Starting /dee2/code/volunteer_pipeline.sh SRR1174002 current disk space = 1524708962304 free memory = 1339054452 SRR1174002 SRAfilesize 9e3168c5f22621716e940b238186453c SRR1174002.sra SRR1174002.sra file validated SRR1174002 is single end SRR1174002 is conventional basespace SRR1174002 read1 length is 42 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR1174002_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 42 %GC 47 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.12475 33.0 33.0 33.0 31.0 33.0 2 32.405 33.0 32.0 34.0 30.0 34.0 3 32.04225 33.0 32.0 34.0 29.0 34.0 4 32.28925 33.0 32.0 34.0 30.0 34.0 5 32.2205 33.0 32.0 34.0 29.0 34.0 6 32.2205 33.0 32.0 34.0 29.0 34.0 7 32.22025 33.0 32.0 34.0 29.0 34.0 8 32.0425 33.0 32.0 34.0 29.0 34.0 9 31.8225 33.0 32.0 34.0 28.0 34.0 10 32.0535 33.0 32.0 34.0 29.0 34.0 11 31.6685 33.0 31.0 34.0 28.0 34.0 12 31.61425 33.0 31.0 34.0 27.0 34.0 13 31.43325 33.0 31.0 33.0 27.0 34.0 14 31.77025 33.0 32.0 34.0 28.0 34.0 15 31.8515 33.0 32.0 34.0 29.0 34.0 16 31.6745 33.0 32.0 34.0 28.0 34.0 17 31.6 33.0 31.0 34.0 28.0 34.0 18 31.553 33.0 31.0 33.0 27.0 34.0 19 31.40975 33.0 31.0 33.0 27.0 34.0 20 31.1045 33.0 31.0 33.0 26.0 34.0 21 31.0325 33.0 31.0 33.0 26.0 34.0 22 30.82975 33.0 30.0 33.0 26.0 34.0 23 31.22625 33.0 31.0 33.0 27.0 34.0 24 30.91975 33.0 31.0 33.0 26.0 34.0 25 31.1835 33.0 31.0 33.0 27.0 34.0 26 30.582 32.0 30.0 33.0 25.0 34.0 27 29.54725 32.0 29.0 33.0 22.0 34.0 28 30.44775 32.0 30.0 33.0 25.0 34.0 29 29.53375 32.0 28.0 33.0 23.0 33.0 30 30.15375 32.0 30.0 33.0 24.0 34.0 31 29.4295 32.0 28.0 33.0 23.0 33.0 32 29.7495 32.0 29.0 33.0 23.0 33.0 33 29.58425 32.0 29.0 33.0 22.0 34.0 34 29.6205 32.0 29.0 33.0 23.0 33.0 35 28.53225 31.0 27.0 33.0 21.0 33.0 36 28.45375 31.0 27.0 33.0 21.0 33.0 37 29.166 32.0 28.0 33.0 22.0 34.0 38 28.12175 31.0 27.0 33.0 19.0 33.0 39 28.11325 31.0 27.0 33.0 19.0 33.0 40 29.01975 32.0 28.0 33.0 21.0 34.0 41 28.225 31.0 28.0 33.0 19.0 33.0 42 26.13425 30.0 24.0 33.0 4.0 33.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 1 1 0.0 1 2 0.0 1 3 0.0 1 4 0.0 1 5 0.0 1 6 0.0 1 7 0.0 1 8 0.0 1 9 0.0 1 10 0.0 1 11 0.0 1 12 0.0 1 13 0.0 1 14 0.0 1 15 0.0 1 16 0.0 1 17 0.0 1 18 0.0 1 19 0.0 1 20 0.0 1 21 0.0 1 22 0.0 1 23 0.0 1 24 0.0 1 25 0.0 1 26 0.0 1 27 0.0 1 28 0.0 1 29 0.0 1 30 0.0 1 31 0.0 1 32 0.0 1 33 0.0 1 34 0.0 1 35 0.0 1 36 0.0 1 37 0.0 1 38 0.0 1 39 0.0 1 40 0.0 1 41 0.0 1 42 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 4 2.0 5 1.0 6 2.0 7 0.0 8 2.0 9 1.0 10 1.0 11 1.0 12 1.0 13 1.0 14 4.0 15 2.0 16 4.0 17 7.0 18 10.0 19 12.0 20 9.0 21 27.0 22 26.0 23 33.0 24 73.0 25 58.0 26 110.0 27 126.0 28 213.0 29 320.0 30 509.0 31 862.0 32 1180.0 33 403.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 33.26592517694641 29.87866531850354 20.222446916076844 16.632962588473205 2 36.05 24.224999999999998 22.875 16.85 3 31.864831038798496 25.131414267834796 17.69712140175219 25.306633291614517 4 35.0 31.55 19.625 13.825000000000001 5 30.14007003501751 27.388694347173587 23.88694347173587 18.584292146073036 6 27.474999999999998 30.025000000000002 27.075 15.425 7 29.475 27.375 27.750000000000004 15.4 8 26.23811905952976 25.41270635317659 32.566283141570786 15.78289144572286 9 24.099999999999998 31.275 28.95 15.675 10 35.71785892946473 28.489244622311155 20.560280140070038 15.232616308154077 11 25.15 24.05 29.025000000000002 21.775 12 21.980495123780948 22.73068267066767 29.782445611402853 25.506376594148538 13 26.138069034517258 23.761880940470235 20.635317658829415 29.464732366183092 14 21.630407601900476 41.98549637409352 23.355838959739934 13.028257064266066 15 26.60665166291573 36.6591647911978 21.005251312828207 15.728932233058265 16 26.775 24.525 33.975 14.725 17 25.431357839459867 24.8062015503876 35.38384596149037 14.378594648662165 18 37.943971985992995 22.886443221610804 21.5607803901951 17.608804402201102 19 34.300000000000004 24.099999999999998 23.925 17.675 20 24.412206103051524 30.965482741370685 29.139569784892444 15.482741370685343 21 22.775000000000002 24.5 26.650000000000002 26.075 22 24.7997997997998 29.52952952952953 21.696696696696698 23.973973973973976 23 30.597948461346007 27.395546659994995 26.26970227670753 15.736802601951464 24 23.386693346673336 29.389694847423716 20.985492746373186 26.23811905952976 25 20.155038759689923 41.18529632408102 22.655663915978995 16.004001000250064 26 16.55 11.774999999999999 47.725 23.95 27 14.757378689344671 13.981990995497748 21.1855927963982 50.07503751875938 28 11.058293720290218 15.761821366024517 50.23767825869402 22.942206654991242 29 22.22222222222222 10.735735735735735 17.14214214214214 49.8998998998999 30 48.225 8.924999999999999 29.299999999999997 13.55 31 19.009504752376188 14.507253626813407 47.57378689344672 18.90945472736368 32 14.307153576788394 39.94497248624312 22.161080540270135 23.58679339669835 33 13.900000000000002 14.224999999999998 51.4 20.474999999999998 34 43.735933983495876 11.177794448612154 25.10627656914228 19.979994998749685 35 10.741111667501253 10.465698547821733 28.592889334001004 50.20030045067602 36 14.107053526763384 14.607303651825912 20.335167583791897 50.95047523761881 37 39.40985246311578 10.127531882970743 34.25856464116029 16.204051012753187 38 10.40260065016254 10.802700675168792 54.363590897724436 24.431107776944234 39 11.852963240810203 12.42810702675669 29.00725181295324 46.71167791947987 40 11.377844461115279 14.50362590647662 57.96449112278069 16.15403850962741 41 15.944931163954942 19.44931163954944 49.912390488110134 14.693366708385483 42 8.979489744872437 19.984992496248125 27.863931965982992 43.17158579289645 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 2.5 26 5.0 27 20.0 28 35.0 29 35.0 30 34.5 31 34.0 32 37.0 33 40.0 34 40.0 35 59.5 36 79.0 37 118.0 38 157.0 39 215.5 40 274.0 41 274.0 42 355.0 43 436.0 44 507.5 45 579.0 46 594.0 47 609.0 48 609.0 49 630.0 50 651.0 51 614.0 52 577.0 53 577.0 54 428.5 55 280.0 56 201.0 57 122.0 58 93.0 59 64.0 60 64.0 61 45.0 62 26.0 63 18.5 64 11.0 65 12.0 66 13.0 67 13.0 68 7.5 69 2.0 70 2.0 71 2.0 72 2.0 73 1.5 74 1.0 75 1.5 76 2.0 77 1.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.5 100 1.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 1.0999999999999999 2 0.0 3 0.125 4 0.0 5 0.05 6 0.0 7 0.0 8 0.05 9 0.0 10 0.05 11 0.0 12 0.025 13 0.05 14 0.025 15 0.025 16 0.0 17 0.025 18 0.05 19 0.0 20 0.05 21 0.0 22 0.1 23 0.075 24 0.05 25 0.025 26 0.0 27 0.05 28 0.075 29 0.1 30 0.0 31 0.05 32 0.05 33 0.0 34 0.025 35 0.15 36 0.05 37 0.025 38 0.025 39 0.025 40 0.025 41 0.125 42 0.05 >>END_MODULE >>Sequence Length Distribution pass #Length Count 42 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 77.225 #Duplication Level Percentage of deduplicated Percentage of total 1 94.8203302039495 73.225 2 2.136613790870832 3.3000000000000003 3 1.0035610229847847 2.325 4 0.32372936225315635 1.0 5 0.4208481709291033 1.625 6 0.19423761735189382 0.8999999999999999 7 0.16186468112657817 0.8750000000000001 8 0.09711880867594691 0.6 9 0.03237293622531564 0.22499999999999998 >10 0.7445775331822596 10.375 >50 0.03237293622531564 1.925 >100 0.03237293622531564 3.6249999999999996 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences fail #Sequence Count Percentage Possible Source GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTATCTCGT 145 3.6249999999999996 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCATCTCGTAT 77 1.925 No Hit TAACGAACGAACGATTTGAACATCTCGTATGCCGTCTTCTGC 32 0.8 Illumina PCR Primer Index 7 (96% over 25bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGATCTCGT 29 0.7250000000000001 No Hit CGAACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTTG 28 0.7000000000000001 RNA PCR Primer, Index 19 (96% over 29bp) TGCTTGGACTACATATGGTTGAGGGTTGTATCGTATGCCGTC 26 0.65 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTATCTCGTAT 26 0.65 No Hit AACGAACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCT 23 0.575 RNA PCR Primer, Index 19 (96% over 27bp) CTAACGAACGAACGATTTGAACATCTCGTATGCCGTCTTCTG 22 0.5499999999999999 RNA PCR Primer, Index 19 (96% over 25bp) AACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTTGAA 21 0.525 RNA PCR Primer, Index 19 (96% over 29bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCATCTCGTA 19 0.475 No Hit ATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAA 17 0.42500000000000004 Illumina Single End Adapter 1 (95% over 24bp) ACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTTGAAA 17 0.42500000000000004 Illumina PCR Primer Index 7 (96% over 28bp) GGGGATGTAGCTCAGAATCTCGTATGCCGTCTTCTGCTTGAA 15 0.375 RNA PCR Primer, Index 40 (100% over 30bp) CGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTTGAAAA 15 0.375 RNA PCR Primer, Index 19 (96% over 29bp) GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGATCTCGTA 15 0.375 No Hit ACGAACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTT 15 0.375 Illumina PCR Primer Index 7 (96% over 27bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCATCTCGTATG 14 0.35000000000000003 No Hit GAACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTTGA 13 0.325 Illumina PCR Primer Index 7 (96% over 28bp) AGGGCTATAGCTCAGTTCGGATCTCGTATGCCGTCTTCTGCT 13 0.325 TruSeq Adapter, Index 9 (96% over 26bp) GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACATCTCGTATG 12 0.3 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGATCTCG 12 0.3 No Hit TTTGGATTGAAGGGAGCTCTGATCTCGTATGCCGTCTTCTGC 11 0.27499999999999997 Illumina PCR Primer Index 9 (96% over 25bp) TGACAGAAGAGAGTGAGCACATCTCGTATGCCGTCTTCTGCT 10 0.25 Illumina PCR Primer Index 9 (96% over 25bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTATCTCGTA 10 0.25 No Hit TCCTAACGAACGAACGATTTGAACATCTCGTATGCCGTCTTC 9 0.22499999999999998 Illumina PCR Primer Index 7 (95% over 22bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAATCTCGT 8 0.2 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGAGA 8 0.2 No Hit TCGCTTGGTGCAGATCGGGACATCTCGTATGCCGTCTTCTGC 8 0.2 Illumina PCR Primer Index 3 (95% over 24bp) CCCCGAGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAA 7 0.17500000000000002 RNA PCR Primer, Index 17 (96% over 28bp) CATCCTAACGAACGAACGATTTGAACATCTCGTATGCCGTCT 7 0.17500000000000002 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATATCTCGTA 7 0.17500000000000002 No Hit GACACGACTCTCGGCAACGGATATCTATCTCGTATGCCGTCT 7 0.17500000000000002 No Hit TCCGTCGTAGTCTAGGATCTCGTATGCCGTCTTCTGCTTGAA 7 0.17500000000000002 RNA PCR Primer, Index 22 (96% over 28bp) AAGGAAGCTATAAGATCTCGTATGCCGTCTTCTGCTTGAAAA 6 0.15 RNA PCR Primer, Index 44 (96% over 31bp) GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTATCTCGTA 6 0.15 No Hit CCTAACGAACGAACGATTTGAACATCTCGTATGCCGTCTTCT 6 0.15 RNA PCR Primer, Index 19 (95% over 24bp) GCACCAGTGGTCTAGTGGTAGAATAGTACCATCTCGTATGCC 6 0.15 No Hit ATCCTAACGAACGAACGATTTGAACATCTCGTATGCCGTCTT 6 0.15 RNA PCR Primer, Index 19 (95% over 22bp) GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACCATCTCGTAT 6 0.15 No Hit GTCGTTGTAGTATAGTGGTATCTCGTATGCCGTCTTCTGCTT 5 0.125 RNA PCR Primer, Index 34 (96% over 27bp) GGGGATGTAGCTCAAAATCTCGTATGCCGTCTTCTGCTTGAA 5 0.125 RNA PCR Primer, Index 40 (96% over 30bp) GGGATTGTAGTTCAATATCTCGTATGCCGTCTTCTGCTTGAA 5 0.125 Illumina PCR Primer Index 6 (96% over 29bp) AGGCATCCTAACGAACGAACGATTTGAACATCTCGTATGCCG 5 0.125 No Hit ACGATTTGAACATCTCGTATGCCGTCTTCTGCTTGAAAAAAA 5 0.125 Illumina PCR Primer Index 7 (96% over 28bp) GTCGTTGTAGTATAGTGGTAAGTATTCCCGCATCTCGTATGC 5 0.125 No Hit AGGGCAAAGAACGCGAGTGAGATCTCGTATGCCGTCTTCTGC 5 0.125 TruSeq Adapter, Index 25 (96% over 25bp) GAACGATTTGAACATCTCGTATGCCGTCTTCTGCTTGAAAAA 5 0.125 RNA PCR Primer, Index 19 (96% over 29bp) GGGGACGTAGCTCATAATCTCGTATGCCGTCTTCTGCTTGAA 5 0.125 RNA PCR Primer, Index 40 (96% over 30bp) CTGAGGCATCCTAACGAACGAACGATTTGAACATCTCGTATG 5 0.125 No Hit GCATCCTAACGAACGAACGATTTGAACATCTCGTATGCCGTC 5 0.125 No Hit TAATTCATGATCTGGATCTCGTATGCCGTCTTCTGCTTGAAA 5 0.125 RNA PCR Primer, Index 23 (96% over 28bp) GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGATCTCGT 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10 0.0 0.0 0.0 0.0 0.0 11 0.0 0.0 0.0 0.0 0.0 12 0.0 0.0 0.0 0.0 0.0 13 0.0 0.0 0.0 0.0 0.0 14 0.0 0.0 0.0 0.0 0.0 15 0.0 0.0 0.0 0.0 0.0 16 0.0 0.0 0.0 0.0 0.0 17 0.0 0.0 0.0 0.0 0.0 18 0.0 0.0 0.0 0.0 0.0 19 0.0 0.0 0.0 0.0 0.0 20 0.0 0.0 0.0 0.0 0.0 21 0.0 0.0 0.0 0.0 0.0 22 0.0 0.0 0.0 0.0 0.0 23 0.0 0.0 0.0 0.0 0.0 24 0.0 0.0 0.0 0.0 0.0 25 0.0 0.0 0.0 0.0 0.0 26 0.0 0.0 0.0 0.0 0.0 27 0.0 0.0 0.0 0.0 0.0 28 0.0 0.0 0.0 0.0 0.0 29 0.0 0.0 0.0 0.0 0.0 30 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AGCCAAG 45 1.7644197E-9 36.36709 10 TAGCTCA 20 0.0017729009 36.36709 8 TAGCCAA 45 1.7644197E-9 36.36709 9 TGTAGCC 40 2.847446E-8 36.36709 7 GCCAAGT 45 1.7644197E-9 36.36709 11 CCAAGTG 45 1.7644197E-9 36.36709 12 GTAGCCA 45 1.7644197E-9 36.36709 8 CAAGTGG 45 1.7644197E-9 36.36709 13 GGATCAA 50 1.2551027E-10 35.912502 18 GGATTAT 40 3.200512E-8 35.912502 31 ATTATCT 35 5.0466224E-7 35.912502 33 GCAGTGG 40 3.200512E-8 35.912502 26 TGGATTA 35 5.0466224E-7 35.912502 30 TGGATCA 50 1.2551027E-10 35.912502 17 GATCAAG 50 1.2551027E-10 35.912502 19 AGGCAGT 40 3.200512E-8 35.912502 24 GATTATC 35 5.0466224E-7 35.912502 32 ATCAAGG 50 1.2551027E-10 35.912502 20 GTGGATT 40 3.200512E-8 35.912502 29 GTGGATC 50 1.2551027E-10 35.912502 16 >>END_MODULE Read 650429 spots for SRR1174002.sra Written 650429 spots for SRR1174002.sra Read 650429 spots for SRR1174002.sra Written 650429 spots for SRR1174002.sra Read 650434 spots for SRR1174002.sra Written 650434 spots for SRR1174002.sra Read 650429 spots for SRR1174002.sra Written 650429 spots for SRR1174002.sra Read 650429 spots for SRR1174002.sra Written 650429 spots for SRR1174002.sra Read 650429 spots for SRR1174002.sra Written 650429 spots for SRR1174002.sra Read 650429 spots for SRR1174002.sra Written 650429 spots for SRR1174002.sra Read 650429 spots for SRR1174002.sra Written 650429 spots for SRR1174002.sra Read 650429 spots for SRR1174002.sra Written 650429 spots for SRR1174002.sra Read 650429 spots for SRR1174002.sra Written 650429 spots for SRR1174002.sra Read 650429 spots for SRR1174002.sra Written 650429 spots for SRR1174002.sra Read 650429 spots for SRR1174002.sra Written 650429 spots for SRR1174002.sra Read 650429 spots for SRR1174002.sra Written 650429 spots for SRR1174002.sra Read 650429 spots for SRR1174002.sra Written 650429 spots for SRR1174002.sra Read 650429 spots for SRR1174002.sra Written 650429 spots for SRR1174002.sra Read 650429 spots for SRR1174002.sra Written 650429 spots for SRR1174002.sra Read 650429 spots for SRR1174002.sra Written 650429 spots for SRR1174002.sra Read 650429 spots for SRR1174002.sra Written 650429 spots for SRR1174002.sra Read 650429 spots for SRR1174002.sra Written 650429 spots for SRR1174002.sra Read 650429 spots for SRR1174002.sra Written 650429 spots for SRR1174002.sra SRR ids: ['SRR1174002.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_sm358wi8 SRR1174002.sra spots: 13008585 blocks: [[1, 650429], [650430, 1300858], [1300859, 1951287], [1951288, 2601716], [2601717, 3252145], [3252146, 3902574], [3902575, 4553003], [4553004, 5203432], [5203433, 5853861], [5853862, 6504290], [6504291, 7154719], [7154720, 7805148], [7805149, 8455577], [8455578, 9106006], [9106007, 9756435], [9756436, 10406864], [10406865, 11057293], [11057294, 11707722], [11707723, 12358151], [12358152, 13008585]] SRR1174002 file size 1815624 SRR1174002 completed basic pipeline successfully skewer v0.2.2 [April 4, 2016] COMMAND LINE: skewer -f sanger -l 18 -q 10 -k inf -t 20 -o SRR1174002 SRR1174002_1.fastq Input file: SRR1174002_1.fastq trimmed: SRR1174002-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- minimum overlap length for adapter detection (-k): inf -- number of concurrent threads (-t): 20 Mon Dec 9 14:12:31 2024 >> started Mon Dec 9 14:13:03 2024 >> done (31.333s) 13008585 reads processed; of these: 52034 ( 0.40%) short reads filtered out after trimming by size control 23452 ( 0.18%) empty reads filtered out after trimming by size control 12933099 (99.42%) reads available; of these: 1706069 (13.19%) trimmed reads available after processing 11227030 (86.81%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 7648 0.06% 19 8938 0.07% 20 9645 0.07% 21 10480 0.08% 22 12728 0.10% 23 18825 0.15% 24 21047 0.16% 25 19686 0.15% 26 25361 0.20% 27 37212 0.29% 28 31434 0.24% 29 40283 0.31% 30 44150 0.34% 31 45619 0.35% 32 46490 0.36% 33 40710 0.31% 34 41815 0.32% 35 44496 0.34% 36 45804 0.35% 37 64823 0.50% 38 73586 0.57% 39 105743 0.82% 40 261245 2.02% 41 648301 5.01% 42 11227030 86.81% 12933099 reads passed initial QC criterion=sequence-density sequence-density=73.07 sequence-density-rank=1 fanout-score=31.89 fanout-score-rank=1 prefix-density=75.96 prefix-fanout=30.7 sequence=ATCTCGTATGCCGTCTTCTGCTTGAAAAAA criterion=fanout-score sequence-density=73.07 sequence-density-rank=1 fanout-score=31.89 fanout-score-rank=1 prefix-density=75.96 prefix-fanout=30.7 sequence=ATCTCGTATGCCGTCTTCTGCTTGAAAAAA Potential 3prime adapter identified. Now checking if in reference sequence Warning: gzbuffer added in zlib v1.2.3.5. Unable to change buffer size from default of 8192. 1 reads; of these: 1 (100.00%) were unpaired; of these: 1 (100.00%) aligned 0 times 0 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate Adapter seq not found in reference. Now shuffling file before clipping skewer v0.2.2 [April 4, 2016] COMMAND LINE: skewer -f sanger -l 18 -t 20 -x ATCTCGTATGCCGTCTTCTGCTTGAAAAAA -o SRR1174002 - Input file: STDIN trimmed: SRR1174002-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): ATCTCGTATGCCGTCTTCTGCTTGAAAAAA -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- minimum overlap length for adapter detection (-k): 3 -- number of concurrent threads (-t): 20 Mon Dec 9 14:14:38 2024 >> started Mon Dec 9 14:15:26 2024 >> done (47.595s) 12583556 reads processed; of these: 2101720 (16.70%) short reads filtered out after trimming by size control 224391 ( 1.78%) empty reads filtered out after trimming by size control 10257445 (81.51%) reads available; of these: 9638872 (93.97%) trimmed reads available after processing 618573 ( 6.03%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 259877 2.53% 19 302931 2.95% 20 331631 3.23% 21 674070 6.57% 22 309714 3.02% 23 798181 7.78% 24 3995365 38.95% 25 282269 2.75% 26 157870 1.54% 27 127168 1.24% 28 107645 1.05% 29 152225 1.48% 30 179242 1.75% 31 165193 1.61% 32 221055 2.16% 33 550727 5.37% 34 307506 3.00% 35 713838 6.96% 36 111742 1.09% 37 56401 0.55% 38 28330 0.28% 39 22270 0.22% 40 12533 0.12% 41 17570 0.17% 42 372092 3.63% criterion=sequence-density sequence-density=6.31 sequence-density-rank=1 fanout-score=1.00 fanout-score-rank=20 prefix-density=0.01 prefix-fanout=1.0 sequence=GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATT criterion=fanout-score sequence-density=0.15 sequence-density-rank=28 fanout-score=42.55 fanout-score-rank=1 prefix-density=6.20 prefix-fanout=1.0 sequence=GATCAAGGCAGGGGATT Started job on | Dec 09 14:17:18 Started mapping on | Dec 09 14:17:19 Finished on | Dec 09 14:19:35 Mapping speed, Million of reads per hour | 280.77 Number of input reads | 10606988 Average input read length | 26 UNIQUE READS: Uniquely mapped reads number | 4112273 Uniquely mapped reads % | 38.77% Average mapped length | 23.79 Number of splices: Total | 35127 Number of splices: Annotated (sjdb) | 4406 Number of splices: GT/AG | 32265 Number of splices: GC/AG | 1231 Number of splices: AT/AC | 15 Number of splices: Non-canonical | 1616 Mismatch rate per base, % | 0.21% Deletion rate per base | 0.00% Deletion average length | 1.21 Insertion rate per base | 0.00% Insertion average length | 1.02 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 4153057 % of reads mapped to multiple loci | 39.15% Number of reads mapped to too many loci | 1526129 % of reads mapped to too many loci | 14.39% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 5.57% % of reads unmapped: other | 2.12% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 2341658 2341658 2341658 N_multimapping 4153057 4153057 4153057 N_noFeature 3420599 3695720 3828176 N_ambiguous 18162 8384 1246 UnstrandedReadsAssigned:673512 PositiveStrandReadsAssigned:408169 NegativeStrandReadsAssigned:282851 Dataset is classified unstranded MeadianReadLen=24 20thPercentileLength=23 echo kmer=19 SRR1174002 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=19 [quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20 [index] k-mer length: 19 [index] number of targets: 52,972 [index] number of k-mers: 65,492,969 [index] number of equivalence classes: 320,172 [quant] running in single-end mode [quant] will process file 1: SRR1174002-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 10,606,988 reads, 3,250,979 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,164 rounds 52973 SRR1174002.ke.tsv 35125 SRR1174002.se.tsv 88098 total ==> SRR1174002.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 0 0 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 3.61881 0.230066 PNS24243 293 194 0 0 KQK14069 1603 1504 25.8035 1.49648 KQK14071 474 375 0 0 ==> SRR1174002.se.tsv <== BRADI_1g14170v3 25 BRADI_1g53295v3 1 BRADI_1g59795v3 1 BRADI_1g07683v3 0 BRADI_1g00485v3 1 BRADI_1g20270v3 10 BRADI_1g74790v3 84 BRADI_1g09890v3 1 BRADI_1g77505v3 0 BRADI_1g48960v3 0 SRR1174002 completed mapping pipeline successfully