/var/spool/slurm/d/job2268256/slurm_script: line 20: fg: no job control
Using an excessive number of cores has a diminishing return! It is recommended not to exceed 8 cores per trimming process (you asked for 8 cores). Please consider re-specifying
Path to Cutadapt set as: '/gscratch/srlab/strigg/bin/anaconda3/bin/cutadapt' (user defined)
Cutadapt seems to be working fine (tested command '/gscratch/srlab/strigg/bin/anaconda3/bin/cutadapt --version')
Cutadapt version: 2.4
Could not detect version of Python used by Cutadapt from the first line of Cutadapt (but found this: >>>#!/bin/sh<<<)
Letting the (modified) Cutadapt deal with the Python version instead
Parallel gzip (pigz) detected. Proceeding with multicore (de)compression using 8 cores

No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default)

Output will be written into the directory: /gscratch/scrubbed/strigg/analyses/20200316/
Setting the option '--clip_r2 2' (to remove methylation bias from the start of Read 2)
Writing report to '/gscratch/scrubbed/strigg/analyses/20200316/EPI-167_S10_L002_R1_001.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /gscratch/srlab/strigg/data/Pgenr/FASTQS/raw/EPI-167_S10_L002_R1_001.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.6.4_dev
Cutadapt version: 2.4
Python version: could not detect
Number of cores used for trimming: 8
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGCACACGTCTGAAC' (user defined)
Maximum trimming error rate: 0.1 (default)
Optional adapter 2 sequence (only used for read 2 of paired-end files): 'AGATCGGAAGAGCGTCGTGTAGGGA'
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
File was specified to be an MspI-digested RRBS sample. Read 1 sequences with adapter contamination will be trimmed a further 2 bp from their 3' end, and Read 2 sequences will be trimmed by 2 bp from their 5' end to remove potential methylation-biased bases from the end-repair reaction
All Read 2 sequences will be trimmed by 2 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications)
Running FastQC on the data once trimming has completed
Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/FASTQC --threads 28'
Output file(s) will be GZIP compressed

Cutadapt seems to be fairly up-to-date (version 2.4). Setting -j 8
  >>> Now performing adaptive quality trimming with a Phred-score cutoff of: 20 <<<

This is cutadapt 2.4 with Python 3.7.6
Command line parameters: -j 8 -e 0.1 -q 20 -a X /gscratch/srlab/strigg/data/Pgenr/FASTQS/raw/EPI-167_S10_L002_R1_001.fastq.gz
Processing reads on 8 cores in single-end mode ...
10000000 sequences processed
20000000 sequences processed
Finished in 62.73 s (3 us/read; 23.78 M reads/minute).

=== Summary ===

Total reads processed:              24,859,230
Reads with adapters:                         0 (0.0%)
Reads written (passing filters):    24,859,230 (100.0%)

Total basepairs processed: 2,510,782,230 bp
Quality-trimmed:              11,488,232 bp (0.5%)
Total written (filtered):  2,499,293,998 bp (99.5%)

=== Adapter 1 ===

Sequence: X; Type: regular 3'; Length: 1; Trimmed: 0 times.

  >>> Quality trimming completed <<<
24859230 sequences processed in total

Writing final adapter and quality trimmed output to EPI-167_S10_L002_R1_001_trimmed.fq.gz


  >>> Now performing adapter trimming for the adapter sequence: 'AGATCGGAAGAGCACACGTCTGAAC' from file EPI-167_S10_L002_R1_001.fastq.gz_qual_trimmed.fastq <<< 
10000000 sequences processed
20000000 sequences processed
This is cutadapt 2.4 with Python 3.7.6
Command line parameters: -j 8 -e 0.1 -O 1 -a AGATCGGAAGAGCACACGTCTGAAC /gscratch/scrubbed/strigg/analyses/20200316/EPI-167_S10_L002_R1_001.fastq.gz_qual_trimmed.fastq
Processing reads on 8 cores in single-end mode ...
Finished in 81.27 s (3 us/read; 18.35 M reads/minute).

=== Summary ===

Total reads processed:              24,859,230
Reads with adapters:                13,310,825 (53.5%)
Reads written (passing filters):    24,859,230 (100.0%)

Total basepairs processed: 2,499,293,998 bp
Total written (filtered):  2,298,441,331 bp (92.0%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGCACACGTCTGAAC; Type: regular 3'; Length: 25; Trimmed: 13310825 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20-25 bp: 2

Bases preceding removed adapters:
  A: 25.5%
  C: 9.5%
  G: 23.7%
  T: 41.3%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	5079588	6214807.5	0	5079588
2	1202251	1553701.9	0	1202251
3	456300	388425.5	0	456300
4	315396	97106.4	0	315396
5	162023	24276.6	0	162023
6	154952	6069.1	0	154952
7	141317	1517.3	0	141317
8	147815	379.3	0	147815
9	156397	94.8	0	154875 1522
10	144818	23.7	1	138784 6034
11	151610	5.9	1	144610 7000
12	144234	1.5	1	137849 6385
13	138279	0.4	1	132093 6186
14	149582	0.1	1	141472 8110
15	139617	0.0	1	132371 7246
16	149533	0.0	1	140718 8815
17	143290	0.0	1	134911 8379
18	132507	0.0	1	123777 8159 571
19	143599	0.0	1	132190 10635 774
20	131755	0.0	2	122046 8589 1120
21	146494	0.0	2	132987 11445 2062
22	135126	0.0	2	124303 9630 1193
23	126194	0.0	2	115663 9314 1217
24	131857	0.0	2	119870 10387 1600
25	122353	0.0	2	112116 9190 1047
26	132356	0.0	2	119736 10869 1751
27	119873	0.0	2	109836 8721 1316
28	113147	0.0	2	103784 8301 1062
29	123716	0.0	2	112992 9263 1461
30	113300	0.0	2	103872 8363 1065
31	120517	0.0	2	109240 9537 1740
32	111072	0.0	2	102015 7969 1088
33	114305	0.0	2	104447 8569 1289
34	108779	0.0	2	99492 8120 1167
35	104061	0.0	2	95648 7427 986
36	99353	0.0	2	91169 7175 1009
37	105972	0.0	2	96779 8018 1175
38	92166	0.0	2	84732 6433 1001
39	93699	0.0	2	85639 6965 1095
40	94449	0.0	2	85795 7662 992
41	129224	0.0	2	119820 8107 1297
42	78034	0.0	2	72578 4766 690
43	35611	0.0	2	31892 3292 427
44	72241	0.0	2	66560 4941 740
45	66871	0.0	2	61637 4601 633
46	63480	0.0	2	58567 4379 534
47	65222	0.0	2	59962 4547 713
48	58338	0.0	2	53531 4197 610
49	59861	0.0	2	54840 4380 641
50	53802	0.0	2	49655 3678 469
51	50397	0.0	2	46525 3380 492
52	46801	0.0	2	43097 3252 452
53	42870	0.0	2	39683 2782 405
54	41405	0.0	2	38238 2746 421
55	40756	0.0	2	37782 2611 363
56	36903	0.0	2	34142 2423 338
57	33898	0.0	2	31227 2360 311
58	31239	0.0	2	28980 2027 232
59	30217	0.0	2	28005 1966 246
60	26732	0.0	2	24878 1668 186
61	26427	0.0	2	24460 1787 180
62	25361	0.0	2	23508 1647 206
63	21705	0.0	2	20154 1396 155
64	19937	0.0	2	18653 1152 132
65	17966	0.0	2	16711 1137 118
66	16513	0.0	2	15317 1088 108
67	15408	0.0	2	14252 1052 104
68	14019	0.0	2	12960 970 89
69	13548	0.0	2	12518 939 91
70	12389	0.0	2	11493 818 78
71	12247	0.0	2	11250 892 105
72	14140	0.0	2	12722 1193 225
73	24750	0.0	2	21535 2947 268
74	80751	0.0	2	75790 4690 271
75	62956	0.0	2	59263 3517 176
76	34298	0.0	2	32139 2050 109
77	19980	0.0	2	18745 1172 63
78	11508	0.0	2	10781 686 41
79	6171	0.0	2	5742 410 19
80	3991	0.0	2	3687 279 25
81	2402	0.0	2	2222 166 14
82	1642	0.0	2	1490 140 12
83	1273	0.0	2	1174 88 11
84	1130	0.0	2	1031 91 8
85	989	0.0	2	903 78 8
86	959	0.0	2	877 76 6
87	835	0.0	2	750 78 7
88	716	0.0	2	643 63 10
89	798	0.0	2	727 62 9
90	871	0.0	2	802 64 5
91	1229	0.0	2	1108 109 12
92	1963	0.0	2	1790 160 13
93	4579	0.0	2	4247 306 26
94	13773	0.0	2	12652 1011 110
95	24682	0.0	2	22814 1730 138
96	11975	0.0	2	11015 885 75
97	8863	0.0	2	8123 684 56
98	3854	0.0	2	3544 284 26
99	4127	0.0	2	3800 310 17
100	4411	0.0	2	4002 383 26
101	8135	0.0	2	7184 899 52
Successfully deleted temporary file EPI-167_S10_L002_R1_001.fastq.gz_qual_trimmed.fastq


RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Pgenr/FASTQS/raw/EPI-167_S10_L002_R1_001.fastq.gz
=============================================
24859230 sequences processed in total
Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20):	2260450 (9.1%)
The length threshold of paired-end sequences gets evaluated later on (in the validation step)
RRBS reads trimmed by additional 2 bp when adapter contamination was detected:	13261661 (53.3%)

Writing report to '/gscratch/scrubbed/strigg/analyses/20200316/EPI-167_S10_L002_R2_001.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /gscratch/srlab/strigg/data/Pgenr/FASTQS/raw/EPI-167_S10_L002_R2_001.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.6.4_dev
Cutadapt version: 2.4
Python version: could not detect
Number of cores used for trimming: 8
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGCACACGTCTGAAC' (user defined)
Maximum trimming error rate: 0.1 (default)
Optional adapter 2 sequence (only used for read 2 of paired-end files): 'AGATCGGAAGAGCGTCGTGTAGGGA'
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
File was specified to be an MspI-digested RRBS sample. Read 1 sequences with adapter contamination will be trimmed a further 2 bp from their 3' end, and Read 2 sequences will be trimmed by 2 bp from their 5' end to remove potential methylation-biased bases from the end-repair reaction
All Read 2 sequences will be trimmed by 2 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications)
Running FastQC on the data once trimming has completed
Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/FASTQC --threads 28'
Output file(s) will be GZIP compressed

Cutadapt seems to be fairly up-to-date (version 2.4). Setting -j -j 8
  >>> Now performing adaptive quality trimming with a Phred-score cutoff of: 20 <<<

This is cutadapt 2.4 with Python 3.7.6
Command line parameters: -j 8 -e 0.1 -q 20 -a X /gscratch/srlab/strigg/data/Pgenr/FASTQS/raw/EPI-167_S10_L002_R2_001.fastq.gz
Processing reads on 8 cores in single-end mode ...
10000000 sequences processed
20000000 sequences processed
Finished in 59.04 s (2 us/read; 25.26 M reads/minute).

=== Summary ===

Total reads processed:              24,859,230
Reads with adapters:                         0 (0.0%)
Reads written (passing filters):    24,859,230 (100.0%)

Total basepairs processed: 2,510,782,230 bp
Quality-trimmed:              22,659,614 bp (0.9%)
Total written (filtered):  2,488,122,616 bp (99.1%)

=== Adapter 1 ===

Sequence: X; Type: regular 3'; Length: 1; Trimmed: 0 times.

  >>> Quality trimming completed <<<
24859230 sequences processed in total

Writing final adapter and quality trimmed output to EPI-167_S10_L002_R2_001_trimmed.fq.gz


  >>> Now performing adapter trimming for the adapter sequence: 'AGATCGGAAGAGCGTCGTGTAGGGA' from file EPI-167_S10_L002_R2_001.fastq.gz_qual_trimmed.fastq <<< 
10000000 sequences processed
20000000 sequences processed
This is cutadapt 2.4 with Python 3.7.6
Command line parameters: -j 8 -e 0.1 -O 1 -a AGATCGGAAGAGCGTCGTGTAGGGA /gscratch/scrubbed/strigg/analyses/20200316/EPI-167_S10_L002_R2_001.fastq.gz_qual_trimmed.fastq
Processing reads on 8 cores in single-end mode ...
Finished in 85.41 s (3 us/read; 17.46 M reads/minute).

=== Summary ===

Total reads processed:              24,859,230
Reads with adapters:                15,363,536 (61.8%)
Reads written (passing filters):    24,859,230 (100.0%)

Total basepairs processed: 2,488,122,616 bp
Total written (filtered):  2,293,251,313 bp (92.2%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGCGTCGTGTAGGGA; Type: regular 3'; Length: 25; Trimmed: 15363536 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20-25 bp: 2

Bases preceding removed adapters:
  A: 40.3%
  C: 20.3%
  G: 7.3%
  T: 32.1%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	8554514	6214807.5	0	8554514
2	247131	1553701.9	0	247131
3	191193	388425.5	0	191193
4	164298	97106.4	0	164298
5	160566	24276.6	0	160566
6	159035	6069.1	0	159035
7	150319	1517.3	0	150319
8	152605	379.3	0	152605
9	152922	94.8	0	152285 637
10	151128	23.7	1	146689 4439
11	146920	5.9	1	141612 5308
12	148837	1.5	1	143363 5474
13	142341	0.4	1	137280 5061
14	151875	0.1	1	146116 5759
15	140621	0.0	1	135080 5541
16	140329	0.0	1	134360 5969
17	147590	0.0	1	141058 6532
18	131268	0.0	1	125180 5970 118
19	137242	0.0	1	130202 6888 152
20	134860	0.0	2	126296 7299 1265
21	136470	0.0	2	126594 8307 1569
22	137929	0.0	2	128046 8405 1478
23	132148	0.0	2	122951 7765 1432
24	137535	0.0	2	127293 8713 1529
25	121830	0.0	2	112500 7874 1456
26	122372	0.0	2	111493 9021 1858
27	122833	0.0	2	110779 9719 2335
28	125558	0.0	2	115435 8627 1496
29	121040	0.0	2	109875 9372 1793
30	127761	0.0	2	117798 8505 1458
31	110644	0.0	2	101253 7874 1517
32	113145	0.0	2	104687 7317 1141
33	117931	0.0	2	107886 8506 1539
34	119747	0.0	2	108853 9087 1807
35	109358	0.0	2	101564 6789 1005
36	102469	0.0	2	93985 7185 1299
37	101986	0.0	2	93931 6852 1203
38	88289	0.0	2	81349 5989 951
39	91384	0.0	2	83980 6298 1106
40	87968	0.0	2	81063 5902 1003
41	85810	0.0	2	79585 5436 789
42	82412	0.0	2	76871 4870 671
43	73026	0.0	2	67328 4920 778
44	72521	0.0	2	67133 4755 633
45	84963	0.0	2	79659 4649 655
46	65401	0.0	2	60883 3896 622
47	46340	0.0	2	42573 3316 451
48	62890	0.0	2	58972 3433 485
49	44178	0.0	2	41087 2712 379
50	45926	0.0	2	42356 3132 438
51	59803	0.0	2	56373 3012 418
52	36947	0.0	2	34103 2470 374
53	36693	0.0	2	33991 2310 392
54	32194	0.0	2	29695 2182 317
55	36861	0.0	2	34493 2101 267
56	34269	0.0	2	31729 2174 366
57	30720	0.0	2	28494 1961 265
58	28380	0.0	2	26339 1776 265
59	26631	0.0	2	24733 1671 227
60	25170	0.0	2	23184 1700 286
61	24593	0.0	2	22735 1596 262
62	24060	0.0	2	22223 1561 276
63	22601	0.0	2	20779 1597 225
64	21649	0.0	2	19897 1515 237
65	22204	0.0	2	20390 1572 242
66	24131	0.0	2	22040 1770 321
67	35937	0.0	2	31177 4455 305
68	129003	0.0	2	123606 5023 374
69	47313	0.0	2	44432 2606 275
70	24870	0.0	2	23330 1358 182
71	12976	0.0	2	11952 904 120
72	8650	0.0	2	7938 594 118
73	6006	0.0	2	5428 500 78
74	4673	0.0	2	4170 423 80
75	3587	0.0	2	3246 292 49
76	2967	0.0	2	2644 260 63
77	2595	0.0	2	2287 248 60
78	2277	0.0	2	1988 229 60
79	1974	0.0	2	1740 196 38
80	1588	0.0	2	1403 150 35
81	1399	0.0	2	1220 147 32
82	1178	0.0	2	1020 129 29
83	1067	0.0	2	929 111 27
84	908	0.0	2	767 111 30
85	844	0.0	2	702 108 34
86	765	0.0	2	629 110 26
87	784	0.0	2	659 101 24
88	797	0.0	2	673 96 28
89	913	0.0	2	759 123 31
90	1123	0.0	2	931 153 39
91	1402	0.0	2	1155 188 59
92	2147	0.0	2	1810 255 82
93	4579	0.0	2	3823 597 159
94	13431	0.0	2	11681 1388 362
95	23741	0.0	2	20778 2421 542
96	11598	0.0	2	10136 1204 258
97	8556	0.0	2	7512 866 178
98	3633	0.0	2	3223 345 65
99	3883	0.0	2	3382 409 92
100	4128	0.0	2	3619 404 105
101	7880	0.0	2	6828 858 194
Successfully deleted temporary file EPI-167_S10_L002_R2_001.fastq.gz_qual_trimmed.fastq


RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Pgenr/FASTQS/raw/EPI-167_S10_L002_R2_001.fastq.gz
=============================================
24859230 sequences processed in total
Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20):	2502338 (10.1%)
The length threshold of paired-end sequences gets evaluated later on (in the validation step)
RRBS reads trimmed by additional 2 bp when adapter contamination was detected:	0 (0.0%)

Validate paired-end files EPI-167_S10_L002_R1_001_trimmed.fq.gz and EPI-167_S10_L002_R2_001_trimmed.fq.gz
file_1: EPI-167_S10_L002_R1_001_trimmed.fq.gz, file_2: EPI-167_S10_L002_R2_001_trimmed.fq.gz


>>>>> Now validing the length of the 2 paired-end infiles: EPI-167_S10_L002_R1_001_trimmed.fq.gz and EPI-167_S10_L002_R2_001_trimmed.fq.gz <<<<<
Writing validated paired-end Read 1 reads to EPI-167_S10_L002_R1_001_val_1.fq.gz
Writing validated paired-end Read 2 reads to EPI-167_S10_L002_R2_001_val_2.fq.gz

Total number of sequences analysed: 24859230

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 375991 (1.51%)


  >>> Now running FastQC on the validated data EPI-167_S10_L002_R1_001_val_1.fq.gz<<<

Started analysis of EPI-167_S10_L002_R1_001_val_1.fq.gz
Approx 5% complete for EPI-167_S10_L002_R1_001_val_1.fq.gz
Approx 10% complete for EPI-167_S10_L002_R1_001_val_1.fq.gz
Approx 15% complete for EPI-167_S10_L002_R1_001_val_1.fq.gz
Approx 20% complete for EPI-167_S10_L002_R1_001_val_1.fq.gz
Approx 25% complete for EPI-167_S10_L002_R1_001_val_1.fq.gz
Approx 30% complete for EPI-167_S10_L002_R1_001_val_1.fq.gz
Approx 35% complete for EPI-167_S10_L002_R1_001_val_1.fq.gz
Approx 40% complete for EPI-167_S10_L002_R1_001_val_1.fq.gz
Approx 45% complete for EPI-167_S10_L002_R1_001_val_1.fq.gz
Approx 50% complete for EPI-167_S10_L002_R1_001_val_1.fq.gz
Approx 55% complete for EPI-167_S10_L002_R1_001_val_1.fq.gz
Approx 60% complete for EPI-167_S10_L002_R1_001_val_1.fq.gz
Approx 65% complete for EPI-167_S10_L002_R1_001_val_1.fq.gz
Approx 70% complete for EPI-167_S10_L002_R1_001_val_1.fq.gz
Approx 75% complete for EPI-167_S10_L002_R1_001_val_1.fq.gz
Approx 80% complete for EPI-167_S10_L002_R1_001_val_1.fq.gz
Approx 85% complete for EPI-167_S10_L002_R1_001_val_1.fq.gz
Approx 90% complete for EPI-167_S10_L002_R1_001_val_1.fq.gz
Approx 95% complete for EPI-167_S10_L002_R1_001_val_1.fq.gz
Analysis complete for EPI-167_S10_L002_R1_001_val_1.fq.gz

  >>> Now running FastQC on the validated data EPI-167_S10_L002_R2_001_val_2.fq.gz<<<

Started analysis of EPI-167_S10_L002_R2_001_val_2.fq.gz
Approx 5% complete for EPI-167_S10_L002_R2_001_val_2.fq.gz
Approx 10% complete for EPI-167_S10_L002_R2_001_val_2.fq.gz
Approx 15% complete for EPI-167_S10_L002_R2_001_val_2.fq.gz
Approx 20% complete for EPI-167_S10_L002_R2_001_val_2.fq.gz
Approx 25% complete for EPI-167_S10_L002_R2_001_val_2.fq.gz
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Analysis complete for EPI-167_S10_L002_R2_001_val_2.fq.gz
Deleting both intermediate output files EPI-167_S10_L002_R1_001_trimmed.fq.gz and EPI-167_S10_L002_R2_001_trimmed.fq.gz

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