Mercurial > repos > iuc > multiqc
view test-data/kallisto_1.txt @ 19:f7985e0479b9 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 2b946616b7d12eed507d95ebbd8fd257ae37d83b"
| author | iuc |
|---|---|
| date | Sat, 21 Nov 2020 12:54:24 +0000 |
| parents | 3bad335ccea9 |
| children |
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-------------------------------------------------------------------------------- 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 [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, 30 minutes, 54 seconds.. ================================================================================ ###CF Run finished at 01:06 15-05-2016