Starting /dee2/code/volunteer_pipeline.sh SRR6941613 current disk space = 1551173799936 free memory = 1597594932 SRR6941613 SRAfilesize 3d4ccc834c5239f15c8f221fe913450d SRR6941613.sra SRR6941613.sra file validated SRR6941613 is paired end SRR6941613 is conventional basespace SRR6941613 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6941613_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 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.9395 34.0 33.0 34.0 32.0 34.0 2 32.85225 34.0 33.0 34.0 32.0 34.0 3 32.92 34.0 33.0 34.0 32.0 34.0 4 33.01825 34.0 33.0 34.0 32.0 34.0 5 33.1995 34.0 33.0 34.0 32.0 34.0 6 36.85775 38.0 37.0 38.0 35.0 38.0 7 37.29925 38.0 38.0 38.0 36.0 38.0 8 37.36175 38.0 38.0 38.0 37.0 38.0 9 37.386 38.0 38.0 38.0 37.0 38.0 10-14 37.388549999999995 38.0 38.0 38.0 37.0 38.0 15-19 37.435649999999995 38.0 38.0 38.0 37.2 38.0 20-24 37.40075 38.0 38.0 38.0 37.4 38.0 25-29 37.286500000000004 38.0 38.0 38.0 37.0 38.0 30-34 37.2762 38.0 38.0 38.0 37.0 38.0 35-39 37.2976 38.0 38.0 38.0 37.0 38.0 40-44 37.2963 38.0 38.0 38.0 37.0 38.0 45-49 37.360350000000004 38.0 38.0 38.0 37.0 38.0 50-54 37.31885 38.0 38.0 38.0 37.0 38.0 55-59 37.2704 38.0 38.0 38.0 37.0 38.0 60-64 37.21339999999999 38.0 38.0 38.0 36.4 38.0 65-69 36.97305 38.0 38.0 38.0 35.8 38.0 70-74 37.0286 38.0 38.0 38.0 36.0 38.0 75-79 37.0552 38.0 38.0 38.0 36.0 38.0 80-84 36.97025 38.0 38.0 38.0 35.8 38.0 85-89 36.8462 38.0 38.0 38.0 35.2 38.0 90-94 36.7935 38.0 38.0 38.0 34.8 38.0 95-99 36.775349999999996 38.0 38.0 38.0 35.0 38.0 100-104 36.589999999999996 38.0 38.0 38.0 34.2 38.0 105-109 36.335899999999995 38.0 37.8 38.0 33.8 38.0 110-114 36.120050000000006 38.0 38.0 38.0 33.6 38.0 115-119 36.1822 38.0 37.8 38.0 33.6 38.0 120-124 36.167249999999996 38.0 37.8 38.0 33.6 38.0 125-129 36.09465 38.0 37.6 38.0 33.2 38.0 130-134 36.02845000000001 38.0 37.2 38.0 33.0 38.0 135-139 35.7496 38.0 36.0 38.0 32.8 38.0 140-144 35.4323 38.0 36.0 38.0 31.0 38.0 145-149 34.9063 38.0 35.4 38.0 30.2 38.0 150-151 30.844749999999998 35.5 29.0 38.0 15.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 3 1.0 4 0.0 5 0.0 6 0.0 7 0.0 8 1.0 9 0.0 10 1.0 11 0.0 12 0.0 13 1.0 14 0.0 15 1.0 16 2.0 17 2.0 18 1.0 19 4.0 20 1.0 21 3.0 22 3.0 23 4.0 24 12.0 25 7.0 26 14.0 27 14.0 28 22.0 29 32.0 30 38.0 31 52.0 32 66.0 33 83.0 34 140.0 35 230.0 36 533.0 37 2732.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 46.54234654234654 10.023310023310025 7.044807044807044 36.38953638953639 2 21.675 12.325 35.525 30.475 3 20.035017508754375 16.333166583291643 25.962981490745374 37.6688344172086 4 25.85 23.125 21.525 29.5 5 26.0 29.075 22.575 22.35 6 23.375 31.624999999999996 23.45 21.55 7 16.775000000000002 25.0 36.95 21.275 8 19.5 25.025 29.875 25.6 9 20.525 21.025 32.45 26.0 10-14 22.939999999999998 26.55 25.22 25.290000000000003 15-19 23.286164308215408 24.88124406220311 26.226311315565777 25.6062803140157 20-24 23.294999999999998 25.650000000000002 25.895000000000003 25.16 25-29 23.466173308665432 25.6262813140657 25.73628681434072 25.171258562928145 30-34 23.51117555877794 24.911245562278115 25.556277813890695 26.021301065053255 35-39 23.397339733973396 25.15751575157516 25.962596259625965 25.48254825482548 40-44 23.13231323132313 25.557555755575557 26.022602260226023 25.28752875287529 45-49 22.93 24.975 25.590000000000003 26.505000000000003 50-54 22.82 25.485000000000003 25.485000000000003 26.21 55-59 23.24 25.169999999999998 26.119999999999997 25.47 60-64 23.06 25.345000000000002 25.465 26.13 65-69 23.1 25.259999999999998 25.46 26.179999999999996 70-74 23.257325732573257 25.30753075307531 25.397539753975394 26.037603760376037 75-79 24.08 24.81 25.695 25.415 80-84 23.462346234623464 25.237523752375235 25.452545254525454 25.84758475847585 85-89 23.546177308865442 25.54127706385319 25.29626481324066 25.616280814040703 90-94 23.955000000000002 25.635 25.385 25.025 95-99 23.575 24.9 25.765 25.759999999999998 100-104 23.36168084042021 25.237618809404704 26.063031515757878 25.337668834417208 105-109 23.445 25.480000000000004 24.955 26.119999999999997 110-114 23.56866877414823 25.385117165939086 25.30483215414722 25.741381905765465 115-119 23.656667835144475 25.664780409634936 25.32425259151685 25.354299163703743 120-124 24.164331465172136 25.255204163330664 24.864891913530823 25.715572457966374 125-129 23.655 25.415 24.845 26.085 130-134 23.345 25.480000000000004 24.795 26.38 135-139 23.825 25.224999999999998 24.89 26.06 140-144 23.630000000000003 25.1 24.955 26.314999999999998 145-149 23.49 25.665 24.8 26.045 150-151 23.7875 25.7375 24.4875 25.9875 >>END_MODULE >>Per sequence GC content fail #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 0.5 25 1.5 26 2.0 27 2.0 28 3.5 29 6.0 30 10.5 31 8.5 32 6.0 33 19.5 34 29.5 35 41.0 36 59.0 37 74.0 38 84.0 39 104.0 40 135.5 41 151.0 42 159.0 43 168.5 44 179.5 45 189.0 46 194.5 47 189.5 48 177.5 49 174.0 50 172.0 51 163.5 52 142.5 53 115.0 54 100.0 55 102.0 56 105.5 57 95.5 58 93.5 59 94.0 60 89.5 61 78.5 62 60.0 63 57.0 64 58.0 65 48.5 66 40.0 67 44.0 68 37.5 69 25.0 70 22.0 71 21.0 72 21.5 73 15.0 74 10.0 75 8.5 76 5.0 77 2.5 78 1.5 79 1.0 80 0.5 81 0.5 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 3.4750000000000005 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 0.005 20-24 0.0 25-29 0.005 30-34 0.005 35-39 0.01 40-44 0.01 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.01 75-79 0.0 80-84 0.01 85-89 0.005 90-94 0.0 95-99 0.0 100-104 0.05 105-109 0.0 110-114 0.35500000000000004 115-119 0.155 120-124 0.08 125-129 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 99.2 #Duplication Level Percentage of deduplicated Percentage of total 1 99.29435483870968 98.5 2 0.6300403225806451 1.25 3 0.05040322580645161 0.15 4 0.025201612903225805 0.1 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 fail #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 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.05 0.0 0.0 0.0 0.0 66-67 0.05 0.0 0.0 0.0 0.0 68-69 0.0875 0.0 0.0 0.0 0.0 70-71 0.125 0.0 0.0 0.0 0.0 72-73 0.16249999999999998 0.0 0.0 0.0 0.0 74-75 0.21250000000000002 0.0 0.0 0.0 0.0 76-77 0.30000000000000004 0.0 0.0 0.0 0.0 78-79 0.325 0.0 0.0 0.0 0.0 80-81 0.4 0.0 0.0 0.0 0.0 82-83 0.4875 0.0 0.0 0.0 0.0 84-85 0.525 0.0 0.0 0.0 0.0 86-87 0.6375 0.0 0.0 0.0 0.0 88-89 0.775 0.0 0.0 0.0 0.0 90-91 0.95 0.0 0.0 0.0 0.0 92-93 1.225 0.0 0.0 0.0 0.0 94-95 1.5125 0.0 0.0 0.0 0.0 96-97 1.725 0.0 0.0 0.0 0.0 98-99 1.925 0.0 0.0 0.0 0.0 100-101 2.2 0.0 0.0 0.0 0.0 102-103 2.4125 0.0 0.0 0.0 0.0 104-105 2.7125 0.0 0.0 0.0 0.0 106-107 2.9875 0.0 0.0 0.0 0.0 108-109 3.3875 0.0 0.0 0.0 0.0 110-111 3.875 0.0 0.0 0.0 0.0 112-113 4.35 0.0 0.0 0.0 0.0 114-115 4.9125 0.0 0.0 0.0 0.0 116-117 5.6375 0.0 0.0 0.0 0.0 118-119 6.15 0.0 0.0 0.0 0.0 120-121 6.775 0.0 0.0 0.0 0.0 122-123 7.4375 0.0 0.0 0.0 0.0 124-125 8.1 0.0 0.0 0.0 0.0 126-127 8.65 0.0 0.0 0.0 0.0 128-129 9.275 0.0 0.0 0.0 0.0 130-131 10.1 0.0 0.0 0.0 0.0 132-133 10.7625 0.0 0.0 0.0 0.0 134-135 11.625 0.0 0.0 0.0 0.0 136-137 12.325 0.0 0.0 0.0 0.0 138-139 13.375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR6941613 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6941613_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 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.87275 33.0 33.0 34.0 32.0 34.0 2 32.98175 34.0 33.0 34.0 32.0 34.0 3 33.0535 34.0 33.0 34.0 32.0 34.0 4 33.02575 34.0 33.0 34.0 32.0 34.0 5 33.063 34.0 33.0 34.0 33.0 34.0 6 37.248 38.0 38.0 38.0 37.0 38.0 7 37.23225 38.0 38.0 38.0 37.0 38.0 8 37.18575 38.0 38.0 38.0 37.0 38.0 9 37.16675 38.0 38.0 38.0 37.0 38.0 10-14 37.21095 38.0 38.0 38.0 37.0 38.0 15-19 37.14735 38.0 38.0 38.0 37.0 38.0 20-24 37.1438 38.0 38.0 38.0 37.0 38.0 25-29 37.12035 38.0 38.0 38.0 37.0 38.0 30-34 37.09765 38.0 38.0 38.0 37.0 38.0 35-39 37.023999999999994 38.0 38.0 38.0 36.6 38.0 40-44 37.039950000000005 38.0 38.0 38.0 36.6 38.0 45-49 37.0429 38.0 38.0 38.0 36.2 38.0 50-54 37.0207 38.0 38.0 38.0 36.2 38.0 55-59 36.877950000000006 38.0 38.0 38.0 36.0 38.0 60-64 36.8597 38.0 38.0 38.0 36.0 38.0 65-69 36.69725 38.0 38.0 38.0 35.2 38.0 70-74 36.81675 38.0 38.0 38.0 35.6 38.0 75-79 36.7711 38.0 38.0 38.0 35.0 38.0 80-84 36.623 38.0 38.0 38.0 35.0 38.0 85-89 36.6082 38.0 38.0 38.0 35.0 38.0 90-94 36.493550000000006 38.0 38.0 38.0 34.6 38.0 95-99 36.293400000000005 38.0 38.0 38.0 34.0 38.0 100-104 36.18915 38.0 38.0 38.0 34.0 38.0 105-109 35.78435 38.0 37.6 38.0 32.6 38.0 110-114 35.191700000000004 38.0 36.0 38.0 28.4 38.0 115-119 35.2916 38.0 36.0 38.0 30.4 38.0 120-124 35.11560000000001 38.0 35.8 38.0 29.2 38.0 125-129 35.10965 38.0 36.0 38.0 29.4 38.0 130-134 35.1388 38.0 36.0 38.0 30.0 38.0 135-139 34.6133 38.0 35.4 38.0 27.6 38.0 140-144 33.990700000000004 38.0 33.2 38.0 24.4 38.0 145-149 32.925349999999995 38.0 33.0 38.0 14.8 38.0 150-151 26.981499999999997 33.0 17.5 37.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 4.0 3 2.0 4 3.0 5 0.0 6 3.0 7 0.0 8 2.0 9 3.0 10 2.0 11 1.0 12 0.0 13 0.0 14 3.0 15 4.0 16 7.0 17 5.0 18 9.0 19 10.0 20 3.0 21 5.0 22 5.0 23 10.0 24 14.0 25 17.0 26 22.0 27 24.0 28 25.0 29 44.0 30 46.0 31 57.0 32 70.0 33 109.0 34 172.0 35 246.0 36 617.0 37 2456.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 42.275 20.0 9.075 28.65 2 28.375 24.025 29.599999999999998 18.0 3 22.425 26.325 27.825 23.425 4 27.450000000000003 30.475 20.225 21.85 5 28.025 33.275 19.225 19.475 6 23.10577644411103 36.084021005251316 20.830207551887973 19.979994998749685 7 23.474999999999998 19.675 33.225 23.625 8 22.900000000000002 24.0 24.925 28.175 9 23.549999999999997 23.849999999999998 27.075 25.525 10-14 25.89 26.505000000000003 23.46 24.145 15-19 25.7 25.64 24.605 24.055 20-24 25.590000000000003 25.795 24.55 24.065 25-29 25.629999999999995 26.115 23.995 24.26 30-34 26.02 25.36 24.645 23.974999999999998 35-39 25.474999999999998 25.385 24.86 24.279999999999998 40-44 25.64 25.615 24.34 24.404999999999998 45-49 25.895000000000003 25.685000000000002 24.3 24.12 50-54 25.765 25.874999999999996 24.59 23.77 55-59 26.07 25.25 24.5 24.18 60-64 26.06 24.759999999999998 25.095 24.085 65-69 26.125 25.19 24.87 23.815 70-74 25.485000000000003 25.380000000000003 24.93 24.205 75-79 25.985000000000003 25.11 24.895 24.01 80-84 25.55511102220444 25.45509101820364 24.64492898579716 24.34486897379476 85-89 26.08630431521576 25.416270813540677 24.846242312115603 23.651182559127957 90-94 25.757575757575758 25.682568256825682 24.437443744374438 24.122412241224122 95-99 25.738860829124366 25.473821073160973 24.948742311346702 23.838575786367954 100-104 26.405 25.840000000000003 24.755 23.0 105-109 26.3 25.305 24.525 23.87 110-114 26.345000000000002 25.945 24.435000000000002 23.275000000000002 115-119 26.724999999999998 26.479999999999997 24.04 22.755 120-124 26.784999999999997 26.040000000000003 24.22 22.955000000000002 125-129 27.694999999999997 26.16 23.82 22.325 130-134 27.787778777877786 26.15261526152615 24.157415741574155 21.902190219021904 135-139 28.11781178117812 26.62266226622662 23.75237523752375 21.507150715071507 140-144 28.274137068534266 26.503251625812908 24.032016008004 21.190595297648823 145-149 28.79151660664266 26.705682272909165 23.519407763105242 20.983393357342937 150-151 29.991248906113267 27.015876984623077 23.24040505063133 19.75246905863233 >>END_MODULE >>Per sequence GC content fail #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 0.5 22 1.0 23 1.0 24 0.5 25 2.0 26 3.5 27 3.0 28 3.0 29 5.0 30 10.0 31 10.0 32 12.0 33 22.5 34 30.0 35 34.5 36 45.5 37 62.0 38 75.5 39 88.0 40 103.5 41 134.0 42 168.5 43 177.5 44 174.0 45 183.5 46 192.0 47 182.5 48 175.5 49 177.5 50 155.5 51 143.0 52 143.5 53 117.0 54 110.0 55 117.0 56 105.0 57 96.0 58 101.5 59 96.0 60 88.5 61 83.5 62 79.5 63 72.0 64 59.0 65 53.0 66 47.5 67 43.5 68 44.5 69 42.0 70 31.0 71 26.5 72 19.0 73 11.0 74 13.0 75 10.5 76 3.5 77 2.5 78 2.5 79 2.0 80 1.0 81 0.0 82 0.0 83 1.0 84 1.0 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 0.025 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 0.02 85-89 0.005 90-94 0.01 95-99 0.015 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.01 135-139 0.01 140-144 0.05 145-149 0.04 150-151 0.0125 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 98.2 #Duplication Level Percentage of deduplicated Percentage of total 1 98.82892057026477 97.05 2 0.8655804480651732 1.7000000000000002 3 0.12729124236252545 0.375 4 0.10183299389002036 0.4 5 0.02545824847250509 0.125 6 0.02545824847250509 0.15 7 0.0 0.0 8 0.02545824847250509 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 AGCACACACAAGCCTAGAAGCCTTCAGCTTAATCTTCTTCCTAAGCAAGT 8 0.2 No Hit CTTGATCATCTGAAAAATCTTAATCCAGATCAGACCAAGCAGAGCAGAGA 6 0.15 No Hit CACAGGCAAAACACAGCTGATTCGTGTACTCGATCTCCCCAGCAAGTTAA 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.025 0.0 0.0 0.0 0.0 2 0.025 0.0 0.0 0.0 0.0 3 0.025 0.0 0.0 0.0 0.0 4 0.025 0.0 0.0 0.0 0.0 5 0.025 0.0 0.0 0.0 0.0 6 0.025 0.0 0.0 0.0 0.0 7 0.025 0.0 0.0 0.0 0.0 8 0.025 0.0 0.0 0.0 0.0 9 0.025 0.0 0.0 0.0 0.0 10-11 0.025 0.0 0.0 0.0 0.0 12-13 0.025 0.0 0.0 0.0 0.0 14-15 0.025 0.0 0.0 0.0 0.0 16-17 0.025 0.0 0.0 0.0 0.0 18-19 0.025 0.0 0.0 0.0 0.0 20-21 0.025 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.075 0.0 0.0 0.0 0.0 62-63 0.075 0.0 0.0 0.0 0.0 64-65 0.075 0.0 0.0 0.0 0.0 66-67 0.075 0.0 0.0 0.0 0.0 68-69 0.1125 0.0 0.0 0.0 0.0 70-71 0.15 0.0 0.0 0.0 0.0 72-73 0.1875 0.0 0.0 0.0 0.0 74-75 0.2375 0.0 0.0 0.0 0.0 76-77 0.32499999999999996 0.0 0.0 0.0 0.0 78-79 0.35 0.0 0.0 0.0 0.0 80-81 0.42500000000000004 0.0 0.0 0.0 0.0 82-83 0.5125 0.0 0.0 0.0 0.0 84-85 0.55 0.0 0.0 0.0 0.0 86-87 0.6625 0.0 0.0 0.0 0.0 88-89 0.825 0.0 0.0 0.0 0.0 90-91 1.0 0.0 0.0 0.0 0.0 92-93 1.275 0.0 0.0 0.0 0.0 94-95 1.5875 0.0 0.0 0.0 0.0 96-97 1.7999999999999998 0.0 0.0 0.0 0.0 98-99 2.0 0.0 0.0 0.0 0.0 100-101 2.3 0.0 0.0 0.0 0.0 102-103 2.525 0.0 0.0 0.0 0.0 104-105 2.875 0.0 0.0 0.0 0.0 106-107 3.1375 0.0 0.0 0.0 0.0 108-109 3.5374999999999996 0.0 0.0 0.0 0.0 110-111 4.0 0.0 0.0 0.0 0.0 112-113 4.5 0.0 0.0 0.0 0.0 114-115 5.1125 0.0 0.0 0.0 0.0 116-117 5.8 0.0 0.0 0.0 0.0 118-119 6.3 0.0 0.0 0.0 0.0 120-121 6.9 0.0 0.0 0.0 0.0 122-123 7.5625 0.0 0.0 0.0 0.0 124-125 8.212499999999999 0.0 0.0 0.0 0.0 126-127 8.7375 0.0 0.0 0.0 0.0 128-129 9.4 0.0 0.0 0.0 0.0 130-131 10.212499999999999 0.0 0.0 0.0 0.0 132-133 10.8625 0.0 0.0 0.0 0.0 134-135 11.7125 0.0 0.0 0.0 0.0 136-137 12.350000000000001 0.0 0.0 0.0 0.0 138-139 13.325 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GTGAAAG 10 0.006830828 145.0 1 >>END_MODULE Read 1288406 spots for SRR6941613.sra Written 1288406 spots for SRR6941613.sra Read 1288406 spots for SRR6941613.sra Written 1288406 spots for SRR6941613.sra Read 1288406 spots for SRR6941613.sra Written 1288406 spots for SRR6941613.sra Read 1288406 spots for SRR6941613.sra Written 1288406 spots for SRR6941613.sra Read 1288406 spots for SRR6941613.sra Written 1288406 spots for SRR6941613.sra Read 1288406 spots for SRR6941613.sra Written 1288406 spots for SRR6941613.sra Read 1288423 spots for SRR6941613.sra Written 1288423 spots for SRR6941613.sra Read 1288406 spots for SRR6941613.sra Written 1288406 spots for SRR6941613.sra Read 1288406 spots for SRR6941613.sra Written 1288406 spots for SRR6941613.sra Read 1288406 spots for SRR6941613.sra Written 1288406 spots for SRR6941613.sra Read 1288406 spots for SRR6941613.sra Written 1288406 spots for SRR6941613.sra Read 1288406 spots for SRR6941613.sra Written 1288406 spots for SRR6941613.sra Read 1288406 spots for SRR6941613.sra Written 1288406 spots for SRR6941613.sra Read 1288406 spots for SRR6941613.sra Written 1288406 spots for SRR6941613.sra Read 1288406 spots for SRR6941613.sra Written 1288406 spots for SRR6941613.sra Read 1288406 spots for SRR6941613.sra Written 1288406 spots for SRR6941613.sra Read 1288406 spots for SRR6941613.sra Written 1288406 spots for SRR6941613.sra Read 1288406 spots for SRR6941613.sra Written 1288406 spots for SRR6941613.sra Read 1288406 spots for SRR6941613.sra Written 1288406 spots for SRR6941613.sra Read 1288406 spots for SRR6941613.sra Written 1288406 spots for SRR6941613.sra SRR ids: ['SRR6941613.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_1oiazzim SRR6941613.sra spots: 25768137 blocks: [[1, 1288406], [1288407, 2576812], [2576813, 3865218], [3865219, 5153624], [5153625, 6442030], [6442031, 7730436], [7730437, 9018842], [9018843, 10307248], [10307249, 11595654], [11595655, 12884060], [12884061, 14172466], [14172467, 15460872], [15460873, 16749278], [16749279, 18037684], [18037685, 19326090], [19326091, 20614496], [20614497, 21902902], [21902903, 23191308], [23191309, 24479714], [24479715, 25768137]] SRR6941613 file size 8710275 SRR6941613 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 SRR6941613 SRR6941613_1.fastq SRR6941613_2.fastq Input file: SRR6941613_1.fastq Paired file: SRR6941613_2.fastq trimmed: SRR6941613-trimmed-pair1.fastq, SRR6941613-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 Fri Dec 6 13:12:24 2024 >> started Fri Dec 6 13:12:54 2024 >> done (30.394s) 25768137 read pairs processed; of these: 15183 ( 0.06%) short read pairs filtered out after trimming by size control 30640 ( 0.12%) empty read pairs filtered out after trimming by size control 25722314 (99.82%) read pairs available; of these: 13808584 (53.68%) trimmed read pairs available after processing 11913730 (46.32%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 10 0.00% 19 8 0.00% 20 15 0.00% 21 16 0.00% 22 14 0.00% 23 13 0.00% 24 20 0.00% 25 15 0.00% 26 25 0.00% 27 14 0.00% 28 23 0.00% 29 31 0.00% 30 26 0.00% 31 25 0.00% 32 25 0.00% 33 25 0.00% 34 36 0.00% 35 29 0.00% 36 50 0.00% 37 44 0.00% 38 37 0.00% 39 57 0.00% 40 64 0.00% 41 69 0.00% 42 69 0.00% 43 68 0.00% 44 83 0.00% 45 112 0.00% 46 121 0.00% 47 150 0.00% 48 145 0.00% 49 191 0.00% 50 191 0.00% 51 234 0.00% 52 295 0.00% 53 318 0.00% 54 353 0.00% 55 383 0.00% 56 450 0.00% 57 514 0.00% 58 584 0.00% 59 713 0.00% 60 834 0.00% 61 944 0.00% 62 1079 0.00% 63 1232 0.00% 64 1435 0.01% 65 1596 0.01% 66 1809 0.01% 67 1988 0.01% 68 2361 0.01% 69 2691 0.01% 70 3112 0.01% 71 3666 0.01% 72 4260 0.02% 73 4841 0.02% 74 5312 0.02% 75 6100 0.02% 76 6711 0.03% 77 7415 0.03% 78 8365 0.03% 79 9408 0.04% 80 10322 0.04% 81 11646 0.05% 82 13463 0.05% 83 14458 0.06% 84 17199 0.07% 85 18996 0.07% 86 20648 0.08% 87 22048 0.09% 88 24419 0.09% 89 25325 0.10% 90 27466 0.11% 91 29489 0.11% 92 31347 0.12% 93 33649 0.13% 94 36471 0.14% 95 38564 0.15% 96 40777 0.16% 97 42621 0.17% 98 44239 0.17% 99 46129 0.18% 100 49189 0.19% 101 50902 0.20% 102 53652 0.21% 103 55938 0.22% 104 57970 0.23% 105 60544 0.24% 106 63829 0.25% 107 64679 0.25% 108 67066 0.26% 109 70141 0.27% 110 70733 0.27% 111 72747 0.28% 112 75971 0.30% 113 78911 0.31% 114 80962 0.31% 115 84699 0.33% 116 86958 0.34% 117 88727 0.34% 118 88969 0.35% 119 90088 0.35% 120 92573 0.36% 121 94152 0.37% 122 96345 0.37% 123 100316 0.39% 124 103199 0.40% 125 104584 0.41% 126 107524 0.42% 127 108570 0.42% 128 110869 0.43% 129 115138 0.45% 130 116270 0.45% 131 118706 0.46% 132 121027 0.47% 133 126424 0.49% 134 129988 0.51% 135 135510 0.53% 136 139240 0.54% 137 143619 0.56% 138 150022 0.58% 139 159126 0.62% 140 164505 0.64% 141 175699 0.68% 142 190752 0.74% 143 208109 0.81% 144 235946 0.92% 145 271491 1.06% 146 323200 1.26% 147 415873 1.62% 148 587833 2.29% 149 1114965 4.33% 150 5704234 22.18% 151 11913730 46.32% 25722314 reads passed initial QC criterion=sequence-density sequence-density=0.69 sequence-density-rank=1 fanout-score=3.16 fanout-score-rank=17 prefix-density=0.75 prefix-fanout=2.9 sequence=GGTGTTGTCGAAGCCGATGATGCGGAC criterion=fanout-score sequence-density=0.05 sequence-density-rank=23 fanout-score=139.80 fanout-score-rank=1 prefix-density=0.60 prefix-fanout=10.7 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.41 sequence-density-rank=1 fanout-score=2.03 fanout-score-rank=27 prefix-density=0.41 prefix-fanout=2.0 sequence=GAAGATGTCTTGC criterion=fanout-score sequence-density=0.04 sequence-density-rank=27 fanout-score=27.46 fanout-score-rank=1 prefix-density=0.20 prefix-fanout=5.0 sequence=GCAGCAGCCATTACTTGATCATCTGAAAAATCTTAATCCAGATCAGACCAAGCAGAGCAGAGATGTCTGCTACCTTCTCGTCCACCGTCGGAGCTCCGGCTTCTACGCCAACCAGCTTCCTTGGGAAGAAGCTCAAGAAGCAGGTGACCTCGGCCGTGAACTACCATGGCAAGAGCACCAAGGCCAACAGATTCACAGTCATGGCCAAGGAGGTGGACGAGTCAAAGCAGACTGACCAGGACAGGTGGAAGGGCCTCGCCTACGATATCTCCGACGACCAGCAGGACATCACCAGGGGGAAGGGTATCGTCGACTCGCTCTTCCAGGCGCCCATGGGCGACGGTACCCACGTGGCCGTCCTCAGCTCCCAAGAGTACATCAGCCAGGGCCTAAGGAAGTACGACTTCGACAACA SRR6941613 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 06 13:14:21 Started mapping on | Dec 06 13:14:21 Finished on | Dec 06 13:18:18 Mapping speed, Million of reads per hour | 390.72 Number of input reads | 25722314 Average input read length | 281 UNIQUE READS: Uniquely mapped reads number | 20759961 Uniquely mapped reads % | 80.71% Average mapped length | 282.73 Number of splices: Total | 22906716 Number of splices: Annotated (sjdb) | 21539219 Number of splices: GT/AG | 22558940 Number of splices: GC/AG | 267431 Number of splices: AT/AC | 9536 Number of splices: Non-canonical | 70809 Mismatch rate per base, % | 0.47% Deletion rate per base | 0.03% Deletion average length | 2.55 Insertion rate per base | 0.03% Insertion average length | 2.58 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 375192 % of reads mapped to multiple loci | 1.46% Number of reads mapped to too many loci | 91330 % of reads mapped to too many loci | 0.36% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 16.20% % of reads unmapped: other | 1.28% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 4602683 4602683 4602683 N_multimapping 375192 375192 375192 N_noFeature 858501 20038092 1085296 N_ambiguous 626070 4152 133328 UnstrandedReadsAssigned:19275390 PositiveStrandReadsAssigned:717717 NegativeStrandReadsAssigned:19541337 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=146 echo kmer=141 SRR6941613 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: 52,972 [index] number of k-mers: 66,720,672 [index] number of equivalence classes: 111,837 [quant] running in paired-end mode [quant] will process pair 1: SRR6941613-trimmed-pair1.fastq SRR6941613-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 25,722,314 reads, 22,717,902 reads pseudoaligned [quant] estimated average fragment length: 226.773 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,232 rounds 52973 SRR6941613.ke.tsv 35125 SRR6941613.se.tsv 88098 total ==> SRR6941613.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 710.761 66.2329 6.2583 PNS24247 1044 818.227 63.0649 5.17632 PNS24249 1928 1702.23 64.0858 2.52843 PNS24246 1044 818.227 63.0649 5.17632 PNS24248 1044 818.227 63.0649 5.17632 PNS24244 1471 1245.23 69.4865 3.74765 PNS24243 293 113.322 0 0 KQK14069 1603 1377.23 3949.14 192.577 KQK14071 474 263.332 72.2305 18.4215 ==> SRR6941613.se.tsv <== BRADI_1g14170v3 3324 BRADI_1g53295v3 674 BRADI_1g59795v3 180 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 506 BRADI_1g74790v3 106 BRADI_1g09890v3 0 BRADI_1g77505v3 265 BRADI_1g48960v3 0 SRR6941613 completed mapping pipeline successfully