
--------------------------------------------------------------------------------
Module:			fastqc
Run File:		HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1.fastq.gz_fastq_kallisto.run
Job ID:			cf_fastq_kallisto_1463255307_fastqc_792
Previous Job ID:	start_000
Date & Time:		20:48, 14-05-2016
--------------------------------------------------------------------------------

---------- FastQC version information ----------
FastQC v0.11.5

------- End of FastQC version information ------

###CFCMD fastqc -q  HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1.fastq.gz

###CF FastQC successfully ran, took 13 minutes, 29 seconds

###CFCMD fastqc -q  HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2.fastq.gz

###CF FastQC successfully ran, took 12 minutes, 27 seconds




--------------------------------------------------------------------------------
Module:			trim_galore
Run File:		HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1.fastq.gz_fastq_kallisto.run
Job ID:			cf_fastq_kallisto_1463255307_trim_galore_160
Previous Job ID:	start_000
Date & Time:		20:48, 14-05-2016
--------------------------------------------------------------------------------

---------- Cutadapt version information ----------
1.8.1

------- End of Cutadapt version information ------
---------- Trim Galore! version information ----------

                          Quality-/Adapter-/RRBS-Trimming
                               (powered by Cutadapt)
                                  version 0.4.1

                             Last update: 20 07 2015


------- End of Trim Galore! version information ------

###CFCMD trim_galore --paired --gzip --phred33       --fastqc HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1.fastq.gz HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2.fastq.gz

Path to Cutadapt set as: 'cutadapt' (default)
1.8.1
Cutadapt seems to be working fine (tested command 'cutadapt --version')


AUTO-DETECTING ADAPTER TYPE
===========================
Attempting to auto-detect adapter type from the first 1 million sequences of the first file (>> HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1.fastq.gz <<)

Found perfect matches for the following adapter sequences:
Adapter type	Count	Sequence	Sequences analysed	Percentage
Illumina	7610	AGATCGGAAGAGC	1000000	0.76
Nextera	8	CTGTCTCTTATA	1000000	0.00
smallRNA	3	TGGAATTCTCGG	1000000	0.00
Using Illumina adapter for trimming (count: 7610). Second best hit was Nextera (count: 8)

Writing report to 'HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.1
Cutadapt version: 1.8.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Running FastQC on the data once trimming has completed
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1.fastq.gz <<< 
10000000 sequences processed
20000000 sequences processed
30000000 sequences processed
40000000 sequences processed
50000000 sequences processed
60000000 sequences processed
70000000 sequences processed
This is cutadapt 1.8.1 with Python 2.7.5
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 1418.14 s (19 us/read; 3.14 M reads/minute).

=== Summary ===

Total reads processed:              74,203,167
Reads with adapters:                24,438,848 (32.9%)
Reads written (passing filters):    74,203,167 (100.0%)

Total basepairs processed: 7,494,519,867 bp
Quality-trimmed:             512,942,133 bp (6.8%)
Total written (filtered):  6,915,434,043 bp (92.3%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 24438848 times.

No. of allowed errors:
0-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 29.1%
  C: 32.5%
  G: 21.5%
  T: 15.6%
  none/other: 1.2%

Overview of removed sequences
length	count	expect	max.err	error counts
1	15780739	18550791.8	0	15780739
2	5577733	4637697.9	0	5577733
3	1416646	1159424.5	0	1416646
4	357832	289856.1	0	357832
5	146943	72464.0	0	146943
6	108165	18116.0	0	108165
7	80461	4529.0	0	80461
8	82845	1132.3	0	82845
9	70563	283.1	0	69432 1131
10	60090	70.8	1	58009 2081
11	47646	17.7	1	46210 1436
12	46325	4.4	1	45426 899
13	36297	1.1	1	35620 677
14	33206	1.1	1	32517 689
15	30200	1.1	1	29537 663
16	26650	1.1	1	25941 709
17	23883	1.1	1	23175 708
18	22814	1.1	1	22206 608
19	15317	1.1	1	14942 375
20	14734	1.1	1	14316 418
21	12981	1.1	1	12572 409
22	10726	1.1	1	10386 340
23	10585	1.1	1	10145 440
24	8211	1.1	1	7813 398
25	7776	1.1	1	7401 375
26	6577	1.1	1	6226 351
27	7824	1.1	1	7188 636
28	6995	1.1	1	6562 433
29	5964	1.1	1	5450 514
30	6235	1.1	1	5759 476
31	4001	1.1	1	3651 350
32	4002	1.1	1	3591 411
33	3627	1.1	1	3171 456
34	4898	1.1	1	3703 1195
35	5262	1.1	1	4277 985
36	5078	1.1	1	3913 1165
37	5358	1.1	1	4348 1010
38	4700	1.1	1	3853 847
39	4403	1.1	1	3314 1089
40	5420	1.1	1	3916 1504
41	6469	1.1	1	5586 883
42	3392	1.1	1	2865 527
43	2475	1.1	1	2072 403
44	2456	1.1	1	1563 893
45	4035	1.1	1	2956 1079
46	3992	1.1	1	3345 647
47	2424	1.1	1	1858 566
48	2639	1.1	1	1947 692
49	2945	1.1	1	2271 674
50	2427	1.1	1	1771 656
51	3773	1.1	1	2342 1431
52	5065	1.1	1	3343 1722
53	4906	1.1	1	4300 606
54	1870	1.1	1	1307 563
55	1999	1.1	1	1388 611
56	2968	1.1	1	1945 1023
57	3724	1.1	1	2617 1107
58	3918	1.1	1	2489 1429
59	4730	1.1	1	3582 1148
60	4028	1.1	1	2633 1395
61	4988	1.1	1	3106 1882
62	8736	1.1	1	4240 4496
63	14165	1.1	1	8720 5445
64	12661	1.1	1	10106 2555
65	6864	1.1	1	4432 2432
66	8136	1.1	1	4501 3635
67	13203	1.1	1	6497 6706
68	25197	1.1	1	12465 12732
69	50150	1.1	1	22596 27554
70	57190	1.1	1	45540 11650
71	24203	1.1	1	17833 6370
72	10860	1.1	1	7925 2935
73	4677	1.1	1	3765 912
74	1417	1.1	1	1054 363
75	588	1.1	1	413 175
76	488	1.1	1	343 145
77	560	1.1	1	379 181
78	531	1.1	1	361 170
79	280	1.1	1	172 108
80	252	1.1	1	156 96
81	202	1.1	1	123 79
82	186	1.1	1	100 86
83	165	1.1	1	93 72
84	176	1.1	1	81 95
85	196	1.1	1	110 86
86	217	1.1	1	116 101
87	235	1.1	1	119 116
88	256	1.1	1	137 119
89	249	1.1	1	132 117
90	276	1.1	1	140 136
91	278	1.1	1	138 140
92	347	1.1	1	176 171
93	314	1.1	1	171 143
94	333	1.1	1	205 128
95	361	1.1	1	228 133
96	461	1.1	1	237 224
97	505	1.1	1	250 255
98	640	1.1	1	312 328
99	628	1.1	1	330 298
100	1356	1.1	1	726 630
101	6374	1.1	1	3751 2623


RUN STATISTICS FOR INPUT FILE: HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1.fastq.gz
=============================================
74203167 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Writing report to 'HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.1
Cutadapt version: 1.8.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Running FastQC on the data once trimming has completed
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2.fastq.gz <<< 
10000000 sequences processed
20000000 sequences processed
30000000 sequences processed
40000000 sequences processed
50000000 sequences processed
60000000 sequences processed
70000000 sequences processed
This is cutadapt 1.8.1 with Python 2.7.5
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 1721.22 s (23 us/read; 2.59 M reads/minute).

=== Summary ===

Total reads processed:              74,203,167
Reads with adapters:                21,064,160 (28.4%)
Reads written (passing filters):    74,203,167 (100.0%)

Total basepairs processed: 7,494,519,867 bp
Quality-trimmed:           2,366,541,609 bp (31.6%)
Total written (filtered):  5,082,419,690 bp (67.8%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 21064160 times.

No. of allowed errors:
0-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 30.1%
  C: 33.0%
  G: 20.7%
  T: 15.2%
  none/other: 0.9%

Overview of removed sequences
length	count	expect	max.err	error counts
1	12550241	18550791.8	0	12550241
2	6853426	4637697.9	0	6853426
3	1004381	1159424.5	0	1004381
4	288343	289856.1	0	288343
5	51798	72464.0	0	51798
6	12267	18116.0	0	12267
7	5590	4529.0	0	5590
8	3548	1132.3	0	3548
9	4029	283.1	0	2533 1496
10	5830	70.8	1	4021 1809
11	2853	17.7	1	1580 1273
12	4735	4.4	1	4249 486
13	2911	1.1	1	2430 481
14	4856	1.1	1	4434 422
15	1804	1.1	1	1593 211
16	2368	1.1	1	2059 309
17	4669	1.1	1	4321 348
18	1030	1.1	1	866 164
19	2547	1.1	1	2321 226
20	1754	1.1	1	1600 154
21	950	1.1	1	868 82
22	1594	1.1	1	1455 139
23	1951	1.1	1	1677 274
24	4690	1.1	1	4305 385
25	1690	1.1	1	1476 214
26	2584	1.1	1	1543 1041
27	1859	1.1	1	1414 445
28	3527	1.1	1	3194 333
29	1791	1.1	1	1440 351
30	5381	1.1	1	4997 384
31	567	1.1	1	440 127
32	1756	1.1	1	1597 159
33	999	1.1	1	858 141
34	1029	1.1	1	911 118
35	2074	1.1	1	1899 175
36	1288	1.1	1	1109 179
37	2081	1.1	1	1892 189
38	1339	1.1	1	1197 142
39	2811	1.1	1	2570 241
40	2661	1.1	1	2354 307
41	3432	1.1	1	3016 416
42	6993	1.1	1	6439 554
43	1468	1.1	1	1286 182
44	2728	1.1	1	2432 296
45	4923	1.1	1	4561 362
46	1119	1.1	1	989 130
47	1665	1.1	1	1489 176
48	1946	1.1	1	1791 155
49	1932	1.1	1	1752 180
50	4384	1.1	1	4019 365
51	3873	1.1	1	3633 240
52	1010	1.1	1	918 92
53	506	1.1	1	432 74
54	2117	1.1	1	1959 158
55	2453	1.1	1	2286 167
56	1117	1.1	1	995 122
57	2284	1.1	1	2007 277
58	5593	1.1	1	5183 410
59	3875	1.1	1	3516 359
60	4107	1.1	1	3667 440
61	5724	1.1	1	5107 617
62	8646	1.1	1	7513 1133
63	18293	1.1	1	16357 1936
64	29353	1.1	1	24721 4632
65	54668	1.1	1	47835 6833
66	30607	1.1	1	28229 2378
67	4181	1.1	1	3499 682
68	1785	1.1	1	1607 178
69	649	1.1	1	581 68
70	386	1.1	1	331 55
71	201	1.1	1	149 52
72	181	1.1	1	161 20
73	238	1.1	1	203 35
74	116	1.1	1	100 16
75	1	1.1	1	0 1
79	2	1.1	1	1 1
80	2	1.1	1	1 1


RUN STATISTICS FOR INPUT FILE: HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2.fastq.gz
=============================================
74203167 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Validate paired-end files HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_trimmed.fq.gz and HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_trimmed.fq.gz
file_1: HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_trimmed.fq.gz, file_2: HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_trimmed.fq.gz


>>>>> Now validing the length of the 2 paired-end infiles: HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_trimmed.fq.gz and HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_trimmed.fq.gz <<<<<
Writing validated paired-end read 1 reads to HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
Writing validated paired-end read 2 reads to HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz

Total number of sequences analysed: 74203167

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 4050544 (5.46%)


  >>> Now running FastQC on the validated data HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz<<<

Started analysis of HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
Approx 5% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
Approx 10% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
Approx 15% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
Approx 20% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
Approx 25% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
Approx 30% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
Approx 35% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
Approx 40% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
Approx 45% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
Approx 50% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
Approx 55% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
Approx 60% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
Approx 65% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
Approx 70% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
Approx 75% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
Approx 80% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
Approx 85% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
Approx 90% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
Approx 95% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
Analysis complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz

  >>> Now running FastQC on the validated data HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz<<<

Started analysis of HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
Approx 5% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
Approx 10% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
Approx 15% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
Approx 20% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
Approx 25% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
Approx 30% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
Approx 35% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
Approx 40% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
Approx 45% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
Approx 50% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
Approx 55% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
Approx 60% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
Approx 65% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
Approx 70% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
Approx 75% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
Approx 80% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
Approx 85% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
Approx 90% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
Approx 95% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
Analysis complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
Deleting both intermediate output files HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_trimmed.fq.gz and HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_trimmed.fq.gz

====================================================================================================

###CF Trim galore (PE mode) successfully exited, took 2 hours, 14 minutes, 51 seconds..




--------------------------------------------------------------------------------
Module:			kallisto
Run File:		HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1.fastq.gz_fastq_kallisto.run
Job ID:			cf_fastq_kallisto_1463255307_kallisto_460
Previous Job ID:	cf_fastq_kallisto_1463255307_trim_galore_160
Date & Time:		23:03, 14-05-2016
--------------------------------------------------------------------------------


Pseudoaligning against /home/rsh46/scratch/Genomes/Homo_sapiens/GRCh38/Homo_sapiens.GRCh38.cdna.all.idx

---------- Kallisto version information ----------
kallisto 0.42.5

------- End of Kallisto version information ------

###CFCMD kallisto quant -t 1 --pseudobam -i /home/rsh46/scratch/Genomes/Homo_sapiens/GRCh38/Homo_sapiens.GRCh38.cdna.all.idx -o HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz_kallisto_output -b 100 HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz | samtools view -Sb - > HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz_kallisto.bam


[quant] fragment length distribution will be estimated from the data
[index] k-mer length: 31
[index] number of targets: 176,241
[index] number of k-mers: 104,600,239
[index] number of equivalence classes: 702,950
[quant] running in paired-end mode
[quant] will process pair 1: HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
                             HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
[quant] finding pseudoalignments for the reads ... done
[quant] processed 70,152,623 reads, 59,280,920 reads pseudoaligned
[quant] estimated average fragment length: 169.418
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,380 rounds
[bstrp] running EM for the bootstrap: 1
[bstrp] running EM for the bootstrap: 2
[bstrp] running EM for the bootstrap: 3
[bstrp] running EM for the bootstrap: 4
[bstrp] running EM for the bootstrap: 5
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[bstrp] running EM for the bootstrap: 97
[bstrp] running EM for the bootstrap: 98
[bstrp] running EM for the bootstrap: 99
[bstrp] running EM for the bootstrap: 100

###CF kallisto (PE mode) successfully exited, took 2 hours, 44 minutes, 36 seconds..



================================================================================





###CF Run finished at 01:48 15-05-2016


###CF Pipeline fastq_kallisto finished at 01:59 15-05-2016

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