Starting /dee2/code/volunteer_pipeline.sh SRR28623285 current disk space = 3049867579392 free memory = 1575387672 SRR28623285 SRAfilesize fca216437fbb46c0ec71b11e00dc516b SRR28623285.sra SRR28623285.sra file validated SRR28623285 is paired end SRR28623285 is conventional basespace SRR28623285 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR28623285_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 43 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.24725 37.0 37.0 37.0 37.0 37.0 2 36.398 37.0 37.0 37.0 37.0 37.0 3 36.5825 37.0 37.0 37.0 37.0 37.0 4 36.609 37.0 37.0 37.0 37.0 37.0 5 36.606 37.0 37.0 37.0 37.0 37.0 6 36.6685 37.0 37.0 37.0 37.0 37.0 7 36.501 37.0 37.0 37.0 37.0 37.0 8 36.417 37.0 37.0 37.0 37.0 37.0 9 36.5375 37.0 37.0 37.0 37.0 37.0 10-14 36.644499999999994 37.0 37.0 37.0 37.0 37.0 15-19 36.5729 37.0 37.0 37.0 37.0 37.0 20-24 36.5607 37.0 37.0 37.0 37.0 37.0 25-29 36.5159 37.0 37.0 37.0 37.0 37.0 30-34 36.4748 37.0 37.0 37.0 37.0 37.0 35-39 36.4599 37.0 37.0 37.0 37.0 37.0 40-44 36.3805 37.0 37.0 37.0 37.0 37.0 45-49 36.376200000000004 37.0 37.0 37.0 37.0 37.0 50-54 36.311899999999994 37.0 37.0 37.0 37.0 37.0 55-59 36.3074 37.0 37.0 37.0 37.0 37.0 60-64 36.2922 37.0 37.0 37.0 37.0 37.0 65-69 36.2911 37.0 37.0 37.0 37.0 37.0 70-74 36.1553 37.0 37.0 37.0 37.0 37.0 75-79 36.1541 37.0 37.0 37.0 37.0 37.0 80-84 36.0301 37.0 37.0 37.0 37.0 37.0 85-89 36.0615 37.0 37.0 37.0 37.0 37.0 90-94 36.056400000000004 37.0 37.0 37.0 37.0 37.0 95-99 35.9157 37.0 37.0 37.0 37.0 37.0 100-104 36.0048 37.0 37.0 37.0 37.0 37.0 105-109 35.93430000000001 37.0 37.0 37.0 37.0 37.0 110-114 35.9153 37.0 37.0 37.0 37.0 37.0 115-119 35.8866 37.0 37.0 37.0 37.0 37.0 120-124 35.7827 37.0 37.0 37.0 37.0 37.0 125-129 35.6233 37.0 37.0 37.0 37.0 37.0 130-134 35.7947 37.0 37.0 37.0 37.0 37.0 135-139 35.625299999999996 37.0 37.0 37.0 37.0 37.0 140-144 35.3748 37.0 37.0 37.0 34.6 37.0 145-149 35.2633 37.0 37.0 37.0 32.2 37.0 150-151 35.1185 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 1101 1 0.0 1101 2 0.0 1101 3 0.0 1101 4 0.0 1101 5 0.0 1101 6 0.0 1101 7 0.0 1101 8 0.0 1101 9 0.0 1101 10-14 0.0 1101 15-19 0.0 1101 20-24 0.0 1101 25-29 0.0 1101 30-34 0.0 1101 35-39 0.0 1101 40-44 0.0 1101 45-49 0.0 1101 50-54 0.0 1101 55-59 0.0 1101 60-64 0.0 1101 65-69 0.0 1101 70-74 0.0 1101 75-79 0.0 1101 80-84 0.0 1101 85-89 0.0 1101 90-94 0.0 1101 95-99 0.0 1101 100-104 0.0 1101 105-109 0.0 1101 110-114 0.0 1101 115-119 0.0 1101 120-124 0.0 1101 125-129 0.0 1101 130-134 0.0 1101 135-139 0.0 1101 140-144 0.0 1101 145-149 0.0 1101 150-151 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 2.0 22 1.0 23 3.0 24 3.0 25 2.0 26 8.0 27 12.0 28 12.0 29 17.0 30 24.0 31 39.0 32 58.0 33 91.0 34 137.0 35 413.0 36 2959.0 37 218.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 31.003268795574552 12.622579834045764 12.446567764646717 43.92758360573297 2 19.35 16.85 34.449999999999996 29.349999999999998 3 18.575 19.05 26.1 36.275 4 22.575 27.750000000000004 23.375 26.3 5 23.724999999999998 33.525 23.25 19.5 6 20.95 36.4 23.05 19.6 7 15.65 25.15 41.449999999999996 17.75 8 19.0 26.174999999999997 31.125000000000004 23.7 9 17.75 23.375 36.125 22.75 10-14 18.345 31.069999999999997 27.134999999999998 23.45 15-19 19.67 28.985 27.35 23.995 20-24 19.645000000000003 29.375 27.560000000000002 23.419999999999998 25-29 19.855 29.39 27.150000000000002 23.605 30-34 19.525000000000002 29.020000000000003 28.005000000000003 23.45 35-39 19.43 29.07 28.044999999999998 23.455000000000002 40-44 20.07 29.409999999999997 27.46 23.06 45-49 20.105 28.79 27.72 23.385 50-54 19.830000000000002 29.315 27.63 23.225 55-59 20.380000000000003 29.2 27.395000000000003 23.025000000000002 60-64 19.900000000000002 28.77 28.084999999999997 23.244999999999997 65-69 19.939999999999998 28.525 28.125 23.41 70-74 19.78 29.349999999999998 27.395000000000003 23.474999999999998 75-79 20.14 28.194999999999997 27.639999999999997 24.025 80-84 19.85 28.89 27.63 23.630000000000003 85-89 19.55 29.325000000000003 27.6 23.525 90-94 20.45 28.68 27.389999999999997 23.48 95-99 20.04 28.925 27.54 23.494999999999997 100-104 20.65 29.225 26.945000000000004 23.18 105-109 20.169999999999998 28.665000000000003 27.825 23.34 110-114 20.97 27.875 27.425 23.73 115-119 20.580000000000002 29.154999999999998 26.765 23.5 120-124 20.765 28.83 26.68 23.724999999999998 125-129 20.77 29.15 25.945 24.135 130-134 20.355 28.29 27.634999999999998 23.72 135-139 21.125 28.915000000000003 25.665 24.295 140-144 21.529999999999998 28.499999999999996 26.095000000000002 23.875 145-149 20.95 28.139999999999997 27.089999999999996 23.82 150-151 21.2375 27.525 27.525 23.7125 >>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 0.5 23 2.0 24 3.0 25 2.0 26 4.0 27 6.5 28 8.5 29 14.5 30 23.0 31 39.5 32 47.5 33 53.0 34 60.0 35 74.0 36 92.0 37 106.5 38 135.0 39 179.5 40 213.0 41 228.5 42 254.5 43 267.5 44 257.0 45 277.0 46 276.0 47 232.0 48 205.5 49 185.0 50 167.5 51 149.0 52 112.5 53 81.0 54 68.5 55 45.5 56 28.0 57 28.5 58 20.0 59 11.5 60 12.0 61 7.0 62 5.0 63 5.0 64 3.5 65 2.0 66 1.0 67 1.0 68 0.5 69 1.0 70 1.0 71 0.5 72 1.0 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 0.0 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 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 83.65 #Duplication Level Percentage of deduplicated Percentage of total 1 84.30962343096235 70.525 2 12.61207411835027 21.099999999999998 3 2.510460251046025 6.3 4 0.4482964734010759 1.5 5 0.059772863120143446 0.25 6 0.029886431560071723 0.15 7 0.029886431560071723 0.17500000000000002 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 warn #Sequence Count Percentage Possible Source CCCTTCTTTGAAGTTGGAGTGTCAGGGCAAGCGCAGGAGTTATGATTAGC 7 0.17500000000000002 No Hit CTCGACAACAGGCTCTACGGGTACTTCCGGCTCCTCTTTTGTCTCCTCAA 6 0.15 No Hit TTGGATTTTTATGCTTGTTATGCGAAGCAGATCCCATGTCTGACAAAGCA 5 0.125 No Hit ACAAGACATATGCAGGAAAGGTAAAAGAGTCTACCACTCGTACATTTCTA 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 0.0 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 0.025 0.0 0.0 0.0 0.0 66-67 0.075 0.0 0.0 0.0 0.0 68-69 0.075 0.0 0.0 0.0 0.0 70-71 0.1 0.0 0.0 0.0 0.0 72-73 0.125 0.0 0.0 0.0 0.0 74-75 0.16249999999999998 0.0 0.0 0.0 0.0 76-77 0.225 0.0 0.0 0.0 0.0 78-79 0.2875 0.0 0.0 0.0 0.0 80-81 0.4375 0.0 0.0 0.0 0.0 82-83 0.525 0.0 0.0 0.0 0.0 84-85 0.6375 0.0 0.0 0.0 0.0 86-87 0.75 0.0 0.0 0.0 0.0 88-89 0.8125 0.0 0.0 0.0 0.0 90-91 0.95 0.0 0.0 0.0 0.0 92-93 1.15 0.0 0.0 0.0 0.0 94-95 1.2999999999999998 0.0 0.0 0.0 0.0 96-97 1.5375 0.0 0.0 0.0 0.0 98-99 1.7125 0.0 0.0 0.0 0.0 100-101 1.925 0.0 0.0 0.0 0.0 102-103 2.3625 0.0 0.0 0.0 0.0 104-105 2.825 0.0 0.0 0.0 0.0 106-107 3.35 0.0 0.0 0.0 0.0 108-109 3.825 0.0 0.0 0.0 0.0 110-111 4.2375 0.0 0.0 0.0 0.0 112-113 4.7 0.0 0.0 0.0 0.0 114-115 5.225 0.0 0.0 0.0 0.0 116-117 5.7125 0.0 0.0 0.0 0.0 118-119 6.1375 0.0 0.0 0.0 0.0 120-121 6.637499999999999 0.0 0.0 0.0 0.0 122-123 7.175000000000001 0.0 0.0 0.0 0.0 124-125 7.65 0.0 0.0 0.0 0.0 126-127 8.175 0.0 0.0 0.0 0.0 128-129 8.75 0.0 0.0 0.0 0.0 130-131 9.35 0.0 0.0 0.0 0.0 132-133 9.9 0.0 0.0 0.0 0.0 134-135 10.337499999999999 0.0 0.0 0.0 0.0 136-137 10.9125 0.0 0.0 0.0 0.0 138-139 11.7375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TCTTCAA 10 0.006830828 145.0 7 >>END_MODULE SRR28623285 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR28623285_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 35.535 37.0 37.0 37.0 37.0 37.0 2 36.176 37.0 37.0 37.0 37.0 37.0 3 36.1405 37.0 37.0 37.0 37.0 37.0 4 36.1425 37.0 37.0 37.0 37.0 37.0 5 36.227 37.0 37.0 37.0 37.0 37.0 6 36.1495 37.0 37.0 37.0 37.0 37.0 7 36.175 37.0 37.0 37.0 37.0 37.0 8 36.215 37.0 37.0 37.0 37.0 37.0 9 36.09 37.0 37.0 37.0 37.0 37.0 10-14 36.1158 37.0 37.0 37.0 37.0 37.0 15-19 36.0903 37.0 37.0 37.0 37.0 37.0 20-24 36.07940000000001 37.0 37.0 37.0 37.0 37.0 25-29 36.062 37.0 37.0 37.0 37.0 37.0 30-34 35.9728 37.0 37.0 37.0 37.0 37.0 35-39 35.997 37.0 37.0 37.0 37.0 37.0 40-44 35.9159 37.0 37.0 37.0 37.0 37.0 45-49 35.9637 37.0 37.0 37.0 37.0 37.0 50-54 35.9058 37.0 37.0 37.0 37.0 37.0 55-59 35.7534 37.0 37.0 37.0 37.0 37.0 60-64 35.727 37.0 37.0 37.0 37.0 37.0 65-69 35.7573 37.0 37.0 37.0 37.0 37.0 70-74 35.8126 37.0 37.0 37.0 37.0 37.0 75-79 35.8337 37.0 37.0 37.0 37.0 37.0 80-84 35.700900000000004 37.0 37.0 37.0 37.0 37.0 85-89 35.613299999999995 37.0 37.0 37.0 37.0 37.0 90-94 35.543 37.0 37.0 37.0 37.0 37.0 95-99 35.521100000000004 37.0 37.0 37.0 34.6 37.0 100-104 35.4047 37.0 37.0 37.0 34.6 37.0 105-109 35.436699999999995 37.0 37.0 37.0 37.0 37.0 110-114 35.4899 37.0 37.0 37.0 37.0 37.0 115-119 35.501200000000004 37.0 37.0 37.0 37.0 37.0 120-124 35.3582 37.0 37.0 37.0 34.6 37.0 125-129 34.824600000000004 37.0 37.0 37.0 25.0 37.0 130-134 35.2132 37.0 37.0 37.0 29.8 37.0 135-139 35.0312 37.0 37.0 37.0 27.4 37.0 140-144 34.9479 37.0 37.0 37.0 27.4 37.0 145-149 34.9743 37.0 37.0 37.0 25.0 37.0 150-151 34.6005 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 1101 1 0.0 1101 2 0.0 1101 3 0.0 1101 4 0.0 1101 5 0.0 1101 6 0.0 1101 7 0.0 1101 8 0.0 1101 9 0.0 1101 10-14 0.0 1101 15-19 0.0 1101 20-24 0.0 1101 25-29 0.0 1101 30-34 0.0 1101 35-39 0.0 1101 40-44 0.0 1101 45-49 0.0 1101 50-54 0.0 1101 55-59 0.0 1101 60-64 0.0 1101 65-69 0.0 1101 70-74 0.0 1101 75-79 0.0 1101 80-84 0.0 1101 85-89 0.0 1101 90-94 0.0 1101 95-99 0.0 1101 100-104 0.0 1101 105-109 0.0 1101 110-114 0.0 1101 115-119 0.0 1101 120-124 0.0 1101 125-129 0.0 1101 130-134 0.0 1101 135-139 0.0 1101 140-144 0.0 1101 145-149 0.0 1101 150-151 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 14 1.0 15 1.0 16 1.0 17 2.0 18 2.0 19 3.0 20 3.0 21 3.0 22 4.0 23 6.0 24 8.0 25 12.0 26 8.0 27 23.0 28 20.0 29 22.0 30 44.0 31 59.0 32 77.0 33 127.0 34 266.0 35 732.0 36 2342.0 37 234.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 34.675 17.849999999999998 16.900000000000002 30.575000000000003 2 28.349999999999998 24.525 29.75 17.375 3 22.25 27.900000000000002 29.75 20.1 4 25.5 33.5 22.975 18.025 5 24.0 36.65 22.25 17.1 6 20.549999999999997 37.5 23.025000000000002 18.925 7 20.424999999999997 19.775000000000002 39.825 19.975 8 20.674999999999997 25.674999999999997 28.325 25.324999999999996 9 22.35 24.85 30.7 22.1 10-14 22.905 29.125 27.02 20.95 15-19 22.74 28.87 27.584999999999997 20.805 20-24 22.97 28.384999999999998 27.900000000000002 20.745 25-29 23.215 27.455000000000002 28.345 20.985 30-34 22.34 28.405 28.455000000000002 20.8 35-39 22.695 28.105000000000004 27.765 21.435000000000002 40-44 22.645 27.595 28.595 21.165 45-49 22.295 28.265 28.335 21.105 50-54 22.994999999999997 28.24 27.925 20.84 55-59 22.945 28.444999999999997 27.950000000000003 20.66 60-64 23.32 28.055000000000003 27.915 20.71 65-69 23.015 28.194999999999997 28.139999999999997 20.65 70-74 23.369999999999997 28.110000000000003 28.035 20.485 75-79 22.71 28.505000000000003 28.29 20.495 80-84 23.76 28.705000000000002 27.51 20.025000000000002 85-89 24.115000000000002 28.325 27.62 19.939999999999998 90-94 23.735 28.549999999999997 27.495000000000005 20.22 95-99 23.794999999999998 27.544999999999998 28.105000000000004 20.555 100-104 24.34 27.71 27.855 20.095 105-109 24.565 27.425 27.975 20.035 110-114 24.85 27.750000000000004 27.839999999999996 19.56 115-119 24.9 27.91 27.1 20.09 120-124 24.7 27.575 27.334999999999997 20.39 125-129 25.655 28.355000000000004 26.93 19.06 130-134 25.16 28.005000000000003 27.060000000000002 19.775000000000002 135-139 25.474999999999998 27.935 26.99 19.6 140-144 25.64 27.905 27.07 19.384999999999998 145-149 26.105 27.279999999999998 27.235 19.38 150-151 26.075 27.787499999999998 27.05 19.0875 >>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 0.5 7 0.5 8 0.0 9 0.0 10 1.0 11 1.0 12 0.0 13 1.0 14 1.0 15 0.0 16 0.5 17 1.0 18 0.5 19 0.0 20 0.0 21 0.0 22 0.0 23 0.5 24 1.0 25 2.0 26 5.5 27 4.0 28 3.5 29 10.0 30 17.0 31 24.0 32 30.5 33 47.0 34 61.0 35 74.5 36 100.5 37 121.0 38 149.0 39 176.0 40 200.0 41 225.0 42 252.0 43 263.5 44 261.5 45 281.0 46 277.5 47 249.5 48 208.0 49 180.5 50 165.5 51 130.5 52 112.5 53 97.0 54 64.5 55 46.5 56 33.5 57 23.0 58 17.5 59 13.0 60 13.5 61 10.5 62 7.5 63 5.5 64 6.0 65 6.0 66 3.0 67 1.5 68 1.5 69 0.5 70 0.5 71 0.0 72 0.0 73 0.5 74 0.5 75 0.0 76 0.0 77 0.0 78 0.5 79 0.5 80 0.0 81 0.0 82 0.5 83 0.5 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.5 91 0.5 92 0.5 93 0.5 94 0.0 95 0.0 96 0.0 97 0.5 98 0.5 99 0.5 100 1.0 >>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 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 84.22500000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 84.98070644108044 71.575 2 12.05105372514099 20.3 3 2.3745918670228554 6.0 4 0.4749183734045711 1.6 5 0.08904719501335707 0.375 6 0.029682398337785694 0.15 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 warn #Sequence Count Percentage Possible Source CATGGGTTCCAGGCCTGGCTCTTTTCTTTACCTTGGTGCCTCTCCACAAC 6 0.15 No Hit TTGGCAGAATTGGATAACAGATCTGGGTCCAAATGTGTGAGGGCCATGTC 5 0.125 No Hit CTTTTTGCTTCTTACAGTTTTCTTTTGTATCCCAGCTGTGCTTTATTTTC 5 0.125 No Hit AATTCATGGATTTCTTGCTGTGAATAATTAACTGGCCGATGATGCTGCCG 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 0.0 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 0.025 0.0 0.0 0.0 0.0 66-67 0.075 0.0 0.0 0.0 0.0 68-69 0.075 0.0 0.0 0.0 0.0 70-71 0.1 0.0 0.0 0.0 0.0 72-73 0.125 0.0 0.0 0.0 0.0 74-75 0.16249999999999998 0.0 0.0 0.0 0.0 76-77 0.225 0.0 0.0 0.0 0.0 78-79 0.2875 0.0 0.0 0.0 0.0 80-81 0.4375 0.0 0.0 0.0 0.0 82-83 0.525 0.0 0.0 0.0 0.0 84-85 0.6499999999999999 0.0 0.0 0.0 0.0 86-87 0.775 0.0 0.0 0.0 0.0 88-89 0.8374999999999999 0.0 0.0 0.0 0.0 90-91 0.975 0.0 0.0 0.0 0.0 92-93 1.175 0.0 0.0 0.0 0.0 94-95 1.3250000000000002 0.0 0.0 0.0 0.0 96-97 1.5625 0.0 0.0 0.0 0.0 98-99 1.7375 0.0 0.0 0.0 0.0 100-101 1.9749999999999999 0.0 0.0 0.0 0.0 102-103 2.3875 0.0 0.0 0.0 0.0 104-105 2.8499999999999996 0.0 0.0 0.0 0.0 106-107 3.375 0.0 0.0 0.0 0.0 108-109 3.8375000000000004 0.0 0.0 0.0 0.0 110-111 4.25 0.0 0.0 0.0 0.0 112-113 4.737500000000001 0.0 0.0 0.0 0.0 114-115 5.3 0.0 0.0 0.0 0.0 116-117 5.8 0.0 0.0 0.0 0.0 118-119 6.2375 0.0 0.0 0.0 0.0 120-121 6.725 0.0 0.0 0.0 0.0 122-123 7.25 0.0 0.0 0.0 0.0 124-125 7.725 0.0 0.0 0.0 0.0 126-127 8.25 0.0 0.0 0.0 0.0 128-129 8.825 0.0 0.0 0.0 0.0 130-131 9.425 0.0 0.0 0.0 0.0 132-133 9.9625 0.0 0.0 0.0 0.0 134-135 10.3875 0.0 0.0 0.0 0.0 136-137 10.95 0.0 0.0 0.0 0.0 138-139 11.8 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 2019639 spots for SRR28623285.sra Written 2019639 spots for SRR28623285.sra Read 2019639 spots for SRR28623285.sra Written 2019639 spots for SRR28623285.sra Read 2019639 spots for SRR28623285.sra Written 2019639 spots for SRR28623285.sra Read 2019639 spots for SRR28623285.sra Written 2019639 spots for SRR28623285.sra Read 2019639 spots for SRR28623285.sra Written 2019639 spots for SRR28623285.sra Read 2019639 spots for SRR28623285.sra Written 2019639 spots for SRR28623285.sra Read 2019639 spots for SRR28623285.sra Written 2019639 spots for SRR28623285.sra Read 2019639 spots for SRR28623285.sra Written 2019639 spots for SRR28623285.sra Read 2019639 spots for SRR28623285.sra Written 2019639 spots for SRR28623285.sra Read 2019639 spots for SRR28623285.sra Written 2019639 spots for SRR28623285.sra Read 2019639 spots for SRR28623285.sra Written 2019639 spots for SRR28623285.sra Read 2019639 spots for SRR28623285.sra Written 2019639 spots for SRR28623285.sra Read 2019639 spots for SRR28623285.sra Written 2019639 spots for SRR28623285.sra Read 2019639 spots for SRR28623285.sra Written 2019639 spots for SRR28623285.sra Read 2019639 spots for SRR28623285.sra Written 2019639 spots for SRR28623285.sra Read 2019639 spots for SRR28623285.sra Written 2019639 spots for SRR28623285.sra Read 2019639 spots for SRR28623285.sra Written 2019639 spots for SRR28623285.sra Read 2019639 spots for SRR28623285.sra Written 2019639 spots for SRR28623285.sra Read 2019639 spots for SRR28623285.sra Written 2019639 spots for SRR28623285.sra Read 2019639 spots for SRR28623285.sra Written 2019639 spots for SRR28623285.sra SRR ids: ['SRR28623285.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_0sk34svg SRR28623285.sra spots: 40392780 blocks: [[1, 2019639], [2019640, 4039278], [4039279, 6058917], [6058918, 8078556], [8078557, 10098195], [10098196, 12117834], [12117835, 14137473], [14137474, 16157112], [16157113, 18176751], [18176752, 20196390], [20196391, 22216029], [22216030, 24235668], [24235669, 26255307], [26255308, 28274946], [28274947, 30294585], [30294586, 32314224], [32314225, 34333863], [34333864, 36353502], [36353503, 38373141], [38373142, 40392780]] SRR28623285 file size 14918134 SRR28623285 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 SRR28623285 SRR28623285_1.fastq SRR28623285_2.fastq Input file: SRR28623285_1.fastq Paired file: SRR28623285_2.fastq trimmed: SRR28623285-trimmed-pair1.fastq, SRR28623285-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 Tue Feb 11 15:06:10 2025 >> started Tue Feb 11 15:07:01 2025 >> done (50.960s) 40392780 read pairs processed; of these: 64 ( 0.00%) short read pairs filtered out after trimming by size control 32965 ( 0.08%) empty read pairs filtered out after trimming by size control 40359751 (99.92%) read pairs available; of these: 5886754 (14.59%) trimmed read pairs available after processing 34472997 (85.41%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 3 0.00% 19 5 0.00% 20 10 0.00% 21 11 0.00% 22 12 0.00% 23 19 0.00% 24 16 0.00% 25 14 0.00% 26 15 0.00% 27 12 0.00% 28 22 0.00% 29 20 0.00% 30 10 0.00% 31 33 0.00% 32 38 0.00% 33 32 0.00% 34 37 0.00% 35 54 0.00% 36 47 0.00% 37 53 0.00% 38 52 0.00% 39 75 0.00% 40 95 0.00% 41 84 0.00% 42 97 0.00% 43 113 0.00% 44 114 0.00% 45 159 0.00% 46 148 0.00% 47 200 0.00% 48 226 0.00% 49 221 0.00% 50 311 0.00% 51 333 0.00% 52 364 0.00% 53 409 0.00% 54 481 0.00% 55 535 0.00% 56 565 0.00% 57 682 0.00% 58 752 0.00% 59 902 0.00% 60 1069 0.00% 61 1281 0.00% 62 1408 0.00% 63 1643 0.00% 64 1891 0.00% 65 2076 0.01% 66 2318 0.01% 67 2599 0.01% 68 3027 0.01% 69 3522 0.01% 70 4050 0.01% 71 4729 0.01% 72 5438 0.01% 73 6302 0.02% 74 7001 0.02% 75 7912 0.02% 76 8582 0.02% 77 9687 0.02% 78 10530 0.03% 79 11952 0.03% 80 13098 0.03% 81 14882 0.04% 82 16600 0.04% 83 18403 0.05% 84 19786 0.05% 85 22085 0.05% 86 23283 0.06% 87 25048 0.06% 88 26792 0.07% 89 28528 0.07% 90 30743 0.08% 91 32982 0.08% 92 35796 0.09% 93 38137 0.09% 94 40874 0.10% 95 43011 0.11% 96 45439 0.11% 97 46844 0.12% 98 48826 0.12% 99 50796 0.13% 100 53109 0.13% 101 55111 0.14% 102 58703 0.15% 103 60586 0.15% 104 63106 0.16% 105 66133 0.16% 106 67576 0.17% 107 69223 0.17% 108 71037 0.18% 109 73649 0.18% 110 74755 0.19% 111 77960 0.19% 112 79810 0.20% 113 82648 0.20% 114 84441 0.21% 115 87427 0.22% 116 89397 0.22% 117 90800 0.22% 118 92946 0.23% 119 94345 0.23% 120 95349 0.24% 121 98257 0.24% 122 99347 0.25% 123 101422 0.25% 124 104012 0.26% 125 105307 0.26% 126 106922 0.26% 127 109019 0.27% 128 109907 0.27% 129 111272 0.28% 130 112987 0.28% 131 113042 0.28% 132 114659 0.28% 133 117922 0.29% 134 118275 0.29% 135 119479 0.30% 136 121400 0.30% 137 122181 0.30% 138 123328 0.31% 139 124681 0.31% 140 124542 0.31% 141 125936 0.31% 142 127810 0.32% 143 128290 0.32% 144 130727 0.32% 145 131441 0.33% 146 131460 0.33% 147 133333 0.33% 148 135116 0.33% 149 134468 0.33% 150 135750 0.34% 151 34472997 85.41% 40359751 reads passed initial QC criterion=sequence-density sequence-density=0.13 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=38 prefix-density=0.13 prefix-fanout=2.0 sequence=TGCGACATGGTTGGCAAGAATCCTTCTGCGAATTTAGCAACAACCGAAGAATCAAGATACTCCTGCAAGCCCTCCAGATCATCAAAGGTAGTTTCAAAAGCATGAGTATATCCGAAATTGAGGTCGTGAATACCCAGATTAGTGCCCCAGTGTAAGCTCTTCAAGGGTTCAACTTGATTGACCAGATGAGTGAAGTCGTTTATGATTTTCTCAATTT criterion=fanout-score sequence-density=0.02 sequence-density-rank=31 fanout-score=118.20 fanout-score-rank=1 prefix-density=0.17 prefix-fanout=15.3 sequence=TCTCCTTCCTCTAAATGATAAGGTTCAGTGGACTTCTCGCGACGTCGCCGGCGGCGAACCGCCCACGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAGACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCAT criterion=sequence-density sequence-density=0.25 sequence-density-rank=1 fanout-score=2.87 fanout-score-rank=32 prefix-density=0.28 prefix-fanout=2.5 sequence=ATAGAGAGAAAGA criterion=fanout-score sequence-density=0.08 sequence-density-rank=21 fanout-score=328.53 fanout-score-rank=1 prefix-density=0.87 prefix-fanout=29.6 sequence=GAAGAAGAAGAAA SRR28623285 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 15:07:41 Started mapping on | Feb 11 15:07:41 Finished on | Feb 11 15:11:26 Mapping speed, Million of reads per hour | 645.76 Number of input reads | 40359751 Average input read length | 294 UNIQUE READS: Uniquely mapped reads number | 38013657 Uniquely mapped reads % | 94.19% Average mapped length | 292.35 Number of splices: Total | 34954227 Number of splices: Annotated (sjdb) | 34268724 Number of splices: GT/AG | 34376585 Number of splices: GC/AG | 446351 Number of splices: AT/AC | 29981 Number of splices: Non-canonical | 101310 Mismatch rate per base, % | 0.44% Deletion rate per base | 0.03% Deletion average length | 2.99 Insertion rate per base | 0.03% Insertion average length | 2.50 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1056742 % of reads mapped to multiple loci | 2.62% Number of reads mapped to too many loci | 146016 % of reads mapped to too many loci | 0.36% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.70% % of reads unmapped: other | 0.13% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1289352 1289352 1289352 N_multimapping 1056742 1056742 1056742 N_noFeature 1272698 37661704 1446511 N_ambiguous 388090 2522 208072 UnstrandedReadsAssigned:36352869 PositiveStrandReadsAssigned:349431 NegativeStrandReadsAssigned:36359074 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR28623285 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: SRR28623285-trimmed-pair1.fastq SRR28623285-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 40,359,751 reads, 36,560,112 reads pseudoaligned [quant] estimated average fragment length: 240.97 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,119 rounds 52401 SRR28623285.ke.tsv 34699 SRR28623285.se.tsv 87100 total ==> SRR28623285.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1778.03 1887 29.0374 Potri.005G024800.1.v4.1 1035 795.03 2620 90.1661 Potri.004G059700.1.v4.1 961 721.049 79 2.9977 Potri.007G009000.2.v4.1 1416 1176.03 0 0 Potri.003G141000.2.v4.1 2943 2703.03 944.632 9.56175 Potri.016G087400.1.v4.1 270 93.7505 2552.92 745.056 Potri.015G069301.1.v4.1 564 332.332 0 0 Potri.010G195200.1.v4.1 1773 1533.03 115 2.05245 Potri.012G127500.1.v4.1 977 737.045 11560 429.131 ==> SRR28623285.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 1612 Potri.001G233950.v4.1 1 Potri.001G122700.v4.1 484 Potri.001G212900.v4.1 419 Potri.001G182400.v4.1 3 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 2 Potri.001G416900.v4.1 1 Potri.001G452600.v4.1 3 SRR28623285 completed mapping pipeline successfully