Mercurial > repos > iuc > multiqc
diff test-data/kallisto_2.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_2.txt Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,496 @@ + +-------------------------------------------------------------------------------- +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 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