Mercurial > repos > iuc > multiqc
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
| author | iuc |
|---|---|
| date | Mon, 02 Sep 2024 14:22:54 +0000 |
| parents | 3bad335ccea9 |
| children |
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-------------------------------------------------------------------------------- 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 [bstrp] running EM for the bootstrap: 6 [bstrp] running EM for the bootstrap: 7 [bstrp] running EM for the bootstrap: 8 [bstrp] running EM for the bootstrap: 9 [bstrp] running EM for the bootstrap: 10 [bstrp] running EM for the bootstrap: 11 [bstrp] running EM for the bootstrap: 12 [bstrp] running EM for the bootstrap: 13 [bstrp] running EM for the bootstrap: 14 [bstrp] running EM for the bootstrap: 15 [bstrp] running EM for the bootstrap: 16 [bstrp] running EM for the bootstrap: 17 [bstrp] running EM for the bootstrap: 18 [bstrp] running EM for the bootstrap: 19 [bstrp] running EM for the bootstrap: 20 [bstrp] running EM for the bootstrap: 21 [bstrp] running EM for the bootstrap: 22 [bstrp] running EM for the 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bootstrap: 96 [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 Sending HTML e-mail with sendmail.. Sent a pipeline e-mail notification to rsh46@cam.ac.uk