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comparison test-data/kallisto_1.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.RHM066_CGATGT_L002_R1.fastq.gz_fastq_kallisto.run
5 Job ID: cf_fastq_kallisto_1463255307_fastqc_732
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.RHM066_CGATGT_L002_R1.fastq.gz
16
17 ###CF FastQC successfully ran, took 12 minutes
18
19 ###CFCMD fastqc -q HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2.fastq.gz
20
21 ###CF FastQC successfully ran, took 11 minutes, 16 seconds
22
23
24
25
26 --------------------------------------------------------------------------------
27 Module: trim_galore
28 Run File: HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1.fastq.gz_fastq_kallisto.run
29 Job ID: cf_fastq_kallisto_1463255307_trim_galore_659
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.RHM066_CGATGT_L002_R1.fastq.gz HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_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.RHM066_CGATGT_L002_R1.fastq.gz <<)
59
60 Found perfect matches for the following adapter sequences:
61 Adapter type Count Sequence Sequences analysed Percentage
62 Illumina 4591 AGATCGGAAGAGC 1000000 0.46
63 Nextera 4 CTGTCTCTTATA 1000000 0.00
64 smallRNA 2 TGGAATTCTCGG 1000000 0.00
65 Using Illumina adapter for trimming (count: 4591). Second best hit was Nextera (count: 4)
66
67 Writing report to 'HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1.fastq.gz_trimming_report.txt'
68
69 SUMMARISING RUN PARAMETERS
70 ==========================
71 Input filename: HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_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.RHM066_CGATGT_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.RHM066_CGATGT_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 This is cutadapt 1.8.1 with Python 2.7.5
95 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1.fastq.gz
96 Trimming 1 adapter with at most 10.0% errors in single-end mode ...
97 Finished in 1129.68 s (19 us/read; 3.20 M reads/minute).
98
99 === Summary ===
100
101 Total reads processed: 60,339,006
102 Reads with adapters: 19,773,783 (32.8%)
103 Reads written (passing filters): 60,339,006 (100.0%)
104
105 Total basepairs processed: 6,094,239,606 bp
106 Quality-trimmed: 318,558,927 bp (5.2%)
107 Total written (filtered): 5,735,844,499 bp (94.1%)
108
109 === Adapter 1 ===
110
111 Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 19773783 times.
112
113 No. of allowed errors:
114 0-9 bp: 0; 10-13 bp: 1
115
116 Bases preceding removed adapters:
117 A: 29.4%
118 C: 32.6%
119 G: 21.6%
120 T: 16.2%
121 none/other: 0.2%
122
123 Overview of removed sequences
124 length count expect max.err error counts
125 1 13107583 15084751.5 0 13107583
126 2 4517008 3771187.9 0 4517008
127 3 1168959 942797.0 0 1168959
128 4 281663 235699.2 0 281663
129 5 104792 58924.8 0 104792
130 6 69263 14731.2 0 69263
131 7 51851 3682.8 0 51851
132 8 51844 920.7 0 51844
133 9 41855 230.2 0 41073 782
134 10 36637 57.5 1 35344 1293
135 11 29587 14.4 1 28680 907
136 12 28042 3.6 1 27586 456
137 13 22536 0.9 1 22227 309
138 14 19927 0.9 1 19661 266
139 15 17329 0.9 1 17095 234
140 16 15643 0.9 1 15353 290
141 17 13807 0.9 1 13539 268
142 18 11603 0.9 1 11389 214
143 19 8338 0.9 1 8198 140
144 20 8131 0.9 1 8001 130
145 21 6942 0.9 1 6778 164
146 22 5839 0.9 1 5731 108
147 23 5474 0.9 1 5341 133
148 24 4736 0.9 1 4599 137
149 25 4504 0.9 1 4393 111
150 26 3852 0.9 1 3728 124
151 27 4425 0.9 1 4203 222
152 28 3575 0.9 1 3433 142
153 29 3316 0.9 1 3165 151
154 30 3370 0.9 1 3209 161
155 31 2266 0.9 1 2167 99
156 32 2158 0.9 1 2035 123
157 33 2462 0.9 1 2308 154
158 34 2879 0.9 1 2595 284
159 35 3667 0.9 1 3330 337
160 36 4027 0.9 1 3697 330
161 37 2582 0.9 1 2341 241
162 38 2056 0.9 1 1830 226
163 39 2926 0.9 1 2733 193
164 40 1401 0.9 1 1278 123
165 41 1847 0.9 1 1733 114
166 42 1508 0.9 1 1413 95
167 43 1211 0.9 1 1130 81
168 44 1112 0.9 1 975 137
169 45 1507 0.9 1 1329 178
170 46 1640 0.9 1 1514 126
171 47 1116 0.9 1 1028 88
172 48 1158 0.9 1 1060 98
173 49 1375 0.9 1 1274 101
174 50 1121 0.9 1 1020 101
175 51 1703 0.9 1 1474 229
176 52 1994 0.9 1 1755 239
177 53 2141 0.9 1 1984 157
178 54 919 0.9 1 835 84
179 55 822 0.9 1 721 101
180 56 1428 0.9 1 1252 176
181 57 1649 0.9 1 1438 211
182 58 1372 0.9 1 1179 193
183 59 1835 0.9 1 1664 171
184 60 1510 0.9 1 1296 214
185 61 1538 0.9 1 1240 298
186 62 2471 0.9 1 1928 543
187 63 3805 0.9 1 3104 701
188 64 4243 0.9 1 3806 437
189 65 2208 0.9 1 1851 357
190 66 2382 0.9 1 1899 483
191 67 3595 0.9 1 2610 985
192 68 6338 0.9 1 4553 1785
193 69 10826 0.9 1 7037 3789
194 70 15641 0.9 1 13860 1781
195 71 6064 0.9 1 5031 1033
196 72 2588 0.9 1 2271 317
197 73 1010 0.9 1 855 155
198 74 466 0.9 1 379 87
199 75 232 0.9 1 169 63
200 76 133 0.9 1 87 46
201 77 123 0.9 1 83 40
202 78 109 0.9 1 73 36
203 79 67 0.9 1 38 29
204 80 62 0.9 1 33 29
205 81 63 0.9 1 21 42
206 82 77 0.9 1 33 44
207 83 59 0.9 1 22 37
208 84 67 0.9 1 23 44
209 85 62 0.9 1 23 39
210 86 72 0.9 1 33 39
211 87 73 0.9 1 22 51
212 88 79 0.9 1 24 55
213 89 54 0.9 1 22 32
214 90 66 0.9 1 31 35
215 91 62 0.9 1 30 32
216 92 85 0.9 1 32 53
217 93 70 0.9 1 27 43
218 94 61 0.9 1 27 34
219 95 56 0.9 1 25 31
220 96 79 0.9 1 35 44
221 97 78 0.9 1 39 39
222 98 125 0.9 1 50 75
223 99 87 0.9 1 43 44
224 100 137 0.9 1 79 58
225 101 547 0.9 1 329 218
226
227
228 RUN STATISTICS FOR INPUT FILE: HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1.fastq.gz
229 =============================================
230 60339006 sequences processed in total
231 The length threshold of paired-end sequences gets evaluated later on (in the validation step)
232
233 Writing report to 'HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2.fastq.gz_trimming_report.txt'
234
235 SUMMARISING RUN PARAMETERS
236 ==========================
237 Input filename: HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2.fastq.gz
238 Trimming mode: paired-end
239 Trim Galore version: 0.4.1
240 Cutadapt version: 1.8.1
241 Quality Phred score cutoff: 20
242 Quality encoding type selected: ASCII+33
243 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
244 Maximum trimming error rate: 0.1 (default)
245 Minimum required adapter overlap (stringency): 1 bp
246 Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
247 Running FastQC on the data once trimming has completed
248 Output file(s) will be GZIP compressed
249
250 Writing final adapter and quality trimmed output to HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_trimmed.fq.gz
251
252
253 >>> 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 <<<
254 10000000 sequences processed
255 20000000 sequences processed
256 30000000 sequences processed
257 40000000 sequences processed
258 50000000 sequences processed
259 60000000 sequences processed
260 This is cutadapt 1.8.1 with Python 2.7.5
261 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2.fastq.gz
262 Trimming 1 adapter with at most 10.0% errors in single-end mode ...
263 Finished in 1357.49 s (22 us/read; 2.67 M reads/minute).
264
265 === Summary ===
266
267 Total reads processed: 60,339,006
268 Reads with adapters: 17,101,385 (28.3%)
269 Reads written (passing filters): 60,339,006 (100.0%)
270
271 Total basepairs processed: 6,094,239,606 bp
272 Quality-trimmed: 1,861,214,185 bp (30.5%)
273 Total written (filtered): 4,202,697,623 bp (69.0%)
274
275 === Adapter 1 ===
276
277 Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 17101385 times.
278
279 No. of allowed errors:
280 0-9 bp: 0; 10-13 bp: 1
281
282 Bases preceding removed adapters:
283 A: 30.1%
284 C: 33.1%
285 G: 21.0%
286 T: 15.6%
287 none/other: 0.2%
288
289 Overview of removed sequences
290 length count expect max.err error counts
291 1 10224232 15084751.5 0 10224232
292 2 5630139 3771187.9 0 5630139
293 3 824951 942797.0 0 824951
294 4 237457 235699.2 0 237457
295 5 42614 58924.8 0 42614
296 6 8620 14731.2 0 8620
297 7 4051 3682.8 0 4051
298 8 2491 920.7 0 2491
299 9 2860 230.2 0 1848 1012
300 10 4289 57.5 1 2932 1357
301 11 1923 14.4 1 1196 727
302 12 3234 3.6 1 2884 350
303 13 1974 0.9 1 1769 205
304 14 3402 0.9 1 3193 209
305 15 1303 0.9 1 1215 88
306 16 1677 0.9 1 1563 114
307 17 3501 0.9 1 3304 197
308 18 753 0.9 1 662 91
309 19 1959 0.9 1 1820 139
310 20 1348 0.9 1 1256 92
311 21 807 0.9 1 745 62
312 22 1343 0.9 1 1262 81
313 23 1485 0.9 1 1358 127
314 24 3748 0.9 1 3541 207
315 25 1313 0.9 1 1219 94
316 26 1605 0.9 1 1405 200
317 27 1260 0.9 1 1122 138
318 28 2828 0.9 1 2673 155
319 29 1187 0.9 1 1064 123
320 30 4440 0.9 1 4243 197
321 31 383 0.9 1 326 57
322 32 1491 0.9 1 1382 109
323 33 753 0.9 1 683 70
324 34 736 0.9 1 649 87
325 35 1840 0.9 1 1717 123
326 36 923 0.9 1 835 88
327 37 1792 0.9 1 1685 107
328 38 875 0.9 1 795 80
329 39 2158 0.9 1 2040 118
330 40 1496 0.9 1 1370 126
331 41 2113 0.9 1 1958 155
332 42 4026 0.9 1 3801 225
333 43 837 0.9 1 761 76
334 44 2041 0.9 1 1906 135
335 45 3100 0.9 1 2934 166
336 46 687 0.9 1 630 57
337 47 1082 0.9 1 1003 79
338 48 1398 0.9 1 1297 101
339 49 1470 0.9 1 1380 90
340 50 2185 0.9 1 2046 139
341 51 3600 0.9 1 3427 173
342 52 786 0.9 1 712 74
343 53 343 0.9 1 290 53
344 54 1810 0.9 1 1687 123
345 55 1581 0.9 1 1462 119
346 56 662 0.9 1 605 57
347 57 1454 0.9 1 1336 118
348 58 2899 0.9 1 2636 263
349 59 1818 0.9 1 1633 185
350 60 1593 0.9 1 1376 217
351 61 1968 0.9 1 1722 246
352 62 2449 0.9 1 2062 387
353 63 4233 0.9 1 3609 624
354 64 5813 0.9 1 4609 1204
355 65 9498 0.9 1 7807 1691
356 66 5265 0.9 1 4540 725
357 67 755 0.9 1 565 190
358 68 303 0.9 1 257 46
359 69 106 0.9 1 84 22
360 70 86 0.9 1 55 31
361 71 51 0.9 1 26 25
362 72 40 0.9 1 20 20
363 73 54 0.9 1 38 16
364 74 32 0.9 1 21 11
365 76 1 0.9 1 0 1
366 77 2 0.9 1 1 1
367 79 3 0.9 1 2 1
368
369
370 RUN STATISTICS FOR INPUT FILE: HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2.fastq.gz
371 =============================================
372 60339006 sequences processed in total
373 The length threshold of paired-end sequences gets evaluated later on (in the validation step)
374
375 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
376 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
377
378
379 >>>>> 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 <<<<<
380 Writing validated paired-end read 1 reads to HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
381 Writing validated paired-end read 2 reads to HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
382
383 Total number of sequences analysed: 60339006
384
385 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 2322959 (3.85%)
386
387
388 >>> Now running FastQC on the validated data HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz<<<
389
390 Started analysis of HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
391 Approx 5% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
392 Approx 10% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
393 Approx 15% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
394 Approx 20% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
395 Approx 25% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
396 Approx 30% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
397 Approx 35% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
398 Approx 40% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
399 Approx 45% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
400 Approx 50% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
401 Approx 55% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
402 Approx 60% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
403 Approx 65% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
404 Approx 70% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
405 Approx 75% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
406 Approx 80% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
407 Approx 85% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
408 Approx 90% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
409 Approx 95% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
410 Analysis complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
411
412 >>> Now running FastQC on the validated data HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz<<<
413
414 Started analysis of HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
415 Approx 5% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
416 Approx 10% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
417 Approx 15% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
418 Approx 20% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
419 Approx 25% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
420 Approx 30% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
421 Approx 35% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
422 Approx 40% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
423 Approx 45% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
424 Approx 50% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
425 Approx 55% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
426 Approx 60% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
427 Approx 65% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
428 Approx 70% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
429 Approx 75% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
430 Approx 80% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
431 Approx 85% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
432 Approx 90% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
433 Approx 95% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
434 Analysis complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
435 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
436
437 ====================================================================================================
438
439 ###CF Trim galore (PE mode) successfully exited, took 1 hours, 45 minutes, 38 seconds..
440
441
442
443
444 --------------------------------------------------------------------------------
445 Module: kallisto
446 Run File: HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1.fastq.gz_fastq_kallisto.run
447 Job ID: cf_fastq_kallisto_1463255307_kallisto_017
448 Previous Job ID: cf_fastq_kallisto_1463255307_trim_galore_659
449 Date & Time: 22:34, 14-05-2016
450 --------------------------------------------------------------------------------
451
452
453 Pseudoaligning against /home/rsh46/scratch/Genomes/Homo_sapiens/GRCh38/Homo_sapiens.GRCh38.cdna.all.idx
454
455 ---------- Kallisto version information ----------
456 kallisto 0.42.5
457
458 ------- End of Kallisto version information ------
459
460 ###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
461
462
463 [quant] fragment length distribution will be estimated from the data
464 [index] k-mer length: 31
465 [index] number of targets: 176,241
466 [index] number of k-mers: 104,600,239
467 [index] number of equivalence classes: 702,950
468 [quant] running in paired-end mode
469 [quant] will process pair 1: HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz
470 HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz
471 [quant] finding pseudoalignments for the reads ... done
472 [quant] processed 58,016,047 reads, 48,531,088 reads pseudoaligned
473 [quant] estimated average fragment length: 167.866
474 [ em] quantifying the abundances ... done
475 [ em] the Expectation-Maximization algorithm ran for 1,210 rounds
476 [bstrp] running EM for the bootstrap: 1
477 [bstrp] running EM for the bootstrap: 2
478 [bstrp] running EM for the bootstrap: 3
479 [bstrp] running EM for the bootstrap: 4
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575 [bstrp] running EM for the bootstrap: 100
576
577 ###CF kallisto (PE mode) successfully exited, took 2 hours, 30 minutes, 54 seconds..
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582 ================================================================================
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588 ###CF Run finished at 01:06 15-05-2016