Starting /dee2/code/volunteer_pipeline.sh SRR6053286 current disk space = 3052645376000 free memory = 1507820616 SRR6053286 SRAfilesize 585e9020ff9a3e6ed670e8144fd68e98 SRR6053286.sra SRR6053286.sra file validated SRR6053286 is paired end SRR6053286 is conventional basespace SRR6053286 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6053286_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 32.11525 34.0 33.0 34.0 32.0 34.0 2 33.212 34.0 33.0 34.0 32.0 34.0 3 33.29275 34.0 33.0 34.0 32.0 34.0 4 33.422 34.0 34.0 34.0 33.0 34.0 5 33.406 34.0 33.0 34.0 33.0 34.0 6 36.87525 38.0 37.0 38.0 35.0 38.0 7 37.25725 38.0 38.0 38.0 36.0 38.0 8 37.305 38.0 38.0 38.0 37.0 38.0 9 37.49225 38.0 38.0 38.0 37.0 38.0 10-14 37.501099999999994 38.0 38.0 38.0 37.0 38.0 15-19 37.433949999999996 38.0 38.0 38.0 37.0 38.0 20-24 37.4131 38.0 38.0 38.0 37.0 38.0 25-29 37.4183 38.0 38.0 38.0 37.0 38.0 30-34 37.420049999999996 38.0 38.0 38.0 37.0 38.0 35-39 37.358050000000006 38.0 38.0 38.0 37.0 38.0 40-44 37.266749999999995 38.0 38.0 38.0 36.8 38.0 45-49 37.25025 38.0 38.0 38.0 36.8 38.0 50-54 37.198249999999994 38.0 38.0 38.0 36.2 38.0 55-59 37.18489999999999 38.0 38.0 38.0 36.2 38.0 60-64 37.17535 38.0 38.0 38.0 36.2 38.0 65-69 37.09085 38.0 38.0 38.0 36.0 38.0 70-74 37.09955 38.0 38.0 38.0 36.0 38.0 75-79 37.05694999999999 38.0 38.0 38.0 36.0 38.0 80-84 36.9944 38.0 38.0 38.0 36.0 38.0 85-89 36.976549999999996 38.0 38.0 38.0 36.0 38.0 90-94 36.86035 38.0 38.0 38.0 35.6 38.0 95-99 36.7607 38.0 38.0 38.0 35.0 38.0 100-104 36.6885 38.0 38.0 38.0 35.0 38.0 105-109 36.6683 38.0 38.0 38.0 34.6 38.0 110-114 36.53955 38.0 38.0 38.0 34.0 38.0 115-119 36.39205 38.0 38.0 38.0 34.0 38.0 120-124 36.34815 38.0 38.0 38.0 34.0 38.0 125-129 36.2399 38.0 38.0 38.0 33.6 38.0 130-134 36.057500000000005 38.0 38.0 38.0 33.2 38.0 135-139 35.87565 38.0 37.4 38.0 33.0 38.0 140-144 35.628099999999996 38.0 36.4 38.0 31.8 38.0 145-149 35.2141 38.0 36.0 38.0 31.2 38.0 150-151 32.7415 37.0 33.5 38.0 16.5 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 16 2.0 17 2.0 18 5.0 19 4.0 20 2.0 21 6.0 22 3.0 23 4.0 24 4.0 25 13.0 26 9.0 27 17.0 28 22.0 29 30.0 30 39.0 31 40.0 32 56.0 33 99.0 34 115.0 35 198.0 36 440.0 37 2890.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 36.45127670661803 12.350182386659718 5.862428348097968 45.33611255862428 2 18.55 15.0 39.550000000000004 26.900000000000002 3 17.275 17.849999999999998 28.249999999999996 36.625 4 21.175 26.55 24.349999999999998 27.925 5 22.425 32.975 24.3 20.3 6 20.4 34.300000000000004 24.775 20.525 7 14.075 26.875 41.375 17.675 8 15.625 25.525 33.0 25.85 9 15.325 24.15 36.675000000000004 23.849999999999998 10-14 18.35 30.220000000000002 28.355000000000004 23.075000000000003 15-19 19.08 29.294999999999998 28.15 23.474999999999998 20-24 18.54 28.775000000000002 28.37 24.315 25-29 19.509999999999998 28.910000000000004 28.544999999999998 23.035 30-34 19.689999999999998 29.310000000000002 27.625 23.375 35-39 19.075 29.37 27.245 24.310000000000002 40-44 19.665 28.494999999999997 28.02 23.82 45-49 19.155 28.904999999999998 28.199999999999996 23.74 50-54 20.075000000000003 29.404999999999998 27.32 23.200000000000003 55-59 19.705000000000002 28.925 27.71 23.66 60-64 19.685 28.83 27.639999999999997 23.845 65-69 19.57 28.715000000000003 27.92 23.794999999999998 70-74 19.005 28.52 28.64 23.835 75-79 19.564999999999998 28.499999999999996 28.465 23.47 80-84 19.759999999999998 28.685 28.294999999999998 23.26 85-89 19.81 28.485 27.735 23.97 90-94 19.650000000000002 29.395 27.500000000000004 23.455000000000002 95-99 19.735 28.84 27.834999999999997 23.59 100-104 20.07 28.395 27.544999999999998 23.990000000000002 105-109 20.455000000000002 28.76 27.134999999999998 23.65 110-114 19.919999999999998 28.26 28.060000000000002 23.76 115-119 20.75 28.410000000000004 27.060000000000002 23.78 120-124 20.565 28.945 26.640000000000004 23.849999999999998 125-129 21.16 28.48 26.33 24.03 130-134 21.62 28.42 26.445 23.515 135-139 21.305 28.52 26.66 23.515 140-144 21.035 28.555000000000003 26.38 24.03 145-149 20.49 29.04 26.090000000000003 24.38 150-151 20.6125 27.825 26.8125 24.75 >>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 0.5 15 0.5 16 0.5 17 1.0 18 0.5 19 0.5 20 1.0 21 0.5 22 0.5 23 1.5 24 3.0 25 3.5 26 3.5 27 6.5 28 14.5 29 20.5 30 20.0 31 27.0 32 34.5 33 44.5 34 65.0 35 81.5 36 97.5 37 131.5 38 154.5 39 181.0 40 213.0 41 230.0 42 253.0 43 266.5 44 273.5 45 270.0 46 249.0 47 240.0 48 231.0 49 193.0 50 158.5 51 128.5 52 101.5 53 79.5 54 57.0 55 43.0 56 38.0 57 29.5 58 17.0 59 10.5 60 6.5 61 5.0 62 2.5 63 2.5 64 2.0 65 0.5 66 0.5 67 0.0 68 0.5 69 0.5 70 0.5 71 0.5 72 0.5 73 0.5 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 4.05 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 99.7 #Duplication Level Percentage of deduplicated Percentage of total 1 99.72417251755266 99.425 2 0.25075225677031093 0.5 3 0.025075225677031094 0.075 4 0.0 0.0 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences pass >>END_MODULE >>Adapter Content 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 0.0 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 0.0625 0.0 0.0 0.0 0.0 74-75 0.0875 0.0 0.0 0.0 0.0 76-77 0.1375 0.0 0.0 0.0 0.0 78-79 0.15 0.0 0.0 0.0 0.0 80-81 0.15 0.0 0.0 0.0 0.0 82-83 0.1875 0.0 0.0 0.0 0.0 84-85 0.2375 0.0 0.0 0.0 0.0 86-87 0.35 0.0 0.0 0.0 0.0 88-89 0.4 0.0 0.0 0.0 0.0 90-91 0.425 0.0 0.0 0.0 0.0 92-93 0.625 0.0 0.0 0.0 0.0 94-95 0.9125 0.0 0.0 0.0 0.0 96-97 1.0625 0.0 0.0 0.0 0.0 98-99 1.3 0.0 0.0 0.0 0.0 100-101 1.5625 0.0 0.0 0.0 0.0 102-103 1.8624999999999998 0.0 0.0 0.0 0.0 104-105 2.1500000000000004 0.0 0.0 0.0 0.0 106-107 2.4000000000000004 0.0 0.0 0.0 0.0 108-109 2.8125 0.0 0.0 0.0 0.0 110-111 3.3625 0.0 0.0 0.0 0.0 112-113 3.8875 0.0 0.0 0.0 0.0 114-115 4.35 0.0 0.0 0.0 0.0 116-117 4.8375 0.0 0.0 0.0 0.0 118-119 5.3 0.0 0.0 0.0 0.0 120-121 6.025 0.0 0.0 0.0 0.0 122-123 6.6625 0.0 0.0 0.0 0.0 124-125 7.075 0.0 0.0 0.0 0.0 126-127 7.7125 0.0 0.0 0.0 0.0 128-129 8.475000000000001 0.0 0.0 0.0 0.0 130-131 9.2875 0.0 0.0 0.0 0.0 132-133 10.2 0.0 0.0 0.0 0.0 134-135 11.125 0.0 0.0 0.0 0.0 136-137 11.9875 0.0 0.0 0.0 0.0 138-139 12.525 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CTCCCCA 10 0.006836113 144.9625 8 TCCCCAA 10 0.006836113 144.9625 9 >>END_MODULE SRR6053286 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6053286_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.836 33.0 33.0 34.0 32.0 34.0 2 32.84175 33.0 33.0 34.0 32.0 34.0 3 32.9745 33.0 33.0 34.0 32.0 34.0 4 32.914 34.0 33.0 34.0 32.0 34.0 5 32.9965 34.0 33.0 34.0 32.0 34.0 6 37.08525 38.0 38.0 38.0 37.0 38.0 7 37.07475 38.0 38.0 38.0 37.0 38.0 8 37.0855 38.0 38.0 38.0 36.0 38.0 9 36.988 38.0 38.0 38.0 36.0 38.0 10-14 37.1318 38.0 38.0 38.0 36.8 38.0 15-19 37.03015 38.0 38.0 38.0 36.2 38.0 20-24 37.088800000000006 38.0 38.0 38.0 36.8 38.0 25-29 37.0757 38.0 38.0 38.0 36.8 38.0 30-34 37.07395 38.0 38.0 38.0 36.4 38.0 35-39 37.089 38.0 38.0 38.0 37.0 38.0 40-44 37.0185 38.0 38.0 38.0 36.2 38.0 45-49 37.03679999999999 38.0 38.0 38.0 36.4 38.0 50-54 37.01845 38.0 38.0 38.0 36.0 38.0 55-59 36.9806 38.0 38.0 38.0 36.0 38.0 60-64 36.901849999999996 38.0 38.0 38.0 36.0 38.0 65-69 36.84740000000001 38.0 38.0 38.0 36.0 38.0 70-74 36.89125 38.0 38.0 38.0 36.0 38.0 75-79 36.80285000000001 38.0 38.0 38.0 35.8 38.0 80-84 36.7923 38.0 38.0 38.0 35.8 38.0 85-89 36.7457 38.0 38.0 38.0 35.6 38.0 90-94 36.6269 38.0 38.0 38.0 35.2 38.0 95-99 36.54915 38.0 38.0 38.0 34.8 38.0 100-104 36.52235 38.0 38.0 38.0 34.8 38.0 105-109 36.43675 38.0 38.0 38.0 34.2 38.0 110-114 36.28595 38.0 38.0 38.0 34.2 38.0 115-119 36.17965 38.0 38.0 38.0 34.0 38.0 120-124 35.897149999999996 38.0 38.0 38.0 33.2 38.0 125-129 35.924549999999996 38.0 38.0 38.0 33.0 38.0 130-134 35.73095 38.0 38.0 38.0 32.6 38.0 135-139 35.62480000000001 38.0 37.8 38.0 33.0 38.0 140-144 35.32405 38.0 36.0 38.0 31.0 38.0 145-149 34.77315 38.0 36.0 38.0 29.8 38.0 150-151 31.692625 36.5 32.0 38.0 15.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 3.0 3 6.0 4 1.0 5 0.0 6 1.0 7 1.0 8 0.0 9 1.0 10 0.0 11 1.0 12 2.0 13 1.0 14 4.0 15 3.0 16 1.0 17 4.0 18 4.0 19 3.0 20 3.0 21 3.0 22 11.0 23 9.0 24 18.0 25 13.0 26 11.0 27 19.0 28 37.0 29 31.0 30 38.0 31 47.0 32 58.0 33 79.0 34 126.0 35 186.0 36 413.0 37 2862.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 32.375 25.825 10.2 31.6 2 25.575 27.05 33.85 13.525 3 18.15 29.049999999999997 32.824999999999996 19.975 4 21.725 35.3 24.6 18.375 5 24.975 36.575 21.7 16.75 6 20.440330247685765 39.15436577433075 23.267450587940957 17.137853390042533 7 19.849812265331664 21.476846057571965 39.774718397997496 18.89862327909887 8 20.275344180225282 25.00625782227785 28.410513141426787 26.307884856070086 9 21.562734785875282 22.890057600801402 33.007763586275985 22.539444027047335 10-14 23.118521856692205 29.02208201892745 26.77882930248861 21.080566821891743 15-19 23.16358720144209 28.040658955485455 28.47629062140103 20.319463221671423 20-24 23.055736391406683 28.879763633632127 27.5176523611598 20.546847613801393 25-29 22.8747371583058 28.50205266846901 28.236707720036048 20.386502453189145 30-34 23.279575277972555 28.648702794751074 27.832314935390162 20.239406991886206 35-39 23.196676177604246 28.247484607298396 27.416529008359614 21.13931020673775 40-44 23.34451173732419 27.819210170679217 28.57500375394164 20.261274338054957 45-49 23.160476524176595 27.560316347982784 28.57142857142857 20.707778556412055 50-54 23.178973717146434 28.370463078848562 28.195244055068834 20.25531914893617 55-59 23.181658907743905 28.087300395454772 28.743054512689593 19.987986184111726 60-64 23.745618427641464 28.15723585378067 27.871807711567353 20.225338007010514 65-69 23.142027243589745 28.114983974358974 28.305288461538463 20.437700320512818 70-74 23.783052884615387 27.564102564102566 28.21514423076923 20.437700320512818 75-79 23.5235185092421 27.676200971797826 28.302359364824923 20.497921154135152 80-84 23.88941753893925 27.670656583362547 28.191516001402313 20.248409876295888 85-89 23.742736926467643 27.880184331797235 27.584652374273695 20.79242636746143 90-94 23.73560340510766 27.86680020030045 28.11717576364547 20.28042063094642 95-99 23.927731344777538 27.88148741304239 27.946549221760677 20.244232020419396 100-104 24.204044853824588 27.828394072887463 27.48798558269924 20.479575490588704 105-109 23.75419442079431 28.872639855762007 27.53042520158261 19.84274052186107 110-114 24.08817635270541 28.051102204408817 27.650300601202403 20.210420841683366 115-119 24.933633859253693 27.913849236163284 26.98722764838467 20.165289256198346 120-124 24.098557692307693 28.740985576923077 27.063301282051285 20.09715544871795 125-129 25.354299163703743 28.414041764735337 26.676348339926886 19.55531073163403 130-134 25.550991785213384 28.446203165698257 26.627930274494087 19.374874774594268 135-139 25.60584818746245 28.229521329861807 26.987782896054473 19.17684758662127 140-144 26.247559937934835 28.449872365984284 26.537864757995894 18.76470293808499 145-149 25.919807778945785 28.532812734644843 26.715723081543775 18.831656404865598 150-151 26.65999749906215 28.310616481180446 26.722520945354507 18.3068650744029 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.5 3 0.5 4 1.0 5 1.0 6 0.5 7 0.5 8 0.0 9 0.0 10 0.0 11 0.5 12 1.0 13 0.5 14 0.5 15 0.5 16 0.0 17 0.0 18 0.0 19 0.0 20 0.5 21 1.0 22 1.5 23 3.0 24 5.0 25 3.5 26 5.5 27 6.5 28 5.0 29 8.5 30 14.5 31 22.5 32 25.5 33 35.0 34 55.0 35 81.0 36 92.0 37 102.0 38 141.5 39 174.5 40 200.0 41 229.5 42 248.0 43 289.0 44 308.0 45 282.0 46 269.0 47 250.0 48 230.5 49 195.5 50 155.5 51 131.5 52 110.5 53 86.5 54 59.0 55 45.0 56 31.5 57 21.5 58 16.5 59 11.0 60 9.5 61 8.5 62 6.0 63 4.0 64 2.5 65 1.5 66 2.0 67 2.0 68 0.5 69 0.0 70 1.0 71 1.5 72 0.5 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 0.075 7 0.125 8 0.125 9 0.17500000000000002 10-14 0.145 15-19 0.145 20-24 0.155 25-29 0.13 30-34 0.16999999999999998 35-39 0.11499999999999999 40-44 0.105 45-49 0.11 50-54 0.125 55-59 0.11499999999999999 60-64 0.15 65-69 0.16 70-74 0.16 75-79 0.185 80-84 0.165 85-89 0.18 90-94 0.15 95-99 0.095 100-104 0.12 105-109 0.165 110-114 0.2 115-119 0.17500000000000002 120-124 0.16 125-129 0.155 130-134 0.18 135-139 0.13999999999999999 140-144 0.105 145-149 0.11499999999999999 150-151 0.0375 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.575 #Duplication Level Percentage of deduplicated Percentage of total 1 99.62339944765253 99.2 2 0.3263871453678132 0.65 3 0.05021340697966357 0.15 4 0.0 0.0 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences pass >>END_MODULE >>Adapter Content 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 0.0 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 0.0625 0.0 0.0 0.0 0.0 74-75 0.0875 0.0 0.0 0.0 0.0 76-77 0.1375 0.0 0.0 0.0 0.0 78-79 0.15 0.0 0.0 0.0 0.0 80-81 0.15 0.0 0.0 0.0 0.0 82-83 0.1875 0.0 0.0 0.0 0.0 84-85 0.2375 0.0 0.0 0.0 0.0 86-87 0.35 0.0 0.0 0.0 0.0 88-89 0.4 0.0 0.0 0.0 0.0 90-91 0.425 0.0 0.0 0.0 0.0 92-93 0.6000000000000001 0.0 0.0 0.0 0.0 94-95 0.9125 0.0 0.0 0.0 0.0 96-97 1.0625 0.0 0.0 0.0 0.0 98-99 1.3125 0.0 0.0 0.0 0.0 100-101 1.5875 0.0 0.0 0.0 0.0 102-103 1.8624999999999998 0.0 0.0 0.0 0.0 104-105 2.1500000000000004 0.0 0.0 0.0 0.0 106-107 2.4000000000000004 0.0 0.0 0.0 0.0 108-109 2.7625 0.0 0.0 0.0 0.0 110-111 3.2875 0.0 0.0 0.0 0.0 112-113 3.8125 0.0 0.0 0.0 0.0 114-115 4.275 0.0 0.0 0.0 0.0 116-117 4.7625 0.0 0.0 0.0 0.0 118-119 5.175000000000001 0.0 0.0 0.0 0.0 120-121 5.875 0.0 0.0 0.0 0.0 122-123 6.4875 0.0 0.0 0.0 0.0 124-125 6.925 0.0 0.0 0.0 0.0 126-127 7.575 0.0 0.0 0.0 0.0 128-129 8.350000000000001 0.0 0.0 0.0 0.0 130-131 9.149999999999999 0.0 0.0 0.0 0.0 132-133 10.075 0.0 0.0 0.0 0.0 134-135 11.0 0.0 0.0 0.0 0.0 136-137 11.8125 0.0 0.0 0.0 0.0 138-139 12.337499999999999 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 2747836 spots for SRR6053286.sra Written 2747836 spots for SRR6053286.sra Read 2747836 spots for SRR6053286.sra Written 2747836 spots for SRR6053286.sra Read 2747836 spots for SRR6053286.sra Written 2747836 spots for SRR6053286.sra Read 2747836 spots for SRR6053286.sra Written 2747836 spots for SRR6053286.sra Read 2747836 spots for SRR6053286.sra Written 2747836 spots for SRR6053286.sra Read 2747836 spots for SRR6053286.sra Written 2747836 spots for SRR6053286.sra Read 2747836 spots for SRR6053286.sra Written 2747836 spots for SRR6053286.sra Read 2747836 spots for SRR6053286.sra Written 2747836 spots for SRR6053286.sra Read 2747836 spots for SRR6053286.sra Written 2747836 spots for SRR6053286.sra Read 2747836 spots for SRR6053286.sra Written 2747836 spots for SRR6053286.sra Read 2747836 spots for SRR6053286.sra Written 2747836 spots for SRR6053286.sra Read 2747836 spots for SRR6053286.sra Written 2747836 spots for SRR6053286.sra Read 2747836 spots for SRR6053286.sra Written 2747836 spots for SRR6053286.sra Read 2747836 spots for SRR6053286.sra Written 2747836 spots for SRR6053286.sra Read 2747836 spots for SRR6053286.sra Written 2747836 spots for SRR6053286.sra Read 2747836 spots for SRR6053286.sra Written 2747836 spots for SRR6053286.sra Read 2747836 spots for SRR6053286.sra Written 2747836 spots for SRR6053286.sra Read 2747836 spots for SRR6053286.sra Written 2747836 spots for SRR6053286.sra Read 2747845 spots for SRR6053286.sra Written 2747845 spots for SRR6053286.sra Read 2747836 spots for SRR6053286.sra Written 2747836 spots for SRR6053286.sra SRR ids: ['SRR6053286.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_ts94q1_8 SRR6053286.sra spots: 54956729 blocks: [[1, 2747836], [2747837, 5495672], [5495673, 8243508], [8243509, 10991344], [10991345, 13739180], [13739181, 16487016], [16487017, 19234852], [19234853, 21982688], [21982689, 24730524], [24730525, 27478360], [27478361, 30226196], [30226197, 32974032], [32974033, 35721868], [35721869, 38469704], [38469705, 41217540], [41217541, 43965376], [43965377, 46713212], [46713213, 49461048], [49461049, 52208884], [52208885, 54956729]] SRR6053286 file size 18601331 SRR6053286 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 SRR6053286 SRR6053286_1.fastq SRR6053286_2.fastq Input file: SRR6053286_1.fastq Paired file: SRR6053286_2.fastq trimmed: SRR6053286-trimmed-pair1.fastq, SRR6053286-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 18:05:29 2025 >> started Tue Feb 11 18:06:34 2025 >> done (65.501s) 54956729 read pairs processed; of these: 66322 ( 0.12%) short read pairs filtered out after trimming by size control 38432 ( 0.07%) empty read pairs filtered out after trimming by size control 54851975 (99.81%) read pairs available; of these: 20804455 (37.93%) trimmed read pairs available after processing 34047520 (62.07%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 38 0.00% 19 38 0.00% 20 32 0.00% 21 33 0.00% 22 31 0.00% 23 34 0.00% 24 25 0.00% 25 41 0.00% 26 34 0.00% 27 18 0.00% 28 30 0.00% 29 29 0.00% 30 32 0.00% 31 31 0.00% 32 37 0.00% 33 33 0.00% 34 30 0.00% 35 38 0.00% 36 44 0.00% 37 48 0.00% 38 45 0.00% 39 57 0.00% 40 65 0.00% 41 75 0.00% 42 104 0.00% 43 122 0.00% 44 105 0.00% 45 139 0.00% 46 153 0.00% 47 188 0.00% 48 204 0.00% 49 269 0.00% 50 277 0.00% 51 351 0.00% 52 384 0.00% 53 452 0.00% 54 518 0.00% 55 536 0.00% 56 606 0.00% 57 724 0.00% 58 807 0.00% 59 959 0.00% 60 1153 0.00% 61 1248 0.00% 62 1510 0.00% 63 1711 0.00% 64 1813 0.00% 65 2169 0.00% 66 2364 0.00% 67 2639 0.00% 68 3053 0.01% 69 3489 0.01% 70 4394 0.01% 71 4724 0.01% 72 5259 0.01% 73 5978 0.01% 74 6686 0.01% 75 7413 0.01% 76 8204 0.01% 77 8814 0.02% 78 9666 0.02% 79 10877 0.02% 80 12304 0.02% 81 13997 0.03% 82 16024 0.03% 83 18343 0.03% 84 21593 0.04% 85 24268 0.04% 86 26160 0.05% 87 28545 0.05% 88 30966 0.06% 89 33816 0.06% 90 36497 0.07% 91 39654 0.07% 92 44360 0.08% 93 49135 0.09% 94 54579 0.10% 95 58431 0.11% 96 62920 0.11% 97 68246 0.12% 98 71204 0.13% 99 75366 0.14% 100 80958 0.15% 101 86170 0.16% 102 91880 0.17% 103 99934 0.18% 104 105733 0.19% 105 113438 0.21% 106 120032 0.22% 107 125157 0.23% 108 129628 0.24% 109 133444 0.24% 110 135882 0.25% 111 143221 0.26% 112 149364 0.27% 113 157004 0.29% 114 165238 0.30% 115 174778 0.32% 116 179880 0.33% 117 185554 0.34% 118 190546 0.35% 119 192704 0.35% 120 197968 0.36% 121 202008 0.37% 122 205474 0.37% 123 212824 0.39% 124 221162 0.40% 125 226894 0.41% 126 235175 0.43% 127 237085 0.43% 128 241983 0.44% 129 242765 0.44% 130 245986 0.45% 131 247814 0.45% 132 254216 0.46% 133 260734 0.48% 134 267015 0.49% 135 274930 0.50% 136 283094 0.52% 137 288419 0.53% 138 296748 0.54% 139 304425 0.55% 140 310071 0.57% 141 322290 0.59% 142 336687 0.61% 143 354441 0.65% 144 384683 0.70% 145 421774 0.77% 146 475562 0.87% 147 568619 1.04% 148 752403 1.37% 149 1295325 2.36% 150 6987948 12.74% 151 34047520 62.07% 54851975 reads passed initial QC criterion=sequence-density sequence-density=0.30 sequence-density-rank=1 fanout-score=7.75 fanout-score-rank=9 prefix-density=0.49 prefix-fanout=4.7 sequence=ACACCAGCAATGATTGTCTGACTTGTGGTGGTCTCGGAGAAACTCAAGTCTGGGTACATGCTGCATCCATTGCAGCCACTGCCGCACTTGCATCCAGAGCCGCAGCCACAGTTTCCTCCACAGCAAGACATTTTCTGTTGGAAAAGAAGGAAAGTGTG criterion=fanout-score sequence-density=0.02 sequence-density-rank=35 fanout-score=112.01 fanout-score-rank=1 prefix-density=0.15 prefix-fanout=15.1 sequence=TCTCCTTCCTCTAAATGATAAGGTTCAGTGGACTTCTCGCGACGTCGCCGGCGGCGAACCGCCCACGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAGACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAA criterion=sequence-density sequence-density=0.45 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=35 prefix-density=0.44 prefix-fanout=2.0 sequence=CACACTTTCCTTCTTTTCCAACAGAAAATGTCTTGCTGTGGAGGAAACTGTGGCTGCGGCTCTGGATGCAAGTGCGGCAGTGGCTGCAATGGATGCAGCATGTACCCAGACTTGAGTTTCTCCGAGACCACCACAAGTCAGACAATCATTGCTGGTGT criterion=fanout-score sequence-density=0.01 sequence-density-rank=39 fanout-score=86.88 fanout-score-rank=1 prefix-density=0.08 prefix-fanout=5.8 sequence=TCCTGCTCTCGCAATCGCTGCTTCTTTGTCTGTCTTTGGGTCGATCCGAAAGAGAGGAGCTCTTCTGCGCAATCATGTTGGTCTATCAAGATCTTCTCTCTGGTGATGAGCTTCTCTCGGATTCGTTCCCATACAAGGAGATTGAGAATGGGATACTGTGGGAAGTTGAAGGAAAGTGGGTTGTTCAAGGAGCCGTTGATGTAGACAT SRR6053286 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 18:07:20 Started mapping on | Feb 11 18:07:20 Finished on | Feb 11 18:14:38 Mapping speed, Million of reads per hour | 450.84 Number of input reads | 54851975 Average input read length | 291 UNIQUE READS: Uniquely mapped reads number | 51143240 Uniquely mapped reads % | 93.24% Average mapped length | 289.21 Number of splices: Total | 45757645 Number of splices: Annotated (sjdb) | 44605369 Number of splices: GT/AG | 44897936 Number of splices: GC/AG | 607001 Number of splices: AT/AC | 43653 Number of splices: Non-canonical | 209055 Mismatch rate per base, % | 0.75% Deletion rate per base | 0.07% Deletion average length | 2.93 Insertion rate per base | 0.05% Insertion average length | 2.72 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1783267 % of reads mapped to multiple loci | 3.25% Number of reads mapped to too many loci | 347026 % of reads mapped to too many loci | 0.63% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.75% % of reads unmapped: other | 0.13% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1954535 1954535 1954535 N_multimapping 1783267 1783267 1783267 N_noFeature 1815643 50342308 2267852 N_ambiguous 750958 4330 400057 UnstrandedReadsAssigned:48576639 PositiveStrandReadsAssigned:796602 NegativeStrandReadsAssigned:48475331 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=147 echo kmer=143 SRR6053286 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: SRR6053286-trimmed-pair1.fastq SRR6053286-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 54,851,975 reads, 47,848,987 reads pseudoaligned [quant] estimated average fragment length: 225.138 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,153 rounds 52401 SRR6053286.ke.tsv 34699 SRR6053286.se.tsv 87100 total ==> SRR6053286.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1793.86 3399.92 34.622 Potri.005G024800.1.v4.1 1035 810.862 2156 48.5706 Potri.004G059700.1.v4.1 961 736.862 72 1.78492 Potri.007G009000.2.v4.1 1416 1191.86 0 0 Potri.003G141000.2.v4.1 2943 2718.86 1870.45 12.567 Potri.016G087400.1.v4.1 270 96.0457 4834.07 919.405 Potri.015G069301.1.v4.1 564 343.713 0 0 Potri.010G195200.1.v4.1 1773 1548.86 654 7.71324 Potri.012G127500.1.v4.1 977 752.862 18708 453.925 ==> SRR6053286.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 1494 Potri.001G233950.v4.1 3 Potri.001G122700.v4.1 1297 Potri.001G212900.v4.1 1 Potri.001G182400.v4.1 5 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 114 SRR6053286 completed mapping pipeline successfully