Starting /dee2/code/volunteer_pipeline.sh SRR12682223 current disk space = 1547641479168 free memory = 1600040972 SRR12682223 SRAfilesize fb8713a34e6be1ed218dc9cd2a6bc19c SRR12682223.sra SRR12682223.sra file validated SRR12682223 is single end SRR12682223 is conventional basespace SRR12682223 read1 length is 57-150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12682223_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 57-150 %GC 52 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.5125 32.0 32.0 32.0 32.0 32.0 2 31.5825 32.0 32.0 32.0 32.0 32.0 3 31.6175 32.0 32.0 32.0 32.0 32.0 4 31.59275 32.0 32.0 32.0 32.0 32.0 5 31.61925 32.0 32.0 32.0 32.0 32.0 6 34.8975 36.0 36.0 36.0 36.0 36.0 7 35.19775 36.0 36.0 36.0 36.0 36.0 8 35.175 36.0 36.0 36.0 36.0 36.0 9 35.18575 36.0 36.0 36.0 36.0 36.0 10-14 35.12595 36.0 36.0 36.0 36.0 36.0 15-19 35.07875 36.0 36.0 36.0 36.0 36.0 20-24 35.00375 36.0 36.0 36.0 35.2 36.0 25-29 34.827099999999994 36.0 36.0 36.0 32.8 36.0 30-34 34.751250000000006 36.0 36.0 36.0 32.0 36.0 35-39 34.77905 36.0 36.0 36.0 32.0 36.0 40-44 34.718900000000005 36.0 36.0 36.0 32.0 36.0 45-49 34.58964999999999 36.0 36.0 36.0 32.0 36.0 50-54 34.548700000000004 36.0 36.0 36.0 32.0 36.0 55-59 34.40568942235559 36.0 36.0 36.0 32.0 36.0 60-64 34.2385409614906 36.0 36.0 36.0 32.0 36.0 65-69 34.14251763416668 36.0 36.0 36.0 32.0 36.0 70-74 34.17026634944695 36.0 36.0 36.0 32.0 36.0 75-79 34.069961792216226 36.0 36.0 36.0 32.0 36.0 80-84 34.0456088927967 36.0 36.0 36.0 30.0 36.0 85-89 33.87117997659001 36.0 36.0 36.0 28.0 36.0 90-94 33.95364471085913 36.0 36.0 36.0 31.0 36.0 95-99 33.86053419211281 36.0 36.0 36.0 27.0 36.0 100-104 33.74615834129095 36.0 36.0 36.0 27.0 36.0 105-109 33.44676462944202 36.0 32.8 36.0 27.0 36.0 110-114 33.38132462461812 36.0 32.0 36.0 27.0 36.0 115-119 33.01986439452576 36.0 32.0 36.0 27.0 36.0 120-124 32.37201085991617 34.4 32.0 36.0 25.8 36.0 125-129 32.2177206249866 34.4 32.0 36.0 24.6 36.0 130-134 31.774887079600916 33.6 32.0 36.0 22.2 36.0 135-139 31.59097549096674 32.0 32.0 36.0 21.0 36.0 140-144 31.81492941870918 35.2 32.0 36.0 21.0 36.0 145-149 31.594573785366237 32.0 32.0 36.0 21.0 36.0 150 26.455445544554454 27.0 21.0 32.0 14.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 18 1.0 19 0.0 20 2.0 21 3.0 22 5.0 23 6.0 24 14.0 25 32.0 26 42.0 27 62.0 28 83.0 29 118.0 30 137.0 31 167.0 32 218.0 33 379.0 34 948.0 35 1783.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 30.15 10.2 7.625 52.025 2 21.875 13.05 30.625000000000004 34.449999999999996 3 19.225 15.075 20.525 45.175 4 27.250000000000004 22.75 17.224999999999998 32.775 5 26.424999999999997 27.650000000000002 22.325 23.599999999999998 6 22.538403424830015 28.3807605137245 25.384034248300175 23.696801813145303 7 17.224999999999998 22.975 39.074999999999996 20.724999999999998 8 20.075000000000003 18.075 31.7 30.15 9 20.3 20.075000000000003 33.95 25.674999999999997 10-14 22.805 24.67 24.37 28.155 15-19 22.61 23.169999999999998 25.685000000000002 28.535 20-24 24.325 23.73 25.835 26.11 25-29 23.235 23.305 24.965 28.494999999999997 30-34 23.685000000000002 22.14 25.729999999999997 28.444999999999997 35-39 22.994999999999997 23.494999999999997 24.959999999999997 28.549999999999997 40-44 24.141207060353018 23.1911595579779 24.546227311365566 28.121406070303518 45-49 23.792379237923793 23.412341234123414 24.81248124812481 27.982798279827982 50-54 22.776138806940345 23.70618530926546 25.056252812640633 28.461423071153558 55-59 23.420855213803453 23.13078269567392 25.05126281570393 28.397099274818704 60-64 23.130443487836622 22.284512964260685 26.043648012814096 28.541395535088597 65-69 22.8117641164387 22.90695926649632 25.67262888922291 28.608647727842072 70-74 23.901484751203853 22.848113964687 25.170545746388445 28.079855537720704 75-79 24.131177179590196 23.12675773402973 23.824829248694254 28.917235837685816 80-84 24.0438808373591 22.59963768115942 24.592391304347828 28.764090177133657 85-89 23.732323232323232 22.666666666666664 25.42929292929293 28.17171717171717 90-94 24.440593302410928 22.748356185330547 24.83306998317957 27.977980529078955 95-99 22.94226995765775 23.505112052049984 25.317566869771763 28.2350511205205 100-104 24.081181975918817 23.650034176349966 23.93921867606078 28.329565171670435 105-109 23.849619221280705 23.211412635417783 25.093853909685727 27.845114233615785 110-114 24.790240671229853 22.687127401192317 25.088319717376905 27.43431221020093 115-119 24.699071420382896 22.6470251060415 25.295196606672015 27.35870686690359 120-124 24.45805560559659 22.842731039452353 24.656218098841048 28.04299525611001 125-129 23.752711496746205 23.669771596274085 23.280592063289525 29.296924843690185 130-134 24.142587091547394 22.37375101269241 24.85822306238185 28.625438833378343 135-139 25.13201084629656 23.00556586270872 23.997431140288285 27.864992150706435 140-144 23.931102812285648 23.580519777455986 23.405228260041156 29.083149150217206 145-149 25.10456750878367 22.134850259327422 23.25581395348837 29.504768278400533 150 25.99009900990099 0.0 32.7970297029703 41.21287128712871 >>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 0.0 23 0.0 24 0.0 25 0.0 26 0.0 27 0.0 28 0.5 29 0.5 30 0.0 31 2.0 32 4.0 33 6.5 34 10.0 35 16.5 36 36.0 37 44.0 38 43.0 39 52.0 40 63.0 41 68.5 42 68.5 43 80.0 44 97.0 45 117.0 46 148.5 47 169.5 48 196.5 49 220.0 50 225.5 51 226.0 52 211.5 53 203.0 54 194.5 55 198.5 56 204.0 57 173.5 58 136.5 59 107.5 60 96.5 61 89.0 62 67.0 63 66.0 64 65.0 65 53.0 66 45.0 67 36.5 68 31.5 69 28.0 70 21.0 71 20.0 72 23.0 73 15.5 74 8.5 75 10.0 76 10.0 77 5.5 78 3.0 79 1.5 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 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.7250000000000001 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 0.005 45-49 0.01 50-54 0.005 55-59 0.015001500150015003 60-64 0.020018016214593135 65-69 0.015028554253080853 70-74 0.015045889964391393 75-79 0.005021845025862502 80-84 0.005031952900920848 85-89 0.010099989900010101 90-94 0.01528896136989094 95-99 0.025811780496618655 100-104 0.021027177627083005 105-109 0.021447721179624665 110-114 0.005519677650825191 115-119 0.011462631820265932 120-124 0.00600456346823586 125-129 0.019136314345856987 130-134 0.006750826976304598 135-139 0.007135212272565109 140-144 0.007620789513793629 145-149 0.01672800267648043 150 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 56-57 1.0 58-59 1.0 60-61 1.0 62-63 3.0 64-65 2.0 66-67 0.0 68-69 2.0 70-71 3.0 72-73 1.0 74-75 3.0 76-77 1.0 78-79 2.0 80-81 5.0 82-83 5.0 84-85 6.0 86-87 8.0 88-89 11.0 90-91 23.0 92-93 16.0 94-95 18.0 96-97 25.0 98-99 29.0 100-101 32.0 102-103 22.0 104-105 28.0 106-107 40.0 108-109 40.0 110-111 49.0 112-113 48.0 114-115 56.0 116-117 62.0 118-119 59.0 120-121 62.0 122-123 77.0 124-125 87.0 126-127 71.0 128-129 80.0 130-131 57.0 132-133 60.0 134-135 67.0 136-137 68.0 138-139 66.0 140-141 72.0 142-143 85.0 144-145 76.0 146-147 110.0 148-149 744.0 150-151 1616.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 74.8 #Duplication Level Percentage of deduplicated Percentage of total 1 85.99598930481284 64.325 2 6.918449197860962 10.35 3 3.0414438502673797 6.825 4 1.5040106951871657 4.5 5 0.6350267379679144 2.375 6 0.6016042780748663 2.7 7 0.3676470588235294 1.925 8 0.30080213903743314 1.7999999999999998 9 0.2339572192513369 1.575 >10 0.4010695187165776 3.6249999999999996 >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 CCCGACTGTCCCTATTAATCATTACTCCGATCCCGAAGGCCAACACAATA 18 0.44999999999999996 No Hit CCGACATCGAAGGATCAAAAAGCAACGTCGCTATGAACGCTTGGCTGCCA 18 0.44999999999999996 No Hit CTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATT 16 0.4 No Hit CCTCGCGGTACTTGTTCGCTATCGGTCTCTCGCCTGTATTTAGCCTTGGA 13 0.325 No Hit CGGCAATTTCAAGCACTCTTTGACTCTCTTTTCAAAGTCCTTTTCATCTT 10 0.25 No Hit CCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAAT 10 0.25 No Hit CTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTG 10 0.25 No Hit CCCGTGTCAGGATTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTG 10 0.25 No Hit CCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGC 10 0.25 No Hit CCGCAGGCTCCACGCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTTC 10 0.25 No Hit GCCGCAGGCTCCACGCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTT 10 0.25 No Hit CTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGG 10 0.25 No Hit CCCGAAGTTACGGATCCGTTTTGCCGACTTCCCTTGCCTACATTGTTCCA 9 0.22499999999999998 No Hit CCCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTAT 9 0.22499999999999998 No Hit CATGAATCATCGGATCAGCGAGCAAAGCCCGCGTCAGCCTTTTATCTAAT 9 0.22499999999999998 No Hit CCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAG 9 0.22499999999999998 No Hit CCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCT 9 0.22499999999999998 No Hit CTCAGAGCCAATCCTTTTCCCGAAGTTACGGATCCGTTTTGCCGACTTCC 9 0.22499999999999998 No Hit ATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATA 9 0.22499999999999998 No Hit CCCCCATCCGCTTCCCTCCCGGCAATTTCAAGCACTCTTTGACTCTCTTT 8 0.2 No Hit GTCGGGGCAGGCGGCGGGCGCAGGCGCCGCTTGCTAGCTTGGATTCTGAC 8 0.2 No Hit CCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACA 8 0.2 No Hit GTCCTTTTCATCTTTCCCTCGCGGTACTTGTTCGCTATCGGTCTCTCGCC 8 0.2 No Hit GTCGGCATCGTTTATGGTTGAGACTAGGACGGTATCTGATCGTCTTCGAG 8 0.2 No Hit CCTAATTCTCCGTCACCCGTCACCACCATGGTAGGCCCCTATCCTACCAT 8 0.2 No Hit GTCGAGTTATCATGAATCATCGGATCAGCGAGCAAAGCCCGCGTCAGCCT 8 0.2 No Hit GCCACGCTTTCACGGTTCGTATTCGTACTGGAAATCAGAATCAAACGAGC 8 0.2 No Hit GGCTTGCTTTGAGCACTCTAATTTCTTCAAAGTAACGATGCCGGAGGCAC 8 0.2 No Hit CTTTTGTTCCACACGAGATTTCTGTTCTCGTTGAGCTCATCTTAGGACAC 7 0.17500000000000002 No Hit CTCTGACTATGAAATACGAATGCCCCCGACTGTCCCTATTAATCATTACT 7 0.17500000000000002 No Hit CAGAGCGATGGCTTGCTTTGAGCACTCTAATTTCTTCAAAGTAACGATGC 7 0.17500000000000002 No Hit CCCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCG 7 0.17500000000000002 No Hit CCCCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTA 7 0.17500000000000002 No Hit GTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGAACCCA 7 0.17500000000000002 No Hit GTTACGACTTCTCCTTCCTCTAAATGATAAGGTTCAATGGACTTCTCGCG 7 0.17500000000000002 No Hit CTAATTCTCCGTCACCCGTCACCACCATGGTAGGCCCCTATCCTACCATC 7 0.17500000000000002 No Hit CAGAAATTTGAATGATGCGTCGCCGGCACGAGGGCCGTGCGATCCGTCGA 7 0.17500000000000002 No Hit CCCTTTTGTTCCACACGAGATTTCTGTTCTCGTTGAGCTCATCTTAGGAC 7 0.17500000000000002 No Hit CAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTG 7 0.17500000000000002 No Hit CCCGATTCCATGGCGCGGCTCACCGGAGCAGCCGCGCCGTCCTACCTATT 6 0.15 No Hit CCGGAATCGAACCCTAATTCTCCGTCACCCGTCACCACCATGGTAGGCCC 6 0.15 No Hit AGAAATTTGAATGATGCGTCGCCGGCACGAGGGCCGTGCGATCCGTCGAG 6 0.15 No Hit CTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGG 6 0.15 No Hit CCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGG 6 0.15 No Hit CTTGTTACGACTTCTCCTTCCTCTAAATGATAAGGTTCAATGGACTTCTC 6 0.15 No Hit AGCCTTGCGACCATACTCCCCCCGGAACCCAAAGACTTTGATTTCTCATA 6 0.15 No Hit CTCATTCCAATTACCAGACACTAATGTGCCCGGTATTGTTATTTATTGTC 6 0.15 No Hit CACGCTTTCACGGTTCGTATTCGTACTGGAAATCAGAATCAAACGAGCTT 6 0.15 No Hit GGCTTTACCTGATAGAACTCGTAATGGGCTCCAGCTATCCTGAGGGAAAC 6 0.15 No Hit CGCGGCACGGTCATCAGTAGGGTAAAACTAACCTGTCTCACGACGGTCTA 6 0.15 No Hit CACCATCTTTCGGGTCCCGACAGGCGTGCTCCAACTCGAACCCTTCACAG 6 0.15 No Hit GCTGGAATTACCGCGGCTGCTGGCACCAGACTTGCCCTCCAATGGATCCT 6 0.15 No Hit CTTGCGACCATACTCCCCCCGGAACCCAAAGACTTTGATTTCTCATAAGG 6 0.15 No Hit GTCGCTATGAACGCTTGGCTGCCACAAGCCAGTTATCCCTGTGGTAACTT 6 0.15 No Hit CCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTATA 6 0.15 No Hit CGCTATTGGAGCTGGAATTACCGCGGCTGCTGGCACCAGACTTGCCCTCC 6 0.15 No Hit CTGGAAATCAGAATCAAACGAGCTTTTACCCTTTTGTTCCACACGAGATT 6 0.15 No Hit CCCTAATTCTCCGTCACCCGTCACCACCATGGTAGGCCCCTATCCTACCA 5 0.125 No Hit CTTTTATCTAATAAATGCGCCCCTCCCAGAAGTCGGGGTTTGTTGCACGT 5 0.125 No Hit CCCTGGTCGGCATCGTTTATGGTTGAGACTAGGACGGTATCTGATCGTCT 5 0.125 No Hit CTTCCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGA 5 0.125 No Hit GTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAG 5 0.125 No Hit CCGCCGTTTACCCGCGCTTGGTTGAATTTCTTCACTTTGACATTCAGAGC 5 0.125 No Hit GTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACT 5 0.125 No Hit CCCATGCTAATGTATCCAGAGCGATGGCTTGCTTTGAGCACTCTAATTTC 5 0.125 No Hit CTGACTATGAAATACGAATGCCCCCGACTGTCCCTATTAATCATTACTCC 5 0.125 No Hit CAACAACTTAAATATACGCTATTGGAGCTGGAATTACCGCGGCTGCTGGC 5 0.125 No Hit TATTAATCATTACTCCGATCCCGAAGGCCAACACAATAGGACCGGAATCC 5 0.125 No Hit CCAGAGCGATGGCTTGCTTTGAGCACTCTAATTTCTTCAAAGTAACGATG 5 0.125 No Hit GCCCGGTCCGTCGCTGAGGACGCCTCTCCAGACTACAATTCGGACGGCAC 5 0.125 No Hit CCGAGTAGCACGTACCATCAAACAAACTATAACTGATTTAATGAGCCATT 5 0.125 No Hit GTCAGCCTTTTATCTAATAAATGCGCCCCTCCCAGAAGTCGGGGTTTGTT 5 0.125 No Hit CATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACC 5 0.125 No Hit GTCCAACTACGAGCTTTTTAACTGCAACAACTTAAATATACGCTATTGGA 5 0.125 No Hit CTTCAAAGTAACGATGCCGGAGGCACGACCCGGCCAATTAAGGCTAGGAG 5 0.125 No Hit CCTGTGGTAACTTTTCTGACACCTCTAGCTTCAAACTCCGAAGATCTAAA 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 1373376 READS because READLEN < 1 Read 1373376 spots for SRR12682223.sra Written 1373376 spots for SRR12682223.sra Rejected 1373376 READS because READLEN < 1 Read 1373376 spots for SRR12682223.sra Written 1373376 spots for SRR12682223.sra Rejected 1373376 READS because READLEN < 1 Read 1373376 spots for SRR12682223.sra Written 1373376 spots for SRR12682223.sra Rejected 1373376 READS because READLEN < 1 Read 1373376 spots for SRR12682223.sra Written 1373376 spots for SRR12682223.sra Rejected 1373376 READS because READLEN < 1 Read 1373376 spots for SRR12682223.sra Written 1373376 spots for SRR12682223.sra Rejected 1373376 READS because READLEN < 1 Read 1373376 spots for SRR12682223.sra Written 1373376 spots for SRR12682223.sra Rejected 1373376 READS because READLEN < 1 Read 1373376 spots for SRR12682223.sra Written 1373376 spots for SRR12682223.sra Rejected 1373376 READS because READLEN < 1 Read 1373376 spots for SRR12682223.sra Written 1373376 spots for SRR12682223.sra Rejected 1373376 READS because READLEN < 1 Read 1373376 spots for SRR12682223.sra Written 1373376 spots for SRR12682223.sra Rejected 1373376 READS because READLEN < 1 Read 1373376 spots for SRR12682223.sra Written 1373376 spots for SRR12682223.sra Rejected 1373376 READS because READLEN < 1 Read 1373376 spots for SRR12682223.sra Written 1373376 spots for SRR12682223.sra Rejected 1373379 READS because READLEN < 1 Read 1373379 spots for SRR12682223.sra Written 1373379 spots for SRR12682223.sra Rejected 1373376 READS because READLEN < 1 Read 1373376 spots for SRR12682223.sra Written 1373376 spots for SRR12682223.sra Rejected 1373376 READS because READLEN < 1 Read 1373376 spots for SRR12682223.sra Written 1373376 spots for SRR12682223.sra Rejected 1373376 READS because READLEN < 1 Read 1373376 spots for SRR12682223.sra Written 1373376 spots for SRR12682223.sra Rejected 1373376 READS because READLEN < 1 Read 1373376 spots for SRR12682223.sra Written 1373376 spots for SRR12682223.sra Rejected 1373376 READS because READLEN < 1 Read 1373376 spots for SRR12682223.sra Written 1373376 spots for SRR12682223.sra Rejected 1373376 READS because READLEN < 1 Read 1373376 spots for SRR12682223.sra Written 1373376 spots for SRR12682223.sra Rejected 1373376 READS because READLEN < 1 Read 1373376 spots for SRR12682223.sra Written 1373376 spots for SRR12682223.sra Rejected 1373376 READS because READLEN < 1 Read 1373376 spots for SRR12682223.sra Written 1373376 spots for SRR12682223.sra SRR ids: ['SRR12682223.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_wv2mzg_5 SRR12682223.sra spots: 27467523 blocks: [[1, 1373376], [1373377, 2746752], [2746753, 4120128], [4120129, 5493504], [5493505, 6866880], [6866881, 8240256], [8240257, 9613632], [9613633, 10987008], [10987009, 12360384], [12360385, 13733760], [13733761, 15107136], [15107137, 16480512], [16480513, 17853888], [17853889, 19227264], [19227265, 20600640], [20600641, 21974016], [21974017, 23347392], [23347393, 24720768], [24720769, 26094144], [26094145, 27467523]] SRR12682223 file size 8647892 SRR12682223 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 SRR12682223 SRR12682223_1.fastq Input file: SRR12682223_1.fastq trimmed: SRR12682223-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 03:15:52 2024 >> started Sat Dec 7 03:16:08 2024 >> done (16.078s) 27467523 reads processed; of these: 1 ( 0.00%) short reads filtered out after trimming by size control 1759 ( 0.01%) empty reads filtered out after trimming by size control 27465763 (99.99%) reads available; of these: 11942 ( 0.04%) trimmed reads available after processing 27453821 (99.96%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 22 17 0.00% 23 18 0.00% 24 18 0.00% 25 20 0.00% 26 41 0.00% 27 49 0.00% 28 64 0.00% 29 85 0.00% 30 86 0.00% 31 93 0.00% 32 105 0.00% 33 127 0.00% 34 153 0.00% 35 183 0.00% 36 211 0.00% 37 259 0.00% 38 333 0.00% 39 450 0.00% 40 421 0.00% 41 531 0.00% 42 562 0.00% 43 602 0.00% 44 576 0.00% 45 585 0.00% 46 715 0.00% 47 838 0.00% 48 1001 0.00% 49 1195 0.00% 50 1403 0.01% 51 1524 0.01% 52 1684 0.01% 53 1643 0.01% 54 1647 0.01% 55 1791 0.01% 56 2139 0.01% 57 2280 0.01% 58 2808 0.01% 59 3073 0.01% 60 3512 0.01% 61 3832 0.01% 62 4362 0.02% 63 4475 0.02% 64 4676 0.02% 65 4931 0.02% 66 5402 0.02% 67 6056 0.02% 68 6502 0.02% 69 6950 0.03% 70 7629 0.03% 71 9038 0.03% 72 10183 0.04% 73 11435 0.04% 74 11686 0.04% 75 12774 0.05% 76 13733 0.05% 77 14515 0.05% 78 15912 0.06% 79 17970 0.07% 80 19432 0.07% 81 20716 0.08% 82 23074 0.08% 83 24529 0.09% 84 27422 0.10% 85 31903 0.12% 86 35927 0.13% 87 37772 0.14% 88 40629 0.15% 89 42525 0.15% 90 46195 0.17% 91 48040 0.17% 92 55541 0.20% 93 60627 0.22% 94 62289 0.23% 95 70436 0.26% 96 76450 0.28% 97 80446 0.29% 98 90749 0.33% 99 91947 0.33% 100 93768 0.34% 101 98282 0.36% 102 106340 0.39% 103 114865 0.42% 104 120658 0.44% 105 122521 0.45% 106 128462 0.47% 107 140300 0.51% 108 134384 0.49% 109 148335 0.54% 110 149992 0.55% 111 160065 0.58% 112 175239 0.64% 113 171034 0.62% 114 185817 0.68% 115 200458 0.73% 116 205627 0.75% 117 196659 0.72% 118 196905 0.72% 119 208520 0.76% 120 225456 0.82% 121 214858 0.78% 122 236750 0.86% 123 247115 0.90% 124 232865 0.85% 125 236030 0.86% 126 242731 0.88% 127 237412 0.86% 128 243181 0.89% 129 259798 0.95% 130 248063 0.90% 131 247389 0.90% 132 251770 0.92% 133 258466 0.94% 134 248886 0.91% 135 253484 0.92% 136 261551 0.95% 137 260849 0.95% 138 248817 0.91% 139 254095 0.93% 140 252458 0.92% 141 242360 0.88% 142 241053 0.88% 143 241538 0.88% 144 253120 0.92% 145 241352 0.88% 146 301958 1.10% 147 491187 1.79% 148 1108182 4.03% 149 3906614 14.22% 150 11026592 40.15% 27465763 reads passed initial QC criterion=sequence-density sequence-density=0.91 sequence-density-rank=1 fanout-score=2.73 fanout-score-rank=32 prefix-density=2.47 prefix-fanout=1.0 sequence=CTTGGATGTGGCAGCCGTTTCTC criterion=fanout-score sequence-density=0.15 sequence-density-rank=19 fanout-score=23.41 fanout-score-rank=1 prefix-density=2.08 prefix-fanout=1.7 sequence=GGCCCGGTCAGCCCGGGCCTTGG Started job on | Dec 07 03:16:30 Started mapping on | Dec 07 03:16:30 Finished on | Dec 07 03:18:13 Mapping speed, Million of reads per hour | 959.97 Number of input reads | 27465763 Average input read length | 138 UNIQUE READS: Uniquely mapped reads number | 8618705 Uniquely mapped reads % | 31.38% Average mapped length | 138.58 Number of splices: Total | 3356143 Number of splices: Annotated (sjdb) | 3167884 Number of splices: GT/AG | 3311220 Number of splices: GC/AG | 39740 Number of splices: AT/AC | 2534 Number of splices: Non-canonical | 2649 Mismatch rate per base, % | 0.26% Deletion rate per base | 0.01% Deletion average length | 1.77 Insertion rate per base | 0.00% Insertion average length | 1.15 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1748765 % of reads mapped to multiple loci | 6.37% Number of reads mapped to too many loci | 14363296 % of reads mapped to too many loci | 52.30% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.80% % of reads unmapped: other | 7.16% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 17098293 17098293 17098293 N_multimapping 1748765 1748765 1748765 N_noFeature 744361 8402697 815749 N_ambiguous 183518 894 39620 UnstrandedReadsAssigned:7690826 PositiveStrandReadsAssigned:215114 NegativeStrandReadsAssigned:7763336 Dataset is classified negative stranded MeadianReadLen=149 20thPercentileLength=125 echo kmer=121 SRR12682223 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: SRR12682223-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 27,465,763 reads, 8,099,543 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,086 rounds 52973 SRR12682223.ke.tsv 35125 SRR12682223.se.tsv 88098 total ==> SRR12682223.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 58.5994 12.4868 PNS24247 1044 945 3.63539 0.686125 PNS24249 1928 1829 63.2957 6.17226 PNS24246 1044 945 3.63539 0.686125 PNS24248 1044 945 3.63539 0.686125 PNS24244 1471 1372 65.1987 8.47557 PNS24243 293 194 0 0 KQK14069 1603 1504 2894.59 343.259 KQK14071 474 375 128.628 61.1768 ==> SRR12682223.se.tsv <== BRADI_1g14170v3 3248 BRADI_1g53295v3 38 BRADI_1g59795v3 124 BRADI_1g07683v3 0 BRADI_1g00485v3 11 BRADI_1g20270v3 493 BRADI_1g74790v3 196 BRADI_1g09890v3 0 BRADI_1g77505v3 83 BRADI_1g48960v3 0 SRR12682223 completed mapping pipeline successfully