Starting /dee2/code/volunteer_pipeline.sh SRR12682213 current disk space = 1547295260672 free memory = 1601978676 SRR12682213 SRAfilesize 999713004c1bf7bdee50e6de917349bb SRR12682213.sra SRR12682213.sra file validated SRR12682213 is single end SRR12682213 is conventional basespace SRR12682213 read1 length is 42-150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12682213_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 42-150 %GC 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.5245 32.0 32.0 32.0 32.0 32.0 2 31.49575 32.0 32.0 32.0 32.0 32.0 3 31.559 32.0 32.0 32.0 32.0 32.0 4 31.6135 32.0 32.0 32.0 32.0 32.0 5 31.587 32.0 32.0 32.0 32.0 32.0 6 34.778 36.0 36.0 36.0 36.0 36.0 7 35.089 36.0 36.0 36.0 36.0 36.0 8 35.01675 36.0 36.0 36.0 36.0 36.0 9 35.1095 36.0 36.0 36.0 36.0 36.0 10-14 35.06265 36.0 36.0 36.0 36.0 36.0 15-19 35.100750000000005 36.0 36.0 36.0 35.2 36.0 20-24 34.9719 36.0 36.0 36.0 36.0 36.0 25-29 34.88295 36.0 36.0 36.0 32.8 36.0 30-34 34.8765 36.0 36.0 36.0 32.8 36.0 35-39 34.812050000000006 36.0 36.0 36.0 32.0 36.0 40-44 34.67721149037259 36.0 36.0 36.0 32.0 36.0 45-49 34.53938484621155 36.0 36.0 36.0 32.0 36.0 50-54 34.50895447723862 36.0 36.0 36.0 32.0 36.0 55-59 34.44172086043021 36.0 36.0 36.0 32.0 36.0 60-64 34.22862134088054 36.0 36.0 36.0 32.0 36.0 65-69 34.08029168245447 36.0 36.0 36.0 32.0 36.0 70-74 34.17104130191646 36.0 36.0 36.0 32.0 36.0 75-79 34.03360141073209 36.0 36.0 36.0 32.0 36.0 80-84 33.99211180535714 36.0 36.0 36.0 30.0 36.0 85-89 33.90148688279011 36.0 36.0 36.0 31.0 36.0 90-94 33.891196492699144 36.0 36.0 36.0 30.0 36.0 95-99 33.795573825404844 36.0 36.0 36.0 27.0 36.0 100-104 33.77352241500574 36.0 36.0 36.0 28.0 36.0 105-109 33.42138987909977 36.0 32.8 36.0 27.0 36.0 110-114 33.28462226833016 36.0 32.8 36.0 27.0 36.0 115-119 32.87394106256951 36.0 32.0 36.0 27.0 36.0 120-124 32.28531807814979 34.4 32.0 36.0 24.6 36.0 125-129 32.01876049193329 33.6 32.0 36.0 23.4 36.0 130-134 31.58291440078271 32.8 32.0 36.0 22.2 36.0 135-139 31.632008379889676 33.6 32.0 36.0 21.0 36.0 140-144 31.916950378689318 35.2 32.0 36.0 22.2 36.0 145-149 31.542614559786074 32.0 32.0 36.0 21.0 36.0 150 26.326726342710998 27.0 21.0 32.0 14.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 17 1.0 18 0.0 19 1.0 20 1.0 21 8.0 22 6.0 23 9.0 24 18.0 25 41.0 26 39.0 27 53.0 28 78.0 29 114.0 30 134.0 31 176.0 32 227.0 33 365.0 34 912.0 35 1817.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 28.475 9.425 7.3 54.800000000000004 2 20.625 13.0 35.675000000000004 30.7 3 20.225 16.2 21.224999999999998 42.35 4 27.3 23.175 18.625 30.9 5 25.4 28.525 23.225 22.85 6 22.328870927001766 32.20510229856024 24.273806516797173 21.192220257640816 7 18.475 21.85 38.35 21.325 8 20.025000000000002 19.5 32.4 28.075 9 21.2 20.0 32.824999999999996 25.974999999999998 10-14 22.985 26.450000000000003 24.240000000000002 26.325 15-19 23.325000000000003 24.12 25.840000000000003 26.715 20-24 23.665 25.03 25.06 26.245 25-29 23.169999999999998 24.635 24.69 27.505000000000003 30-34 23.5 23.474999999999998 24.845 28.18 35-39 23.445 24.55 24.26 27.744999999999997 40-44 23.85238523852385 24.327432743274326 24.59245924592459 27.22772277227723 45-49 23.640910227556887 23.840960240060017 25.08627156789197 27.431857964491122 50-54 22.99649824912456 24.772386193096548 24.777388694347174 27.453726863431715 55-59 23.28664332166083 23.961980990495245 24.59729864932466 28.154077038519258 60-64 23.397227365997697 22.906761423352183 25.94464741504429 27.751363795605826 65-69 22.465835711067726 24.21284477148721 24.953696751263955 28.36762276618111 70-74 24.336793540945788 24.37189709643448 24.622636778496563 26.668672584123165 75-79 24.317393271986727 24.12128526172877 24.166540956403683 27.394780509880828 80-84 24.096142193496263 23.37406584528378 24.136538073116544 28.393253888103416 85-89 23.744801704026777 23.689015113094634 24.885891064002436 27.680292118876153 90-94 24.166666666666668 23.537832310838446 24.468302658486706 27.827198364008183 95-99 23.340925561652345 24.050108706905476 25.028470856196293 27.580494875245886 100-104 23.77070733631344 23.844333420983435 24.664738364449118 27.72022087825401 105-109 24.097424291410714 23.801056148291842 25.439163702985233 26.66235585731221 110-114 24.389298177588213 23.741206447681826 25.092782363042154 26.776713011687807 115-119 24.65824238943136 23.394600804135553 25.08902929350948 26.85812751292361 120-124 24.67869426175104 23.496047788571772 24.395100464611115 27.43015748506607 125-129 23.939355331889413 23.588992228309337 23.506179131099504 28.965473308701746 130-134 24.96452942368759 23.464630768191338 23.90379028444024 27.66704952368083 135-139 25.098913747212432 23.02712035105388 24.87590820804259 26.998057693691102 140-144 23.965609887157445 24.56436631611269 23.87349351347202 27.59653028325785 145-149 25.634560430324427 21.751554883173643 24.357034795763994 28.25684989073794 150 26.15089514066496 0.0 34.71867007672634 39.130434782608695 >>END_MODULE >>Per sequence GC content warn #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 0.5 24 0.5 25 1.0 26 1.0 27 3.5 28 5.0 29 2.0 30 2.0 31 7.0 32 9.5 33 13.0 34 15.5 35 23.0 36 54.0 37 68.5 38 59.0 39 61.0 40 77.5 41 90.5 42 95.0 43 101.0 44 117.5 45 136.5 46 159.5 47 186.0 48 191.5 49 200.5 50 207.5 51 178.0 52 179.0 53 200.5 54 174.5 55 167.5 56 168.0 57 141.5 58 119.5 59 96.0 60 75.0 61 63.0 62 60.0 63 71.5 64 70.5 65 57.5 66 47.0 67 44.0 68 43.0 69 29.0 70 26.5 71 30.5 72 22.5 73 17.0 74 14.0 75 11.0 76 9.5 77 7.5 78 5.5 79 2.5 80 1.0 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 0.5 95 0.5 96 0.0 97 0.0 98 0.0 99 0.5 100 0.5 >>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 1.0250000000000001 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 40-44 1.0 45-49 1.0 50-54 0.0 55-59 1.0 60-64 1.0 65-69 4.0 70-74 10.0 75-79 13.0 80-84 18.0 85-89 28.0 90-94 38.0 95-99 54.0 100-104 80.0 105-109 96.0 110-114 110.0 115-119 158.0 120-124 181.0 125-129 164.0 130-134 192.0 135-139 178.0 140-144 164.0 145-149 944.0 150-151 1564.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 80.425 #Duplication Level Percentage of deduplicated Percentage of total 1 89.36897730805097 71.875 2 5.502020516008703 8.85 3 2.0205160087037615 4.875 4 1.1812247435498913 3.8 5 0.7460366801367734 3.0 6 0.4973577867578489 2.4 7 0.24867889337892446 1.4000000000000001 8 0.12433944668946223 0.8 9 0.062169723344731115 0.44999999999999996 >10 0.24867889337892446 2.55 >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 CTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATT 15 0.375 No Hit CCGACATCGAAGGATCAAAAAGCAACGTCGCTATGAACGCTTGGCTGCCA 15 0.375 No Hit CTAGAATTACTACGGTTATCCGAGTAGCACGTACCATCAAACAAACTATA 14 0.35000000000000003 No Hit CCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAG 13 0.325 No Hit CTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGG 13 0.325 No Hit CCCCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTA 11 0.27499999999999997 No Hit CCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTATA 11 0.27499999999999997 No Hit CCTAATTCTCCGTCACCCGTCACCACCATGGTAGGCCCCTATCCTACCAT 10 0.25 No Hit CCACGCTTTCACGGTTCGTATTCGTACTGGAAATCAGAATCAAACGAGCT 9 0.22499999999999998 No Hit CTCAGAGCCAATCCTTTTCCCGAAGTTACGGATCCGTTTTGCCGACTTCC 9 0.22499999999999998 No Hit CCCTTTTGTTCCACACGAGATTTCTGTTCTCGTTGAGCTCATCTTAGGAC 8 0.2 No Hit CTCCAATGGATCCTCGTTAAGGGATTTAGATTGTACTCATTCCAATTACC 8 0.2 No Hit CTCTGACTATGAAATACGAATGCCCCCGACTGTCCCTATTAATCATTACT 8 0.2 No Hit CCCGACTGTCCCTATTAATCATTACTCCGATCCCGAAGGCCAACACAATA 8 0.2 No Hit CTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAAC 7 0.17500000000000002 No Hit CCCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTAT 7 0.17500000000000002 No Hit CCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGC 7 0.17500000000000002 No Hit CCCGAAGTTACGGATCCGTTTTGCCGACTTCCCTTGCCTACATTGTTCCA 7 0.17500000000000002 No Hit CTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTG 7 0.17500000000000002 No Hit CAGAAATTTGAATGATGCGTCGCCGGCACGAGGGCCGTGCGATCCGTCGA 7 0.17500000000000002 No Hit GTCGAGTTATCATGAATCATCGGATCAGCGAGCAAAGCCCGCGTCAGCCT 7 0.17500000000000002 No Hit ATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATA 7 0.17500000000000002 No Hit CTCGTAATGGGCTCCAGCTATCCTGAGGGAAACTTCGGAGGGAACCAGCT 6 0.15 No Hit CTTGTTACGACTTCTCCTTCCTCTAAATGATAAGGTTCAATGGACTTCTC 6 0.15 No Hit CTCATCTTAGGACACCTGCGTTATCTTTTAACAGATGTGCCGCCCCAGCC 6 0.15 No Hit CCCGAGCCCAGTCCTCAGAGCCAATCCTTTTCCCGAAGTTACGGATCCGT 6 0.15 No Hit CCGGTATTGTTATTTATTGTCACTACCTCCCCGTGTCAGGATTGGGTAAT 6 0.15 No Hit CGCCCCTATACCCAAGTCAGACGAACGATTTGCACGTCAGTATCGCTTCG 6 0.15 No Hit CCGAAGGCCAACACAATAGGACCGGAATCCTATGATGTTATCCCATGCTA 6 0.15 No Hit CTTTTGTTCCACACGAGATTTCTGTTCTCGTTGAGCTCATCTTAGGACAC 6 0.15 No Hit GTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACT 6 0.15 No Hit CAACAACTTAAATATACGCTATTGGAGCTGGAATTACCGCGGCTGCTGGC 6 0.15 No Hit CTAATTCTCCGTCACCCGTCACCACCATGGTAGGCCCCTATCCTACCATC 6 0.15 No Hit CTCCGTCACCCGTCACCACCATGGTAGGCCCCTATCCTACCATCGAAAGT 6 0.15 No Hit TATTAATCATTACTCCGATCCCGAAGGCCAACACAATAGGACCGGAATCC 6 0.15 No Hit CGCGGCACGGTCATCAGTAGGGTAAAACTAACCTGTCTCACGACGGTCTA 6 0.15 No Hit CTGGAAATCAGAATCAAACGAGCTTTTACCCTTTTGTTCCACACGAGATT 6 0.15 No Hit GTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGA 6 0.15 No Hit CCTAGATGTCCAGTCAACTGCTGCGCCTCAACGCATTTCGGGGAGAACCA 5 0.125 No Hit CCCCGCTCAGGCATAGTTCACCATCTTTCGGGTCCCGACAGGCGTGCTCC 5 0.125 No Hit CTTCCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGA 5 0.125 No Hit CAGCCTTGCGACCATACTCCCCCCGGAACCCAAAGACTTTGATTTCTCAT 5 0.125 No Hit CTGTATTTAGCCTTGGACGGAGTCTACCGCCCGATTTGGGCTGCATTCCC 5 0.125 No Hit CCAGAGCGATGGCTTGCTTTGAGCACTCTAATTTCTTCAAAGTAACGATG 5 0.125 No Hit CCCGTGTCAGGATTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTG 5 0.125 No Hit CCCGATTCCATGGCGCGGCTCACCGGAGCAGCCGCGCCGTCCTACCTATT 5 0.125 No Hit CTTTTATCTAATAAATGCGCCCCTCCCAGAAGTCGGGGTTTGTTGCACGT 5 0.125 No Hit CTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGAACCCAAAGACTTT 5 0.125 No Hit CCCTGGTCGGCATCGTTTATGGTTGAGACTAGGACGGTATCTGATCGTCT 5 0.125 No Hit CCCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCG 5 0.125 No Hit CCAACTACGAGCTTTTTAACTGCAACAACTTAAATATACGCTATTGGAGC 5 0.125 No Hit CAGCCTTTTATCTAATAAATGCGCCCCTCCCAGAAGTCGGGGTTTGTTGC 5 0.125 No Hit CGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGAACCC 5 0.125 No Hit CTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCCGGA 5 0.125 No Hit CCTCGCGGTACTTGTTCGCTATCGGTCTCTCGCCTGTATTTAGCCTTGGA 5 0.125 No Hit CCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGC 5 0.125 No Hit GTGCGACGTGGGGCTGGATCTCAGTGGATCGTGGCAGCAAGGCCACTCTG 5 0.125 No Hit CAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGG 5 0.125 No Hit CTTGCGACCATACTCCCCCCGGAACCCAAAGACTTTGATTTCTCATAAGG 5 0.125 No Hit CCCACTTATCCTACACCTCTCAAGTCATTTCACAAAGTCGGACTAGAGTC 5 0.125 No Hit CTATGATGTTATCCCATGCTAATGTATCCAGAGCGATGGCTTGCTTTGAG 5 0.125 No Hit CCCCGACTGTCCCTATTAATCATTACTCCGATCCCGAAGGCCAACACAAT 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 82-83 0.0 0.0 0.0 0.0 0.0 84-85 0.0 0.0 0.0 0.0 0.0 86-87 0.0 0.0 0.0 0.0 0.0 88-89 0.0 0.0 0.0 0.0 0.0 90-91 0.0 0.0 0.0 0.0 0.0 92-93 0.0 0.0 0.0 0.0 0.0 94-95 0.0 0.0 0.0 0.0 0.0 96-97 0.0 0.0 0.0 0.0 0.0 98-99 0.0 0.0 0.0 0.0 0.0 100-101 0.0 0.0 0.0 0.0 0.0 102-103 0.0 0.0 0.0 0.0 0.0 104-105 0.0 0.0 0.0 0.0 0.0 106-107 0.0 0.0 0.0 0.0 0.0 108-109 0.0 0.0 0.0 0.0 0.0 110-111 0.0 0.0 0.0 0.0 0.0 112-113 0.0 0.0 0.0 0.0 0.0 114-115 0.0 0.0 0.0 0.0 0.0 116-117 0.0 0.0 0.0 0.0 0.0 118-119 0.0 0.0 0.0 0.0 0.0 120-121 0.0 0.0 0.0 0.0 0.0 122-123 0.0 0.0 0.0 0.0 0.0 124-125 0.0 0.0 0.0 0.0 0.0 126-127 0.0 0.0 0.0 0.0 0.0 128-129 0.0 0.0 0.0 0.0 0.0 130-131 0.0 0.0 0.0 0.0 0.0 132-133 0.0 0.0 0.0 0.0 0.0 134-135 0.0 0.0 0.0 0.0 0.0 136-137 0.0 0.0 0.0 0.0 0.0 138 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Rejected 1385897 READS because READLEN < 1 Read 1385897 spots for SRR12682213.sra Written 1385897 spots for SRR12682213.sra Rejected 1385897 READS because READLEN < 1 Read 1385897 spots for SRR12682213.sra Written 1385897 spots for SRR12682213.sra Rejected 1385897 READS because READLEN < 1 Read 1385897 spots for SRR12682213.sra Written 1385897 spots for SRR12682213.sra Rejected 1385897 READS because READLEN < 1 Read 1385897 spots for SRR12682213.sra Written 1385897 spots for SRR12682213.sra Rejected 1385897 READS because READLEN < 1 Read 1385897 spots for SRR12682213.sra Written 1385897 spots for SRR12682213.sra Rejected 1385897 READS because READLEN < 1 Read 1385897 spots for SRR12682213.sra Written 1385897 spots for SRR12682213.sra Rejected 1385897 READS because READLEN < 1 Read 1385897 spots for SRR12682213.sra Written 1385897 spots for SRR12682213.sra Rejected 1385897 READS because READLEN < 1 Read 1385897 spots for SRR12682213.sra Written 1385897 spots for SRR12682213.sra Rejected 1385897 READS because READLEN < 1 Read 1385897 spots for SRR12682213.sra Written 1385897 spots for SRR12682213.sra Rejected 1385897 READS because READLEN < 1 Read 1385897 spots for SRR12682213.sra Written 1385897 spots for SRR12682213.sra Rejected 1385897 READS because READLEN < 1 Read 1385897 spots for SRR12682213.sra Written 1385897 spots for SRR12682213.sra Rejected 1385897 READS because READLEN < 1 Read 1385897 spots for SRR12682213.sra Written 1385897 spots for SRR12682213.sra Rejected 1385897 READS because READLEN < 1 Read 1385897 spots for SRR12682213.sra Written 1385897 spots for SRR12682213.sra Rejected 1385897 READS because READLEN < 1 Read 1385897 spots for SRR12682213.sra Written 1385897 spots for SRR12682213.sra Rejected 1385897 READS because READLEN < 1 Read 1385897 spots for SRR12682213.sra Written 1385897 spots for SRR12682213.sra Rejected 1385897 READS because READLEN < 1 Read 1385897 spots for SRR12682213.sra Written 1385897 spots for SRR12682213.sra Rejected 1385916 READS because READLEN < 1 Read 1385916 spots for SRR12682213.sra Written 1385916 spots for SRR12682213.sra Rejected 1385897 READS because READLEN < 1 Read 1385897 spots for SRR12682213.sra Written 1385897 spots for SRR12682213.sra Rejected 1385897 READS because READLEN < 1 Read 1385897 spots for SRR12682213.sra Written 1385897 spots for SRR12682213.sra Rejected 1385897 READS because READLEN < 1 Read 1385897 spots for SRR12682213.sra Written 1385897 spots for SRR12682213.sra SRR ids: ['SRR12682213.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_8hyrk2ma SRR12682213.sra spots: 27717959 blocks: [[1, 1385897], [1385898, 2771794], [2771795, 4157691], [4157692, 5543588], [5543589, 6929485], [6929486, 8315382], [8315383, 9701279], [9701280, 11087176], [11087177, 12473073], [12473074, 13858970], [13858971, 15244867], [15244868, 16630764], [16630765, 18016661], [18016662, 19402558], [19402559, 20788455], [20788456, 22174352], [22174353, 23560249], [23560250, 24946146], [24946147, 26332043], [26332044, 27717959]] SRR12682213 file size 8722507 SRR12682213 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 SRR12682213 SRR12682213_1.fastq Input file: SRR12682213_1.fastq trimmed: SRR12682213-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- 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 -- minimum overlap length for adapter detection (-k): inf -- number of concurrent threads (-t): 20 Sat Dec 7 02:48:12 2024 >> started Sat Dec 7 02:48:28 2024 >> done (16.018s) 27717959 reads processed; of these: 0 ( 0.00%) short reads filtered out after trimming by size control 769 ( 0.00%) empty reads filtered out after trimming by size control 27717190 (100.00%) reads available; of these: 11645 ( 0.04%) trimmed reads available after processing 27705545 (99.96%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 20 1 0.00% 21 1 0.00% 22 17 0.00% 23 17 0.00% 24 29 0.00% 25 30 0.00% 26 50 0.00% 27 61 0.00% 28 102 0.00% 29 94 0.00% 30 100 0.00% 31 115 0.00% 32 162 0.00% 33 195 0.00% 34 216 0.00% 35 267 0.00% 36 322 0.00% 37 350 0.00% 38 423 0.00% 39 542 0.00% 40 641 0.00% 41 691 0.00% 42 686 0.00% 43 734 0.00% 44 692 0.00% 45 796 0.00% 46 920 0.00% 47 1093 0.00% 48 1335 0.00% 49 1553 0.01% 50 1818 0.01% 51 1859 0.01% 52 2062 0.01% 53 2092 0.01% 54 2064 0.01% 55 2323 0.01% 56 2562 0.01% 57 2921 0.01% 58 3596 0.01% 59 3647 0.01% 60 4061 0.01% 61 4578 0.02% 62 5128 0.02% 63 5217 0.02% 64 5354 0.02% 65 5768 0.02% 66 6370 0.02% 67 6900 0.02% 68 7478 0.03% 69 8034 0.03% 70 8616 0.03% 71 10290 0.04% 72 11230 0.04% 73 12464 0.04% 74 12832 0.05% 75 13723 0.05% 76 15446 0.06% 77 16324 0.06% 78 17275 0.06% 79 19958 0.07% 80 21554 0.08% 81 22883 0.08% 82 25829 0.09% 83 27462 0.10% 84 30012 0.11% 85 34736 0.13% 86 39489 0.14% 87 40524 0.15% 88 43748 0.16% 89 45828 0.17% 90 49765 0.18% 91 51843 0.19% 92 59162 0.21% 93 63957 0.23% 94 65968 0.24% 95 73458 0.27% 96 79835 0.29% 97 83195 0.30% 98 92808 0.33% 99 94110 0.34% 100 97051 0.35% 101 100990 0.36% 102 108909 0.39% 103 117598 0.42% 104 123212 0.44% 105 124680 0.45% 106 129936 0.47% 107 141788 0.51% 108 137447 0.50% 109 149846 0.54% 110 150487 0.54% 111 160751 0.58% 112 173475 0.63% 113 171637 0.62% 114 185717 0.67% 115 198589 0.72% 116 205298 0.74% 117 197627 0.71% 118 196952 0.71% 119 207947 0.75% 120 225602 0.81% 121 214651 0.77% 122 232718 0.84% 123 243460 0.88% 124 230113 0.83% 125 231241 0.83% 126 239812 0.87% 127 233187 0.84% 128 238908 0.86% 129 253016 0.91% 130 242790 0.88% 131 243103 0.88% 132 246856 0.89% 133 250956 0.91% 134 240654 0.87% 135 246347 0.89% 136 256478 0.93% 137 255575 0.92% 138 243807 0.88% 139 250394 0.90% 140 244780 0.88% 141 234963 0.85% 142 232838 0.84% 143 232257 0.84% 144 243383 0.88% 145 236690 0.85% 146 292112 1.05% 147 500628 1.81% 148 1137630 4.10% 149 3999968 14.43% 150 11181945 40.34% 27717190 reads passed initial QC criterion=sequence-density sequence-density=0.70 sequence-density-rank=1 fanout-score=2.73 fanout-score-rank=36 prefix-density=1.90 prefix-fanout=1.0 sequence=CTTGGATGTGGCAGCCGTTTCTC criterion=fanout-score sequence-density=0.02 sequence-density-rank=38 fanout-score=81.76 fanout-score-rank=1 prefix-density=1.52 prefix-fanout=1.1 sequence=CAAACTCCCCAGTGCAGAGAGCTTGATCAAATGTACCAATTACACACACAGACACACAGATACATACATACTCACAAGGAAGGATACACCAATTAAGAGCAAGTAAACAACAACACAATCACACCACACGCTCTGACTCGGCGCTTATTTACTAACCACAAGTTCATCATGATTAATGGACTAACAGTTACAAGGGTTGCACTTGCAGTTGTCGCCGCAGCTGCACCCTTCGCCGGACACGCCGGCCATCTCGAACTGCTCCTGTTTCTTCTC Started job on | Dec 07 02:48:54 Started mapping on | Dec 07 02:48:54 Finished on | Dec 07 02:50:06 Mapping speed, Million of reads per hour | 1385.86 Number of input reads | 27717190 Average input read length | 138 UNIQUE READS: Uniquely mapped reads number | 12745284 Uniquely mapped reads % | 45.98% Average mapped length | 138.51 Number of splices: Total | 5079456 Number of splices: Annotated (sjdb) | 4787949 Number of splices: GT/AG | 5011412 Number of splices: GC/AG | 60132 Number of splices: AT/AC | 3543 Number of splices: Non-canonical | 4369 Mismatch rate per base, % | 0.23% Deletion rate per base | 0.01% Deletion average length | 1.60 Insertion rate per base | 0.00% Insertion average length | 1.14 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1434107 % of reads mapped to multiple loci | 5.17% Number of reads mapped to too many loci | 11693476 % of reads mapped to too many loci | 42.19% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.24% % of reads unmapped: other | 5.41% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 13537799 13537799 13537799 N_multimapping 1434107 1434107 1434107 N_noFeature 859006 12412793 966776 N_ambiguous 270050 1537 46495 UnstrandedReadsAssigned:11616228 PositiveStrandReadsAssigned:330954 NegativeStrandReadsAssigned:11732013 Dataset is classified negative stranded MeadianReadLen=149 20thPercentileLength=125 echo kmer=121 SRR12682213 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=31 [quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20 [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 single-end mode [quant] will process file 1: SRR12682213-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 27,717,190 reads, 12,091,836 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,144 rounds 52973 SRR12682213.ke.tsv 35125 SRR12682213.se.tsv 88098 total ==> SRR12682213.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 17.0447 2.62612 PNS24247 1044 945 36.0786 4.92344 PNS24249 1928 1829 90.8726 6.40723 PNS24246 1044 945 36.0786 4.92344 PNS24248 1044 945 36.0786 4.92344 PNS24244 1471 1372 118.847 11.1708 PNS24243 293 194 0 0 KQK14069 1603 1504 8210.46 703.997 KQK14071 474 375 346.205 119.057 ==> SRR12682213.se.tsv <== BRADI_1g14170v3 9023 BRADI_1g53295v3 98 BRADI_1g59795v3 282 BRADI_1g07683v3 0 BRADI_1g00485v3 13 BRADI_1g20270v3 531 BRADI_1g74790v3 335 BRADI_1g09890v3 1 BRADI_1g77505v3 124 BRADI_1g48960v3 0 SRR12682213 completed mapping pipeline successfully