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comparison test-data/kallisto_2.txt @ 0:3bad335ccea9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
author iuc
date Tue, 24 Oct 2017 06:29:59 -0400
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-1:000000000000 0:3bad335ccea9
1
2 --------------------------------------------------------------------------------
3 Module: fastqc
4 Run File: HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1.fastq.gz_fastq_kallisto.run
5 Job ID: cf_fastq_kallisto_1463255307_fastqc_792
6 Previous Job ID: start_000
7 Date & Time: 20:48, 14-05-2016
8 --------------------------------------------------------------------------------
9
10 ---------- FastQC version information ----------
11 FastQC v0.11.5
12
13 ------- End of FastQC version information ------
14
15 ###CFCMD fastqc -q HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1.fastq.gz
16
17 ###CF FastQC successfully ran, took 13 minutes, 29 seconds
18
19 ###CFCMD fastqc -q HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2.fastq.gz
20
21 ###CF FastQC successfully ran, took 12 minutes, 27 seconds
22
23
24
25
26 --------------------------------------------------------------------------------
27 Module: trim_galore
28 Run File: HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1.fastq.gz_fastq_kallisto.run
29 Job ID: cf_fastq_kallisto_1463255307_trim_galore_160
30 Previous Job ID: start_000
31 Date & Time: 20:48, 14-05-2016
32 --------------------------------------------------------------------------------
33
34 ---------- Cutadapt version information ----------
35 1.8.1
36
37 ------- End of Cutadapt version information ------
38 ---------- Trim Galore! version information ----------
39
40 Quality-/Adapter-/RRBS-Trimming
41 (powered by Cutadapt)
42 version 0.4.1
43
44 Last update: 20 07 2015
45
46
47 ------- End of Trim Galore! version information ------
48
49 ###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
50
51 Path to Cutadapt set as: 'cutadapt' (default)
52 1.8.1
53 Cutadapt seems to be working fine (tested command 'cutadapt --version')
54
55
56 AUTO-DETECTING ADAPTER TYPE
57 ===========================
58 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 <<)
59
60 Found perfect matches for the following adapter sequences:
61 Adapter type Count Sequence Sequences analysed Percentage
62 Illumina 7610 AGATCGGAAGAGC 1000000 0.76
63 Nextera 8 CTGTCTCTTATA 1000000 0.00
64 smallRNA 3 TGGAATTCTCGG 1000000 0.00
65 Using Illumina adapter for trimming (count: 7610). Second best hit was Nextera (count: 8)
66
67 Writing report to 'HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1.fastq.gz_trimming_report.txt'
68
69 SUMMARISING RUN PARAMETERS
70 ==========================
71 Input filename: HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1.fastq.gz
72 Trimming mode: paired-end
73 Trim Galore version: 0.4.1
74 Cutadapt version: 1.8.1
75 Quality Phred score cutoff: 20
76 Quality encoding type selected: ASCII+33
77 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
78 Maximum trimming error rate: 0.1 (default)
79 Minimum required adapter overlap (stringency): 1 bp
80 Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
81 Running FastQC on the data once trimming has completed
82 Output file(s) will be GZIP compressed
83
84 Writing final adapter and quality trimmed output to HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_trimmed.fq.gz
85
86
87 >>> 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 <<<
88 10000000 sequences processed
89 20000000 sequences processed
90 30000000 sequences processed
91 40000000 sequences processed
92 50000000 sequences processed
93 60000000 sequences processed
94 70000000 sequences processed
95 This is cutadapt 1.8.1 with Python 2.7.5
96 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1.fastq.gz
97 Trimming 1 adapter with at most 10.0% errors in single-end mode ...
98 Finished in 1418.14 s (19 us/read; 3.14 M reads/minute).
99
100 === Summary ===
101
102 Total reads processed: 74,203,167
103 Reads with adapters: 24,438,848 (32.9%)
104 Reads written (passing filters): 74,203,167 (100.0%)
105
106 Total basepairs processed: 7,494,519,867 bp
107 Quality-trimmed: 512,942,133 bp (6.8%)
108 Total written (filtered): 6,915,434,043 bp (92.3%)
109
110 === Adapter 1 ===
111
112 Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 24438848 times.
113
114 No. of allowed errors:
115 0-9 bp: 0; 10-13 bp: 1
116
117 Bases preceding removed adapters:
118 A: 29.1%
119 C: 32.5%
120 G: 21.5%
121 T: 15.6%
122 none/other: 1.2%
123
124 Overview of removed sequences
125 length count expect max.err error counts
126 1 15780739 18550791.8 0 15780739
127 2 5577733 4637697.9 0 5577733
128 3 1416646 1159424.5 0 1416646
129 4 357832 289856.1 0 357832
130 5 146943 72464.0 0 146943
131 6 108165 18116.0 0 108165
132 7 80461 4529.0 0 80461
133 8 82845 1132.3 0 82845
134 9 70563 283.1 0 69432 1131
135 10 60090 70.8 1 58009 2081
136 11 47646 17.7 1 46210 1436
137 12 46325 4.4 1 45426 899
138 13 36297 1.1 1 35620 677
139 14 33206 1.1 1 32517 689
140 15 30200 1.1 1 29537 663
141 16 26650 1.1 1 25941 709
142 17 23883 1.1 1 23175 708
143 18 22814 1.1 1 22206 608
144 19 15317 1.1 1 14942 375
145 20 14734 1.1 1 14316 418
146 21 12981 1.1 1 12572 409
147 22 10726 1.1 1 10386 340
148 23 10585 1.1 1 10145 440
149 24 8211 1.1 1 7813 398
150 25 7776 1.1 1 7401 375
151 26 6577 1.1 1 6226 351
152 27 7824 1.1 1 7188 636
153 28 6995 1.1 1 6562 433
154 29 5964 1.1 1 5450 514
155 30 6235 1.1 1 5759 476
156 31 4001 1.1 1 3651 350
157 32 4002 1.1 1 3591 411
158 33 3627 1.1 1 3171 456
159 34 4898 1.1 1 3703 1195
160 35 5262 1.1 1 4277 985
161 36 5078 1.1 1 3913 1165
162 37 5358 1.1 1 4348 1010
163 38 4700 1.1 1 3853 847
164 39 4403 1.1 1 3314 1089
165 40 5420 1.1 1 3916 1504
166 41 6469 1.1 1 5586 883
167 42 3392 1.1 1 2865 527
168 43 2475 1.1 1 2072 403
169 44 2456 1.1 1 1563 893
170 45 4035 1.1 1 2956 1079
171 46 3992 1.1 1 3345 647
172 47 2424 1.1 1 1858 566
173 48 2639 1.1 1 1947 692
174 49 2945 1.1 1 2271 674
175 50 2427 1.1 1 1771 656
176 51 3773 1.1 1 2342 1431
177 52 5065 1.1 1 3343 1722
178 53 4906 1.1 1 4300 606
179 54 1870 1.1 1 1307 563
180 55 1999 1.1 1 1388 611
181 56 2968 1.1 1 1945 1023
182 57 3724 1.1 1 2617 1107
183 58 3918 1.1 1 2489 1429
184 59 4730 1.1 1 3582 1148
185 60 4028 1.1 1 2633 1395
186 61 4988 1.1 1 3106 1882
187 62 8736 1.1 1 4240 4496
188 63 14165 1.1 1 8720 5445
189 64 12661 1.1 1 10106 2555
190 65 6864 1.1 1 4432 2432
191 66 8136 1.1 1 4501 3635
192 67 13203 1.1 1 6497 6706
193 68 25197 1.1 1 12465 12732
194 69 50150 1.1 1 22596 27554
195 70 57190 1.1 1 45540 11650
196 71 24203 1.1 1 17833 6370
197 72 10860 1.1 1 7925 2935
198 73 4677 1.1 1 3765 912
199 74 1417 1.1 1 1054 363
200 75 588 1.1 1 413 175
201 76 488 1.1 1 343 145
202 77 560 1.1 1 379 181
203 78 531 1.1 1 361 170
204 79 280 1.1 1 172 108
205 80 252 1.1 1 156 96
206 81 202 1.1 1 123 79
207 82 186 1.1 1 100 86
208 83 165 1.1 1 93 72
209 84 176 1.1 1 81 95
210 85 196 1.1 1 110 86
211 86 217 1.1 1 116 101
212 87 235 1.1 1 119 116
213 88 256 1.1 1 137 119
214 89 249 1.1 1 132 117
215 90 276 1.1 1 140 136
216 91 278 1.1 1 138 140
217 92 347 1.1 1 176 171
218 93 314 1.1 1 171 143
219 94 333 1.1 1 205 128
220 95 361 1.1 1 228 133
221 96 461 1.1 1 237 224
222 97 505 1.1 1 250 255
223 98 640 1.1 1 312 328
224 99 628 1.1 1 330 298
225 100 1356 1.1 1 726 630
226 101 6374 1.1 1 3751 2623
227
228
229 RUN STATISTICS FOR INPUT FILE: HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1.fastq.gz
230 =============================================
231 74203167 sequences processed in total
232 The length threshold of paired-end sequences gets evaluated later on (in the validation step)
233
234 Writing report to 'HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2.fastq.gz_trimming_report.txt'
235
236 SUMMARISING RUN PARAMETERS
237 ==========================
238 Input filename: HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2.fastq.gz
239 Trimming mode: paired-end
240 Trim Galore version: 0.4.1
241 Cutadapt version: 1.8.1
242 Quality Phred score cutoff: 20
243 Quality encoding type selected: ASCII+33
244 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
245 Maximum trimming error rate: 0.1 (default)
246 Minimum required adapter overlap (stringency): 1 bp
247 Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
248 Running FastQC on the data once trimming has completed
249 Output file(s) will be GZIP compressed
250
251 Writing final adapter and quality trimmed output to HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_trimmed.fq.gz
252
253
254 >>> 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 <<<
255 10000000 sequences processed
256 20000000 sequences processed
257 30000000 sequences processed
258 40000000 sequences processed
259 50000000 sequences processed
260 60000000 sequences processed
261 70000000 sequences processed
262 This is cutadapt 1.8.1 with Python 2.7.5
263 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2.fastq.gz
264 Trimming 1 adapter with at most 10.0% errors in single-end mode ...
265 Finished in 1721.22 s (23 us/read; 2.59 M reads/minute).
266
267 === Summary ===
268
269 Total reads processed: 74,203,167
270 Reads with adapters: 21,064,160 (28.4%)
271 Reads written (passing filters): 74,203,167 (100.0%)
272
273 Total basepairs processed: 7,494,519,867 bp
274 Quality-trimmed: 2,366,541,609 bp (31.6%)
275 Total written (filtered): 5,082,419,690 bp (67.8%)
276
277 === Adapter 1 ===
278
279 Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 21064160 times.
280
281 No. of allowed errors:
282 0-9 bp: 0; 10-13 bp: 1
283
284 Bases preceding removed adapters:
285 A: 30.1%
286 C: 33.0%
287 G: 20.7%
288 T: 15.2%
289 none/other: 0.9%
290
291 Overview of removed sequences
292 length count expect max.err error counts
293 1 12550241 18550791.8 0 12550241
294 2 6853426 4637697.9 0 6853426
295 3 1004381 1159424.5 0 1004381
296 4 288343 289856.1 0 288343
297 5 51798 72464.0 0 51798
298 6 12267 18116.0 0 12267
299 7 5590 4529.0 0 5590
300 8 3548 1132.3 0 3548
301 9 4029 283.1 0 2533 1496
302 10 5830 70.8 1 4021 1809
303 11 2853 17.7 1 1580 1273
304 12 4735 4.4 1 4249 486
305 13 2911 1.1 1 2430 481
306 14 4856 1.1 1 4434 422
307 15 1804 1.1 1 1593 211
308 16 2368 1.1 1 2059 309
309 17 4669 1.1 1 4321 348
310 18 1030 1.1 1 866 164
311 19 2547 1.1 1 2321 226
312 20 1754 1.1 1 1600 154
313 21 950 1.1 1 868 82
314 22 1594 1.1 1 1455 139
315 23 1951 1.1 1 1677 274
316 24 4690 1.1 1 4305 385
317 25 1690 1.1 1 1476 214
318 26 2584 1.1 1 1543 1041
319 27 1859 1.1 1 1414 445
320 28 3527 1.1 1 3194 333
321 29 1791 1.1 1 1440 351
322 30 5381 1.1 1 4997 384
323 31 567 1.1 1 440 127
324 32 1756 1.1 1 1597 159
325 33 999 1.1 1 858 141
326 34 1029 1.1 1 911 118
327 35 2074 1.1 1 1899 175
328 36 1288 1.1 1 1109 179
329 37 2081 1.1 1 1892 189
330 38 1339 1.1 1 1197 142
331 39 2811 1.1 1 2570 241
332 40 2661 1.1 1 2354 307
333 41 3432 1.1 1 3016 416
334 42 6993 1.1 1 6439 554
335 43 1468 1.1 1 1286 182
336 44 2728 1.1 1 2432 296
337 45 4923 1.1 1 4561 362
338 46 1119 1.1 1 989 130
339 47 1665 1.1 1 1489 176
340 48 1946 1.1 1 1791 155
341 49 1932 1.1 1 1752 180
342 50 4384 1.1 1 4019 365
343 51 3873 1.1 1 3633 240
344 52 1010 1.1 1 918 92
345 53 506 1.1 1 432 74
346 54 2117 1.1 1 1959 158
347 55 2453 1.1 1 2286 167
348 56 1117 1.1 1 995 122
349 57 2284 1.1 1 2007 277
350 58 5593 1.1 1 5183 410
351 59 3875 1.1 1 3516 359
352 60 4107 1.1 1 3667 440
353 61 5724 1.1 1 5107 617
354 62 8646 1.1 1 7513 1133
355 63 18293 1.1 1 16357 1936
356 64 29353 1.1 1 24721 4632
357 65 54668 1.1 1 47835 6833
358 66 30607 1.1 1 28229 2378
359 67 4181 1.1 1 3499 682
360 68 1785 1.1 1 1607 178
361 69 649 1.1 1 581 68
362 70 386 1.1 1 331 55
363 71 201 1.1 1 149 52
364 72 181 1.1 1 161 20
365 73 238 1.1 1 203 35
366 74 116 1.1 1 100 16
367 75 1 1.1 1 0 1
368 79 2 1.1 1 1 1
369 80 2 1.1 1 1 1
370
371
372 RUN STATISTICS FOR INPUT FILE: HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2.fastq.gz
373 =============================================
374 74203167 sequences processed in total
375 The length threshold of paired-end sequences gets evaluated later on (in the validation step)
376
377 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
378 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
379
380
381 >>>>> 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 <<<<<
382 Writing validated paired-end read 1 reads to HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
383 Writing validated paired-end read 2 reads to HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
384
385 Total number of sequences analysed: 74203167
386
387 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 4050544 (5.46%)
388
389
390 >>> Now running FastQC on the validated data HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz<<<
391
392 Started analysis of HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
393 Approx 5% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
394 Approx 10% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
395 Approx 15% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
396 Approx 20% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
397 Approx 25% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
398 Approx 30% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
399 Approx 35% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
400 Approx 40% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
401 Approx 45% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
402 Approx 50% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
403 Approx 55% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
404 Approx 60% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
405 Approx 65% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
406 Approx 70% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
407 Approx 75% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
408 Approx 80% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
409 Approx 85% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
410 Approx 90% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
411 Approx 95% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
412 Analysis complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
413
414 >>> Now running FastQC on the validated data HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz<<<
415
416 Started analysis of HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
417 Approx 5% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
418 Approx 10% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
419 Approx 15% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
420 Approx 20% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
421 Approx 25% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
422 Approx 30% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
423 Approx 35% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
424 Approx 40% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
425 Approx 45% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
426 Approx 50% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
427 Approx 55% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
428 Approx 60% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
429 Approx 65% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
430 Approx 70% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
431 Approx 75% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
432 Approx 80% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
433 Approx 85% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
434 Approx 90% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
435 Approx 95% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
436 Analysis complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
437 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
438
439 ====================================================================================================
440
441 ###CF Trim galore (PE mode) successfully exited, took 2 hours, 14 minutes, 51 seconds..
442
443
444
445
446 --------------------------------------------------------------------------------
447 Module: kallisto
448 Run File: HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1.fastq.gz_fastq_kallisto.run
449 Job ID: cf_fastq_kallisto_1463255307_kallisto_460
450 Previous Job ID: cf_fastq_kallisto_1463255307_trim_galore_160
451 Date & Time: 23:03, 14-05-2016
452 --------------------------------------------------------------------------------
453
454
455 Pseudoaligning against /home/rsh46/scratch/Genomes/Homo_sapiens/GRCh38/Homo_sapiens.GRCh38.cdna.all.idx
456
457 ---------- Kallisto version information ----------
458 kallisto 0.42.5
459
460 ------- End of Kallisto version information ------
461
462 ###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
463
464
465 [quant] fragment length distribution will be estimated from the data
466 [index] k-mer length: 31
467 [index] number of targets: 176,241
468 [index] number of k-mers: 104,600,239
469 [index] number of equivalence classes: 702,950
470 [quant] running in paired-end mode
471 [quant] will process pair 1: HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz
472 HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz
473 [quant] finding pseudoalignments for the reads ... done
474 [quant] processed 70,152,623 reads, 59,280,920 reads pseudoaligned
475 [quant] estimated average fragment length: 169.418
476 [ em] quantifying the abundances ... done
477 [ em] the Expectation-Maximization algorithm ran for 1,380 rounds
478 [bstrp] running EM for the bootstrap: 1
479 [bstrp] running EM for the bootstrap: 2
480 [bstrp] running EM for the bootstrap: 3
481 [bstrp] running EM for the bootstrap: 4
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573 [bstrp] running EM for the bootstrap: 96
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575 [bstrp] running EM for the bootstrap: 98
576 [bstrp] running EM for the bootstrap: 99
577 [bstrp] running EM for the bootstrap: 100
578
579 ###CF kallisto (PE mode) successfully exited, took 2 hours, 44 minutes, 36 seconds..
580
581
582
583 ================================================================================
584
585
586
587
588
589 ###CF Run finished at 01:48 15-05-2016
590
591
592 ###CF Pipeline fastq_kallisto finished at 01:59 15-05-2016
593
594 Sending HTML e-mail with sendmail..
595 Sent a pipeline e-mail notification to rsh46@cam.ac.uk