 Jun 2016 18:09:48: Finished 'FE'! Please check '/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf_FE.bdg'! 
INFO  @ Wed, 22 Jun 2016 18:13:24: Read and build treatment bedGraph... 
INFO  @ Wed, 22 Jun 2016 18:14:02: Read and build control bedGraph... 
INFO  @ Wed, 22 Jun 2016 18:14:19: Build scoreTrackII... 
INFO  @ Wed, 22 Jun 2016 18:14:33: Values in your input bedGraph files will be multiplied by 25.297818 ... 
INFO  @ Wed, 22 Jun 2016 18:16:41: Calculate scores comparing treatment and control by 'ppois'... 
INFO  @ Wed, 22 Jun 2016 18:17:07: Write bedGraph of scores... 
INFO  @ Wed, 22 Jun 2016 18:18:20: Finished 'ppois'! Please check '/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf_ppois.bdg'!

Num	14
ID	task.callpeak_macs2.macs2_atac_rep1.pval0.1.line_64.id_19
Name	macs2_atac rep1.pval0.1
Thread	thread_20
PID	73873

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-06-22 17:57:54
End	2016-06-22 18:08:02
Elapsed	00:10:07
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.tagAlign.gz
Output files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.narrowPeak.gz /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.gappedPeak.gz
Dependencies

 
# SYS command. line 66

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/dskim89/git/bds_atac/.:/users/dskim89/git/bds_atac/modules:/users/dskim89/git/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 67

 export LC_COLLATE=C

# SYS command. line 69

 macs2 callpeak \
			-t /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1" -g "hs" -p 0.1 \
			--nomodel --shift -75 --extsize 150 --broad --keep-dup all

# SYS command. line 74

 sort -k 8gr,8gr "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.broadPeak.gz

# SYS command. line 75

 sort -k 14gr,14gr "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.gappedPeak.gz

# SYS command. line 76

 rm -f "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1"_peaks.broadPeak

# SYS command. line 77

 rm -f "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1"_peaks.gappedPeak

# SYS command. line 79

 macs2 callpeak \
			-t /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1" -g "hs" -p 0.1 \
			--nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits

# SYS command. line 84

 sort -k 8gr,8gr "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1"_peaks.narrowPeak

# SYS command. line 86

 rm -f "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1"_peaks.xls

# SYS command. line 87

 rm -f "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1"_summits.bed

# SYS command. line 90

 if [[ false == "true" ]]; then \
			\
			macs2 bdgcmp -t "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1" -m FE;\
			slopBed -i "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1"_FE.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.fc.signal.bedgraph; \
			rm -f "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1"_FE.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.fc.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/signal/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.fc.signal.bigwig"; \
			rm -f /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.fc.signal.bedgraph /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
			\
			sval=$(wc -l <(zcat -f "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1"_ppois.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.pval.signal.bedgraph; \
			rm -f "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1"_ppois.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.pval.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/signal/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.pval.signal.bigwig"; \
			rm -f /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.pval.signal.bedgraph /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
			\
			fi

# SYS command. line 115

 rm -f "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1"_control_lambda.bdg

# SYS command. line 117

 TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."

   
--------------------Stdout--------------------
Task has finished (607 seconds).

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH
INFO  @ Wed, 22 Jun 2016 17:57:57: 
# Command line: callpeak -t /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 --broad --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-01
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is on
 
INFO  @ Wed, 22 Jun 2016 17:57:57: #1 read tag files... 
INFO  @ Wed, 22 Jun 2016 17:57:57: #1 read treatment tags... 
INFO  @ Wed, 22 Jun 2016 17:57:58:  1000000 
INFO  @ Wed, 22 Jun 2016 17:58:00:  2000000 
INFO  @ Wed, 22 Jun 2016 17:58:01:  3000000 
INFO  @ Wed, 22 Jun 2016 17:58:03:  4000000 
INFO  @ Wed, 22 Jun 2016 17:58:04:  5000000 
INFO  @ Wed, 22 Jun 2016 17:58:06:  6000000 
INFO  @ Wed, 22 Jun 2016 17:58:07:  7000000 
INFO  @ Wed, 22 Jun 2016 17:58:09:  8000000 
INFO  @ Wed, 22 Jun 2016 17:58:10:  9000000 
INFO  @ Wed, 22 Jun 2016 17:58:12:  10000000 
INFO  @ Wed, 22 Jun 2016 17:58:13:  11000000 
INFO  @ Wed, 22 Jun 2016 17:58:15:  12000000 
INFO  @ Wed, 22 Jun 2016 17:58:16:  13000000 
INFO  @ Wed, 22 Jun 2016 17:58:18:  14000000 
INFO  @ Wed, 22 Jun 2016 17:58:19:  15000000 
INFO  @ Wed, 22 Jun 2016 17:58:21:  16000000 
INFO  @ Wed, 22 Jun 2016 17:58:22:  17000000 
INFO  @ Wed, 22 Jun 2016 17:58:24:  18000000 
INFO  @ Wed, 22 Jun 2016 17:58:25:  19000000 
INFO  @ Wed, 22 Jun 2016 17:58:27:  20000000 
INFO  @ Wed, 22 Jun 2016 17:58:28:  21000000 
INFO  @ Wed, 22 Jun 2016 17:58:30:  22000000 
INFO  @ Wed, 22 Jun 2016 17:58:31:  23000000 
INFO  @ Wed, 22 Jun 2016 17:58:33:  24000000 
INFO  @ Wed, 22 Jun 2016 17:58:34:  25000000 
INFO  @ Wed, 22 Jun 2016 17:58:36: #1 tag size is determined as 59 bps 
INFO  @ Wed, 22 Jun 2016 17:58:36: #1 tag size = 59 
INFO  @ Wed, 22 Jun 2016 17:58:36: #1  total tags in treatment: 25297818 
INFO  @ Wed, 22 Jun 2016 17:58:36: #1 finished! 
INFO  @ Wed, 22 Jun 2016 17:58:36: #2 Build Peak Model... 
INFO  @ Wed, 22 Jun 2016 17:58:36: #2 Skipped... 
INFO  @ Wed, 22 Jun 2016 17:58:36: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Wed, 22 Jun 2016 17:58:36: #2 Use 150 as fragment length 
INFO  @ Wed, 22 Jun 2016 17:58:36: #3 Call peaks... 
INFO  @ Wed, 22 Jun 2016 17:58:36: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Wed, 22 Jun 2016 17:58:36: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 22 Jun 2016 17:59:26: #3 Call peaks for each chromosome... 
INFO  @ Wed, 22 Jun 2016 18:00:49: #4 Write output xls file... /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1_peaks.xls 
INFO  @ Wed, 22 Jun 2016 18:00:51: #4 Write broad peak in broadPeak format file... /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1_peaks.broadPeak 
INFO  @ Wed, 22 Jun 2016 18:00:54: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1_peaks.gappedPeak 
INFO  @ Wed, 22 Jun 2016 18:00:55: Done! 
INFO  @ Wed, 22 Jun 2016 18:01:05: 
# Command line: callpeak -t /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits
# ARGUMENTS LIST:
# name = /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is off
# Searching for subpeak summits is on
# MACS will save fragment pileup signal per million reads
 
INFO  @ Wed, 22 Jun 2016 18:01:05: #1 read tag files... 
INFO  @ Wed, 22 Jun 2016 18:01:05: #1 read treatment tags... 
INFO  @ Wed, 22 Jun 2016 18:01:07:  1000000 
INFO  @ Wed, 22 Jun 2016 18:01:08:  2000000 
INFO  @ Wed, 22 Jun 2016 18:01:10:  3000000 
INFO  @ Wed, 22 Jun 2016 18:01:11:  4000000 
INFO  @ Wed, 22 Jun 2016 18:01:13:  5000000 
INFO  @ Wed, 22 Jun 2016 18:01:15:  6000000 
INFO  @ Wed, 22 Jun 2016 18:01:16:  7000000 
INFO  @ Wed, 22 Jun 2016 18:01:18:  8000000 
INFO  @ Wed, 22 Jun 2016 18:01:19:  9000000 
INFO  @ Wed, 22 Jun 2016 18:01:21:  10000000 
INFO  @ Wed, 22 Jun 2016 18:01:22:  11000000 
INFO  @ Wed, 22 Jun 2016 18:01:24:  12000000 
INFO  @ Wed, 22 Jun 2016 18:01:26:  13000000 
INFO  @ Wed, 22 Jun 2016 18:01:27:  14000000 
INFO  @ Wed, 22 Jun 2016 18:01:29:  15000000 
INFO  @ Wed, 22 Jun 2016 18:01:30:  16000000 
INFO  @ Wed, 22 Jun 2016 18:01:32:  17000000 
INFO  @ Wed, 22 Jun 2016 18:01:34:  18000000 
INFO  @ Wed, 22 Jun 2016 18:01:35:  19000000 
INFO  @ Wed, 22 Jun 2016 18:01:37:  20000000 
INFO  @ Wed, 22 Jun 2016 18:01:38:  21000000 
INFO  @ Wed, 22 Jun 2016 18:01:40:  22000000 
INFO  @ Wed, 22 Jun 2016 18:01:41:  23000000 
INFO  @ Wed, 22 Jun 2016 18:01:43:  24000000 
INFO  @ Wed, 22 Jun 2016 18:01:45:  25000000 
INFO  @ Wed, 22 Jun 2016 18:01:47: #1 tag size is determined as 59 bps 
INFO  @ Wed, 22 Jun 2016 18:01:47: #1 tag size = 59 
INFO  @ Wed, 22 Jun 2016 18:01:47: #1  total tags in treatment: 25297818 
INFO  @ Wed, 22 Jun 2016 18:01:47: #1 finished! 
INFO  @ Wed, 22 Jun 2016 18:01:47: #2 Build Peak Model... 
INFO  @ Wed, 22 Jun 2016 18:01:47: #2 Skipped... 
INFO  @ Wed, 22 Jun 2016 18:01:47: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Wed, 22 Jun 2016 18:01:47: #2 Use 150 as fragment length 
INFO  @ Wed, 22 Jun 2016 18:01:47: #3 Call peaks... 
INFO  @ Wed, 22 Jun 2016 18:01:47: #3 Going to call summits inside each peak ... 
INFO  @ Wed, 22 Jun 2016 18:01:47: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Wed, 22 Jun 2016 18:01:47: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 22 Jun 2016 18:02:31: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Wed, 22 Jun 2016 18:02:31: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1_treat_pileup.bdg 
INFO  @ Wed, 22 Jun 2016 18:02:31: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1_control_lambda.bdg 
INFO  @ Wed, 22 Jun 2016 18:02:31: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Wed, 22 Jun 2016 18:02:31: #3 Call peaks for each chromosome... 
INFO  @ Wed, 22 Jun 2016 18:07:49: #4 Write output xls file... /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1_peaks.xls 
INFO  @ Wed, 22 Jun 2016 18:07:53: #4 Write peak in narrowPeak format file... /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1_peaks.narrowPeak 
INFO  @ Wed, 22 Jun 2016 18:07:56: #4 Write summits bed file... /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1_summits.bed 
INFO  @ Wed, 22 Jun 2016 18:07:57: Done!

Num	15
ID	task.callpeak_macs2.macs2_atac_rep1_pr1.pval0.1.line_64.id_20
Name	macs2_atac rep1-pr1.pval0.1
Thread	thread_20
PID	73931

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-06-22 17:57:55
End	2016-06-22 18:06:24
Elapsed	00:08:28
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz
Output files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.narrowPeak.gz /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.gappedPeak.gz
Dependencies

 
# SYS command. line 66

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/dskim89/git/bds_atac/.:/users/dskim89/git/bds_atac/modules:/users/dskim89/git/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 67

 export LC_COLLATE=C

# SYS command. line 69

 macs2 callpeak \
			-t /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz -f BED -n "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1" -g "hs" -p 0.1 \
			--nomodel --shift -75 --extsize 150 --broad --keep-dup all

# SYS command. line 74

 sort -k 8gr,8gr "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.broadPeak.gz

# SYS command. line 75

 sort -k 14gr,14gr "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.gappedPeak.gz

# SYS command. line 76

 rm -f "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_peaks.broadPeak

# SYS command. line 77

 rm -f "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_peaks.gappedPeak

# SYS command. line 79

 macs2 callpeak \
			-t /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz -f BED -n "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1" -g "hs" -p 0.1 \
			--nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits

# SYS command. line 84

 sort -k 8gr,8gr "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_peaks.narrowPeak

# SYS command. line 86

 rm -f "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_peaks.xls

# SYS command. line 87

 rm -f "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_summits.bed

# SYS command. line 90

 if [[ false == "true" ]]; then \
			\
			macs2 bdgcmp -t "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1" -m FE;\
			slopBed -i "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_FE.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.fc.signal.bedgraph; \
			rm -f "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_FE.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.fc.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/signal/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.fc.signal.bigwig"; \
			rm -f /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.fc.signal.bedgraph /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
			\
			sval=$(wc -l <(zcat -f "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_ppois.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.pval.signal.bedgraph; \
			rm -f "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_ppois.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.pval.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/signal/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.pval.signal.bigwig"; \
			rm -f /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.pval.signal.bedgraph /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
			\
			fi

# SYS command. line 115

 rm -f "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1"_control_lambda.bdg

# SYS command. line 117

 TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."

   
--------------------Stdout--------------------
Task has finished (508 seconds).

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH
INFO  @ Wed, 22 Jun 2016 17:57:58: 
# Command line: callpeak -t /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz -f BED -n /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 --broad --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-01
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is on
 
INFO  @ Wed, 22 Jun 2016 17:57:58: #1 read tag files... 
INFO  @ Wed, 22 Jun 2016 17:57:58: #1 read treatment tags... 
INFO  @ Wed, 22 Jun 2016 17:57:59:  1000000 
INFO  @ Wed, 22 Jun 2016 17:58:01:  2000000 
INFO  @ Wed, 22 Jun 2016 17:58:02:  3000000 
INFO  @ Wed, 22 Jun 2016 17:58:04:  4000000 
INFO  @ Wed, 22 Jun 2016 17:58:05:  5000000 
INFO  @ Wed, 22 Jun 2016 17:58:07:  6000000 
INFO  @ Wed, 22 Jun 2016 17:58:08:  7000000 
INFO  @ Wed, 22 Jun 2016 17:58:10:  8000000 
INFO  @ Wed, 22 Jun 2016 17:58:11:  9000000 
INFO  @ Wed, 22 Jun 2016 17:58:13:  10000000 
INFO  @ Wed, 22 Jun 2016 17:58:14:  11000000 
INFO  @ Wed, 22 Jun 2016 17:58:16:  12000000 
INFO  @ Wed, 22 Jun 2016 17:58:17:  13000000 
INFO  @ Wed, 22 Jun 2016 17:58:18: #1 tag size is determined as 67 bps 
INFO  @ Wed, 22 Jun 2016 17:58:18: #1 tag size = 67 
INFO  @ Wed, 22 Jun 2016 17:58:18: #1  total tags in treatment: 13167502 
INFO  @ Wed, 22 Jun 2016 17:58:18: #1 finished! 
INFO  @ Wed, 22 Jun 2016 17:58:18: #2 Build Peak Model... 
INFO  @ Wed, 22 Jun 2016 17:58:18: #2 Skipped... 
INFO  @ Wed, 22 Jun 2016 17:58:18: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Wed, 22 Jun 2016 17:58:18: #2 Use 150 as fragment length 
INFO  @ Wed, 22 Jun 2016 17:58:18: #3 Call peaks... 
INFO  @ Wed, 22 Jun 2016 17:58:18: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Wed, 22 Jun 2016 17:58:18: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 22 Jun 2016 17:58:44: #3 Call peaks for each chromosome... 
INFO  @ Wed, 22 Jun 2016 17:59:44: #4 Write output xls file... /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_peaks.xls 
INFO  @ Wed, 22 Jun 2016 17:59:48: #4 Write broad peak in broadPeak format file... /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_peaks.broadPeak 
INFO  @ Wed, 22 Jun 2016 17:59:50: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_peaks.gappedPeak 
INFO  @ Wed, 22 Jun 2016 17:59:52: Done! 
INFO  @ Wed, 22 Jun 2016 18:00:05: 
# Command line: callpeak -t /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz -f BED -n /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits
# ARGUMENTS LIST:
# name = /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is off
# Searching for subpeak summits is on
# MACS will save fragment pileup signal per million reads
 
INFO  @ Wed, 22 Jun 2016 18:00:05: #1 read tag files... 
INFO  @ Wed, 22 Jun 2016 18:00:05: #1 read treatment tags... 
INFO  @ Wed, 22 Jun 2016 18:00:07:  1000000 
INFO  @ Wed, 22 Jun 2016 18:00:08:  2000000 
INFO  @ Wed, 22 Jun 2016 18:00:10:  3000000 
INFO  @ Wed, 22 Jun 2016 18:00:11:  4000000 
INFO  @ Wed, 22 Jun 2016 18:00:13:  5000000 
INFO  @ Wed, 22 Jun 2016 18:00:14:  6000000 
INFO  @ Wed, 22 Jun 2016 18:00:16:  7000000 
INFO  @ Wed, 22 Jun 2016 18:00:17:  8000000 
INFO  @ Wed, 22 Jun 2016 18:00:19:  9000000 
INFO  @ Wed, 22 Jun 2016 18:00:20:  10000000 
INFO  @ Wed, 22 Jun 2016 18:00:22:  11000000 
INFO  @ Wed, 22 Jun 2016 18:00:23:  12000000 
INFO  @ Wed, 22 Jun 2016 18:00:25:  13000000 
INFO  @ Wed, 22 Jun 2016 18:00:26: #1 tag size is determined as 67 bps 
INFO  @ Wed, 22 Jun 2016 18:00:26: #1 tag size = 67 
INFO  @ Wed, 22 Jun 2016 18:00:26: #1  total tags in treatment: 13167502 
INFO  @ Wed, 22 Jun 2016 18:00:26: #1 finished! 
INFO  @ Wed, 22 Jun 2016 18:00:26: #2 Build Peak Model... 
INFO  @ Wed, 22 Jun 2016 18:00:26: #2 Skipped... 
INFO  @ Wed, 22 Jun 2016 18:00:26: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Wed, 22 Jun 2016 18:00:26: #2 Use 150 as fragment length 
INFO  @ Wed, 22 Jun 2016 18:00:26: #3 Call peaks... 
INFO  @ Wed, 22 Jun 2016 18:00:26: #3 Going to call summits inside each peak ... 
INFO  @ Wed, 22 Jun 2016 18:00:26: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Wed, 22 Jun 2016 18:00:26: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 22 Jun 2016 18:00:56: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Wed, 22 Jun 2016 18:00:56: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_treat_pileup.bdg 
INFO  @ Wed, 22 Jun 2016 18:00:56: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_control_lambda.bdg 
INFO  @ Wed, 22 Jun 2016 18:00:56: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Wed, 22 Jun 2016 18:00:56: #3 Call peaks for each chromosome... 
INFO  @ Wed, 22 Jun 2016 18:06:07: #4 Write output xls file... /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_peaks.xls 
INFO  @ Wed, 22 Jun 2016 18:06:11: #4 Write peak in narrowPeak format file... /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_peaks.narrowPeak 
INFO  @ Wed, 22 Jun 2016 18:06:15: #4 Write summits bed file... /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1_summits.bed 
INFO  @ Wed, 22 Jun 2016 18:06:17: Done!

Num	16
ID	task.callpeak_macs2.macs2_atac_rep1_pr2.pval0.1.line_64.id_21
Name	macs2_atac rep1-pr2.pval0.1
Thread	thread_20
PID	74111

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-06-22 18:02:00
End	2016-06-22 18:10:10
Elapsed	00:08:10
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz
Output files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.narrowPeak.gz /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.gappedPeak.gz
Dependencies

 
# SYS command. line 66

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/dskim89/git/bds_atac/.:/users/dskim89/git/bds_atac/modules:/users/dskim89/git/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 67

 export LC_COLLATE=C

# SYS command. line 69

 macs2 callpeak \
			-t /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz -f BED -n "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1" -g "hs" -p 0.1 \
			--nomodel --shift -75 --extsize 150 --broad --keep-dup all

# SYS command. line 74

 sort -k 8gr,8gr "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_peaks.broadPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.broadPeak.gz

# SYS command. line 75

 sort -k 14gr,14gr "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_peaks.gappedPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.gappedPeak.gz

# SYS command. line 76

 rm -f "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_peaks.broadPeak

# SYS command. line 77

 rm -f "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_peaks.gappedPeak

# SYS command. line 79

 macs2 callpeak \
			-t /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz -f BED -n "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1" -g "hs" -p 0.1 \
			--nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits

# SYS command. line 84

 sort -k 8gr,8gr "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -c > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.narrowPeak.gz

# SYS command. line 85

 rm -f "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_peaks.narrowPeak

# SYS command. line 86

 rm -f "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_peaks.xls

# SYS command. line 87

 rm -f "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_summits.bed

# SYS command. line 90

 if [[ false == "true" ]]; then \
			\
			macs2 bdgcmp -t "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1" -m FE;\
			slopBed -i "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_FE.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.fc.signal.bedgraph; \
			rm -f "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_FE.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.fc.signal.bedgraph > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.fc.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/signal/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.fc.signal.bigwig"; \
			rm -f /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.fc.signal.bedgraph /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.fc.signal.srt.bedgraph; \
			\
			sval=$(wc -l <(zcat -f "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz") | awk '{printf "%f", $1/1000000}'); \
			\
			macs2 bdgcmp \
				-t "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_treat_pileup.bdg -c "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_control_lambda.bdg \
				--o-prefix "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1" -m ppois -S "${sval}"; \
			slopBed -i "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_ppois.bdg -g "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" -b 0 | bedClip stdin "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.pval.signal.bedgraph; \
			rm -f "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_ppois.bdg; \
			\
			sort -k1,1 -k2,2n /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.pval.signal.bedgraph > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
			bedGraphToBigWig /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.pval.signal.srt.bedgraph "/mnt/data/annotations/by_release/hg19.GRCh37/hg19.chrom.sizes" "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/signal/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.pval.signal.bigwig"; \
			rm -f /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.pval.signal.bedgraph /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.pval.signal.srt.bedgraph; \
			\
			fi

# SYS command. line 115

 rm -f "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_treat_pileup.bdg "/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1"_control_lambda.bdg

# SYS command. line 117

 TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."

   
--------------------Stdout--------------------
Task has finished (490 seconds).

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH
INFO  @ Wed, 22 Jun 2016 18:02:02: 
# Command line: callpeak -t /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz -f BED -n /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 --broad --keep-dup all
# ARGUMENTS LIST:
# name = /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff for narrow/strong regions = 1.00e-01
# pvalue cutoff for broad/weak regions = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is on
 
INFO  @ Wed, 22 Jun 2016 18:02:02: #1 read tag files... 
INFO  @ Wed, 22 Jun 2016 18:02:02: #1 read treatment tags... 
INFO  @ Wed, 22 Jun 2016 18:02:03:  1000000 
INFO  @ Wed, 22 Jun 2016 18:02:05:  2000000 
INFO  @ Wed, 22 Jun 2016 18:02:06:  3000000 
INFO  @ Wed, 22 Jun 2016 18:02:08:  4000000 
INFO  @ Wed, 22 Jun 2016 18:02:09:  5000000 
INFO  @ Wed, 22 Jun 2016 18:02:11:  6000000 
INFO  @ Wed, 22 Jun 2016 18:02:13:  7000000 
INFO  @ Wed, 22 Jun 2016 18:02:14:  8000000 
INFO  @ Wed, 22 Jun 2016 18:02:16:  9000000 
INFO  @ Wed, 22 Jun 2016 18:02:17:  10000000 
INFO  @ Wed, 22 Jun 2016 18:02:19:  11000000 
INFO  @ Wed, 22 Jun 2016 18:02:20:  12000000 
INFO  @ Wed, 22 Jun 2016 18:02:22:  13000000 
INFO  @ Wed, 22 Jun 2016 18:02:23: #1 tag size is determined as 82 bps 
INFO  @ Wed, 22 Jun 2016 18:02:23: #1 tag size = 82 
INFO  @ Wed, 22 Jun 2016 18:02:23: #1  total tags in treatment: 13167500 
INFO  @ Wed, 22 Jun 2016 18:02:23: #1 finished! 
INFO  @ Wed, 22 Jun 2016 18:02:23: #2 Build Peak Model... 
INFO  @ Wed, 22 Jun 2016 18:02:23: #2 Skipped... 
INFO  @ Wed, 22 Jun 2016 18:02:23: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Wed, 22 Jun 2016 18:02:23: #2 Use 150 as fragment length 
INFO  @ Wed, 22 Jun 2016 18:02:23: #3 Call peaks... 
INFO  @ Wed, 22 Jun 2016 18:02:23: #3 Call broad peaks with given level1 -log10pvalue cutoff and level2: 1.00000, 1.00000... 
INFO  @ Wed, 22 Jun 2016 18:02:23: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 22 Jun 2016 18:02:48: #3 Call peaks for each chromosome... 
INFO  @ Wed, 22 Jun 2016 18:03:48: #4 Write output xls file... /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_peaks.xls 
INFO  @ Wed, 22 Jun 2016 18:03:51: #4 Write broad peak in broadPeak format file... /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_peaks.broadPeak 
INFO  @ Wed, 22 Jun 2016 18:03:54: #4 Write broad peak in bed12/gappedPeak format file... /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_peaks.gappedPeak 
INFO  @ Wed, 22 Jun 2016 18:03:56: Done! 
INFO  @ Wed, 22 Jun 2016 18:04:07: 
# Command line: callpeak -t /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz -f BED -n /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1 -g hs -p 0.1 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits
# ARGUMENTS LIST:
# name = /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1
# format = BED
# ChIP-seq file = ['/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.tagAlign.gz']
# control file = None
# effective genome size = 2.70e+09
# band width = 300
# model fold = [5, 50]
# pvalue cutoff = 1.00e-01
# qvalue will not be calculated and reported as -1 in the final output.
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 10000 bps
# Broad region calling is off
# Searching for subpeak summits is on
# MACS will save fragment pileup signal per million reads
 
INFO  @ Wed, 22 Jun 2016 18:04:07: #1 read tag files... 
INFO  @ Wed, 22 Jun 2016 18:04:07: #1 read treatment tags... 
INFO  @ Wed, 22 Jun 2016 18:04:09:  1000000 
INFO  @ Wed, 22 Jun 2016 18:04:11:  2000000 
INFO  @ Wed, 22 Jun 2016 18:04:12:  3000000 
INFO  @ Wed, 22 Jun 2016 18:04:14:  4000000 
INFO  @ Wed, 22 Jun 2016 18:04:16:  5000000 
INFO  @ Wed, 22 Jun 2016 18:04:17:  6000000 
INFO  @ Wed, 22 Jun 2016 18:04:19:  7000000 
INFO  @ Wed, 22 Jun 2016 18:04:20:  8000000 
INFO  @ Wed, 22 Jun 2016 18:04:22:  9000000 
INFO  @ Wed, 22 Jun 2016 18:04:24:  10000000 
INFO  @ Wed, 22 Jun 2016 18:04:25:  11000000 
INFO  @ Wed, 22 Jun 2016 18:04:27:  12000000 
INFO  @ Wed, 22 Jun 2016 18:04:29:  13000000 
INFO  @ Wed, 22 Jun 2016 18:04:30: #1 tag size is determined as 82 bps 
INFO  @ Wed, 22 Jun 2016 18:04:30: #1 tag size = 82 
INFO  @ Wed, 22 Jun 2016 18:04:30: #1  total tags in treatment: 13167500 
INFO  @ Wed, 22 Jun 2016 18:04:30: #1 finished! 
INFO  @ Wed, 22 Jun 2016 18:04:30: #2 Build Peak Model... 
INFO  @ Wed, 22 Jun 2016 18:04:30: #2 Skipped... 
INFO  @ Wed, 22 Jun 2016 18:04:30: #2 Sequencing ends will be shifted towards 5' by 75 bp(s) 
INFO  @ Wed, 22 Jun 2016 18:04:30: #2 Use 150 as fragment length 
INFO  @ Wed, 22 Jun 2016 18:04:30: #3 Call peaks... 
INFO  @ Wed, 22 Jun 2016 18:04:30: #3 Going to call summits inside each peak ... 
INFO  @ Wed, 22 Jun 2016 18:04:30: #3 Call peaks with given -log10pvalue cutoff: 1.00000 ... 
INFO  @ Wed, 22 Jun 2016 18:04:30: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Wed, 22 Jun 2016 18:04:57: #3 In the peak calling step, the following will be performed simultaneously: 
INFO  @ Wed, 22 Jun 2016 18:04:57: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_treat_pileup.bdg 
INFO  @ Wed, 22 Jun 2016 18:04:57: #3   Write bedGraph files for control lambda (after scaling if necessary)... /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_control_lambda.bdg 
INFO  @ Wed, 22 Jun 2016 18:04:57: #3   --SPMR is requested, so pileup will be normalized by sequencing depth in million reads. 
INFO  @ Wed, 22 Jun 2016 18:04:57: #3 Call peaks for each chromosome... 
INFO  @ Wed, 22 Jun 2016 18:09:55: #4 Write output xls file... /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_peaks.xls 
INFO  @ Wed, 22 Jun 2016 18:10:00: #4 Write peak in narrowPeak format file... /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_peaks.narrowPeak 
INFO  @ Wed, 22 Jun 2016 18:10:04: #4 Write summits bed file... /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1_summits.bed 
INFO  @ Wed, 22 Jun 2016 18:10:06: Done!

Num	17
ID	task.callpeak_etc.filt_top_peaks_rep1.line_27.id_22
Name	filt_top_peaks rep1
Thread	thread_Root
PID	74368

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-06-22 18:21:53
End	2016-06-22 18:21:59
Elapsed	00:00:06
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.narrowPeak.gz
Output files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.narrowPeak.gz
Dependencies

 
# SYS command. line 29

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/dskim89/git/bds_atac/.:/users/dskim89/git/bds_atac/modules:/users/dskim89/git/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 32

 set +o pipefail

# SYS command. line 35

 zcat /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.narrowPeak.gz | sort -grk8 | head -n 500000 | gzip -c > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.narrowPeak.gz

# SYS command. line 37

 TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."

   
--------------------Stdout--------------------
Task has finished (5 seconds).

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	18
ID	task.callpeak_etc.filt_top_peaks_rep1.line_27.id_23
Name	filt_top_peaks rep1
Thread	thread_Root
PID	74400

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-06-22 18:21:53
End	2016-06-22 18:21:59
Elapsed	00:00:06
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.gappedPeak.gz
Output files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.gappedPeak.gz
Dependencies

 
# SYS command. line 29

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/dskim89/git/bds_atac/.:/users/dskim89/git/bds_atac/modules:/users/dskim89/git/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 32

 set +o pipefail

# SYS command. line 35

 zcat /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.gappedPeak.gz | sort -grk8 | head -n 500000 | gzip -c > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.gappedPeak.gz

# SYS command. line 37

 TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."

   
--------------------Stdout--------------------
Task has finished (6 seconds).

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	19
ID	task.callpeak_etc.filt_top_peaks_rep1_pr1.line_27.id_24
Name	filt_top_peaks rep1-pr1
Thread	thread_Root
PID	74490

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-06-22 18:21:55
End	2016-06-22 18:22:02
Elapsed	00:00:06
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.narrowPeak.gz
Output files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.500000.narrowPeak.gz
Dependencies

 
# SYS command. line 29

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/dskim89/git/bds_atac/.:/users/dskim89/git/bds_atac/modules:/users/dskim89/git/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 32

 set +o pipefail

# SYS command. line 35

 zcat /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.narrowPeak.gz | sort -grk8 | head -n 500000 | gzip -c > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.500000.narrowPeak.gz

# SYS command. line 37

 TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."

   
--------------------Stdout--------------------
Task has finished (6 seconds).

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	20
ID	task.callpeak_etc.filt_top_peaks_rep1_pr2.line_27.id_25
Name	filt_top_peaks rep1-pr2
Thread	thread_Root
PID	74552

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-06-22 18:21:57
End	2016-06-22 18:22:03
Elapsed	00:00:06
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.narrowPeak.gz
Output files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.500000.narrowPeak.gz
Dependencies

 
# SYS command. line 29

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/dskim89/git/bds_atac/.:/users/dskim89/git/bds_atac/modules:/users/dskim89/git/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 32

 set +o pipefail

# SYS command. line 35

 zcat /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.narrowPeak.gz | sort -grk8 | head -n 500000 | gzip -c > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.500000.narrowPeak.gz

# SYS command. line 37

 TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."

   
--------------------Stdout--------------------
Task has finished (5 seconds).

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	21
ID	task.callpeak_etc.filt_top_peaks_rep1_pr1.line_27.id_26
Name	filt_top_peaks rep1-pr1
Thread	thread_Root
PID	74613

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-06-22 18:21:58
End	2016-06-22 18:22:04
Elapsed	00:00:06
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.gappedPeak.gz
Output files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.500000.gappedPeak.gz
Dependencies

 
# SYS command. line 29

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/dskim89/git/bds_atac/.:/users/dskim89/git/bds_atac/modules:/users/dskim89/git/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 32

 set +o pipefail

# SYS command. line 35

 zcat /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.gappedPeak.gz | sort -grk8 | head -n 500000 | gzip -c > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.500000.gappedPeak.gz

# SYS command. line 37

 TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."

   
--------------------Stdout--------------------
Task has finished (6 seconds).

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	22
ID	task.callpeak_etc.filt_top_peaks_rep1_pr2.line_27.id_27
Name	filt_top_peaks rep1-pr2
Thread	thread_Root
PID	74674

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-06-22 18:21:59
End	2016-06-22 18:22:05
Elapsed	00:00:06
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.gappedPeak.gz
Output files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.500000.gappedPeak.gz
Dependencies

 
# SYS command. line 29

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/dskim89/git/bds_atac/.:/users/dskim89/git/bds_atac/modules:/users/dskim89/git/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 32

 set +o pipefail

# SYS command. line 35

 zcat /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.gappedPeak.gz | sort -grk8 | head -n 500000 | gzip -c > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.500000.gappedPeak.gz

# SYS command. line 37

 TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."

   
--------------------Stdout--------------------
Task has finished (6 seconds).

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	23
ID	task.callpeak_etc.naive_overlap_thresh_peak.line_68.id_28
Name	naive_overlap_thresh peak
Thread	thread_Root
PID	74741

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-06-22 18:22:07
End	2016-06-22 18:22:19
Elapsed	00:00:11
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.500000.narrowPeak.gz
Output files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/overlap/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.naive_overlap.narrowPeak.gz
Dependencies

 
# SYS command. line 70

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/dskim89/git/bds_atac/.:/users/dskim89/git/bds_atac/modules:/users/dskim89/git/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 73

 intersectBed -wo -a /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.narrowPeak.gz -b /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.500000.narrowPeak.gz | \
			awk 'BEGIN{FS="\t";OFS="\t"} {s1=$3-$2; s2=$13-$12; if (($21/s1 >= 0.5) || ($21/s2 >= 0.5)) {print $0}}' | cut -f 1-10 | sort | uniq | \
			intersectBed -wo -a stdin -b /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.500000.narrowPeak.gz | \
			awk 'BEGIN{FS="\t";OFS="\t"} {s1=$3-$2; s2=$13-$12; if (($21/s1 >= 0.5) || ($21/s2 >= 0.5)) {print $0}}' | cut -f 1-10 | sort | uniq | gzip -c > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/overlap/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.PooledInRep1AndRep2.narrowPeak.gz

# SYS command. line 79

 zcat /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/overlap/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.PooledInRep1AndRep2.narrowPeak.gz | sort | uniq | gzip -c > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/overlap/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.naive_overlap.narrowPeak.gz

# SYS command. line 81

 rm -f /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/overlap/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.PooledInRep1AndRep2.narrowPeak.gz

# SYS command. line 83

 TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."

   
--------------------Stdout--------------------
Task has finished (12 seconds).

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	24
ID	task.callpeak_etc.naive_overlap_thresh_gpeak.line_68.id_29
Name	naive_overlap_thresh gpeak
Thread	thread_Root
PID	74810

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-06-22 18:22:09
End	2016-06-22 18:22:23
Elapsed	00:00:14
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.gappedPeak.gz /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.500000.gappedPeak.gz /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.500000.gappedPeak.gz
Output files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/overlap/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.naive_overlap.gappedPeak.gz
Dependencies

 
# SYS command. line 70

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/dskim89/git/bds_atac/.:/users/dskim89/git/bds_atac/modules:/users/dskim89/git/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 73

 intersectBed -wo -a /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.gappedPeak.gz -b /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.500000.gappedPeak.gz | \
			awk 'BEGIN{FS="\t";OFS="\t"} {s1=$3-$2; s2=$18-$17; if (($31/s1 >= 0.5) || ($31/s2 >= 0.5)) {print $0}}' | cut -f 1-15 | sort | uniq | \
			intersectBed -wo -a stdin -b /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.500000.gappedPeak.gz | \
			awk 'BEGIN{FS="\t";OFS="\t"} {s1=$3-$2; s2=$18-$17; if (($31/s1 >= 0.5) || ($31/s2 >= 0.5)) {print $0}}' | cut -f 1-15 | sort | uniq | gzip -c > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/overlap/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.PooledInRep1AndRep2.gappedPeak.gz

# SYS command. line 79

 zcat /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/overlap/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.PooledInRep1AndRep2.gappedPeak.gz | sort | uniq | gzip -c > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/overlap/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.naive_overlap.gappedPeak.gz

# SYS command. line 81

 rm -f /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/overlap/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.PooledInRep1AndRep2.gappedPeak.gz

# SYS command. line 83

 TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."

   
--------------------Stdout--------------------
Task has finished (14 seconds).

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	25
ID	task.idr.idr2_rep1_pr.line_73.id_30
Name	idr2 rep1-pr
Thread	thread_Root
PID	74879

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-06-22 18:22:10
End	2016-06-22 18:24:59
Elapsed	00:02:49
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.narrowPeak.gz
Output files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/idr/pseudo_reps/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_rep1-pr.IDR0.1.filt.narrowPeak.gz /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/idr/pseudo_reps/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_rep1-pr.unthresholded-peaks.txt.png /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/idr/pseudo_reps/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_rep1-pr.unthresholded-peaks.txt.gz /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/idr/pseudo_reps/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_rep1-pr.IDR0.1.filt.12-col.bed.gz
Dependencies

 
# SYS command. line 75

 if [[ -f $(which activate) ]]; then source activate bds_atac_py3; fi;  export PATH=/users/dskim89/git/bds_atac/.:/users/dskim89/git/bds_atac/modules:/users/dskim89/git/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 77

 idr --samples /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr1.tn5.pf.pval0.1.500000.narrowPeak.gz /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/pseudo_reps/rep1/pr2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pr2.tn5.pf.pval0.1.500000.narrowPeak.gz --peak-list /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.narrowPeak.gz --input-file-type narrowPeak \
			--output-file /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/idr/pseudo_reps/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_rep1-pr.unthresholded-peaks.txt --rank p.value --soft-idr-threshold 0.1 \
			--plot --use-best-multisummit-IDR

# SYS command. line 81

 idr_thresh_transformed=$(awk -v p=0.1 'BEGIN{print -log(p)/log(10)}')

# SYS command. line 84

 awk 'BEGIN{OFS="\t"} $12>='"${idr_thresh_transformed}"' {if ($2<0) $2=0; print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12,"0"}' /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/idr/pseudo_reps/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_rep1-pr.unthresholded-peaks.txt \
			| sort | uniq | sort -k7n,7n | gzip -c > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/idr/pseudo_reps/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_rep1-pr.IDR0.1.13-col.bed.gz

# SYS command. line 87

 zcat /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/idr/pseudo_reps/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_rep1-pr.IDR0.1.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -c > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/idr/pseudo_reps/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_rep1-pr.IDR0.1.narrowPeak.gz

# SYS command. line 88

 zcat /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/idr/pseudo_reps/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_rep1-pr.IDR0.1.13-col.bed.gz | awk 'BEGIN{OFS="\t"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -c > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/idr/pseudo_reps/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_rep1-pr.IDR0.1.12-col.bed.gz

# SYS command. line 90

 bedtools intersect -v -a /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/idr/pseudo_reps/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_rep1-pr.IDR0.1.13-col.bed.gz -b /mnt/data/ENCODE/blacklists/wgEncodeDacMapabilityConsensusExcludable.bed.gz | gzip -c > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/idr/pseudo_reps/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_rep1-pr.IDR0.1.filt.13-col.bed.gz

# SYS command. line 91

 zcat /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/idr/pseudo_reps/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_rep1-pr.IDR0.1.filt.13-col.bed.gz | awk 'BEGIN{OFS="	"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10}' | gzip -c > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/idr/pseudo_reps/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_rep1-pr.IDR0.1.filt.narrowPeak.gz

# SYS command. line 92

 zcat /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/idr/pseudo_reps/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_rep1-pr.IDR0.1.filt.13-col.bed.gz | awk 'BEGIN{OFS="	"} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12}' | gzip -c > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/idr/pseudo_reps/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_rep1-pr.IDR0.1.filt.12-col.bed.gz

# SYS command. line 94

 gzip -f /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/idr/pseudo_reps/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_rep1-pr.unthresholded-peaks.txt

# SYS command. line 95

 rm -f /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/idr/pseudo_reps/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_rep1-pr.IDR0.1.13-col.bed.gz /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/idr/pseudo_reps/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_rep1-pr.IDR0.1.filt.13-col.bed.gz

# SYS command. line 97

 TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."

   
--------------------Stdout--------------------
Task has finished (169 seconds).

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac_py3/bin to PATH
Initial parameter values: [0.10 1.00 0.20 0.50]
Final parameter values: [1.73 0.68 0.91 0.37]
Number of reported peaks - 179914/179914 (100.0%)

Number of peaks passing IDR cutoff of 0.1 - 90653/179914 (50.4%)

Num	26
ID	task.idr.idr_final_qc.line_214.id_33
Name	idr final qc
Thread	thread_Root
PID	74987

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-06-22 18:25:01
End	2016-06-22 18:25:02
Elapsed	00:00:00
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/idr/pseudo_reps/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_rep1-pr.IDR0.1.filt.narrowPeak.gz
Output files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/qc/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_IDR_final.qc
Dependencies

 
# SYS command. line 216

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/dskim89/git/bds_atac/.:/users/dskim89/git/bds_atac/modules:/users/dskim89/git/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 218

 echo -e "Nt\tN1	""Np\tconservative_set\toptimal_set\trescue_ratio\tself_consistency_ratio\treproducibility" > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/qc/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_IDR_final.qc

# SYS command. line 219

 echo -e "0\t90385	""0\tN/A\tN/A\tNaN\t1.0\t1" >> /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/qc/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_IDR_final.qc

# SYS command. line 221

 TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."

   
--------------------Stdout--------------------
Task has finished (0 seconds).

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	27
ID	task.atac.ataqc_rep1.line_951.id_34
Name	ataqc rep1
Thread	thread_61
PID	75045

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-06-22 18:25:04
End	2016-06-22 19:28:28
Elapsed	01:03:24
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/www/kundaje/dskim89/epinomics/fastqs_2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.fastq.gz /srv/www/kundaje/dskim89/epinomics/fastqs_2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_2_pf.fastq.gz /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.bam /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/qc/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.align.log /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/qc/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pbc.qc /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/qc/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.dup.qc /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.bam /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.tagAlign.gz /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/signal/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval.signal.bigwig /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.narrowPeak.gz
Output files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/qc/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.PE2SE_qc.html /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/qc/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.PE2SE_qc.txt
Dependencies

 
# SYS command. line 953

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/dskim89/git/bds_atac/.:/users/dskim89/git/bds_atac/modules:/users/dskim89/git/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 957

 export _JAVA_OPTIONS="-Xms256M -Xmx4096M -XX:ParallelGCThreads=1"

# SYS command. line 959

 cd /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/qc/rep1

# SYS command. line 961

 /users/dskim89/git/bds_atac/ataqc/run_ataqc.py \
		    --workdir /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/qc/rep1 \
		    --outdir /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/qc/rep1 \
		    --outprefix 151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.PE2SE \
		    --genome hg19 \
		    --ref /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/encodeHg19Male.fa \
		    --tss /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/hg19_RefSeq_stranded.bed.gz \
		    --dnase /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_all_p10_ucsc.bed.gz \
		    --blacklist /mnt/data/ENCODE/blacklists/wgEncodeDacMapabilityConsensusExcludable.bed.gz \
		    --prom /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_prom_p2.bed.gz \
		    --enh /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/reg2map_honeybadger2_dnase_enh_p2.bed.gz \
		    --reg2map /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/dnase_avgs_reg2map_p10_merged_named.pvals.gz \
		    --meta /mnt/lab_data/kundaje/users/dskim89/ataqc/annotations/hg19/eid_to_mnemonic.txt \
		    --pbc /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/qc/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.pbc.qc\
		    --fastq1 /srv/www/kundaje/dskim89/epinomics/fastqs_2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.fastq.gz --fastq2 /srv/www/kundaje/dskim89/epinomics/fastqs_2/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_2_pf.fastq.gz \
		    --alignedbam /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.bam \
		    --alignmentlog /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/qc/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.align.log \
		    --coordsortbam /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.bam \
		    --duplog /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/qc/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.dup.qc \
		    --finalbam /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.bam \
		    --finalbed /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/align/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.tagAlign.gz \
		    --bigwig /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/signal/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval.signal.bigwig \
		    --peaks /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.narrowPeak.gz \
		    --naive_overlap_peaks /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/overlap/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.naive_overlap.narrowPeak.gz \
		    --idr_peaks /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/idr/pseudo_reps/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_rep1-pr.IDR0.1.filt.narrowPeak.gz

   
--------------------Stdout--------------------
Run time: 1:03:18

 
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH
/software/miniconda3/envs/bds_atac/lib/python2.7/site-packages/matplotlib/font_manager.py:273: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment.
  warnings.warn('Matplotlib is building the font cache using fc-list. This may take a moment.')
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
ERROR	2016-06-22 18:28:21	ProcessExecutor	Warning messages:
ERROR	2016-06-22 18:28:21	ProcessExecutor	1: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH,  :
ERROR	2016-06-22 18:28:21	ProcessExecutor	  zero-length arrow is of indeterminate angle and so skipped
ERROR	2016-06-22 18:28:21	ProcessExecutor	2: In arrows(metrics$GC, metrics$NORMALIZED_COVERAGE - metrics$ERROR_BAR_WIDTH,  :
ERROR	2016-06-22 18:28:21	ProcessExecutor	  zero-length arrow is of indeterminate angle and so skipped
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
[bam_sort_core] merging from 30 files...
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
Picked up _JAVA_OPTIONS: -Xms256M -Xmx4096M -XX:ParallelGCThreads=1
processing chromosomes
/users/dskim89/git/bds_atac/ataqc/run_ataqc.py:851: FutureWarning: sort(columns=....) is deprecated, use sort_values(by=.....)
  sorted_results = merged.sort('corr', ascending=True)

Num	28
ID	task.report.peak2hammock.line_422.id_35
Name	peak2hammock
Thread	thread_Root
PID	76214

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-06-22 19:28:30
End	2016-06-22 19:28:36
Elapsed	00:00:06
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/overlap/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.naive_overlap.narrowPeak.gz
Output files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/overlap/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.naive_overlap.narrowPeak.hammock.gz
Dependencies

 
# SYS command. line 424

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/dskim89/git/bds_atac/.:/users/dskim89/git/bds_atac/modules:/users/dskim89/git/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 425

 zcat /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/overlap/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.naive_overlap.narrowPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/overlap/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.naive_overlap.narrowPeak.tmp

# SYS command. line 427

 /users/dskim89/git/bds_atac/utils/narrowpeak.py /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/overlap/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.naive_overlap.narrowPeak.tmp /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/overlap/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.naive_overlap.narrowPeak.hammock

# SYS command. line 428

 rm -f /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/overlap/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.naive_overlap.narrowPeak.tmp

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	29
ID	task.report.peak2hammock.line_422.id_36
Name	peak2hammock
Thread	thread_Root
PID	76286

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-06-22 19:28:37
End	2016-06-22 19:28:43
Elapsed	00:00:05
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/overlap/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.naive_overlap.gappedPeak.gz
Output files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/overlap/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.naive_overlap.gappedPeak.hammock.gz
Dependencies

 
# SYS command. line 424

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/dskim89/git/bds_atac/.:/users/dskim89/git/bds_atac/modules:/users/dskim89/git/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 425

 zcat /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/overlap/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.naive_overlap.gappedPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/overlap/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.naive_overlap.gappedPeak.tmp

# SYS command. line 427

 /users/dskim89/git/bds_atac/utils/gappedpeak.py /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/overlap/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.naive_overlap.gappedPeak.tmp /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/overlap/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.naive_overlap.gappedPeak.hammock

# SYS command. line 428

 rm -f /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/overlap/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.pval0.1.500000.naive_overlap.gappedPeak.tmp

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	30
ID	task.report.peak2hammock.line_422.id_37
Name	peak2hammock
Thread	thread_Root
PID	76356

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-06-22 19:28:44
End	2016-06-22 19:28:48
Elapsed	00:00:04
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.narrowPeak.gz
Output files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.narrowPeak.hammock.gz
Dependencies

 
# SYS command. line 424

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/dskim89/git/bds_atac/.:/users/dskim89/git/bds_atac/modules:/users/dskim89/git/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 425

 zcat /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.narrowPeak.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.narrowPeak.tmp

# SYS command. line 427

 /users/dskim89/git/bds_atac/utils/narrowpeak.py /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.narrowPeak.tmp /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.narrowPeak.hammock

# SYS command. line 428

 rm -f /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/macs2/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.tn5.pf.narrowPeak.tmp

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	31
ID	task.report.peak2hammock.line_422.id_38
Name	peak2hammock
Thread	thread_Root
PID	76427

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-06-22 19:28:49
End	2016-06-22 19:28:52
Elapsed	00:00:03
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/idr/pseudo_reps/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_rep1-pr.IDR0.1.filt.12-col.bed.gz
Output files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/idr/pseudo_reps/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_rep1-pr.IDR0.1.filt.12-col.bed.hammock.gz
Dependencies

 
# SYS command. line 424

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/dskim89/git/bds_atac/.:/users/dskim89/git/bds_atac/modules:/users/dskim89/git/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 425

 zcat /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/idr/pseudo_reps/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_rep1-pr.IDR0.1.filt.12-col.bed.gz | sed '/^\(chr\)/!d' | sort -k1,1V -k2,2n > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/idr/pseudo_reps/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_rep1-pr.IDR0.1.filt.12-col.bed.tmp

# SYS command. line 427

 /users/dskim89/git/bds_atac/utils/narrowpeak.py /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/idr/pseudo_reps/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_rep1-pr.IDR0.1.filt.12-col.bed.tmp /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/idr/pseudo_reps/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_rep1-pr.IDR0.1.filt.12-col.bed.hammock

# SYS command. line 428

 rm -f /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/peak/idr/pseudo_reps/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_rep1-pr.IDR0.1.filt.12-col.bed.tmp

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	32
ID	task.report_graphviz.report.line_108.id_39
Name	report
Thread	thread_Root
PID	76505

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-06-22 19:28:53
End	2016-06-22 19:28:56
Elapsed	00:00:03
Timeout	00:00:-1
Wall Timeout	100 days

Input files
Output files
Dependencies

 
# SYS command. line 109

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/dskim89/git/bds_atac/.:/users/dskim89/git/bds_atac/modules:/users/dskim89/git/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 110

 dot -Tsvg /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/report/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_workflow.dot > /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/report/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_workflow.svg

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Num	33
ID	task.report.pdf2png.line_385.id_42
Name	pdf2png
Thread	thread_Root
PID	76510

OK	true
Exit Code	0
Retries
State	FINISHED
Dep.	OK
Cpus	1
Mem

Start	2016-06-22 19:28:53
End	2016-06-22 19:28:55
Elapsed	00:00:02
Timeout	00:00:-1
Wall Timeout	100 days

Input files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/qc/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.25M.cc.plot.pdf
Output files	/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/qc/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.25M.cc.plot.png
Dependencies

 
# SYS command. line 386

 if [[ -f $(which activate) ]]; then source activate bds_atac; fi;  export PATH=/users/dskim89/git/bds_atac/.:/users/dskim89/git/bds_atac/modules:/users/dskim89/git/bds_atac/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

# SYS command. line 387

 gs -dFirstPage=1 -dLastPage=1 -dTextAlphaBits=4 -dGraphicsAlphaBits=4 -r110x110 \
			-dUseCropBox -dQUIET -dSAFER -dBATCH -dNOPAUSE -dNOPROMPT -sDEVICE=png16m \
			-sOutputFile=/srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/qc/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.25M.cc.plot.png \
			-r144 /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA/qc/rep1/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.trim.PE2SE.nodup.25M.cc.plot.pdf

    
--------------------Stderr--------------------
discarding /software/miniconda3/bin from PATH
prepending /software/miniconda3/envs/bds_atac/bin to PATH

Type	Name	Value
string	_	/usr/bin/bds
string	_JAVA_OPTIONS	-Xms256M -Xmx1024M -XX:ParallelGCThreads=1
bool	allowEmpty	false
string[]	args	[-adapter1_1, CTGTCTCTTATACACATCT, -adapter1_2, CTGTCTCTTATACACATCT, -fastq1_1, 151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_1_pf.fastq.gz, -fastq1_2, 151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA_2_pf.fastq.gz, -out_dir, /srv/scratch/dskim89/ataqc/results/epinomics.atac.2016-06-22.test_run/151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA, -title, 151202_BRISCOE_0269_AC83PEACXX_L3_AGGCAGAA, -species, hg19, -multimapping, 4]
string	BASH_FUNC_module%%	() { eval `/software/env_module/$MODULE_VERSION/bin/modulecmd sh $*`\n}
bool	canFail	false
int	cpus	1
int	cpusLocal	48
int	day	86400
string	DEEPLEARN_SCRIPTS_DIR	/users/nadinehu/deeplearning
real	E	2.718281828459045
int	G	1073741824
string	HOME	/users/dskim89/
int	hour	3600
int	K	1024
string	KERAS_DIR	/users/nadinehu/keras
string	KRB5CCNAME	FILE:/tmp/krb5cc_1060_0IWBck
string	LANG	en_US.UTF-8
string	LD_LIBRARY_PATH	/usr/local/cuda/lib64:
string	LOADEDMODULES
string	LOGNAME	dskim89
int	M	1048576
string	MAIL	/var/mail/dskim89
string	MALLOC_ARENA_MAX	4
string	MAX_JAVA_MEM	8G
int	mem	-1
int	minute	60
string	MODULE_VERSION	3.2.10
string	MODULE_VERSION_STACK	3.2.10
string	MODULEPATH	/usr/local/Modules/versions\t\t\t\t:/usr/local/Modules/$MODULE_VERSION/modulefiles\t:/modules/\t\t\t\t:/software/modulefiles
string	MODULESHOME	/software/env_module/3.2.10
string	node
int	P	1125899906842624
string	PATH	/software/miniconda3/bin:/users/dskim89/anaconda2/bin:/usr/local/cuda/bin:/users/nadinehu/deeplearning/exec:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/software/miniconda3/bin:/users/dskim89//.bds
real	PI	3.141592653589793
string	ppwd	/srv/www/kundaje/dskim89/epinomics/fastqs_2
string	programName	atac.bds
string	programPath	/users/dskim89/git/bds_atac/atac.bds
string	PWD	/srv/www/kundaje/dskim89/epinomics/fastqs_2
string	queue
int	retry	0
string	SHELL	/bin/bash
string	SHLVL	2
string	SSH_CLIENT	10.39.64.210 58224 22
string	SSH_CONNECTION	10.39.64.210 58224 171.65.76.236 22
string	SSH_TTY	/dev/pts/13
string	STY	71770.pts-13.mitra
string	system	local
int	T	1099511627776
string	TERM	screen
string	TERMCAP	SC\|screen\|VT 100/ANSI X3.64 virtual terminal:\\\n\t:DO=\\E[%dB:LE=\\E[%dD:RI=\\E[%dC:UP=\\E[%dA:bs:bt=\\E[Z:\\\n\t:cd=\\E[J:ce=\\E[K:cl=\\E[H\\E[J:cm=\\E[%i%d;%dH:ct=\\E[3g:\\\n\t:do=^J:nd=\\E[C:pt:rc=\\E8:rs=\\Ec:sc=\\E7:st=\\EH:up=\\EM:\\\n\t:le=^H:bl=^G:cr=^M:it#8:ho=\\E[H:nw=\\EE:ta=^I:is=\\E)0:\\\n\t:li#60:co#226:am:xn:xv:LP:sr=\\EM:al=\\E[L:AL=\\E[%dL:\\\n\t:cs=\\E[%i%d;%dr:dl=\\E[M:DL=\\E[%dM:dc=\\E[P:DC=\\E[%dP:\\\n\t:im=\\E[4h:ei=\\E[4l:mi:IC=\\E[%d@:ks=\\E[?1h\\E=:\\\n\t:ke=\\E[?1l\\E>:vi=\\E[?25l:ve=\\E[34h\\E[?25h:vs=\\E[34l:\\\n\t:ti=\\E[?1049h:te=\\E[?1049l:us=\\E[4m:ue=\\E[24m:so=\\E[3m:\\\n\t:se=\\E[23m:mb=\\E[5m:md=\\E[1m:mr=\\E[7m:me=\\E[m:ms:\\\n\t:Co#8:pa#64:AF=\\E[3%dm:AB=\\E[4%dm:op=\\E[39;49m:AX:\\\n\t:vb=\\Eg:G0:as=\\E(0:ae=\\E(B:\\\n\t:ac=\\140\\140aaffggjjkkllmmnnooppqqrrssttuuvvwwxxyyzz{{\|\|}}~~..--++,,hhII00:\\\n\t:po=\\E[5i:pf=\\E[4i:Km=\\E[M:k0=\\E[10~:k1=\\EOP:k2=\\EOQ:\\\n\t:k3=\\EOR:k4=\\EOS:k5=\\E[15~:k6=\\E[17~:k7=\\E[18~:\\\n\t:k8=\\E[19~:k9=\\E[20~:k;=\\E[21~:F1=\\E[23~:F2=\\E[24~:\\\n\t:F3=\\E[1;2P:F4=\\E[1;2Q:F5=\\E[1;2R:F6=\\E[1;2S:\\\n\t:F7=\\E[15;2~:F8=\\E[17;2~:F9=\\E[18;2~:FA=\\E[19;2~:kb=:\\\n\t:K2=\\EOE:kB=\\E[Z:kF=\\E[1;2B:kR=\\E[1;2A:4=\\E[3;2~:\\\n\t:7=\\E[1;2F:#2=\\E[1;2H:#3=\\E[2;2~:#4=\\E[1;2D:%c=\\E[6;2~:\\\n\t:%e=\\E[5;2~:%i=\\E[1;2C:kh=\\E[1~:@1=\\E[1~:kH=\\E[4~:\\\n\t:@7=\\E[4~:kN=\\E[6~:kP=\\E[5~:kI=\\E[2~:kD=\\E[3~:ku=\\EOA:\\\n\t:kd=\\EOB:kr=\\EOC:kl=\\EOD:km:
int	timeout	-1
string	USER	dskim89
string	UTIL_SCRIPTS_DIR	/users/dskim89/git/av_scripts
int	walltimeout	8640000
int	week	604800
string	WINDOW	0
string	XAUTHORITY	/users/dskim89//.Xauthority
string	XDG_RUNTIME_DIR	/run/user/1060
string	XDG_SESSION_ID	4257

BigDataScript report: atac.bds

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