
--------------------------------------------------------------------------------
Module:			fastqc
Run File:		HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1.fastq.gz_fastq_kallisto.run
Job ID:			cf_fastq_kallisto_1463255307_fastqc_732
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.RHM066_CGATGT_L002_R1.fastq.gz

###CF FastQC successfully ran, took 12 minutes

###CFCMD fastqc -q  HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2.fastq.gz

###CF FastQC successfully ran, took 11 minutes, 16 seconds




--------------------------------------------------------------------------------
Module:			trim_galore
Run File:		HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1.fastq.gz_fastq_kallisto.run
Job ID:			cf_fastq_kallisto_1463255307_trim_galore_659
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.RHM066_CGATGT_L002_R1.fastq.gz HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_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.RHM066_CGATGT_L002_R1.fastq.gz <<)

Found perfect matches for the following adapter sequences:
Adapter type	Count	Sequence	Sequences analysed	Percentage
Illumina	4591	AGATCGGAAGAGC	1000000	0.46
Nextera	4	CTGTCTCTTATA	1000000	0.00
smallRNA	2	TGGAATTCTCGG	1000000	0.00
Using Illumina adapter for trimming (count: 4591). Second best hit was Nextera (count: 4)

Writing report to 'HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_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.RHM066_CGATGT_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.RHM066_CGATGT_L002_R1.fastq.gz <<<
10000000 sequences processed
20000000 sequences processed
30000000 sequences processed
40000000 sequences processed
50000000 sequences processed
60000000 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.RHM066_CGATGT_L002_R1.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 1129.68 s (19 us/read; 3.20 M reads/minute).

=== Summary ===

Total reads processed:              60,339,006
Reads with adapters:                19,773,783 (32.8%)
Reads written (passing filters):    60,339,006 (100.0%)

Total basepairs processed: 6,094,239,606 bp
Quality-trimmed:             318,558,927 bp (5.2%)
Total written (filtered):  5,735,844,499 bp (94.1%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 19773783 times.

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

Bases preceding removed adapters:
  A: 29.4%
  C: 32.6%
  G: 21.6%
  T: 16.2%
  none/other: 0.2%

Overview of removed sequences
length	count	expect	max.err	error counts
1	13107583	15084751.5	0	13107583
2	4517008	3771187.9	0	4517008
3	1168959	942797.0	0	1168959
4	281663	235699.2	0	281663
5	104792	58924.8	0	104792
6	69263	14731.2	0	69263
7	51851	3682.8	0	51851
8	51844	920.7	0	51844
9	41855	230.2	0	41073 782
10	36637	57.5	1	35344 1293
11	29587	14.4	1	28680 907
12	28042	3.6	1	27586 456
13	22536	0.9	1	22227 309
14	19927	0.9	1	19661 266
15	17329	0.9	1	17095 234
16	15643	0.9	1	15353 290
17	13807	0.9	1	13539 268
18	11603	0.9	1	11389 214
19	8338	0.9	1	8198 140
20	8131	0.9	1	8001 130
21	6942	0.9	1	6778 164
22	5839	0.9	1	5731 108
23	5474	0.9	1	5341 133
24	4736	0.9	1	4599 137
25	4504	0.9	1	4393 111
26	3852	0.9	1	3728 124
27	4425	0.9	1	4203 222
28	3575	0.9	1	3433 142
29	3316	0.9	1	3165 151
30	3370	0.9	1	3209 161
31	2266	0.9	1	2167 99
32	2158	0.9	1	2035 123
33	2462	0.9	1	2308 154
34	2879	0.9	1	2595 284
35	3667	0.9	1	3330 337
36	4027	0.9	1	3697 330
37	2582	0.9	1	2341 241
38	2056	0.9	1	1830 226
39	2926	0.9	1	2733 193
40	1401	0.9	1	1278 123
41	1847	0.9	1	1733 114
42	1508	0.9	1	1413 95
43	1211	0.9	1	1130 81
44	1112	0.9	1	975 137
45	1507	0.9	1	1329 178
46	1640	0.9	1	1514 126
47	1116	0.9	1	1028 88
48	1158	0.9	1	1060 98
49	1375	0.9	1	1274 101
50	1121	0.9	1	1020 101
51	1703	0.9	1	1474 229
52	1994	0.9	1	1755 239
53	2141	0.9	1	1984 157
54	919	0.9	1	835 84
55	822	0.9	1	721 101
56	1428	0.9	1	1252 176
57	1649	0.9	1	1438 211
58	1372	0.9	1	1179 193
59	1835	0.9	1	1664 171
60	1510	0.9	1	1296 214
61	1538	0.9	1	1240 298
62	2471	0.9	1	1928 543
63	3805	0.9	1	3104 701
64	4243	0.9	1	3806 437
65	2208	0.9	1	1851 357
66	2382	0.9	1	1899 483
67	3595	0.9	1	2610 985
68	6338	0.9	1	4553 1785
69	10826	0.9	1	7037 3789
70	15641	0.9	1	13860 1781
71	6064	0.9	1	5031 1033
72	2588	0.9	1	2271 317
73	1010	0.9	1	855 155
74	466	0.9	1	379 87
75	232	0.9	1	169 63
76	133	0.9	1	87 46
77	123	0.9	1	83 40
78	109	0.9	1	73 36
79	67	0.9	1	38 29
80	62	0.9	1	33 29
81	63	0.9	1	21 42
82	77	0.9	1	33 44
83	59	0.9	1	22 37
84	67	0.9	1	23 44
85	62	0.9	1	23 39
86	72	0.9	1	33 39
87	73	0.9	1	22 51
88	79	0.9	1	24 55
89	54	0.9	1	22 32
90	66	0.9	1	31 35
91	62	0.9	1	30 32
92	85	0.9	1	32 53
93	70	0.9	1	27 43
94	61	0.9	1	27 34
95	56	0.9	1	25 31
96	79	0.9	1	35 44
97	78	0.9	1	39 39
98	125	0.9	1	50 75
99	87	0.9	1	43 44
100	137	0.9	1	79 58
101	547	0.9	1	329 218


RUN STATISTICS FOR INPUT FILE: HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1.fastq.gz
=============================================
60339006 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.RHM066_CGATGT_L002_R2.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_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.RHM066_CGATGT_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.RHM066_CGATGT_L002_R2.fastq.gz <<<
10000000 sequences processed
20000000 sequences processed
30000000 sequences processed
40000000 sequences processed
50000000 sequences processed
60000000 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.RHM066_CGATGT_L002_R2.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 1357.49 s (22 us/read; 2.67 M reads/minute).

=== Summary ===

Total reads processed:              60,339,006
Reads with adapters:                17,101,385 (28.3%)
Reads written (passing filters):    60,339,006 (100.0%)

Total basepairs processed: 6,094,239,606 bp
Quality-trimmed:           1,861,214,185 bp (30.5%)
Total written (filtered):  4,202,697,623 bp (69.0%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 17101385 times.

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

Bases preceding removed adapters:
  A: 30.1%
  C: 33.1%
  G: 21.0%
  T: 15.6%
  none/other: 0.2%

Overview of removed sequences
length	count	expect	max.err	error counts
1	10224232	15084751.5	0	10224232
2	5630139	3771187.9	0	5630139
3	824951	942797.0	0	824951
4	237457	235699.2	0	237457
5	42614	58924.8	0	42614
6	8620	14731.2	0	8620
7	4051	3682.8	0	4051
8	2491	920.7	0	2491
9	2860	230.2	0	1848 1012
10	4289	57.5	1	2932 1357
11	1923	14.4	1	1196 727
12	3234	3.6	1	2884 350
13	1974	0.9	1	1769 205
14	3402	0.9	1	3193 209
15	1303	0.9	1	1215 88
16	1677	0.9	1	1563 114
17	3501	0.9	1	3304 197
18	753	0.9	1	662 91
19	1959	0.9	1	1820 139
20	1348	0.9	1	1256 92
21	807	0.9	1	745 62
22	1343	0.9	1	1262 81
23	1485	0.9	1	1358 127
24	3748	0.9	1	3541 207
25	1313	0.9	1	1219 94
26	1605	0.9	1	1405 200
27	1260	0.9	1	1122 138
28	2828	0.9	1	2673 155
29	1187	0.9	1	1064 123
30	4440	0.9	1	4243 197
31	383	0.9	1	326 57
32	1491	0.9	1	1382 109
33	753	0.9	1	683 70
34	736	0.9	1	649 87
35	1840	0.9	1	1717 123
36	923	0.9	1	835 88
37	1792	0.9	1	1685 107
38	875	0.9	1	795 80
39	2158	0.9	1	2040 118
40	1496	0.9	1	1370 126
41	2113	0.9	1	1958 155
42	4026	0.9	1	3801 225
43	837	0.9	1	761 76
44	2041	0.9	1	1906 135
45	3100	0.9	1	2934 166
46	687	0.9	1	630 57
47	1082	0.9	1	1003 79
48	1398	0.9	1	1297 101
49	1470	0.9	1	1380 90
50	2185	0.9	1	2046 139
51	3600	0.9	1	3427 173
52	786	0.9	1	712 74
53	343	0.9	1	290 53
54	1810	0.9	1	1687 123
55	1581	0.9	1	1462 119
56	662	0.9	1	605 57
57	1454	0.9	1	1336 118
58	2899	0.9	1	2636 263
59	1818	0.9	1	1633 185
60	1593	0.9	1	1376 217
61	1968	0.9	1	1722 246
62	2449	0.9	1	2062 387
63	4233	0.9	1	3609 624
64	5813	0.9	1	4609 1204
65	9498	0.9	1	7807 1691
66	5265	0.9	1	4540 725
67	755	0.9	1	565 190
68	303	0.9	1	257 46
69	106	0.9	1	84 22
70	86	0.9	1	55 31
71	51	0.9	1	26 25
72	40	0.9	1	20 20
73	54	0.9	1	38 16
74	32	0.9	1	21 11
76	1	0.9	1	0 1
77	2	0.9	1	1 1
79	3	0.9	1	2 1


RUN STATISTICS FOR INPUT FILE: HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2.fastq.gz
=============================================
60339006 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.RHM066_CGATGT_L002_R1_trimmed.fq.gz and HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_trimmed.fq.gz
file_1: HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_trimmed.fq.gz, file_2: HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_trimmed.fq.gz


>>>>> Now validing the length of the 2 paired-end infiles: HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_trimmed.fq.gz and HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_trimmed.fq.gz <<<<<
Writing validated paired-end read 1 reads to HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
Writing validated paired-end read 2 reads to HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz

Total number of sequences analysed: 60339006

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 2322959 (3.85%)


  >>> Now running FastQC on the validated data HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz<<<

Started analysis of HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
Approx 5% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
Approx 10% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
Approx 15% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
Approx 20% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
Approx 25% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
Approx 30% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
Approx 35% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
Approx 40% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
Approx 45% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
Approx 50% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
Approx 55% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
Approx 60% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
Approx 65% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
Approx 70% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
Approx 75% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
Approx 80% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
Approx 85% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
Approx 90% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
Approx 95% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
Analysis complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz

  >>> Now running FastQC on the validated data HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz<<<

Started analysis of HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
Approx 5% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
Approx 10% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
Approx 15% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
Approx 20% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
Approx 25% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
Approx 30% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
Approx 35% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
Approx 40% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
Approx 45% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
Approx 50% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
Approx 55% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
Approx 60% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
Approx 65% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
Approx 70% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
Approx 75% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
Approx 80% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
Approx 85% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
Approx 90% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
Approx 95% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
Analysis complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
Deleting both intermediate output files HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_trimmed.fq.gz and HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_trimmed.fq.gz

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

###CF Trim galore (PE mode) successfully exited, took 1 hours, 45 minutes, 38 seconds..




--------------------------------------------------------------------------------
Module:			kallisto
Run File:		HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1.fastq.gz_fastq_kallisto.run
Job ID:			cf_fastq_kallisto_1463255307_kallisto_017
Previous Job ID:	cf_fastq_kallisto_1463255307_trim_galore_659
Date & Time:		22:34, 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.RHM066_CGATGT_L002_R1_val_1.fq.gz_kallisto_output -b 100 HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz | samtools view -Sb - > HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_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.RHM066_CGATGT_L002_R1_val_1.fq.gz
                             HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
[quant] finding pseudoalignments for the reads ... done
[quant] processed 58,016,047 reads, 48,531,088 reads pseudoaligned
[quant] estimated average fragment length: 167.866
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,210 rounds
[bstrp] running EM for the bootstrap: 1
[bstrp] running EM for the bootstrap: 2
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[bstrp] running EM for the bootstrap: 99
[bstrp] running EM for the bootstrap: 100

###CF kallisto (PE mode) successfully exited, took 2 hours, 30 minutes, 54 seconds..




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###CF Run finished at 01:06 15-05-2016
