Mercurial > repos > iuc > multiqc
diff test-data/kallisto_1.txt @ 0:3bad335ccea9 draft
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 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kallisto_1.txt Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,489 @@ + +-------------------------------------------------------------------------------- +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 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