Starting /dee2/code/volunteer_pipeline.sh SRR21835919 current disk space = 3088620269568 free memory = 1498741480 SRR21835919 SRAfilesize e8ab026afb2326239d7b91cf21b30e68 SRR21835919.sra SRR21835919.sra file validated SRR21835919 is paired end SRR21835919 is conventional basespace SRR21835919 read1 length is 100-150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR21835919_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 100-150 %GC 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.6995 37.0 37.0 37.0 37.0 37.0 2 36.5275 37.0 37.0 37.0 37.0 37.0 3 36.7035 37.0 37.0 37.0 37.0 37.0 4 36.7545 37.0 37.0 37.0 37.0 37.0 5 36.6855 37.0 37.0 37.0 37.0 37.0 6 36.6805 37.0 37.0 37.0 37.0 37.0 7 36.736 37.0 37.0 37.0 37.0 37.0 8 36.7675 37.0 37.0 37.0 37.0 37.0 9 36.69 37.0 37.0 37.0 37.0 37.0 10-14 36.702999999999996 37.0 37.0 37.0 37.0 37.0 15-19 36.6827 37.0 37.0 37.0 37.0 37.0 20-24 36.628600000000006 37.0 37.0 37.0 37.0 37.0 25-29 36.601699999999994 37.0 37.0 37.0 37.0 37.0 30-34 36.573499999999996 37.0 37.0 37.0 37.0 37.0 35-39 36.5011 37.0 37.0 37.0 37.0 37.0 40-44 36.5205 37.0 37.0 37.0 37.0 37.0 45-49 36.5034 37.0 37.0 37.0 37.0 37.0 50-54 36.480900000000005 37.0 37.0 37.0 37.0 37.0 55-59 36.4594 37.0 37.0 37.0 37.0 37.0 60-64 36.40690000000001 37.0 37.0 37.0 37.0 37.0 65-69 36.4079 37.0 37.0 37.0 37.0 37.0 70-74 36.4202 37.0 37.0 37.0 37.0 37.0 75-79 36.3301 37.0 37.0 37.0 37.0 37.0 80-84 36.361599999999996 37.0 37.0 37.0 37.0 37.0 85-89 36.2173 37.0 37.0 37.0 37.0 37.0 90-94 36.1995 37.0 37.0 37.0 37.0 37.0 95-99 36.255 37.0 37.0 37.0 37.0 37.0 100-104 36.15070958407564 37.0 37.0 37.0 37.0 37.0 105-109 36.18149458973265 37.0 37.0 37.0 37.0 37.0 110-114 36.15185746586941 37.0 37.0 37.0 37.0 37.0 115-119 36.03170597320506 37.0 37.0 37.0 37.0 37.0 120-124 35.97171580880138 37.0 37.0 37.0 37.0 37.0 125-129 36.02827021695303 37.0 37.0 37.0 37.0 37.0 130-134 35.96353578253935 37.0 37.0 37.0 37.0 37.0 135-139 35.85103465721007 37.0 37.0 37.0 37.0 37.0 140-144 35.8148990066894 37.0 37.0 37.0 37.0 37.0 145-149 35.749678702674565 37.0 37.0 37.0 37.0 37.0 150 35.64642196989701 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 23 1.0 24 0.0 25 3.0 26 4.0 27 4.0 28 9.0 29 11.0 30 11.0 31 33.0 32 39.0 33 57.0 34 108.0 35 305.0 36 3147.0 37 268.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 37.95 14.85 13.475000000000001 33.725 2 21.55 20.925 34.125 23.400000000000002 3 22.336168084042022 24.937468734367183 28.564282141070535 24.16208104052026 4 26.950000000000003 28.749999999999996 20.7 23.599999999999998 5 25.25 32.275 23.05 19.425 6 18.8 36.3 26.0 18.9 7 18.125 19.175 44.224999999999994 18.475 8 19.625 22.900000000000002 31.874999999999996 25.6 9 19.975 24.925 31.775 23.325000000000003 10-14 21.215 29.060000000000002 27.134999999999998 22.59 15-19 21.45 27.595 28.015 22.939999999999998 20-24 21.305 28.425 28.105000000000004 22.165000000000003 25-29 21.91 27.915 27.815 22.36 30-34 21.125 28.335 27.21 23.330000000000002 35-39 21.41 28.48 27.63 22.48 40-44 21.709999999999997 28.084999999999997 27.72 22.485 45-49 21.88 27.85 27.29 22.98 50-54 22.225 27.29 27.650000000000002 22.835 55-59 21.22 27.33 28.605000000000004 22.845 60-64 21.66 27.900000000000002 27.589999999999996 22.85 65-69 22.185 27.505000000000003 27.805000000000003 22.505 70-74 22.259999999999998 27.985 27.32 22.435 75-79 21.29 28.389999999999997 27.384999999999998 22.935 80-84 22.255 27.589999999999996 27.389999999999997 22.765 85-89 22.57 27.865000000000002 27.1 22.465 90-94 22.28 28.139999999999997 27.38 22.2 95-99 22.66 28.27 26.450000000000003 22.62 100-104 22.29126992081788 28.07457151448331 27.65360328756139 21.980555277137416 105-109 21.717908720374375 28.07829718713833 27.650581190560057 22.55321290192724 110-114 22.37127439608654 27.943920520449844 27.278228856725 22.406576226738615 115-119 21.92654052413235 27.780026307801275 27.699079226955376 22.594353941111 120-124 22.35999593454619 28.3412948470373 26.699867872751298 22.59884134566521 125-129 22.444501148252105 27.93059453942332 26.86909926001531 22.755805052309263 130-134 21.722654649733716 27.662843097091354 27.980335927898402 22.634166325276524 135-139 22.011511974509197 28.58464384828862 27.536231884057973 21.86761229314421 140-144 21.901317489020926 27.708602428313096 28.21493154223715 22.17514854042883 145-149 22.24434199497066 26.93839061190277 28.185247275775353 22.632020117351214 150 22.524425666754688 27.832057037232637 27.964087668339054 21.67942962767362 >>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 0.0 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 1.5 23 2.5 24 1.5 25 2.0 26 4.5 27 6.5 28 6.0 29 8.5 30 14.0 31 22.0 32 29.5 33 40.0 34 56.0 35 61.0 36 65.0 37 97.5 38 140.5 39 167.0 40 170.0 41 188.5 42 226.0 43 251.5 44 292.0 45 297.0 46 258.0 47 222.5 48 223.5 49 213.5 50 169.5 51 139.0 52 124.5 53 107.5 54 84.0 55 71.0 56 60.0 57 53.0 58 38.5 59 25.5 60 18.5 61 10.5 62 6.5 63 6.5 64 5.5 65 3.0 66 1.5 67 1.0 68 1.0 69 1.0 70 1.5 71 1.0 72 0.5 73 0.5 74 0.5 75 0.5 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 0.0 2 0.0 3 0.05 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 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 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 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 100-101 9.0 102-103 8.0 104-105 6.0 106-107 8.0 108-109 2.0 110-111 0.0 112-113 3.0 114-115 7.0 116-117 7.0 118-119 9.0 120-121 6.0 122-123 4.0 124-125 7.0 126-127 10.0 128-129 6.0 130-131 2.0 132-133 3.0 134-135 9.0 136-137 6.0 138-139 5.0 140-141 10.0 142-143 22.0 144-145 12.0 146-147 36.0 148-149 16.0 150-151 3787.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 76.525 #Duplication Level Percentage of deduplicated Percentage of total 1 77.29500163345313 59.150000000000006 2 16.7265599477295 25.6 3 4.4429924861156485 10.2 4 1.2414243711205488 3.8 5 0.19601437438745506 0.75 6 0.06533812479581835 0.3 7 0.0 0.0 8 0.03266906239790918 0.2 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 warn #Sequence Count Percentage Possible Source CTCGGTCACTGCTTTCCATGCCTCTGGCTTGTCAGGCCACCTTGAATAGT 8 0.2 No Hit CCTGCTTGCAGCTGCATGATTTGAAAAACTAAGCTCCAAAAATTTCCCAA 6 0.15 No Hit CTTTTTGCCCTTGCTGTCTCAGATATAGTATTGATTAACATGTGGTGTCA 6 0.15 No Hit GCCAGTTGAAGATGATAGGTGGCATCAGAATGAAGTAACAAAAGGTAACA 5 0.125 No Hit CGTTGATTAAGTTTTGGCGGGCTAAGGCATTGATCTCTAGTGTATATCTC 5 0.125 No Hit GGCGTTTCAGCACTTGCTCCCCTCTCTGAAACAGAGGAATTTGGAGGGAC 5 0.125 No Hit TTCTTGTTTCACAACTACGTGGCAAACGTTTTAAACTCCCACCTGGTCCT 5 0.125 No Hit CTCCATTTCCCAAATCGGGTCGGGTGATGTAGCTACAATACGCCCACAAC 5 0.125 No Hit GCCCCATATCCTCCAGCAGCTCTGTGCAACAGAGTTGATGGGAAGTATGT 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 10-11 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 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 82-83 0.0 0.0 0.0 0.0 0.0 84-85 0.0 0.0 0.0 0.0 0.0 86-87 0.0 0.0 0.0 0.0 0.0 88-89 0.0 0.0 0.0 0.0 0.0 90-91 0.0 0.0 0.0 0.0 0.0 92-93 0.0 0.0 0.0 0.0 0.0 94-95 0.0 0.0 0.0 0.0 0.0 96-97 0.0 0.0 0.0 0.0 0.0 98-99 0.0 0.0 0.0 0.0 0.0 100-101 0.0 0.0 0.0 0.0 0.0 102-103 0.0 0.0 0.0 0.0 0.0 104-105 0.0 0.0 0.0 0.0 0.0 106-107 0.0 0.0 0.0 0.0 0.0 108-109 0.0 0.0 0.0 0.0 0.0 110-111 0.0 0.0 0.0 0.0 0.0 112-113 0.0 0.0 0.0 0.0 0.0 114-115 0.0 0.0 0.0 0.0 0.0 116-117 0.0 0.0 0.0 0.0 0.0 118-119 0.0 0.0 0.0 0.0 0.0 120-121 0.0 0.0 0.0 0.0 0.0 122-123 0.0 0.0 0.0 0.0 0.0 124-125 0.0 0.0 0.0 0.0 0.0 126-127 0.0 0.0 0.0 0.0 0.0 128-129 0.0 0.0 0.0 0.0 0.0 130-131 0.0 0.0 0.0 0.0 0.0 132-133 0.0 0.0 0.0 0.0 0.0 134-135 0.0 0.0 0.0 0.0 0.0 136-137 0.0 0.0 0.0 0.0 0.0 138 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CTCACCA 10 0.00707415 143.3125 2 GCTCACC 10 0.00707415 143.3125 1 >>END_MODULE SRR21835919 read2 length is 100-150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR21835919_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 100-150 %GC 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.5575 37.0 37.0 37.0 37.0 37.0 2 36.5445 37.0 37.0 37.0 37.0 37.0 3 36.5725 37.0 37.0 37.0 37.0 37.0 4 36.5745 37.0 37.0 37.0 37.0 37.0 5 36.4655 37.0 37.0 37.0 37.0 37.0 6 36.582 37.0 37.0 37.0 37.0 37.0 7 36.5685 37.0 37.0 37.0 37.0 37.0 8 36.575 37.0 37.0 37.0 37.0 37.0 9 36.531 37.0 37.0 37.0 37.0 37.0 10-14 36.579600000000006 37.0 37.0 37.0 37.0 37.0 15-19 36.5746 37.0 37.0 37.0 37.0 37.0 20-24 36.49229999999999 37.0 37.0 37.0 37.0 37.0 25-29 36.3708 37.0 37.0 37.0 37.0 37.0 30-34 36.489799999999995 37.0 37.0 37.0 37.0 37.0 35-39 36.458299999999994 37.0 37.0 37.0 37.0 37.0 40-44 36.3429 37.0 37.0 37.0 37.0 37.0 45-49 36.342200000000005 37.0 37.0 37.0 37.0 37.0 50-54 36.3821 37.0 37.0 37.0 37.0 37.0 55-59 36.3168 37.0 37.0 37.0 37.0 37.0 60-64 36.283500000000004 37.0 37.0 37.0 37.0 37.0 65-69 36.266200000000005 37.0 37.0 37.0 37.0 37.0 70-74 36.2412 37.0 37.0 37.0 37.0 37.0 75-79 36.1871 37.0 37.0 37.0 37.0 37.0 80-84 36.1585 37.0 37.0 37.0 37.0 37.0 85-89 36.1514 37.0 37.0 37.0 37.0 37.0 90-94 36.1503 37.0 37.0 37.0 37.0 37.0 95-99 36.075599999999994 37.0 37.0 37.0 37.0 37.0 100-104 36.075017338265255 37.0 37.0 37.0 37.0 37.0 105-109 35.97494988185128 37.0 37.0 37.0 37.0 37.0 110-114 35.914113052257306 37.0 37.0 37.0 37.0 37.0 115-119 35.851235398712376 37.0 37.0 37.0 37.0 37.0 120-124 35.747148733642995 37.0 37.0 37.0 37.0 37.0 125-129 35.79579004466783 37.0 37.0 37.0 37.0 37.0 130-134 35.60806023711571 37.0 37.0 37.0 37.0 37.0 135-139 35.73885998040602 37.0 37.0 37.0 37.0 37.0 140-144 35.761157715154134 37.0 37.0 37.0 37.0 37.0 145-149 35.49007323112616 37.0 37.0 37.0 37.0 37.0 150 35.425666754687086 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 2.0 21 0.0 22 1.0 23 4.0 24 2.0 25 3.0 26 9.0 27 4.0 28 6.0 29 7.0 30 28.0 31 17.0 32 31.0 33 45.0 34 129.0 35 502.0 36 3051.0 37 159.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 37.275000000000006 15.675 13.15 33.900000000000006 2 20.875 22.325 33.85 22.95 3 22.175 25.074999999999996 28.675 24.075 4 26.05 29.15 20.95 23.849999999999998 5 24.4 32.824999999999996 24.025 18.75 6 19.75 34.300000000000004 25.874999999999996 20.075000000000003 7 17.45 19.725 43.25 19.575 8 19.975 23.3 31.4 25.324999999999996 9 21.625 22.625 32.45 23.3 10-14 21.584999999999997 29.134999999999998 27.46 21.82 15-19 21.47 27.57 27.735 23.225 20-24 21.69 28.335 28.249999999999996 21.725 25-29 22.105 28.134999999999998 27.71 22.05 30-34 21.475 28.08 27.76 22.685 35-39 21.785 28.199999999999996 27.825 22.189999999999998 40-44 21.985 28.349999999999998 27.485 22.18 45-49 22.095000000000002 27.865000000000002 27.615000000000002 22.425 50-54 21.310000000000002 27.435 27.915 23.34 55-59 21.64 28.365000000000002 27.345000000000002 22.650000000000002 60-64 21.560000000000002 27.845 27.700000000000003 22.895 65-69 21.69 27.639999999999997 27.36 23.31 70-74 21.33 27.445000000000004 28.17 23.055 75-79 21.81 28.000000000000004 27.939999999999998 22.25 80-84 21.615000000000002 27.85 28.16 22.375 85-89 21.7 27.950000000000003 27.665 22.685 90-94 21.584999999999997 28.244999999999997 27.72 22.45 95-99 22.035 28.22 27.700000000000003 22.045 100-104 21.41926430790819 28.20487120376867 27.94427182519795 22.431592663125187 105-109 21.55688622754491 28.158808433553062 27.575101897046245 22.709203441855784 110-114 22.083816632205355 27.87835997781028 28.029653537747745 22.008169852236623 115-119 22.245269654963067 28.26570879287666 26.98067388444804 22.508347667712233 120-124 22.080495985364365 27.90934038011993 27.355422299014126 22.654741335501573 125-129 22.189334013779025 27.542740495024244 27.28757336055116 22.980352130645574 130-134 22.444694797214257 28.185170012290044 27.632117984432607 21.73801720606309 135-139 22.35070408058382 27.21245760098674 28.02960222016651 22.407236098262924 140-144 22.392146732110564 27.16610694910876 27.6052699560837 22.836476362696978 145-149 21.819991617770327 27.939019279128246 27.95997485331098 22.28101424979044 150 22.709268550303673 26.855030367045153 28.254555056773174 22.181146025878004 >>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 0.0 14 0.0 15 0.5 16 1.0 17 0.5 18 0.0 19 0.0 20 0.0 21 0.0 22 1.0 23 1.5 24 1.0 25 1.5 26 4.0 27 5.5 28 5.0 29 6.0 30 11.5 31 17.0 32 26.5 33 40.5 34 43.0 35 58.5 36 90.0 37 110.5 38 132.5 39 165.5 40 192.0 41 205.5 42 234.5 43 269.5 44 267.5 45 271.5 46 274.0 47 254.0 48 232.5 49 214.5 50 190.0 51 137.0 52 109.0 53 94.0 54 79.0 55 65.5 56 47.0 57 40.0 58 28.0 59 23.0 60 19.5 61 11.0 62 7.5 63 4.5 64 1.5 65 1.5 66 2.0 67 1.0 68 0.5 69 0.0 70 0.0 71 0.0 72 0.0 73 0.0 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 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 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 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 100-101 9.0 102-103 8.0 104-105 6.0 106-107 8.0 108-109 2.0 110-111 0.0 112-113 3.0 114-115 7.0 116-117 7.0 118-119 9.0 120-121 6.0 122-123 4.0 124-125 7.0 126-127 10.0 128-129 6.0 130-131 2.0 132-133 3.0 134-135 9.0 136-137 6.0 138-139 5.0 140-141 10.0 142-143 22.0 144-145 12.0 146-147 36.0 148-149 16.0 150-151 3787.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 76.64999999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 77.56033920417482 59.45 2 16.601435094585778 25.45 3 4.305283757338552 9.9 4 1.1741682974559686 3.5999999999999996 5 0.228310502283105 0.8750000000000001 6 0.06523157208088715 0.3 7 0.0 0.0 8 0.03261578604044357 0.2 9 0.03261578604044357 0.22499999999999998 >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 warn #Sequence Count Percentage Possible Source CACATATAGAGGGTGTAATAGCTAAGTAGCCTGTAAGAGATGGCTTCCTC 9 0.22499999999999998 No Hit GGAATGGGGAGTTTTTCAAATTGTTGATCATGGGGTTGATGCTAAGCTGG 8 0.2 No Hit CTTCCCGGTGTGTATGGAAGGGGACTGTCTGTGAGAGGTCCCATCTCATC 6 0.15 No Hit GCTGTCTCAAACTAGCAACCTGCTCCTTGAATTGCTCTTCTTTTTCTTCA 6 0.15 No Hit GATCAAAGCGAGTGGTTACACCTCCAGTGGATGCAACTGGCAGTTGGATT 5 0.125 No Hit CTTCCATTGCAAGCAATGGCGGAAGAGTTCAATGCATGCAGGTGTGGCCT 5 0.125 No Hit GTCACCCCTTGAAGTACAACATATTCACCAAAATACCACTCGAAGGTGTA 5 0.125 No Hit GACAATTTATACCCTTACGTCCATCTCCTCCCCAACAGTAAATTATTTGT 5 0.125 No Hit ACACAGATAGAGCTCTAACATGAGCTATTGTTTCAGCTTCCAAAGCCCCA 5 0.125 No Hit AACAACTGTCATCCCTCTCAAATCCAGTAACTAATCCAATGGGAAATGCT 5 0.125 No Hit CTCCAATGTTCACCATAGACAGTGAAAACCATGTCTTGACCTTTCCCAGT 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 10-11 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 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 82-83 0.0 0.0 0.0 0.0 0.0 84-85 0.0 0.0 0.0 0.0 0.0 86-87 0.0 0.0 0.0 0.0 0.0 88-89 0.0 0.0 0.0 0.0 0.0 90-91 0.0 0.0 0.0 0.0 0.0 92-93 0.0 0.0 0.0 0.0 0.0 94-95 0.0 0.0 0.0 0.0 0.0 96-97 0.0 0.0 0.0 0.0 0.0 98-99 0.0 0.0 0.0 0.0 0.0 100-101 0.0 0.0 0.0 0.0 0.0 102-103 0.0 0.0 0.0 0.0 0.0 104-105 0.0 0.0 0.0 0.0 0.0 106-107 0.0 0.0 0.0 0.0 0.0 108-109 0.0 0.0 0.0 0.0 0.0 110-111 0.0 0.0 0.0 0.0 0.0 112-113 0.0 0.0 0.0 0.0 0.0 114-115 0.0 0.0 0.0 0.0 0.0 116-117 0.0 0.0 0.0 0.0 0.0 118-119 0.0 0.0 0.0 0.0 0.0 120-121 0.0 0.0 0.0 0.0 0.0 122-123 0.0 0.0 0.0 0.0 0.0 124-125 0.0 0.0 0.0 0.0 0.0 126-127 0.0 0.0 0.0 0.0 0.0 128-129 0.0 0.0 0.0 0.0 0.0 130-131 0.0 0.0 0.0 0.0 0.0 132-133 0.0 0.0 0.0 0.0 0.0 134-135 0.0 0.0 0.0 0.0 0.0 136-137 0.0 0.0 0.0 0.0 0.0 138 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CCAACTG 10 0.00707415 143.3125 2 ATGTAAT 10 0.00707415 143.3125 6 >>END_MODULE Read 1154566 spots for SRR21835919.sra Written 1154566 spots for SRR21835919.sra Read 1154566 spots for SRR21835919.sra Written 1154566 spots for SRR21835919.sra Read 1154566 spots for SRR21835919.sra Written 1154566 spots for SRR21835919.sra Read 1154566 spots for SRR21835919.sra Written 1154566 spots for SRR21835919.sra Read 1154566 spots for SRR21835919.sra Written 1154566 spots for SRR21835919.sra Read 1154566 spots for SRR21835919.sra Written 1154566 spots for SRR21835919.sra Read 1154566 spots for SRR21835919.sra Written 1154566 spots for SRR21835919.sra Read 1154566 spots for SRR21835919.sra Written 1154566 spots for SRR21835919.sra Read 1154566 spots for SRR21835919.sra Written 1154566 spots for SRR21835919.sra Read 1154566 spots for SRR21835919.sra Written 1154566 spots for SRR21835919.sra Read 1154566 spots for SRR21835919.sra Written 1154566 spots for SRR21835919.sra Read 1154566 spots for SRR21835919.sra Written 1154566 spots for SRR21835919.sra Read 1154566 spots for SRR21835919.sra Written 1154566 spots for SRR21835919.sra Read 1154566 spots for SRR21835919.sra Written 1154566 spots for SRR21835919.sra Read 1154566 spots for SRR21835919.sra Written 1154566 spots for SRR21835919.sra Read 1154566 spots for SRR21835919.sra Written 1154566 spots for SRR21835919.sra Read 1154566 spots for SRR21835919.sra Written 1154566 spots for SRR21835919.sra Read 1154566 spots for SRR21835919.sra Written 1154566 spots for SRR21835919.sra Read 1154566 spots for SRR21835919.sra Written 1154566 spots for SRR21835919.sra Read 1154568 spots for SRR21835919.sra Written 1154568 spots for SRR21835919.sra SRR ids: ['SRR21835919.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_u0b6e6qx SRR21835919.sra spots: 23091322 blocks: [[1, 1154566], [1154567, 2309132], [2309133, 3463698], [3463699, 4618264], [4618265, 5772830], [5772831, 6927396], [6927397, 8081962], [8081963, 9236528], [9236529, 10391094], [10391095, 11545660], [11545661, 12700226], [12700227, 13854792], [13854793, 15009358], [15009359, 16163924], [16163925, 17318490], [17318491, 18473056], [18473057, 19627622], [19627623, 20782188], [20782189, 21936754], [21936755, 23091322]] SRR21835919 file size 7732454 SRR21835919 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 SRR21835919 SRR21835919_1.fastq SRR21835919_2.fastq Input file: SRR21835919_1.fastq Paired file: SRR21835919_2.fastq trimmed: SRR21835919-trimmed-pair1.fastq, SRR21835919-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 17:40:11 2025 >> started Thu Feb 13 17:40:37 2025 >> done (26.135s) 23091322 read pairs processed; of these: 0 ( 0.00%) short read pairs filtered out after trimming by size control 1 ( 0.00%) empty read pairs filtered out after trimming by size control 23091321 (100.00%) read pairs available; of these: 1089 ( 0.00%) trimmed read pairs available after processing 23090232 (100.00%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 55 1 0.00% 56 0 0.00% 57 0 0.00% 58 0 0.00% 59 0 0.00% 60 0 0.00% 61 0 0.00% 62 0 0.00% 63 1 0.00% 64 0 0.00% 65 0 0.00% 66 0 0.00% 67 0 0.00% 68 1 0.00% 69 0 0.00% 70 0 0.00% 71 0 0.00% 72 0 0.00% 73 0 0.00% 74 1 0.00% 75 0 0.00% 76 0 0.00% 77 0 0.00% 78 0 0.00% 79 0 0.00% 80 0 0.00% 81 0 0.00% 82 0 0.00% 83 0 0.00% 84 0 0.00% 85 0 0.00% 86 0 0.00% 87 0 0.00% 88 0 0.00% 89 0 0.00% 90 1 0.00% 91 0 0.00% 92 0 0.00% 93 1 0.00% 94 0 0.00% 95 1 0.00% 96 0 0.00% 97 0 0.00% 98 2 0.00% 99 3 0.00% 100 13224 0.06% 101 14017 0.06% 102 14174 0.06% 103 14077 0.06% 104 14470 0.06% 105 15136 0.07% 106 15305 0.07% 107 15140 0.07% 108 15347 0.07% 109 15422 0.07% 110 15532 0.07% 111 16128 0.07% 112 16635 0.07% 113 16250 0.07% 114 17187 0.07% 115 17714 0.08% 116 17829 0.08% 117 17647 0.08% 118 17802 0.08% 119 17692 0.08% 120 18389 0.08% 121 19094 0.08% 122 19470 0.08% 123 19855 0.09% 124 20347 0.09% 125 20410 0.09% 126 20438 0.09% 127 20637 0.09% 128 21102 0.09% 129 21668 0.09% 130 21988 0.10% 131 22103 0.10% 132 22935 0.10% 133 23250 0.10% 134 23450 0.10% 135 24554 0.11% 136 22618 0.10% 137 25467 0.11% 138 27088 0.12% 139 28415 0.12% 140 31517 0.14% 141 39992 0.17% 142 50353 0.22% 143 104252 0.45% 144 31123 0.13% 145 61075 0.26% 146 186776 0.81% 147 25735 0.11% 148 26000 0.11% 149 26278 0.11% 150 21748202 94.18% 23091321 reads passed initial QC criterion=sequence-density sequence-density=0.28 sequence-density-rank=1 fanout-score=1.98 fanout-score-rank=30 prefix-density=0.28 prefix-fanout=2.0 sequence=TGAGATGCCTCAGTGCATCCAAACATGGGTAG criterion=fanout-score sequence-density=0.01 sequence-density-rank=32 fanout-score=92.46 fanout-score-rank=1 prefix-density=0.10 prefix-fanout=7.7 sequence=CAAAACCACATATAGAGGGTGTAATAGCTAAGTAGCCTGTAAGAGATGGCTTCCTCTGTGATTTCATCGGCGGCCGTTGCCACAGTTAACCGCACCCCTGCACAGGCCAACATGGTTGCACCATTCAACGGCCTCAAGTCTACCTCAGCTTTCCCGGTCACCAGAAAGGCTAACAATGACATTACTTCCATTGCAAGCAATGGCGGAAGAGTTCAATGCATGCAGGTGTGGCCTCCAACTGGATTGAAGAAGTTCGAGACTCTTTCTTACCTTCCAGATCTCAC criterion=sequence-density sequence-density=0.22 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=28 prefix-density=0.21 prefix-fanout=2.0 sequence=GTTAGGGTAAGCTTTCTT criterion=fanout-score sequence-density=0.11 sequence-density-rank=23 fanout-score=82.81 fanout-score-rank=1 prefix-density=0.42 prefix-fanout=21.4 sequence=CAGCAGCAGCAAGCACAAGCTCTGGCTGTAGACTGAATGT SRR21835919 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 13 17:41:14 Started mapping on | Feb 13 17:41:15 Finished on | Feb 13 17:43:28 Mapping speed, Million of reads per hour | 625.03 Number of input reads | 23091321 Average input read length | 297 UNIQUE READS: Uniquely mapped reads number | 21709447 Uniquely mapped reads % | 94.02% Average mapped length | 295.77 Number of splices: Total | 21691321 Number of splices: Annotated (sjdb) | 21292696 Number of splices: GT/AG | 21301439 Number of splices: GC/AG | 326426 Number of splices: AT/AC | 14466 Number of splices: Non-canonical | 48990 Mismatch rate per base, % | 0.28% Deletion rate per base | 0.01% Deletion average length | 2.74 Insertion rate per base | 0.01% Insertion average length | 2.17 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 524364 % of reads mapped to multiple loci | 2.27% Number of reads mapped to too many loci | 65723 % of reads mapped to too many loci | 0.28% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.36% % of reads unmapped: other | 0.07% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 857510 857510 857510 N_multimapping 524364 524364 524364 N_noFeature 647865 11301541 10912767 N_ambiguous 257927 56885 58463 UnstrandedReadsAssigned:20803655 PositiveStrandReadsAssigned:10351021 NegativeStrandReadsAssigned:10738217 Dataset is classified unstranded MeadianReadLen=150 20thPercentileLength=150 echo kmer=145 SRR21835919 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: SRR21835919-trimmed-pair1.fastq SRR21835919-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 23,091,321 reads, 21,235,852 reads pseudoaligned [quant] estimated average fragment length: 270.301 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,204 rounds 52401 SRR21835919.ke.tsv 34699 SRR21835919.se.tsv 87100 total ==> SRR21835919.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1748.7 677 17.3259 Potri.005G024800.1.v4.1 1035 765.699 153 8.94241 Potri.004G059700.1.v4.1 961 691.712 73 4.72301 Potri.007G009000.2.v4.1 1416 1146.7 0 0 Potri.003G141000.2.v4.1 2943 2673.7 571.219 9.56118 Potri.016G087400.1.v4.1 270 62.7511 875 624.033 Potri.015G069301.1.v4.1 564 295.449 0 0 Potri.010G195200.1.v4.1 1773 1503.7 18 0.535714 Potri.012G127500.1.v4.1 977 707.712 4082 258.129 ==> SRR21835919.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 362 Potri.001G233950.v4.1 1 Potri.001G122700.v4.1 205 Potri.001G212900.v4.1 140 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 332 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 10 SRR21835919 completed mapping pipeline successfully