Starting /dee2/code/volunteer_pipeline.sh SRR7171467 current disk space = 3087497592832 free memory = 1450203176 SRR7171467 SRAfilesize c39b059a4b1d664e9314aef7e47e71bf SRR7171467.sra SRR7171467.sra file validated SRR7171467 is paired end SRR7171467 is conventional basespace SRR7171467 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7171467_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.87225 34.0 33.0 34.0 32.0 34.0 2 33.1885 34.0 33.0 34.0 32.0 34.0 3 32.99625 34.0 33.0 34.0 32.0 34.0 4 33.031 34.0 33.0 34.0 32.0 34.0 5 33.12625 34.0 33.0 34.0 32.0 34.0 6 36.59325 38.0 37.0 38.0 34.0 38.0 7 37.26875 38.0 38.0 38.0 36.0 38.0 8 37.4735 38.0 38.0 38.0 37.0 38.0 9 37.56425 38.0 38.0 38.0 38.0 38.0 10-14 37.521699999999996 38.0 38.0 38.0 37.6 38.0 15-19 37.455400000000004 38.0 38.0 38.0 37.4 38.0 20-24 37.54535 38.0 38.0 38.0 37.8 38.0 25-29 37.44075 38.0 38.0 38.0 37.0 38.0 30-34 37.42695 38.0 38.0 38.0 37.0 38.0 35-39 37.4011 38.0 38.0 38.0 37.0 38.0 40-44 37.425850000000004 38.0 38.0 38.0 37.0 38.0 45-49 37.46155 38.0 38.0 38.0 37.2 38.0 50-54 37.3963 38.0 38.0 38.0 37.0 38.0 55-59 37.3577 38.0 38.0 38.0 37.0 38.0 60-64 37.3229 38.0 38.0 38.0 37.0 38.0 65-69 37.28775 38.0 38.0 38.0 37.0 38.0 70-74 37.1132 38.0 38.0 38.0 36.2 38.0 75-79 37.06665 38.0 38.0 38.0 36.0 38.0 80-84 37.07405 38.0 38.0 38.0 36.0 38.0 85-89 37.0661 38.0 38.0 38.0 36.0 38.0 90-94 36.939 38.0 38.0 38.0 35.8 38.0 95-99 36.67809999999999 38.0 38.0 38.0 34.6 38.0 100-104 36.486149999999995 38.0 38.0 38.0 34.2 38.0 105-109 36.57065 38.0 38.0 38.0 34.0 38.0 110-114 36.4228 38.0 38.0 38.0 34.0 38.0 115-119 36.54559999999999 38.0 38.0 38.0 34.0 38.0 120-124 36.4683 38.0 38.0 38.0 34.0 38.0 125-129 36.38199999999999 38.0 37.8 38.0 34.0 38.0 130-134 36.09625 38.0 37.2 38.0 32.6 38.0 135-139 35.8917 38.0 36.0 38.0 31.8 38.0 140-144 35.725750000000005 38.0 36.0 38.0 31.0 38.0 145-149 35.60195 38.0 36.0 38.0 31.0 38.0 150-151 33.375625 36.5 31.5 38.0 21.5 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 22 1.0 23 2.0 24 3.0 25 9.0 26 5.0 27 16.0 28 12.0 29 37.0 30 39.0 31 42.0 32 63.0 33 85.0 34 148.0 35 219.0 36 509.0 37 2810.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 42.368619562484284 11.541362836308776 9.278350515463918 36.811667085743025 2 22.3 15.925 33.275 28.499999999999996 3 20.25 22.2 26.6 30.95 4 23.150000000000002 28.875 23.025000000000002 24.95 5 21.075 34.175 23.674999999999997 21.075 6 19.825 36.1 24.375 19.7 7 14.725 25.4 42.8 17.075000000000003 8 16.8 25.4 30.725 27.075 9 18.099999999999998 23.674999999999997 34.575 23.65 10-14 19.925 29.475 27.134999999999998 23.465 15-19 19.415 28.74 27.785 24.060000000000002 20-24 19.400000000000002 29.165000000000003 27.800000000000004 23.635 25-29 19.657948692303844 28.709306395959395 27.689153373005954 23.94359153873081 30-34 19.808914011305088 28.943024360962433 27.662448101645744 23.58561352608674 35-39 20.184082837276772 29.18313240958431 27.332299534790653 23.300485218348257 40-44 19.833925266369867 29.2981841828823 26.767045170326647 24.10084538042119 45-49 20.19403880776155 28.740748149629923 27.600520104020802 23.464692938587717 50-54 20.271013550677534 28.596429821491075 27.611380569028455 23.52117605880294 55-59 19.439999999999998 29.04 27.715 23.805 60-64 19.72 28.910000000000004 27.500000000000004 23.87 65-69 19.91 27.97 28.065 24.055 70-74 19.865 28.560000000000002 27.815 23.76 75-79 20.169999999999998 28.73 27.665 23.435 80-84 20.255000000000003 28.205000000000002 27.85 23.69 85-89 20.51 28.27 27.67 23.549999999999997 90-94 20.424999999999997 28.249999999999996 27.555000000000003 23.77 95-99 20.31 28.09 28.24 23.36 100-104 20.375 28.225 27.395000000000003 24.005000000000003 105-109 20.375 27.865000000000002 27.889999999999997 23.87 110-114 20.145 28.22 28.125 23.51 115-119 20.485 28.365000000000002 27.26 23.89 120-124 20.7 28.52 26.855 23.925 125-129 20.595 28.244999999999997 27.515 23.645 130-134 20.655 28.310000000000002 27.3 23.735 135-139 20.69 28.505000000000003 27.22 23.585 140-144 21.05 27.99 27.425 23.535 145-149 20.565 28.384999999999998 26.950000000000003 24.099999999999998 150-151 21.224999999999998 28.4 26.2875 24.087500000000002 >>END_MODULE >>Per sequence GC content pass #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 0.5 14 0.5 15 0.5 16 0.5 17 0.0 18 0.0 19 0.0 20 0.5 21 1.0 22 0.5 23 0.5 24 1.0 25 2.0 26 3.5 27 5.0 28 9.5 29 13.0 30 17.5 31 23.5 32 32.5 33 44.0 34 59.5 35 72.5 36 91.0 37 112.5 38 130.0 39 170.5 40 185.0 41 206.0 42 240.5 43 257.5 44 284.0 45 284.5 46 275.5 47 270.0 48 240.0 49 198.5 50 166.5 51 133.5 52 113.0 53 99.0 54 70.0 55 48.0 56 34.0 57 21.5 58 19.5 59 20.0 60 12.0 61 6.5 62 6.5 63 4.0 64 3.5 65 3.5 66 1.5 67 0.0 68 0.5 69 0.5 70 0.0 71 1.0 72 1.5 73 0.5 74 0.0 75 0.0 76 0.0 77 0.0 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 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.575 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.015 30-34 0.045 35-39 0.045 40-44 0.045 45-49 0.02 50-54 0.005 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.85000000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 99.84977466199298 99.7 2 0.15022533800701052 0.3 3 0.0 0.0 4 0.0 0.0 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences pass >>END_MODULE >>Adapter Content warn #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 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.025 0.0 0.0 0.0 0.0 80-81 0.025 0.0 0.0 0.0 0.0 82-83 0.05 0.0 0.0 0.0 0.0 84-85 0.05 0.0 0.0 0.0 0.0 86-87 0.05 0.0 0.0 0.0 0.0 88-89 0.0625 0.0 0.0 0.0 0.0 90-91 0.1 0.0 0.0 0.0 0.0 92-93 0.16249999999999998 0.0 0.0 0.0 0.0 94-95 0.175 0.0 0.0 0.0 0.0 96-97 0.225 0.0 0.0 0.0 0.0 98-99 0.2875 0.0 0.0 0.0 0.0 100-101 0.3625 0.0 0.0 0.0 0.0 102-103 0.4375 0.0 0.0 0.0 0.0 104-105 0.5875 0.0 0.0 0.0 0.0 106-107 0.6875 0.0 0.0 0.0 0.0 108-109 0.8125 0.0 0.0 0.0 0.0 110-111 1.0 0.0 0.0 0.0 0.0 112-113 1.2 0.0 0.0 0.0 0.0 114-115 1.45 0.0 0.0 0.0 0.0 116-117 1.7625000000000002 0.0 0.0 0.0 0.0 118-119 1.8875 0.0 0.0 0.0 0.0 120-121 2.05 0.0 0.0 0.0 0.0 122-123 2.4375 0.0 0.0 0.0 0.0 124-125 2.6875 0.0 0.0 0.0 0.0 126-127 2.95 0.0 0.0 0.0 0.0 128-129 3.325 0.0 0.0 0.0 0.0 130-131 3.6875 0.0 0.0 0.0 0.0 132-133 4.075 0.0 0.0 0.0 0.0 134-135 4.5875 0.0 0.0 0.0 0.0 136-137 5.0875 0.0 0.0 0.0 0.0 138-139 5.6 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR7171467 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7171467_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.561 33.0 33.0 34.0 32.0 34.0 2 32.60025 33.0 33.0 34.0 31.0 34.0 3 32.66325 34.0 33.0 34.0 32.0 34.0 4 32.4245 34.0 33.0 34.0 31.0 34.0 5 32.4875 34.0 33.0 34.0 32.0 34.0 6 36.59825 38.0 38.0 38.0 34.0 38.0 7 36.51175 38.0 38.0 38.0 34.0 38.0 8 36.47675 38.0 38.0 38.0 34.0 38.0 9 36.51975 38.0 38.0 38.0 34.0 38.0 10-14 36.58819999999999 38.0 38.0 38.0 34.4 38.0 15-19 36.88635 38.0 38.0 38.0 36.0 38.0 20-24 36.95325 38.0 38.0 38.0 36.2 38.0 25-29 37.03315 38.0 38.0 38.0 36.4 38.0 30-34 36.96475 38.0 38.0 38.0 36.0 38.0 35-39 36.9382 38.0 38.0 38.0 36.0 38.0 40-44 36.8963 38.0 38.0 38.0 36.0 38.0 45-49 36.932100000000005 38.0 38.0 38.0 36.0 38.0 50-54 36.786350000000006 38.0 38.0 38.0 35.8 38.0 55-59 36.8261 38.0 38.0 38.0 36.0 38.0 60-64 36.77275 38.0 38.0 38.0 35.6 38.0 65-69 36.8803 38.0 38.0 38.0 36.0 38.0 70-74 36.8899 38.0 38.0 38.0 36.0 38.0 75-79 36.8779 38.0 38.0 38.0 36.0 38.0 80-84 36.7893 38.0 38.0 38.0 35.4 38.0 85-89 36.70139999999999 38.0 38.0 38.0 35.0 38.0 90-94 36.570449999999994 38.0 38.0 38.0 34.4 38.0 95-99 36.5101 38.0 38.0 38.0 34.0 38.0 100-104 36.402499999999996 38.0 38.0 38.0 34.0 38.0 105-109 36.287549999999996 38.0 38.0 38.0 34.0 38.0 110-114 36.23285 38.0 38.0 38.0 33.8 38.0 115-119 35.8991 38.0 37.2 38.0 31.8 38.0 120-124 35.9191 38.0 37.4 38.0 32.4 38.0 125-129 35.8809 38.0 37.0 38.0 32.2 38.0 130-134 35.5971 38.0 36.2 38.0 31.0 38.0 135-139 35.4345 38.0 36.0 38.0 30.0 38.0 140-144 35.0086 38.0 35.4 38.0 27.2 38.0 145-149 34.6964 38.0 35.0 38.0 24.0 38.0 150-151 32.319125 35.5 28.0 38.0 19.5 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 1.0 3 2.0 4 1.0 5 0.0 6 0.0 7 0.0 8 1.0 9 2.0 10 1.0 11 0.0 12 0.0 13 0.0 14 0.0 15 2.0 16 1.0 17 4.0 18 10.0 19 7.0 20 6.0 21 5.0 22 10.0 23 8.0 24 8.0 25 21.0 26 21.0 27 26.0 28 28.0 29 41.0 30 49.0 31 53.0 32 74.0 33 88.0 34 139.0 35 234.0 36 470.0 37 2687.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 40.54054054054054 21.646646646646648 13.763763763763764 24.04904904904905 2 25.131414267834796 26.458072590738425 29.86232790988736 18.548185231539424 3 20.22022022022022 27.77777777777778 32.28228228228228 19.71971971971972 4 24.174174174174173 33.33333333333333 23.5985985985986 18.893893893893893 5 24.092161282243925 35.83771600300526 23.140495867768596 16.929626846982217 6 21.047356552242547 37.434227010774244 23.552994237033325 17.965422199949888 7 19.71442885771543 22.62024048096192 37.5250501002004 20.140280561122246 8 22.019038076152306 25.926853707414832 26.427855711422843 25.626252505010022 9 22.294589178356713 26.603206412825653 28.53206412825651 22.57014028056112 10-14 24.11166240665564 28.376685210244073 26.437127249035232 21.074525134065052 15-19 22.936607366574794 29.085442245051368 27.321473314958656 20.656477073415182 20-24 23.338345864661655 28.516290726817044 27.383458646616543 20.761904761904763 25-29 23.332832306227765 29.139736459742473 26.975299363695576 20.552131870334183 30-34 23.555622309001702 28.286772804646038 27.816161009312108 20.341443877040152 35-39 23.270125581628058 28.72867363786461 27.472857357282233 20.528343423225095 40-44 23.95311560809457 28.676617912242037 27.494490082147866 19.875776397515526 45-49 23.38677354709419 28.45190380761523 27.750501002004007 20.41082164328657 50-54 23.611946281820003 27.861294848667068 28.03166967328122 20.49508919623171 55-59 23.614035087719298 28.24561403508772 27.819548872180448 20.32080200501253 60-64 23.36874812067756 27.7939260298687 27.934248772176005 20.903077077277736 65-69 23.147452277168195 28.31805200661356 28.28799038027957 20.246505335938675 70-74 23.930896344516775 28.82824236354532 27.045568352528793 20.19529293940911 75-79 23.74687343671836 27.048524262131064 28.66933466733367 20.535267633816908 80-84 24.024609843937576 27.77611044417767 28.281312525010005 19.917967186874748 85-89 23.87006356674508 27.568947394764503 28.24465688973422 20.316332148756196 90-94 23.418323899213544 28.01683113760457 27.791414116114808 20.773430847067072 95-99 23.39146121467228 27.72098616957306 28.9035878933654 19.983964722389256 100-104 23.979745312343326 28.32648150005014 27.08813797252582 20.605635215080717 105-109 24.08865266008123 27.40309883167026 28.451085593942736 20.05716291430577 110-114 23.59725216868074 27.949656521085092 27.819284962142106 20.63380634809206 115-119 24.293020457280385 27.822904131568393 27.983353389490574 19.90072202166065 120-124 24.433754259370616 28.021647624774502 27.715975145319703 19.82862297053518 125-129 24.221331997996995 28.437656484727093 27.325988983475213 20.0150225338007 130-134 24.521782674011018 27.786680020030047 27.466199298948425 20.225338007010514 135-139 24.478957915831664 28.016032064128254 27.5751503006012 19.929859719438877 140-144 25.297037148443373 27.70842733243094 27.232165237880384 19.7623702812453 145-149 25.260730044123548 27.787805856397913 27.035699959887687 19.915764139590856 150-151 25.958886939082475 27.112058159939835 26.986713462020557 19.942341438957133 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 1.0 1 0.5 2 0.0 3 0.0 4 0.5 5 1.0 6 0.5 7 0.5 8 0.5 9 0.0 10 0.5 11 1.0 12 0.5 13 0.5 14 1.0 15 0.5 16 0.0 17 0.5 18 1.0 19 1.0 20 0.5 21 0.0 22 0.5 23 0.5 24 0.0 25 0.5 26 2.0 27 6.0 28 8.0 29 9.0 30 10.0 31 15.5 32 22.0 33 29.5 34 47.0 35 67.0 36 81.0 37 102.5 38 133.0 39 159.0 40 196.0 41 237.0 42 269.0 43 300.0 44 313.5 45 293.5 46 278.0 47 270.5 48 235.0 49 191.5 50 152.0 51 121.0 52 100.0 53 77.5 54 65.0 55 51.0 56 35.5 57 29.5 58 23.5 59 17.0 60 12.5 61 7.0 62 6.0 63 5.5 64 1.0 65 1.0 66 2.0 67 1.5 68 1.0 69 0.5 70 0.5 71 0.5 72 0.5 73 0.5 74 0.0 75 0.0 76 0.0 77 0.0 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 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.1 2 0.125 3 0.1 4 0.1 5 0.17500000000000002 6 0.22499999999999998 7 0.2 8 0.2 9 0.2 10-14 0.23500000000000001 15-19 0.22499999999999998 20-24 0.25 25-29 0.20500000000000002 30-34 0.13 35-39 0.065 40-44 0.18 45-49 0.2 50-54 0.22 55-59 0.25 60-64 0.22999999999999998 65-69 0.20500000000000002 70-74 0.15 75-79 0.05 80-84 0.04 85-89 0.105 90-94 0.185 95-99 0.22 100-104 0.27 105-109 0.28500000000000003 110-114 0.28500000000000003 115-119 0.27999999999999997 120-124 0.22 125-129 0.15 130-134 0.15 135-139 0.2 140-144 0.265 145-149 0.27999999999999997 150-151 0.27499999999999997 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.825 #Duplication Level Percentage of deduplicated Percentage of total 1 99.82469321312296 99.65 2 0.1753067868770348 0.35000000000000003 3 0.0 0.0 4 0.0 0.0 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences pass >>END_MODULE >>Adapter Content warn #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 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.025 0.0 0.0 0.0 0.0 80-81 0.025 0.0 0.0 0.0 0.0 82-83 0.05 0.0 0.0 0.0 0.0 84-85 0.05 0.0 0.0 0.0 0.0 86-87 0.05 0.0 0.0 0.0 0.0 88-89 0.0625 0.0 0.0 0.0 0.0 90-91 0.1 0.0 0.0 0.0 0.0 92-93 0.16249999999999998 0.0 0.0 0.0 0.0 94-95 0.175 0.0 0.0 0.0 0.0 96-97 0.225 0.0 0.0 0.0 0.0 98-99 0.2875 0.0 0.0 0.0 0.0 100-101 0.3625 0.0 0.0 0.0 0.0 102-103 0.4375 0.0 0.0 0.0 0.0 104-105 0.5875 0.0 0.0 0.0 0.0 106-107 0.6625 0.0 0.0 0.0 0.0 108-109 0.7875 0.0 0.0 0.0 0.0 110-111 0.9750000000000001 0.0 0.0 0.0 0.0 112-113 1.175 0.0 0.0 0.0 0.0 114-115 1.425 0.0 0.0 0.0 0.0 116-117 1.7 0.0 0.0 0.0 0.0 118-119 1.8125 0.0 0.0 0.0 0.0 120-121 1.975 0.0 0.0 0.0 0.0 122-123 2.3375000000000004 0.0 0.0 0.0 0.0 124-125 2.5875000000000004 0.0 0.0 0.0 0.0 126-127 2.8499999999999996 0.0 0.0 0.0 0.0 128-129 3.2249999999999996 0.0 0.0 0.0 0.0 130-131 3.5625 0.0 0.0 0.0 0.0 132-133 3.9875 0.0 0.0 0.0 0.0 134-135 4.475 0.0 0.0 0.0 0.0 136-137 4.9625 0.0 0.0 0.0 0.0 138-139 5.475 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TAAGAAC 10 0.00682755 145.0 6 AAAGTCG 10 0.00682755 145.0 3 >>END_MODULE Read 1117834 spots for SRR7171467.sra Written 1117834 spots for SRR7171467.sra Read 1117834 spots for SRR7171467.sra Written 1117834 spots for SRR7171467.sra Read 1117834 spots for SRR7171467.sra Written 1117834 spots for SRR7171467.sra Read 1117834 spots for SRR7171467.sra Written 1117834 spots for SRR7171467.sra Read 1117834 spots for SRR7171467.sra Written 1117834 spots for SRR7171467.sra Read 1117849 spots for SRR7171467.sra Written 1117849 spots for SRR7171467.sra Read 1117834 spots for SRR7171467.sra Written 1117834 spots for SRR7171467.sra Read 1117834 spots for SRR7171467.sra Written 1117834 spots for SRR7171467.sra Read 1117834 spots for SRR7171467.sra Written 1117834 spots for SRR7171467.sra Read 1117834 spots for SRR7171467.sra Written 1117834 spots for SRR7171467.sra Read 1117834 spots for SRR7171467.sra Written 1117834 spots for SRR7171467.sra Read 1117834 spots for SRR7171467.sra Written 1117834 spots for SRR7171467.sra Read 1117834 spots for SRR7171467.sra Written 1117834 spots for SRR7171467.sra Read 1117834 spots for SRR7171467.sra Written 1117834 spots for SRR7171467.sra Read 1117834 spots for SRR7171467.sra Written 1117834 spots for SRR7171467.sra Read 1117834 spots for SRR7171467.sra Written 1117834 spots for SRR7171467.sra Read 1117834 spots for SRR7171467.sra Written 1117834 spots for SRR7171467.sra Read 1117834 spots for SRR7171467.sra Written 1117834 spots for SRR7171467.sra Read 1117834 spots for SRR7171467.sra Written 1117834 spots for SRR7171467.sra Read 1117834 spots for SRR7171467.sra Written 1117834 spots for SRR7171467.sra SRR ids: ['SRR7171467.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_e_jnjn9_ SRR7171467.sra spots: 22356695 blocks: [[1, 1117834], [1117835, 2235668], [2235669, 3353502], [3353503, 4471336], [4471337, 5589170], [5589171, 6707004], [6707005, 7824838], [7824839, 8942672], [8942673, 10060506], [10060507, 11178340], [11178341, 12296174], [12296175, 13414008], [13414009, 14531842], [14531843, 15649676], [15649677, 16767510], [16767511, 17885344], [17885345, 19003178], [19003179, 20121012], [20121013, 21238846], [21238847, 22356695]] SRR7171467 file size 7554249 SRR7171467 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 SRR7171467 SRR7171467_1.fastq SRR7171467_2.fastq Input file: SRR7171467_1.fastq Paired file: SRR7171467_2.fastq trimmed: SRR7171467-trimmed-pair1.fastq, SRR7171467-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA -- 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 -- number of concurrent threads (-t): 20 Thu Feb 13 19:04:48 2025 >> started Thu Feb 13 19:05:14 2025 >> done (25.775s) 22356695 read pairs processed; of these: 946 ( 0.00%) short read pairs filtered out after trimming by size control 2548 ( 0.01%) empty read pairs filtered out after trimming by size control 22353201 (99.98%) read pairs available; of these: 2103510 ( 9.41%) trimmed read pairs available after processing 20249691 (90.59%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 1 0.00% 19 7 0.00% 20 2 0.00% 21 2 0.00% 22 2 0.00% 23 4 0.00% 24 1 0.00% 25 1 0.00% 26 4 0.00% 27 1 0.00% 28 2 0.00% 29 0 0.00% 30 4 0.00% 31 2 0.00% 32 3 0.00% 33 2 0.00% 34 2 0.00% 35 3 0.00% 36 4 0.00% 37 2 0.00% 38 8 0.00% 39 8 0.00% 40 5 0.00% 41 2 0.00% 42 10 0.00% 43 6 0.00% 44 6 0.00% 45 10 0.00% 46 8 0.00% 47 5 0.00% 48 21 0.00% 49 13 0.00% 50 19 0.00% 51 19 0.00% 52 13 0.00% 53 26 0.00% 54 27 0.00% 55 25 0.00% 56 50 0.00% 57 46 0.00% 58 49 0.00% 59 59 0.00% 60 77 0.00% 61 91 0.00% 62 101 0.00% 63 121 0.00% 64 150 0.00% 65 127 0.00% 66 140 0.00% 67 198 0.00% 68 237 0.00% 69 243 0.00% 70 365 0.00% 71 377 0.00% 72 463 0.00% 73 499 0.00% 74 611 0.00% 75 687 0.00% 76 771 0.00% 77 901 0.00% 78 1018 0.00% 79 1073 0.00% 80 1321 0.01% 81 1533 0.01% 82 1824 0.01% 83 2048 0.01% 84 2301 0.01% 85 2598 0.01% 86 2891 0.01% 87 3025 0.01% 88 3362 0.02% 89 3715 0.02% 90 4180 0.02% 91 4707 0.02% 92 5281 0.02% 93 5775 0.03% 94 6397 0.03% 95 7008 0.03% 96 7583 0.03% 97 8017 0.04% 98 8480 0.04% 99 9047 0.04% 100 10000 0.04% 101 10805 0.05% 102 11783 0.05% 103 12726 0.06% 104 13750 0.06% 105 14708 0.07% 106 15461 0.07% 107 16193 0.07% 108 16954 0.08% 109 17478 0.08% 110 18351 0.08% 111 19583 0.09% 112 21275 0.10% 113 22256 0.10% 114 23934 0.11% 115 26082 0.12% 116 27751 0.12% 117 31993 0.14% 118 31701 0.14% 119 29481 0.13% 120 29788 0.13% 121 30745 0.14% 122 32460 0.15% 123 34083 0.15% 124 36025 0.16% 125 37550 0.17% 126 39073 0.17% 127 39875 0.18% 128 40826 0.18% 129 41361 0.19% 130 42510 0.19% 131 44066 0.20% 132 46102 0.21% 133 47600 0.21% 134 50035 0.22% 135 51612 0.23% 136 53338 0.24% 137 54385 0.24% 138 54918 0.25% 139 55762 0.25% 140 57166 0.26% 141 63771 0.29% 142 66205 0.30% 143 63808 0.29% 144 67474 0.30% 145 73830 0.33% 146 67511 0.30% 147 73082 0.33% 148 70055 0.31% 149 71670 0.32% 150 74732 0.33% 151 20249691 90.59% 22353201 reads passed initial QC criterion=sequence-density sequence-density=0.25 sequence-density-rank=1 fanout-score=7.20 fanout-score-rank=14 prefix-density=0.50 prefix-fanout=3.5 sequence=TTGCAGCCATTCTCAGCACCAAAGTTCATCTCAGAGCTCTCGTAGAACATCCTAACTGGAGC criterion=fanout-score sequence-density=0.02 sequence-density-rank=26 fanout-score=181.58 fanout-score-rank=1 prefix-density=0.19 prefix-fanout=15.4 sequence=CTCCTTCCTCTAAATGATAAGGTTCAGTGGACTTCTCGCGACGTCGCCGGCGGCGAACCGCCCACGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAGACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAA criterion=sequence-density sequence-density=0.29 sequence-density-rank=1 fanout-score=4.03 fanout-score-rank=24 prefix-density=0.37 prefix-fanout=3.2 sequence=TGCAAGTGCGGCAGTGGCTGCAA criterion=fanout-score sequence-density=0.02 sequence-density-rank=36 fanout-score=37.59 fanout-score-rank=1 prefix-density=0.07 prefix-fanout=9.5 sequence=AGGATCTGTTTAATTTGAGACAGAAAACATGAAATCCTCCTACACTTTCTTCATTCTTTTCTCACTCTTTTCGTTTGCTAACGTGATCGGTGCTAGAAAAGACACTGGAGAGTATTGGAGAGCTGTCATGAAAGATCAGCCCATGCCAGAAGCAATACATGGCCTTATTCGCGAAACCACATTGTCATCAGTCTCCAATGAGAAAGCCGATTGCCACACAACCGAGTCCAATGAAAAGAATAATTTTGTCAAGGATTTTGGCCCACAGCCTACTGCTACATCTTATGACAA SRR7171467 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 13 19:06:06 Started mapping on | Feb 13 19:06:06 Finished on | Feb 13 19:08:36 Mapping speed, Million of reads per hour | 536.48 Number of input reads | 22353201 Average input read length | 298 UNIQUE READS: Uniquely mapped reads number | 20714027 Uniquely mapped reads % | 92.67% Average mapped length | 296.70 Number of splices: Total | 20187131 Number of splices: Annotated (sjdb) | 19784741 Number of splices: GT/AG | 19850915 Number of splices: GC/AG | 263308 Number of splices: AT/AC | 17146 Number of splices: Non-canonical | 55762 Mismatch rate per base, % | 0.43% Deletion rate per base | 0.03% Deletion average length | 2.60 Insertion rate per base | 0.02% Insertion average length | 2.65 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 503674 % of reads mapped to multiple loci | 2.25% Number of reads mapped to too many loci | 208338 % of reads mapped to too many loci | 0.93% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.92% % of reads unmapped: other | 0.23% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1135503 1135503 1135503 N_multimapping 503674 503674 503674 N_noFeature 602145 20513984 675644 N_ambiguous 234255 1830 106461 UnstrandedReadsAssigned:19877627 PositiveStrandReadsAssigned:198213 NegativeStrandReadsAssigned:19931922 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR7171467 Starting Kallisto paired end mapping to ensembl reference transcriptome [quant] fragment length distribution will be estimated from the data [index] k-mer length: 31 [index] number of targets: 52,400 [index] number of k-mers: 62,057,036 [index] number of equivalence classes: 130,681 [quant] running in paired-end mode [quant] will process pair 1: SRR7171467-trimmed-pair1.fastq SRR7171467-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 22,353,201 reads, 20,086,068 reads pseudoaligned [quant] estimated average fragment length: 240.958 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,140 rounds 52401 SRR7171467.ke.tsv 34699 SRR7171467.se.tsv 87100 total ==> SRR7171467.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1778.04 1470 38.7172 Potri.005G024800.1.v4.1 1035 795.042 282 16.6107 Potri.004G059700.1.v4.1 961 721.067 57 3.70193 Potri.007G009000.2.v4.1 1416 1176.04 0 0 Potri.003G141000.2.v4.1 2943 2703.04 731.288 12.6696 Potri.016G087400.1.v4.1 270 78.9201 1519.55 901.691 Potri.015G069301.1.v4.1 564 328.407 0 0 Potri.010G195200.1.v4.1 1773 1533.04 332 10.1417 Potri.012G127500.1.v4.1 977 737.062 15262 969.697 ==> SRR7171467.se.tsv <== Potri.001G166300.v4.1 1 Potri.001G448400.v4.1 344 Potri.001G233950.v4.1 3 Potri.001G122700.v4.1 761 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 2 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 3 Potri.001G452600.v4.1 447 SRR7171467 completed mapping pipeline successfully