Starting /dee2/code/volunteer_pipeline.sh SRR8096908 current disk space = 1539620233216 free memory = 1421458352 SRR8096908 SRAfilesize 458d6aa4284041f14f2a1d3625be0a75 SRR8096908.sra SRR8096908.sra file validated SRR8096908 is paired end SRR8096908 is conventional basespace SRR8096908 read1 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8096908_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 47 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.78175 34.0 33.0 34.0 32.0 34.0 2 32.82725 34.0 33.0 34.0 29.0 34.0 3 32.9035 34.0 33.0 34.0 30.0 34.0 4 33.08825 34.0 33.0 34.0 32.0 34.0 5 33.199 34.0 33.0 34.0 32.0 34.0 6 36.95975 38.0 38.0 38.0 36.0 38.0 7 37.215 38.0 38.0 38.0 36.0 38.0 8 37.30025 38.0 38.0 38.0 37.0 38.0 9 37.40275 38.0 38.0 38.0 37.0 38.0 10-14 37.269999999999996 38.0 38.0 38.0 37.0 38.0 15-19 37.33655 38.0 38.0 38.0 37.0 38.0 20-24 37.237 38.0 38.0 38.0 36.8 38.0 25-29 37.23095 38.0 38.0 38.0 36.8 38.0 30-34 37.1102 38.0 38.0 38.0 36.6 38.0 35-39 37.0815 38.0 38.0 38.0 37.0 38.0 40-44 36.97595 38.0 38.0 38.0 36.0 38.0 45-49 36.9506 38.0 38.0 38.0 36.2 38.0 50-54 36.892849999999996 38.0 38.0 38.0 36.0 38.0 55-59 36.8317 38.0 38.0 38.0 36.0 38.0 60-64 36.576350000000005 38.0 38.0 38.0 35.0 38.0 65-69 36.00825 38.0 38.0 38.0 33.0 38.0 70-74 36.013 38.0 38.0 38.0 33.0 38.0 75-79 35.337199999999996 38.0 38.0 38.0 30.8 38.0 80-84 35.38145 38.0 38.0 38.0 31.8 38.0 85-89 35.4294 38.0 38.0 38.0 33.2 38.0 90-94 35.33775 38.0 38.0 38.0 32.6 38.0 95-99 35.2115 38.0 38.0 38.0 31.6 38.0 100-104 34.979749999999996 38.0 38.0 38.0 29.0 38.0 105-109 34.5773 38.0 37.8 38.0 25.8 38.0 110-114 34.3749 38.0 37.0 38.0 24.2 38.0 115-119 34.13805000000001 38.0 36.8 38.0 22.6 38.0 120-124 33.90735 38.0 36.2 38.0 20.6 38.0 125-129 33.30049999999999 38.0 35.6 38.0 14.2 38.0 130-134 32.9815 38.0 35.4 38.0 13.2 38.0 135-139 32.670899999999996 38.0 34.8 38.0 8.6 38.0 140-144 32.34075 38.0 33.2 38.0 2.0 38.0 145-149 31.645050000000005 38.0 33.0 38.0 2.0 38.0 150 24.95125 33.0 2.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 6 4.0 7 3.0 8 2.0 9 1.0 10 5.0 11 2.0 12 5.0 13 4.0 14 10.0 15 3.0 16 11.0 17 12.0 18 36.0 19 70.0 20 7.0 21 16.0 22 18.0 23 25.0 24 14.0 25 27.0 26 26.0 27 40.0 28 47.0 29 62.0 30 51.0 31 70.0 32 67.0 33 84.0 34 113.0 35 181.0 36 469.0 37 2515.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 42.65935214211076 12.304075235109718 7.340647857889238 37.69592476489028 2 21.45 22.3 34.425 21.825 3 19.650000000000002 19.125 29.95 31.275 4 23.5 26.35 20.849999999999998 29.299999999999997 5 29.425 29.099999999999998 22.875 18.6 6 24.775 31.1 23.225 20.9 7 15.299999999999999 28.349999999999998 38.25 18.099999999999998 8 17.150000000000002 26.974999999999998 29.549999999999997 26.325 9 24.4 20.775 30.425 24.4 10-14 21.665 27.794999999999998 25.215 25.324999999999996 15-19 22.175 26.155 26.14 25.53 20-24 21.415 27.060000000000002 26.950000000000003 24.575 25-29 21.735 26.029999999999998 26.419999999999998 25.814999999999998 30-34 20.455000000000002 26.784999999999997 26.945000000000004 25.814999999999998 35-39 22.18 25.755 27.46 24.605 40-44 20.485 25.985000000000003 27.29 26.240000000000002 45-49 23.02 25.96 27.450000000000003 23.57 50-54 22.18 24.625 26.26 26.935 55-59 22.055 24.69 28.285 24.97 60-64 22.259999999999998 25.5 26.939999999999998 25.3 65-69 20.838125718857828 30.754613191978798 24.71370705605841 23.693554033104967 70-74 21.335 30.28 24.51 23.875 75-79 21.64 28.410000000000004 24.775 25.174999999999997 80-84 22.115000000000002 25.785000000000004 26.855 25.245 85-89 21.740000000000002 26.724999999999998 25.85 25.685000000000002 90-94 22.115000000000002 25.955000000000002 26.064999999999998 25.865 95-99 21.59 26.595000000000002 26.35 25.465 100-104 22.205 27.61 25.765 24.42 105-109 22.86 26.895000000000003 25.685000000000002 24.560000000000002 110-114 22.34 27.375 25.415 24.87 115-119 22.365 26.945000000000004 25.785000000000004 24.905 120-124 22.830000000000002 26.479999999999997 25.624999999999996 25.064999999999998 125-129 22.225 28.15 25.14 24.485 130-134 21.72 29.020000000000003 24.825 24.435000000000002 135-139 21.82 28.244999999999997 24.560000000000002 25.374999999999996 140-144 22.175 26.995 25.040000000000003 25.790000000000003 145-149 22.7 27.125 24.985 25.19 150 21.625 27.250000000000004 26.450000000000003 24.675 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 9.0 1 6.5 2 3.5 3 1.5 4 1.5 5 1.5 6 0.0 7 1.5 8 1.5 9 1.0 10 1.5 11 1.0 12 0.5 13 0.0 14 1.0 15 1.5 16 0.5 17 0.0 18 0.5 19 1.0 20 0.5 21 0.5 22 0.5 23 0.5 24 1.0 25 1.0 26 2.0 27 5.0 28 7.5 29 10.5 30 11.5 31 14.0 32 18.5 33 25.0 34 38.0 35 58.5 36 73.0 37 80.0 38 106.0 39 127.0 40 145.0 41 158.0 42 171.0 43 193.5 44 198.5 45 209.5 46 243.0 47 237.0 48 206.0 49 194.5 50 167.5 51 129.5 52 106.5 53 95.5 54 85.5 55 82.0 56 82.0 57 82.5 58 75.5 59 69.5 60 65.0 61 63.5 62 60.5 63 47.0 64 38.5 65 39.0 66 33.0 67 26.0 68 23.5 69 16.0 70 9.5 71 9.0 72 8.0 73 3.5 74 4.0 75 5.0 76 3.0 77 1.0 78 0.5 79 1.0 80 0.5 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 4.3 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 0.015 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 pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 91.175 #Duplication Level Percentage of deduplicated Percentage of total 1 98.1354537976419 89.47500000000001 2 1.4806690430490814 2.7 3 0.16451878256100905 0.44999999999999996 4 0.054839594187003016 0.2 5 0.0 0.0 6 0.027419797093501508 0.15 7 0.027419797093501508 0.17500000000000002 8 0.0 0.0 9 0.027419797093501508 0.22499999999999998 >10 0.054839594187003016 0.65 >50 0.0 0.0 >100 0.027419797093501508 5.975 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences fail #Sequence Count Percentage Possible Source GATCGGAAGAGCACACGTCTGAACTCCAGTCACATGTCAATCTCGTATGC 239 5.975 TruSeq Adapter, Index 15 (98% over 50bp) TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 16 0.4 No Hit NATCGGAAGAGCACACGTCTGAACTCCAGTCACATGTCAATCTCGTATGC 10 0.25 TruSeq Adapter, Index 15 (97% over 39bp) AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGTCAATCTCGTATG 9 0.22499999999999998 TruSeq Adapter, Index 15 (97% over 49bp) CACACGTCTGAACTCCAGTCACATGTCAATCTCGTATGCCGTCTTCTGCT 7 0.17500000000000002 TruSeq Adapter, Index 15 (98% over 50bp) AGAGCACACGTCTGAACTCCAGTCACATGTCAATCTCGTATGCCGTCTTC 6 0.15 TruSeq Adapter, Index 15 (98% over 50bp) >>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 0.225 0.0 0.0 0.0 0.0 2 0.225 0.0 0.0 0.0 0.0 3 0.225 0.0 0.0 0.0 0.0 4 0.225 0.0 0.0 0.0 0.0 5 0.225 0.0 0.0 0.0 0.0 6 0.225 0.0 0.0 0.0 0.0 7 0.225 0.0 0.0 0.0 0.0 8 0.225 0.0 0.0 0.0 0.0 9 0.225 0.0 0.0 0.0 0.0 10-11 0.225 0.0 0.0 0.0 0.0 12-13 0.225 0.0 0.0 0.0 0.0 14-15 0.225 0.0 0.0 0.0 0.0 16-17 0.225 0.0 0.0 0.0 0.0 18-19 0.225 0.0 0.0 0.0 0.0 20-21 0.225 0.0 0.0 0.0 0.0 22-23 0.225 0.0 0.0 0.0 0.0 24-25 0.225 0.0 0.0 0.0 0.0 26-27 0.225 0.0 0.0 0.0 0.0 28-29 0.225 0.0 0.0 0.0 0.0 30-31 0.25 0.0 0.0 0.0 0.0 32-33 0.25 0.0 0.0 0.0 0.0 34-35 0.25 0.0 0.0 0.0 0.0 36-37 0.275 0.0 0.0 0.0 0.0 38-39 0.3 0.0 0.0 0.0 0.0 40-41 0.325 0.0 0.0 0.0 0.0 42-43 0.375 0.0 0.0 0.0 0.0 44-45 0.4 0.0 0.0 0.0 0.0 46-47 0.4 0.0 0.0 0.0 0.0 48-49 0.425 0.0 0.0 0.0 0.0 50-51 0.4625 0.0 0.0 0.0 0.0 52-53 0.4875 0.0 0.0 0.0 0.0 54-55 0.5 0.0 0.0 0.0 0.0 56-57 0.5 0.0 0.0 0.0 0.0 58-59 0.5 0.0 0.0 0.0 0.0 60-61 0.525 0.0 0.0 0.0 0.0 62-63 0.5375000000000001 0.0 0.0 0.0 0.0 64-65 0.55 0.0 0.0 0.0 0.0 66-67 0.55 0.0 0.0 0.0 0.0 68-69 0.55 0.0 0.0 0.0 0.0 70-71 0.55 0.0 0.0 0.0 0.0 72-73 0.55 0.0 0.0 0.0 0.0 74-75 0.55 0.0 0.0 0.0 0.0 76-77 0.55 0.0 0.0 0.0 0.0 78-79 0.55 0.0 0.0 0.0 0.0 80-81 0.55 0.0 0.0 0.0 0.0 82-83 0.5625 0.0 0.0 0.0 0.0 84-85 0.575 0.0 0.0 0.0 0.0 86-87 0.575 0.0 0.0 0.0 0.0 88-89 0.575 0.0 0.0 0.0 0.0 90-91 0.6 0.0 0.0 0.0 0.0 92-93 0.675 0.0 0.0 0.0 0.0 94-95 0.7375 0.0 0.0 0.0 0.0 96-97 0.775 0.0 0.0 0.0 0.0 98-99 0.8125 0.0 0.0 0.0 0.0 100-101 0.875 0.0 0.0 0.0 0.0 102-103 0.9125000000000001 0.0 0.0 0.0 0.0 104-105 0.925 0.0 0.0 0.0 0.0 106-107 0.9874999999999999 0.0 0.0 0.0 0.0 108-109 1.1875 0.0 0.0 0.0 0.0 110-111 1.3624999999999998 0.0 0.0 0.0 0.0 112-113 1.4625 0.0 0.0 0.0 0.0 114-115 1.5375 0.0 0.0 0.0 0.0 116-117 1.65 0.0 0.0 0.0 0.0 118-119 1.8 0.0 0.0 0.0 0.0 120-121 2.0625 0.0 0.0 0.0 0.0 122-123 2.3375 0.0 0.0 0.0 0.0 124-125 2.5250000000000004 0.0 0.0 0.0 0.0 126-127 2.6875 0.0 0.0 0.0 0.0 128-129 2.775 0.0 0.0 0.0 0.0 130-131 2.9625000000000004 0.0 0.0 0.0 0.0 132-133 3.0875000000000004 0.0 0.0 0.0 0.0 134-135 3.2375 0.0 0.0 0.0 0.0 136-137 3.5125 0.0 0.0 0.0 0.0 138 3.625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GATCGGA 35 1.8872561E-7 106.83673 1 GAAGAGC 45 8.811185E-9 95.975 6 TCGGAAG 40 5.292204E-7 89.97656 3 ATCGGAA 40 5.292204E-7 89.97656 2 GGAAGAG 40 5.292204E-7 89.97656 5 AAGAGCA 50 1.9967101E-6 71.98125 7 GAGCACA 50 1.9967101E-6 71.98125 9 CGGAAGA 50 1.9967101E-6 71.98125 4 AGAGCAC 55 3.5178728E-6 65.4375 8 >>END_MODULE SRR8096908 read2 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8096908_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 48 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.385 33.0 31.0 33.0 18.0 34.0 2 30.70575 33.0 31.0 33.0 25.0 34.0 3 30.5475 33.0 31.0 34.0 18.0 34.0 4 30.75575 33.0 31.0 34.0 25.0 34.0 5 29.00275 33.0 28.0 33.0 15.0 34.0 6 34.0405 38.0 34.0 38.0 26.0 38.0 7 34.47725 38.0 36.0 38.0 26.0 38.0 8 34.61625 38.0 36.0 38.0 26.0 38.0 9 34.36025 38.0 36.0 38.0 16.0 38.0 10-14 34.2921 38.0 35.8 38.0 20.0 38.0 15-19 34.0903 38.0 36.0 38.0 18.0 38.0 20-24 34.06385 38.0 35.8 38.0 17.8 38.0 25-29 33.77225 38.0 35.4 38.0 16.0 38.0 30-34 33.5655 38.0 34.8 38.0 16.0 38.0 35-39 33.290949999999995 38.0 34.2 38.0 16.0 38.0 40-44 33.29765 38.0 34.2 38.0 16.0 38.0 45-49 33.04515 38.0 34.0 38.0 16.0 38.0 50-54 32.891549999999995 38.0 33.8 38.0 16.0 38.0 55-59 32.66675 38.0 33.4 38.0 16.0 38.0 60-64 32.33115 38.0 32.6 38.0 15.4 38.0 65-69 32.06079999999999 38.0 32.2 38.0 14.8 38.0 70-74 31.181150000000002 38.0 29.6 38.0 8.8 38.0 75-79 30.729149999999997 37.4 29.0 38.0 2.0 38.0 80-84 30.35055 37.0 28.6 38.0 2.0 38.0 85-89 30.0939 37.0 27.6 38.0 2.0 38.0 90-94 29.58035 37.0 25.6 38.0 2.0 38.0 95-99 28.83605 36.0 22.8 38.0 2.0 38.0 100-104 28.5468 36.0 21.8 38.0 2.0 38.0 105-109 27.7668 35.2 16.2 38.0 2.0 38.0 110-114 26.82355 34.0 15.0 38.0 2.0 38.0 115-119 26.32855 34.0 15.0 38.0 2.0 38.0 120-124 25.495350000000002 33.6 14.0 38.0 2.0 38.0 125-129 24.62075 32.6 13.2 38.0 2.0 38.0 130-134 23.33625 31.0 6.4 37.2 2.0 38.0 135-139 22.0668 27.0 2.0 36.2 2.0 38.0 140-144 20.361800000000002 23.4 2.0 35.4 2.0 38.0 145-149 17.6796 12.2 2.0 33.8 2.0 38.0 150 11.97075 2.0 2.0 29.0 2.0 35.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 86.0 3 29.0 4 19.0 5 8.0 6 21.0 7 19.0 8 17.0 9 11.0 10 22.0 11 27.0 12 39.0 13 45.0 14 42.0 15 42.0 16 64.0 17 42.0 18 49.0 19 50.0 20 35.0 21 53.0 22 56.0 23 63.0 24 66.0 25 87.0 26 65.0 27 92.0 28 104.0 29 138.0 30 157.0 31 164.0 32 243.0 33 283.0 34 407.0 35 509.0 36 585.0 37 261.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 39.546027742749054 18.764186633039092 8.953341740226985 32.73644388398487 2 24.10489157841654 30.23197175995966 28.895612708018152 16.767523953605647 3 22.844175491679273 22.970247100353 31.820474029248615 22.365103378719112 4 25.245901639344265 29.02900378310214 18.865069356872635 26.86002522068096 5 31.37452711223203 33.114754098360656 18.31021437578815 17.200504413619168 6 27.490542244640604 33.2156368221942 19.722572509457756 19.57124842370744 7 20.832282471626733 24.186633039092058 33.694829760403536 21.28625472887768 8 20.504413619167718 28.297604035308954 24.312736443883985 26.885245901639344 9 29.508196721311474 20.983606557377048 24.91803278688525 24.59016393442623 10-14 26.926568489005447 25.665725237038533 23.083518257010287 24.324188016945733 15-19 26.159975791809565 24.304014524914265 25.514424046802503 24.021585636473674 20-24 27.276853252647506 27.423096318709028 23.338376197680283 21.961674230963187 25-29 26.150975745045635 28.707579042912613 22.72200090766981 22.419444304371943 30-34 27.258975393303754 25.161355385235986 25.44372730939895 22.135941912061316 35-39 25.119749911763222 25.442444410830433 25.06932889628397 24.36847678112237 40-44 28.63120746155785 24.05344088732039 25.08192588858079 22.23342576254096 45-49 25.312626058894715 24.067164179104477 24.96974586526825 25.650463896732557 50-54 25.526979324256178 25.103378719112456 25.153807362581947 24.215834594049422 55-59 24.10993444276349 26.944024205748867 25.985879979828542 22.9601613716591 60-64 23.817448310640444 31.00353000504286 23.02067574382249 22.1583459404942 65-69 24.26489130983003 30.236546123972364 22.852675644323398 22.64588692187421 70-74 24.978566745675526 29.30051944122245 23.18825961974885 22.532654193353167 75-79 24.78942855701821 28.405709386190548 23.392343773642 23.412518283149243 80-84 25.448860197700224 27.925156344563245 23.562638692757716 23.06334476497882 85-89 25.231995158361915 27.884809360500302 23.996368771434334 22.88682670970345 90-94 24.871381014829012 27.67073539796227 24.26107132048825 23.196812266720467 95-99 24.321597901745186 28.568546353273476 23.701200443861595 23.40865530111974 100-104 25.33662817086086 28.13555902970397 23.985072368752835 22.542740430682333 105-109 24.292702607292348 29.214786423924554 22.99662111049473 23.495889858288365 110-114 24.4855759531975 28.888440589065965 23.50716158967117 23.11882186806536 115-119 24.572466326993897 28.366039449124752 23.341572920345055 23.719921303536296 120-124 24.04399152456866 29.32600141257189 23.39319947533044 23.236807587529007 125-129 23.91808736003228 29.723595278926663 23.82729748814688 22.531019872894177 130-134 23.81600847329399 29.631310838755233 23.51339083068543 23.039289857265345 135-139 24.544858540521457 29.502244187805736 23.470674264965457 22.482223006707347 140-144 23.692571486207072 30.087245952897273 23.087397246457208 23.132785314438447 145-149 24.10949200566687 29.85731633272617 22.586520947176687 23.446670714430276 150 23.883984867591426 32.88776796973518 20.201765447667086 23.026481715006305 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 33.0 1 16.5 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 0.0 11 0.5 12 0.5 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.5 20 0.5 21 0.5 22 1.5 23 2.0 24 2.5 25 2.0 26 1.5 27 3.0 28 7.5 29 10.0 30 14.0 31 14.5 32 20.0 33 26.5 34 26.0 35 34.5 36 56.5 37 76.0 38 86.0 39 99.5 40 125.5 41 151.5 42 164.5 43 176.0 44 183.5 45 189.0 46 196.0 47 196.5 48 193.5 49 180.0 50 157.5 51 140.0 52 125.0 53 109.5 54 99.0 55 90.5 56 85.5 57 84.5 58 88.5 59 93.0 60 85.5 61 86.0 62 81.5 63 63.0 64 51.0 65 54.5 66 52.0 67 44.0 68 37.0 69 26.0 70 20.5 71 18.0 72 13.5 73 7.5 74 4.0 75 2.0 76 1.5 77 1.5 78 1.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.5 84 0.5 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 0.8750000000000001 2 0.8500000000000001 3 0.8500000000000001 4 0.8750000000000001 5 0.8750000000000001 6 0.8750000000000001 7 0.8750000000000001 8 0.8750000000000001 9 0.8750000000000001 10-14 0.86 15-19 0.86 20-24 0.8500000000000001 25-29 0.845 30-34 0.84 35-39 0.835 40-44 0.8250000000000001 45-49 0.84 50-54 0.8500000000000001 55-59 0.8500000000000001 60-64 0.8500000000000001 65-69 0.865 70-74 0.855 75-79 0.865 80-84 0.86 85-89 0.86 90-94 0.8699999999999999 95-99 0.8699999999999999 100-104 0.855 105-109 0.855 110-114 0.86 115-119 0.885 120-124 0.89 125-129 0.8699999999999999 130-134 0.865 135-139 0.855 140-144 0.855 145-149 1.18 150 0.8750000000000001 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 94.69999999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 98.52164730728616 93.30000000000001 2 1.1879619852164731 2.25 3 0.07919746568109821 0.22499999999999998 4 0.07919746568109821 0.3 5 0.05279831045406547 0.25 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.026399155227032733 0.22499999999999998 >10 0.026399155227032733 0.8250000000000001 >50 0.0 0.0 >100 0.026399155227032733 2.625 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences fail #Sequence Count Percentage Possible Source GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG 105 2.625 Illumina Single End PCR Primer 1 (100% over 50bp) NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 33 0.8250000000000001 No Hit AAGCAGAAGACGGCATACGAGATTGACATGTGACTGGAGTTCAGACGTGT 9 0.22499999999999998 TruSeq Adapter, Index 15 (98% over 50bp) AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC 5 0.125 Illumina Single End PCR Primer 1 (100% over 50bp) GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTAGCCG 5 0.125 Illumina Single End PCR Primer 1 (98% over 50bp) >>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 0.225 0.0 0.0 0.0 0.0 2 0.225 0.0 0.0 0.0 0.0 3 0.225 0.0 0.0 0.0 0.0 4 0.225 0.0 0.0 0.0 0.0 5 0.225 0.0 0.0 0.0 0.0 6 0.225 0.0 0.0 0.0 0.0 7 0.225 0.0 0.0 0.0 0.0 8 0.225 0.0 0.0 0.0 0.0 9 0.225 0.0 0.0 0.0 0.0 10-11 0.225 0.0 0.0 0.0 0.0 12-13 0.225 0.0 0.0 0.0 0.0 14-15 0.225 0.0 0.0 0.0 0.0 16-17 0.225 0.0 0.0 0.0 0.0 18-19 0.225 0.0 0.0 0.0 0.0 20-21 0.225 0.0 0.0 0.0 0.0 22-23 0.225 0.0 0.0 0.0 0.0 24-25 0.225 0.0 0.0 0.0 0.0 26-27 0.225 0.0 0.0 0.0 0.0 28-29 0.225 0.0 0.0 0.0 0.0 30-31 0.225 0.0 0.0 0.0 0.0 32-33 0.225 0.0 0.0 0.0 0.0 34-35 0.25 0.0 0.0 0.0 0.0 36-37 0.275 0.0 0.0 0.0 0.0 38-39 0.3125 0.0 0.0 0.0 0.0 40-41 0.325 0.0 0.0 0.0 0.0 42-43 0.3875 0.0 0.0 0.0 0.0 44-45 0.4 0.0 0.0 0.0 0.0 46-47 0.4375 0.0 0.0 0.0 0.0 48-49 0.4875 0.0 0.0 0.0 0.0 50-51 0.5 0.0 0.0 0.0 0.0 52-53 0.5874999999999999 0.0 0.0 0.0 0.0 54-55 0.625 0.0 0.0 0.0 0.0 56-57 0.7 0.0 0.0 0.0 0.0 58-59 0.75 0.0 0.0 0.0 0.0 60-61 0.75 0.0 0.0 0.0 0.0 62-63 0.775 0.0 0.0 0.0 0.0 64-65 0.775 0.0 0.0 0.0 0.0 66-67 0.775 0.0 0.0 0.0 0.0 68-69 0.775 0.0 0.0 0.0 0.0 70-71 0.775 0.0 0.0 0.0 0.0 72-73 0.775 0.0 0.0 0.0 0.0 74-75 0.775 0.0 0.0 0.0 0.0 76-77 0.775 0.0 0.0 0.0 0.0 78-79 0.775 0.0 0.0 0.0 0.0 80-81 0.775 0.0 0.0 0.0 0.0 82-83 0.7875000000000001 0.0 0.0 0.0 0.0 84-85 0.8 0.0 0.0 0.0 0.0 86-87 0.8 0.0 0.0 0.0 0.0 88-89 0.8 0.0 0.0 0.0 0.0 90-91 0.8125 0.0 0.0 0.0 0.0 92-93 0.825 0.0 0.0 0.0 0.0 94-95 0.8374999999999999 0.0 0.0 0.0 0.0 96-97 0.875 0.0 0.0 0.0 0.0 98-99 0.9125000000000001 0.0 0.0 0.0 0.0 100-101 0.95 0.0 0.0 0.0 0.0 102-103 0.95 0.0 0.0 0.0 0.0 104-105 0.95 0.0 0.0 0.0 0.0 106-107 0.975 0.0 0.0 0.0 0.0 108-109 1.0750000000000002 0.0 0.0 0.0 0.0 110-111 1.2 0.0 0.0 0.0 0.0 112-113 1.275 0.0 0.0 0.0 0.0 114-115 1.35 0.0 0.0 0.0 0.0 116-117 1.4375 0.0 0.0 0.0 0.0 118-119 1.55 0.0 0.0 0.0 0.0 120-121 1.7625000000000002 0.0 0.0 0.0 0.0 122-123 1.9874999999999998 0.0 0.0 0.0 0.0 124-125 2.1125 0.0 0.0 0.0 0.0 126-127 2.2125000000000004 0.0 0.0 0.0 0.0 128-129 2.25 0.0 0.0 0.0 0.0 130-131 2.3875 0.0 0.0 0.0 0.0 132-133 2.5374999999999996 0.0 0.0 0.0 0.0 134-135 2.6375 0.0 0.0 0.0 0.0 136-137 2.7375 0.0 0.0 0.0 0.0 138 2.8 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GAGCGTC 20 3.6916917E-4 107.97188 9 CGGAAGA 20 3.6916917E-4 107.97188 4 AGAGCGT 25 8.965498E-4 86.377495 8 AAGAGCG 35 3.1452495E-5 82.26428 7 GAAGAGC 35 3.1452495E-5 82.26428 6 GGAAGAG 35 0.003408044 61.69821 5 GGGAAAG 20 0.006147062 28.792501 20-24 >>END_MODULE Read 1950005 spots for SRR8096908.sra Written 1950005 spots for SRR8096908.sra Read 1949991 spots for SRR8096908.sra Written 1949991 spots for SRR8096908.sra Read 1949991 spots for SRR8096908.sra Written 1949991 spots for SRR8096908.sra Read 1949991 spots for SRR8096908.sra Written 1949991 spots for SRR8096908.sra Read 1949991 spots for SRR8096908.sra Written 1949991 spots for SRR8096908.sra Read 1949991 spots for SRR8096908.sra Written 1949991 spots for SRR8096908.sra Read 1949991 spots for SRR8096908.sra Written 1949991 spots for SRR8096908.sra Read 1949991 spots for SRR8096908.sra Written 1949991 spots for SRR8096908.sra Read 1949991 spots for SRR8096908.sra Written 1949991 spots for SRR8096908.sra Read 1949991 spots for SRR8096908.sra Written 1949991 spots for SRR8096908.sra Read 1949991 spots for SRR8096908.sra Written 1949991 spots for SRR8096908.sra Read 1949991 spots for SRR8096908.sra Written 1949991 spots for SRR8096908.sra Read 1949991 spots for SRR8096908.sra Written 1949991 spots for SRR8096908.sra Read 1949991 spots for SRR8096908.sra Written 1949991 spots for SRR8096908.sra Read 1949991 spots for SRR8096908.sra Written 1949991 spots for SRR8096908.sra Read 1949991 spots for SRR8096908.sra Written 1949991 spots for SRR8096908.sra Read 1949991 spots for SRR8096908.sra Written 1949991 spots for SRR8096908.sra Read 1949991 spots for SRR8096908.sra Written 1949991 spots for SRR8096908.sra Read 1949991 spots for SRR8096908.sra Written 1949991 spots for SRR8096908.sra Read 1949991 spots for SRR8096908.sra Written 1949991 spots for SRR8096908.sra SRR ids: ['SRR8096908.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_gti1_isc SRR8096908.sra spots: 38999834 blocks: [[1, 1949991], [1949992, 3899982], [3899983, 5849973], [5849974, 7799964], [7799965, 9749955], [9749956, 11699946], [11699947, 13649937], [13649938, 15599928], [15599929, 17549919], [17549920, 19499910], [19499911, 21449901], [21449902, 23399892], [23399893, 25349883], [25349884, 27299874], [27299875, 29249865], [29249866, 31199856], [31199857, 33149847], [33149848, 35099838], [35099839, 37049829], [37049830, 38999834]] SRR8096908 file size 13117892 SRR8096908 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 SRR8096908 SRR8096908_1.fastq SRR8096908_2.fastq Input file: SRR8096908_1.fastq Paired file: SRR8096908_2.fastq trimmed: SRR8096908-trimmed-pair1.fastq, SRR8096908-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 Sat Dec 7 23:45:16 2024 >> started Sat Dec 7 23:50:33 2024 >> done (316.611s) 38999834 read pairs processed; of these: 163582 ( 0.42%) short read pairs filtered out after trimming by size control 3210474 ( 8.23%) empty read pairs filtered out after trimming by size control 35625778 (91.35%) read pairs available; of these: 18685106 (52.45%) trimmed read pairs available after processing 16940672 (47.55%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 218 0.00% 19 344 0.00% 20 182 0.00% 21 325 0.00% 22 434 0.00% 23 279 0.00% 24 374 0.00% 25 303 0.00% 26 407 0.00% 27 416 0.00% 28 665 0.00% 29 1384 0.00% 30 6296 0.02% 31 5229 0.01% 32 3472 0.01% 33 2593 0.01% 34 12761 0.04% 35 11536 0.03% 36 20061 0.06% 37 6843 0.02% 38 10148 0.03% 39 14701 0.04% 40 30092 0.08% 41 23388 0.07% 42 17667 0.05% 43 10711 0.03% 44 12570 0.04% 45 11070 0.03% 46 23082 0.06% 47 17579 0.05% 48 9142 0.03% 49 17089 0.05% 50 13408 0.04% 51 28158 0.08% 52 17767 0.05% 53 18505 0.05% 54 16496 0.05% 55 19651 0.06% 56 19611 0.06% 57 10202 0.03% 58 8292 0.02% 59 7016 0.02% 60 6277 0.02% 61 17235 0.05% 62 10538 0.03% 63 3930 0.01% 64 3558 0.01% 65 3943 0.01% 66 3965 0.01% 67 4135 0.01% 68 4683 0.01% 69 5544 0.02% 70 6380 0.02% 71 6677 0.02% 72 5980 0.02% 73 6583 0.02% 74 5461 0.02% 75 5974 0.02% 76 6388 0.02% 77 7306 0.02% 78 9084 0.03% 79 9073 0.03% 80 8769 0.02% 81 8776 0.02% 82 9351 0.03% 83 12067 0.03% 84 21555 0.06% 85 20641 0.06% 86 23293 0.07% 87 24697 0.07% 88 24156 0.07% 89 23829 0.07% 90 22560 0.06% 91 22673 0.06% 92 22767 0.06% 93 22760 0.06% 94 23839 0.07% 95 24693 0.07% 96 26874 0.08% 97 29087 0.08% 98 31200 0.09% 99 33461 0.09% 100 33408 0.09% 101 35187 0.10% 102 36835 0.10% 103 39287 0.11% 104 42656 0.12% 105 42934 0.12% 106 44689 0.13% 107 46516 0.13% 108 47951 0.13% 109 48542 0.14% 110 49260 0.14% 111 50506 0.14% 112 51171 0.14% 113 52565 0.15% 114 53768 0.15% 115 55899 0.16% 116 58590 0.16% 117 61356 0.17% 118 62761 0.18% 119 66328 0.19% 120 69242 0.19% 121 73110 0.21% 122 75724 0.21% 123 80160 0.23% 124 84264 0.24% 125 88280 0.25% 126 93283 0.26% 127 98617 0.28% 128 103526 0.29% 129 109440 0.31% 130 116605 0.33% 131 123586 0.35% 132 129021 0.36% 133 135918 0.38% 134 145270 0.41% 135 154818 0.43% 136 165001 0.46% 137 176690 0.50% 138 194043 0.54% 139 212524 0.60% 140 232814 0.65% 141 261381 0.73% 142 291586 0.82% 143 334092 0.94% 144 406752 1.14% 145 503296 1.41% 146 664435 1.87% 147 995702 2.79% 148 1929514 5.42% 149 8655974 24.30% 150 16940672 47.55% 35625778 reads passed initial QC criterion=sequence-density sequence-density=1.04 sequence-density-rank=1 fanout-score=2.07 fanout-score-rank=30 prefix-density=1.06 prefix-fanout=2.0 sequence=AACATGGAGAACATGGCGAGGCGGCCGTTCTTGATCTCCTTCACCTTGAGCTCAGCGAA criterion=fanout-score sequence-density=0.09 sequence-density-rank=32 fanout-score=13.91 fanout-score-rank=1 prefix-density=0.48 prefix-fanout=2.6 sequence=GCCGGGAACGATTCCCTGCTCGACAAGGATGTCAACAATCTTCTTGCCATCAACAGTCGATTGGTAGAGGGTCTCCTCGAAGAGGATAGCACCAGAGATGTAATTTCCCAGGCCTGGTGGAGTGACAAGGAGGGTACGGTAAGCCTGGCGGTTAGCCTCAGTGTTCTCAAGGCCAATCGAGTCAAGTCTCTTTCCACAGGTAGCATTGGACTCATCCATGGCTAGGATGCCCCTTCCTGGTGATGCGATGGTTTTCGCGGTCTTGACAAGTTCATCAGCGTATGCGCTGGCACGGACAACCATGGAGACGGTCATCTGCTTGGGAGTGGCAGCCTGGCGGGTGGTGCCCCATTCGGACTTCTTGGGAAGGAAAGACGATTTGAGGATAGTAGCCGAGGCCATTGTTTCTGGCTCCAAAGGCAAGAGGATCAG criterion=sequence-density sequence-density=0.66 sequence-density-rank=1 fanout-score=3.29 fanout-score-rank=19 prefix-density=0.76 prefix-fanout=2.8 sequence=GAGTTCAGCAAGGTCGG criterion=fanout-score sequence-density=0.02 sequence-density-rank=31 fanout-score=46.54 fanout-score-rank=1 prefix-density=0.10 prefix-fanout=7.3 sequence=GCAGCAGCCATTACTTGATCATCTGAAAAATCTTAATCCAGATCAGACCAAGCAGAGCAGAGATGTCTGCTACCTTCTCGTCCACCGTCGGAGCTCCGGCTTCTACGCCAACCAGCTTCCTTGGGAAGAAGCTCAAGAAGCAGGTGACCTCGGCCGTGAACTACCATGGCAAGAGCACCAAGGCCAACAGATTCACAGTCATGGCCAAGGAGGTGGACGAGTCAAAGCAGACTGACCAGGACAGGTGGAAGGGCCTCGCCTACGATATCTCCGACGACCAGCAGGACATCACCAGGGGGAAGGGTATCGTCGACTCGCTCTTCCAGGCGCCCATGGGCGACGGTACCCACGTGGCCGTCCTCAGCTCCCAAGAGTACATCAGCCAGGGCCTAAGGAAGTACGACTTCGACAACA SRR8096908 testing PE reads STAR mapping to Ensembl genome Unpaired reads removal Started job on | Dec 08 03:08:12 Started mapping on | Dec 08 03:08:13 Finished on | Dec 08 03:32:16 Mapping speed, Million of reads per hour | 88.55 Number of input reads | 35494746 Average input read length | 269 UNIQUE READS: Uniquely mapped reads number | 31554104 Uniquely mapped reads % | 88.90% Average mapped length | 272.12 Number of splices: Total | 31929053 Number of splices: Annotated (sjdb) | 30239336 Number of splices: GT/AG | 31512579 Number of splices: GC/AG | 364893 Number of splices: AT/AC | 9449 Number of splices: Non-canonical | 42132 Mismatch rate per base, % | 0.32% Deletion rate per base | 0.01% Deletion average length | 1.87 Insertion rate per base | 0.01% Insertion average length | 1.77 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 381792 % of reads mapped to multiple loci | 1.08% Number of reads mapped to too many loci | 10848 % of reads mapped to too many loci | 0.03% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 9.83% % of reads unmapped: other | 0.16% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 3716056 3716056 3716056 N_multimapping 381792 381792 381792 N_noFeature 1108878 30579375 1348489 N_ambiguous 886862 4015 155055 UnstrandedReadsAssigned:29558364 PositiveStrandReadsAssigned:970714 NegativeStrandReadsAssigned:30050560 Dataset is classified negative stranded MeadianReadLen=130 20thPercentileLength=129 echo kmer=125 SRR8096908 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: SRR8096908-trimmed-pair1.fastq SRR8096908-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 35,494,746 reads, 32,416,045 reads pseudoaligned [quant] estimated average fragment length: 252.655 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,189 rounds 52973 SRR8096908.ke.tsv 35125 SRR8096908.se.tsv 88098 total ==> SRR8096908.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 684.741 0 0 PNS24247 1044 792.345 92.9218 5.03418 PNS24249 1928 1676.34 30.3114 0.776189 PNS24246 1044 792.345 92.9218 5.03418 PNS24248 1044 792.345 92.9218 5.03418 PNS24244 1471 1219.34 253.923 8.93923 PNS24243 293 93.4704 0 0 KQK14069 1603 1351.34 6344.77 201.546 KQK14071 474 237.201 108.106 19.5639 ==> SRR8096908.se.tsv <== BRADI_1g14170v3 6381 BRADI_1g53295v3 25 BRADI_1g59795v3 1586 BRADI_1g07683v3 0 BRADI_1g00485v3 4 BRADI_1g20270v3 213 BRADI_1g74790v3 97 BRADI_1g09890v3 0 BRADI_1g77505v3 531 BRADI_1g48960v3 0 SRR8096908 completed mapping pipeline successfully