Starting /dee2/code/volunteer_pipeline.sh SRR11389840 current disk space = 1544463974400 free memory = 1479690868 SRR11389840 SRAfilesize 30124563d862aeb95aa8cf14668ee1fd SRR11389840.sra SRR11389840.sra file validated SRR11389840 is paired end SRR11389840 is conventional basespace SRR11389840 read1 length is 35-76 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11389840_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 35-76 %GC 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.76125 32.0 32.0 32.0 32.0 32.0 2 30.85575 32.0 32.0 32.0 32.0 32.0 3 30.831 32.0 32.0 32.0 32.0 32.0 4 30.99525 32.0 32.0 32.0 32.0 32.0 5 30.972 32.0 32.0 32.0 32.0 32.0 6 33.653 36.0 36.0 36.0 32.0 36.0 7 33.63525 36.0 36.0 36.0 32.0 36.0 8 33.8315 36.0 36.0 36.0 32.0 36.0 9 33.84675 36.0 36.0 36.0 32.0 36.0 10-11 33.783875 36.0 36.0 36.0 32.0 36.0 12-13 33.7815 36.0 36.0 36.0 32.0 36.0 14-15 33.88775 36.0 36.0 36.0 32.0 36.0 16-17 33.790125 36.0 36.0 36.0 32.0 36.0 18-19 33.744 36.0 36.0 36.0 32.0 36.0 20-21 33.728 36.0 36.0 36.0 32.0 36.0 22-23 33.650125 36.0 36.0 36.0 29.5 36.0 24-25 33.523624999999996 36.0 36.0 36.0 27.0 36.0 26-27 33.3905 36.0 36.0 36.0 24.0 36.0 28-29 33.338750000000005 36.0 36.0 36.0 24.0 36.0 30-31 33.218 36.0 36.0 36.0 21.0 36.0 32-33 33.226 36.0 36.0 36.0 17.5 36.0 34-35 33.147999999999996 36.0 36.0 36.0 17.5 36.0 36-37 33.23238550578762 36.0 36.0 36.0 17.5 36.0 38-39 33.34046300956216 36.0 36.0 36.0 21.0 36.0 40-41 33.33392048314042 36.0 36.0 36.0 17.5 36.0 42-43 33.19287871162557 36.0 36.0 36.0 21.0 36.0 44-45 33.10996255423657 36.0 36.0 36.0 17.5 36.0 46-47 33.027696076007246 36.0 36.0 36.0 14.0 36.0 48-49 32.947858942065494 36.0 36.0 36.0 17.5 36.0 50-51 32.765113350125944 36.0 34.0 36.0 14.0 36.0 52-53 32.62229219143577 36.0 34.0 36.0 14.0 36.0 54-55 32.2965104243022 36.0 32.0 36.0 14.0 36.0 56-57 32.44608213655833 36.0 32.0 36.0 14.0 36.0 58-59 32.26890120967742 36.0 32.0 36.0 14.0 36.0 60-61 32.13625525891448 36.0 32.0 36.0 14.0 36.0 62-63 32.087663975782036 36.0 32.0 36.0 14.0 36.0 64-65 32.19164774160989 36.0 32.0 36.0 14.0 36.0 66-67 31.98875519904932 36.0 32.0 36.0 14.0 36.0 68-69 32.03528539529155 36.0 32.0 36.0 14.0 36.0 70-71 31.910794948344428 36.0 32.0 36.0 14.0 36.0 72-73 31.891037834808202 36.0 32.0 36.0 14.0 36.0 74-75 31.614243888872593 36.0 32.0 36.0 14.0 36.0 76 30.279940674823877 36.0 27.0 36.0 14.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 26.0 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 1.0 21 1.0 22 6.0 23 20.0 24 16.0 25 35.0 26 63.0 27 98.0 28 124.0 29 203.0 30 237.0 31 317.0 32 454.0 33 631.0 34 905.0 35 863.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 31.78158027176648 10.291897332662305 13.714141922496225 44.21238047307499 2 24.081529944640163 13.663814796175139 31.55510820332159 30.699547055863107 3 25.037745344740813 17.614494212380475 21.640664318067437 35.70709612481127 4 27.805737292400607 26.245596376446905 19.501761449421238 26.446904881731253 5 26.623049823855062 28.938097634625066 22.118772018117767 22.320080523402115 6 21.540010065425264 33.4675390035229 25.56618017111223 19.426270759939605 7 18.72169099144439 27.201811776547558 33.694011071967786 20.382486160040262 8 18.948163059889282 24.63512833417212 31.177654755913437 25.23905385002516 9 18.87267237040765 20.206341217916457 36.08454957221943 24.836436839456468 10-11 22.458480120785104 29.365878208354303 24.182184197282336 23.993457473578257 12-13 23.754403623553095 25.47810770005033 25.943633618520384 24.823855057876195 14-15 22.320080523402115 25.30196275792652 26.91243080020131 25.465525918470057 16-17 23.238550578761952 26.04428787116256 25.44036235530951 25.27679919476598 18-19 22.395571212883745 25.968797181680927 25.754906894816305 25.880724710619024 20-21 23.666331152491193 24.987418218419727 26.49723200805234 24.849018621036738 22-23 23.20080523402114 26.0694514343231 24.874182184197284 25.855561147458477 24-25 22.596879718168093 24.86160040261701 26.421741318570707 26.119778560644185 26-27 22.420734776044288 25.893306492199297 26.28334172118772 25.402617010568697 28-29 23.540513336688477 25.72974333165576 25.54101660795169 25.188726723704075 30-31 22.861097131353798 25.402617010568697 26.13236034222446 25.603925515853042 32-33 23.21338701560141 25.06290890790136 26.7362858580775 24.987418218419727 34-35 23.31404126824358 25.377453447408154 26.5601409159537 24.748364368394565 36-37 23.112732762959233 24.86160040261701 26.056869652742826 25.968797181680927 38-39 23.80473074987418 25.641670860593862 26.031706089582286 24.521892299949673 40-41 24.157020634121793 25.0880724710619 25.855561147458477 24.899345747357827 42-43 23.21338701560141 25.12581781580272 25.84297936587821 25.817815802717664 44-45 23.06530766326916 25.481313703284258 26.06014848370454 25.393230149742042 46-47 23.366486214276723 25.94737504721138 25.95996474883545 24.726173989676443 48-49 23.249370277078086 24.38287153652393 26.68765743073048 25.680100755667507 50-51 23.2367758186398 25.1007556675063 26.926952141057935 24.73551637279597 52-53 23.476070528967256 25.088161209068012 25.239294710327453 26.19647355163728 54-55 22.91220556745182 24.499307217533694 26.149389091825164 26.439098123189318 56-57 23.721340388007054 25.27084908037289 25.560594608213655 25.447215923406404 58-59 23.109879032258064 24.810987903225808 26.272681451612907 25.806451612903224 60-61 24.527350642803125 24.665994454247542 25.283589614318124 25.52306528863121 62-63 23.46115035317861 25.70635721493441 26.059535822401614 24.77295660948537 64-65 24.337623012869038 24.741357557406005 25.775927327781982 25.14509210194297 66-67 23.494508269157937 24.554980431763664 25.741699280393888 26.208812018684508 68-69 23.893805309734514 24.905183312262956 25.95448798988622 25.24652338811631 70-71 23.857739526642195 24.19946842171877 26.237185166434628 25.705606885204404 72-73 23.554086691241896 25.43536290835134 24.9523325282827 26.05821787212406 74-75 23.292092522861754 22.8214093598709 27.19203873050027 26.69445938676708 76 25.843529847979234 0.0 36.59621802002225 37.56025213199852 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 56.0 1 31.0 2 4.0 3 1.0 4 0.0 5 0.0 6 1.0 7 2.0 8 2.0 9 1.5 10 0.5 11 0.5 12 1.0 13 0.5 14 0.0 15 0.0 16 0.5 17 1.5 18 7.5 19 15.5 20 18.0 21 18.5 22 14.0 23 12.0 24 11.0 25 8.0 26 11.0 27 14.5 28 15.0 29 14.5 30 21.0 31 35.0 32 48.0 33 55.0 34 59.5 35 68.0 36 80.5 37 99.0 38 117.0 39 137.5 40 165.5 41 182.5 42 198.5 43 205.5 44 206.0 45 202.5 46 195.5 47 204.0 48 196.0 49 173.0 50 167.5 51 157.0 52 134.0 53 123.5 54 122.0 55 112.0 56 108.0 57 112.0 58 110.5 59 106.0 60 97.0 61 98.5 62 101.0 63 93.5 64 81.5 65 73.0 66 61.5 67 49.0 68 50.0 69 53.5 70 48.5 71 40.5 72 38.0 73 34.0 74 30.0 75 29.0 76 22.5 77 12.5 78 14.0 79 19.0 80 12.0 81 4.5 82 3.5 83 4.0 84 3.5 85 3.0 86 2.0 87 1.0 88 0.5 89 0.0 90 0.5 91 1.0 92 1.0 93 0.5 94 0.0 95 0.0 96 0.0 97 0.0 98 0.5 99 0.5 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.65 2 0.65 3 0.65 4 0.65 5 0.65 6 0.65 7 0.65 8 0.65 9 0.65 10-11 0.65 12-13 0.65 14-15 0.65 16-17 0.65 18-19 0.65 20-21 0.65 22-23 0.65 24-25 0.65 26-27 0.65 28-29 0.65 30-31 0.65 32-33 0.65 34-35 0.65 36-37 0.0 38-39 0.0 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0 54-55 0.0 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0 66-67 0.0 68-69 0.0 70-71 0.0 72-73 0.0 74-75 0.0 76 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 35 26.0 36 0.0 37 0.0 38 0.0 39 0.0 40 0.0 41 0.0 42 0.0 43 0.0 44 1.0 45 1.0 46 1.0 47 1.0 48 0.0 49 0.0 50 0.0 51 0.0 52 0.0 53 0.0 54 1.0 55 0.0 56 0.0 57 1.0 58 0.0 59 0.0 60 2.0 61 2.0 62 0.0 63 1.0 64 0.0 65 2.0 66 1.0 67 4.0 68 2.0 69 2.0 70 3.0 71 8.0 72 15.0 73 81.0 74 254.0 75 894.0 76 2697.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 96.1 #Duplication Level Percentage of deduplicated Percentage of total 1 98.02289281997919 94.19999999999999 2 1.4047866805411031 2.7 3 0.31217481789802287 0.8999999999999999 4 0.07804370447450572 0.3 5 0.052029136316337155 0.25 6 0.052029136316337155 0.3 7 0.026014568158168577 0.17500000000000002 8 0.0 0.0 9 0.0 0.0 >10 0.052029136316337155 1.175 >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 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 26 0.65 No Hit TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 21 0.525 No Hit GTCAATTAGAAGAATAAAGAAGAATTACTGCATTTCGTAACTTATTTTTT 7 0.17500000000000002 No Hit CTTCCATACTTCACAAGCTGCGGCTAGTTCAGGACTCCATTTGCAAGCTGCTCGGATAATTTCATTACCTTCACG 6 0.15 No Hit GCAGTCAATTAGAAGAATAAAGAAGAATTACTGCATTTCGTAACTTATTT 6 0.15 No Hit GTAACTTATTTTTTCTCTTTTTATTTTGTTTCTTTTTATTTAGACCTTCT 5 0.125 No Hit TGCAGTCAATTAGAAGAATAAAGAAGAATTACTGCATTTCGTAACTTATT 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 0.0 0.0 0.0 0.0 0.0 11 0.0 0.0 0.0 0.0 0.0 12 0.0 0.0 0.0 0.0 0.0 13 0.0 0.0 0.0 0.0 0.0 14 0.0 0.0 0.0 0.0 0.0 15 0.0 0.0 0.0 0.0 0.0 16 0.0 0.0 0.0 0.0 0.0 17 0.0 0.0 0.0 0.0 0.0 18 0.0 0.0 0.0 0.0 0.0 19 0.0 0.0 0.0 0.0 0.0 20 0.0 0.0 0.0 0.0 0.0 21 0.0 0.0 0.0 0.0 0.0 22 0.0 0.0 0.0 0.0 0.0 23 0.0 0.0 0.0 0.0 0.0 24 0.0 0.0 0.0 0.0 0.0 25 0.0 0.0 0.0 0.0 0.0 26 0.0 0.0 0.0 0.0 0.0 27 0.0 0.0 0.0 0.0 0.0 28 0.0 0.0 0.0 0.0 0.0 29 0.0 0.0 0.0 0.0 0.0 30 0.0 0.0 0.0 0.0 0.0 31 0.0 0.0 0.0 0.0 0.0 32 0.0 0.0 0.0 0.0 0.0 33 0.0 0.0 0.0 0.0 0.0 34 0.0 0.0 0.0 0.0 0.0 35 0.0 0.0 0.0 0.0 0.0 36 0.0 0.0 0.0 0.0 0.0 37 0.0 0.0 0.0 0.0 0.0 38 0.0 0.0 0.0 0.0 0.0 39 0.0 0.0 0.0 0.0 0.0 40 0.0 0.0 0.0 0.0 0.0 41 0.0 0.0 0.0 0.0 0.0 42 0.0 0.0 0.0 0.0 0.0 43 0.0 0.0 0.0 0.0 0.0 44 0.0 0.0 0.0 0.0 0.0 45 0.0 0.0 0.0 0.0 0.0 46 0.0 0.0 0.0 0.0 0.0 47 0.0 0.0 0.0 0.0 0.0 48 0.0 0.0 0.0 0.0 0.0 49 0.0 0.0 0.0 0.0 0.0 50 0.0 0.0 0.0 0.0 0.0 51 0.0 0.0 0.0 0.0 0.0 52 0.0 0.0 0.0 0.0 0.0 53 0.0 0.0 0.0 0.0 0.0 54 0.0 0.0 0.0 0.0 0.0 55 0.0 0.0 0.0 0.0 0.0 56 0.0 0.0 0.0 0.0 0.0 57 0.0 0.0 0.0 0.0 0.0 58 0.0 0.0 0.0 0.0 0.0 59 0.0 0.0 0.0 0.0 0.0 60 0.0 0.0 0.0 0.0 0.0 61 0.0 0.0 0.0 0.0 0.0 62 0.0 0.0 0.0 0.0 0.0 63 0.0 0.0 0.0 0.0 0.0 64 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR11389840 read2 length is 35-76 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11389840_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 35-76 %GC 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.39025 32.0 32.0 32.0 27.0 32.0 2 30.08 32.0 32.0 32.0 21.0 32.0 3 30.242 32.0 32.0 32.0 21.0 32.0 4 30.114 32.0 32.0 32.0 21.0 32.0 5 30.1045 32.0 32.0 32.0 21.0 32.0 6 33.21075 36.0 36.0 36.0 21.0 36.0 7 33.37675 36.0 36.0 36.0 21.0 36.0 8 32.926 36.0 36.0 36.0 14.0 36.0 9 32.94825 36.0 36.0 36.0 14.0 36.0 10-11 33.195125000000004 36.0 36.0 36.0 21.0 36.0 12-13 33.128 36.0 36.0 36.0 21.0 36.0 14-15 33.098625 36.0 36.0 36.0 21.0 36.0 16-17 33.15925 36.0 36.0 36.0 21.0 36.0 18-19 33.04575 36.0 36.0 36.0 17.5 36.0 20-21 32.890874999999994 36.0 36.0 36.0 14.0 36.0 22-23 32.83375 36.0 36.0 36.0 14.0 36.0 24-25 32.714375000000004 36.0 36.0 36.0 14.0 36.0 26-27 32.862625 36.0 36.0 36.0 14.0 36.0 28-29 32.6595 36.0 36.0 36.0 14.0 36.0 30-31 32.682 36.0 36.0 36.0 14.0 36.0 32-33 32.669250000000005 36.0 36.0 36.0 14.0 36.0 34-35 32.45125 36.0 36.0 36.0 14.0 36.0 36-37 32.654136283630876 36.0 36.0 36.0 14.0 36.0 38-39 32.4972340960523 36.0 36.0 36.0 14.0 36.0 40-41 32.40382197636409 36.0 34.0 36.0 14.0 36.0 42-43 32.420165954236865 36.0 34.0 36.0 14.0 36.0 44-45 32.39682980963478 36.0 36.0 36.0 14.0 36.0 46-47 32.3380380333805 36.0 34.0 36.0 14.0 36.0 48-49 32.17266549207148 36.0 32.0 36.0 14.0 36.0 50-51 32.00868361439718 36.0 32.0 36.0 14.0 36.0 52-53 32.079033475962746 36.0 32.0 36.0 14.0 36.0 54-55 32.008903565836775 36.0 32.0 36.0 14.0 36.0 56-57 31.794687814702918 36.0 32.0 36.0 14.0 36.0 58-59 31.766809367917404 36.0 32.0 36.0 14.0 36.0 60-61 31.68862061738991 36.0 32.0 36.0 14.0 36.0 62-63 31.635996975044115 36.0 32.0 36.0 14.0 36.0 64-65 31.579677256681794 36.0 32.0 36.0 14.0 36.0 66-67 31.439076690211905 36.0 32.0 36.0 14.0 36.0 68-69 31.589947637520396 36.0 32.0 36.0 14.0 36.0 70-71 31.52264304159104 36.0 32.0 36.0 14.0 36.0 72-73 31.37773870955226 36.0 32.0 36.0 14.0 36.0 74-75 31.320302586331103 36.0 32.0 36.0 14.0 36.0 76 30.044554455445546 32.0 27.0 36.0 14.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 23.0 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 5.0 15 16.0 16 11.0 17 11.0 18 10.0 19 5.0 20 11.0 21 13.0 22 10.0 23 38.0 24 36.0 25 48.0 26 79.0 27 119.0 28 161.0 29 182.0 30 269.0 31 318.0 32 444.0 33 610.0 34 855.0 35 726.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 31.53130500377169 18.280110636157907 12.974603972843852 37.213980387226556 2 27.835051546391753 27.65903947699271 25.270304249434243 19.235604727181293 3 27.181292431481012 29.34372642695499 19.91450842343475 23.560472718129244 4 30.198642192607494 32.28564244405331 17.525773195876287 19.989942167462914 5 31.20442544631632 31.53130500377169 19.059592657782247 18.204676892129747 6 23.661051043500127 35.051546391752574 20.543122957002765 20.74427960774453 7 22.479255720392256 18.959014332411364 34.47322102087001 24.088508926326377 8 23.937641438270052 22.881569021875787 26.20065375911491 26.98013578073925 9 24.214231833039978 22.22780990696505 28.337943173246167 25.220015086748802 10-11 27.772190093034947 27.671611767664068 20.505406084988685 24.050792054312296 12-13 27.2818707568519 22.96957505657531 23.76162936887101 25.986924817701784 14-15 25.39602715614785 25.04400301734976 25.01885843600704 24.54111139049535 16-17 27.017852652753334 24.2393764143827 23.547900427457883 25.194870505406087 18-19 25.01885843600704 25.13200905204928 25.546894644204176 24.3022378677395 20-21 25.949207945687704 26.21322604978627 24.402816193110386 23.43474981141564 22-23 26.615539351269803 25.33316570279105 23.711340206185564 24.339954739753583 24-25 26.452099572542114 24.893135529293435 25.04400301734976 23.610761880814685 26-27 27.219009303495096 25.572039225546895 23.987930600955494 23.221020870002516 28-29 26.338948956499873 25.911491073673627 23.258737742016596 24.490822227809907 30-31 24.767412622579833 26.791551420668846 23.81191853155645 24.62911742519487 32-33 26.16293688710083 24.62911742519487 24.000502891626855 25.207442796077444 34-35 25.823485038974102 25.6977621322605 24.251948705054062 24.22680412371134 36-37 26.062358561729948 25.094292180035204 24.478249937138546 24.365099321096302 38-39 25.785768166960022 25.99949710837314 23.082725672617553 25.13200905204928 40-41 26.640683932612525 24.62911742519487 23.472466683429722 25.257731958762886 42-43 25.836057329645463 24.867990947950716 24.075936635655015 25.220015086748802 44-45 26.518294983025275 25.688419464353075 23.513139695712308 24.280145856909343 46-47 26.16681343565228 24.770411372499684 24.204302427978362 24.858472763869667 48-49 25.572615152277876 25.132141958217975 25.03146237100428 24.263780518499875 50-51 26.541656179209667 25.899823810722378 23.256984646362948 24.30153536370501 52-53 27.49811225773974 25.106972061414552 22.94236093632016 24.45255474452555 54-55 25.852737570799246 26.557583385777217 23.952171176840782 23.63750786658276 56-57 25.805639476334342 25.490936555891235 24.307653575025174 24.395770392749245 58-59 26.391337194661297 25.421808108788717 23.835305968269957 24.351548728280033 60-61 25.730478589420652 26.09571788413098 24.34508816120907 23.828715365239294 62-63 26.695235694479457 26.002016637257373 23.796319637005293 23.50642803125788 64-65 26.374180534543623 25.74382249117499 23.676248108925872 24.205748865355524 66-67 25.693743693239153 26.07214934409687 23.890010090817356 24.344096871846617 68-69 25.432504104053542 26.089152670791766 24.270741255208993 24.2076019699457 70-71 27.142857142857142 24.437420986093553 24.34892541087231 24.07079646017699 72-73 25.975842339478707 25.2638270820089 25.111252383979654 23.64907819453274 74-75 26.542131433947052 21.71751108721946 26.421179948931595 25.319177529901893 76 28.25590251332826 0.0 36.1005331302361 35.64356435643564 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 48.0 1 24.5 2 1.0 3 1.0 4 1.0 5 0.5 6 1.0 7 1.0 8 0.0 9 2.0 10 2.5 11 1.5 12 2.0 13 2.5 14 2.0 15 1.0 16 0.5 17 1.0 18 3.0 19 3.5 20 3.0 21 5.0 22 7.0 23 9.0 24 13.5 25 10.0 26 5.5 27 9.5 28 14.5 29 18.0 30 20.0 31 27.5 32 36.0 33 37.0 34 54.5 35 76.0 36 85.5 37 98.0 38 109.0 39 126.5 40 140.5 41 160.0 42 180.0 43 183.5 44 202.0 45 207.5 46 188.5 47 165.5 48 162.0 49 177.0 50 179.0 51 164.5 52 137.5 53 124.5 54 124.0 55 122.0 56 119.0 57 129.5 58 134.0 59 136.0 60 143.5 61 132.5 62 113.0 63 100.5 64 96.0 65 86.0 66 73.0 67 66.5 68 68.5 69 68.5 70 54.5 71 42.0 72 49.5 73 50.0 74 33.5 75 26.5 76 24.5 77 19.0 78 16.5 79 14.0 80 8.5 81 5.5 82 5.0 83 3.5 84 2.5 85 1.5 86 1.5 87 2.0 88 1.0 89 0.0 90 0.5 91 0.5 92 0.0 93 0.5 94 0.5 95 0.0 96 0.0 97 0.0 98 1.0 99 3.5 100 5.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.575 2 0.575 3 0.575 4 0.575 5 0.575 6 0.575 7 0.575 8 0.575 9 0.575 10-11 0.575 12-13 0.575 14-15 0.575 16-17 0.575 18-19 0.575 20-21 0.575 22-23 0.575 24-25 0.575 26-27 0.575 28-29 0.575 30-31 0.575 32-33 0.575 34-35 0.575 36-37 0.0 38-39 0.0 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0 54-55 0.0 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0 66-67 0.0 68-69 0.0 70-71 0.0 72-73 0.0 74-75 0.0 76 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 35 23.0 36 0.0 37 0.0 38 0.0 39 0.0 40 0.0 41 0.0 42 0.0 43 0.0 44 1.0 45 1.0 46 1.0 47 1.0 48 0.0 49 0.0 50 0.0 51 0.0 52 0.0 53 0.0 54 1.0 55 0.0 56 0.0 57 1.0 58 0.0 59 0.0 60 2.0 61 2.0 62 0.0 63 1.0 64 0.0 65 2.0 66 0.0 67 3.0 68 3.0 69 2.0 70 2.0 71 9.0 72 25.0 73 71.0 74 257.0 75 966.0 76 2626.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 96.325 #Duplication Level Percentage of deduplicated Percentage of total 1 97.94964962366987 94.35 2 1.4534129249935115 2.8000000000000003 3 0.3893070334804049 1.125 4 0.05190760446405398 0.2 5 0.0 0.0 6 0.05190760446405398 0.3 7 0.02595380223202699 0.17500000000000002 8 0.02595380223202699 0.2 9 0.0 0.0 >10 0.05190760446405398 0.8500000000000001 >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 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 23 0.575 No Hit AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 11 0.27499999999999997 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACA 8 0.2 No Hit TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 7 0.17500000000000002 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 6 0.15 No Hit GAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTAC 6 0.15 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 0.0 0.0 0.0 0.0 0.0 11 0.0 0.0 0.0 0.0 0.0 12 0.0 0.0 0.0 0.0 0.0 13 0.0 0.0 0.0 0.0 0.0 14 0.0 0.0 0.0 0.0 0.0 15 0.0 0.0 0.0 0.0 0.0 16 0.0 0.0 0.0 0.0 0.0 17 0.0 0.0 0.0 0.0 0.0 18 0.0 0.0 0.0 0.0 0.0 19 0.0 0.0 0.0 0.0 0.0 20 0.0 0.0 0.0 0.0 0.0 21 0.0 0.0 0.0 0.0 0.0 22 0.0 0.0 0.0 0.0 0.0 23 0.0 0.0 0.0 0.0 0.0 24 0.0 0.0 0.0 0.0 0.0 25 0.0 0.0 0.0 0.0 0.0 26 0.0 0.0 0.0 0.0 0.0 27 0.0 0.0 0.0 0.0 0.0 28 0.0 0.0 0.0 0.0 0.0 29 0.0 0.0 0.0 0.0 0.0 30 0.0 0.0 0.0 0.0 0.0 31 0.0 0.0 0.0 0.0 0.0 32 0.0 0.0 0.0 0.0 0.0 33 0.0 0.0 0.0 0.0 0.0 34 0.0 0.0 0.0 0.0 0.0 35 0.0 0.0 0.0 0.0 0.0 36 0.0 0.0 0.0 0.0 0.0 37 0.0 0.0 0.0 0.0 0.0 38 0.0 0.0 0.0 0.0 0.0 39 0.0 0.0 0.0 0.0 0.0 40 0.0 0.0 0.0 0.0 0.0 41 0.0 0.0 0.0 0.0 0.0 42 0.0 0.0 0.0 0.0 0.0 43 0.0 0.0 0.0 0.0 0.0 44 0.0 0.0 0.0 0.0 0.0 45 0.0 0.0 0.0 0.0 0.0 46 0.0 0.0 0.0 0.0 0.0 47 0.0 0.0 0.0 0.0 0.0 48 0.0 0.0 0.0 0.0 0.0 49 0.0 0.0 0.0 0.0 0.0 50 0.0 0.0 0.0 0.0 0.0 51 0.0 0.0 0.0 0.0 0.0 52 0.0 0.0 0.0 0.0 0.0 53 0.0 0.0 0.0 0.0 0.0 54 0.0 0.0 0.0 0.0 0.0 55 0.0 0.0 0.0 0.0 0.0 56 0.0 0.0 0.0 0.0 0.0 57 0.0 0.0 0.0 0.0 0.0 58 0.0 0.0 0.0 0.0 0.0 59 0.0 0.0 0.0 0.0 0.0 60 0.0 0.0 0.0 0.0 0.0 61 0.0 0.0 0.0 0.0 0.0 62 0.0 0.0 0.0 0.0 0.0 63 0.0 0.0 0.0 0.0 0.0 64 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 508407 spots for SRR11389840.sra Written 508407 spots for SRR11389840.sra Read 508407 spots for SRR11389840.sra Written 508407 spots for SRR11389840.sra Read 508407 spots for SRR11389840.sra Written 508407 spots for SRR11389840.sra Read 508407 spots for SRR11389840.sra Written 508407 spots for SRR11389840.sra Read 508407 spots for SRR11389840.sra Written 508407 spots for SRR11389840.sra Read 508407 spots for SRR11389840.sra Written 508407 spots for SRR11389840.sra Read 508407 spots for SRR11389840.sra Written 508407 spots for SRR11389840.sra Read 508407 spots for SRR11389840.sra Written 508407 spots for SRR11389840.sra Read 508407 spots for SRR11389840.sra Written 508407 spots for SRR11389840.sra Read 508407 spots for SRR11389840.sra Written 508407 spots for SRR11389840.sra Read 508407 spots for SRR11389840.sra Written 508407 spots for SRR11389840.sra Read 508407 spots for SRR11389840.sra Written 508407 spots for SRR11389840.sra Read 508413 spots for SRR11389840.sra Written 508413 spots for SRR11389840.sra Read 508407 spots for SRR11389840.sra Written 508407 spots for SRR11389840.sra Read 508407 spots for SRR11389840.sra Written 508407 spots for SRR11389840.sra Read 508407 spots for SRR11389840.sra Written 508407 spots for SRR11389840.sra Read 508407 spots for SRR11389840.sra Written 508407 spots for SRR11389840.sra Read 508407 spots for SRR11389840.sra Written 508407 spots for SRR11389840.sra Read 508407 spots for SRR11389840.sra Written 508407 spots for SRR11389840.sra Read 508407 spots for SRR11389840.sra Written 508407 spots for SRR11389840.sra SRR ids: ['SRR11389840.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_qqgw8ega SRR11389840.sra spots: 10168146 blocks: [[1, 508407], [508408, 1016814], [1016815, 1525221], [1525222, 2033628], [2033629, 2542035], [2542036, 3050442], [3050443, 3558849], [3558850, 4067256], [4067257, 4575663], [4575664, 5084070], [5084071, 5592477], [5592478, 6100884], [6100885, 6609291], [6609292, 7117698], [7117699, 7626105], [7626106, 8134512], [8134513, 8642919], [8642920, 9151326], [9151327, 9659733], [9659734, 10168146]] SRR11389840 file size 1913561 SRR11389840 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 SRR11389840 SRR11389840_1.fastq SRR11389840_2.fastq Input file: SRR11389840_1.fastq Paired file: SRR11389840_2.fastq trimmed: SRR11389840-trimmed-pair1.fastq, SRR11389840-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 07:51:47 2024 >> started Sat Dec 7 07:52:35 2024 >> done (48.132s) 10168146 read pairs processed; of these: 375 ( 0.00%) short read pairs filtered out after trimming by size control 155775 ( 1.53%) empty read pairs filtered out after trimming by size control 10011996 (98.46%) read pairs available; of these: 65243 ( 0.65%) trimmed read pairs available after processing 9946753 (99.35%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 885 0.01% 19 7 0.00% 20 798 0.01% 21 8 0.00% 22 604 0.01% 23 8 0.00% 24 469 0.00% 25 1 0.00% 26 392 0.00% 27 4 0.00% 28 339 0.00% 29 5 0.00% 30 232 0.00% 31 7 0.00% 32 200 0.00% 33 8 0.00% 34 130 0.00% 35 172 0.00% 36 613 0.01% 37 202 0.00% 38 507 0.01% 39 349 0.00% 40 578 0.01% 41 479 0.00% 42 657 0.01% 43 595 0.01% 44 728 0.01% 45 718 0.01% 46 786 0.01% 47 882 0.01% 48 1037 0.01% 49 1022 0.01% 50 1246 0.01% 51 1387 0.01% 52 1554 0.02% 53 1723 0.02% 54 1903 0.02% 55 2184 0.02% 56 2468 0.02% 57 2624 0.03% 58 2925 0.03% 59 3086 0.03% 60 3390 0.03% 61 3684 0.04% 62 3995 0.04% 63 4447 0.04% 64 4894 0.05% 65 5581 0.06% 66 5756 0.06% 67 6329 0.06% 68 6597 0.07% 69 7193 0.07% 70 8274 0.08% 71 9892 0.10% 72 17692 0.18% 73 90243 0.90% 74 740149 7.39% 75 4448177 44.43% 76 4611181 46.06% 10011996 reads passed initial QC criterion=sequence-density sequence-density=0.82 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=26 prefix-density=0.80 prefix-fanout=2.0 sequence=TTCAAATGTACA criterion=fanout-score sequence-density=0.01 sequence-density-rank=32 fanout-score=33.10 fanout-score-rank=1 prefix-density=0.16 prefix-fanout=2.5 sequence=TCTTTTTATTTTGTTTCTTTTTATTTAGACCTTCTTCATATTTAGTTTTATCTATTAATCGATAGTATCTACCGGCGCGAACTCGAATTTGATCGCCTTCCATACTTCACAAGCTGCGGCTAGTTCAGGACTCCATTTGCAAGCTGCTCGGATAATTTCATTACCTTCACGAGCAAGATCGCGCCCTTCGTTACGAGCTTGTACACAGGCTTCTAAAGCCACTCGATTAGCTGCTGCACCAGGTGCATTTCCCCAAGGATGTCCTAAAGTTCCTCCACCAAATTGTAATACAGAATCATCCCCAAAGATTTCGGTCAGAGCTGGCATATGCCAAACATGAATACCACCTGAAGCTACTGGTATAACACCTGGCATGGATACCCAGTCCTGAGTGAAAAAGATACCGCGAGCACGATCTTTTTCAATAAAATCGTCGCGCAATAAATCAACAAAACCTAAAGTGATTTCGCGTTCCCCTTCTAACTTACCTACTACTGTACCGGCGTGGATA criterion=sequence-density sequence-density=0.67 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=26 prefix-density=0.66 prefix-fanout=2.0 sequence=GACGCCTATGTCCGCATCATCGGCTTCGACAACACCCGGCAGGTGCAGTGCATCAGCTTCATCGCCTTCAAGCC criterion=fanout-score sequence-density=0.14 sequence-density-rank=25 fanout-score=47.36 fanout-score-rank=1 prefix-density=0.49 prefix-fanout=13.4 sequence=CGGCGGCGGCGCCCTCCTCGTCTACAACACCAGCGCTCTCGCCGGCTAATTA SRR11389840 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 07:56:01 Started mapping on | Dec 07 07:56:02 Finished on | Dec 07 08:03:21 Mapping speed, Million of reads per hour | 82.10 Number of input reads | 10011996 Average input read length | 150 UNIQUE READS: Uniquely mapped reads number | 8352393 Uniquely mapped reads % | 83.42% Average mapped length | 149.97 Number of splices: Total | 3450483 Number of splices: Annotated (sjdb) | 3277694 Number of splices: GT/AG | 3403554 Number of splices: GC/AG | 41005 Number of splices: AT/AC | 1057 Number of splices: Non-canonical | 4867 Mismatch rate per base, % | 0.76% Deletion rate per base | 0.01% Deletion average length | 1.67 Insertion rate per base | 0.01% Insertion average length | 1.66 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1042369 % of reads mapped to multiple loci | 10.41% Number of reads mapped to too many loci | 28260 % of reads mapped to too many loci | 0.28% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.52% % of reads unmapped: other | 1.36% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 617234 617234 617234 N_multimapping 1042369 1042369 1042369 N_noFeature 319814 8069521 432822 N_ambiguous 224878 1373 59721 UnstrandedReadsAssigned:7807701 PositiveStrandReadsAssigned:281499 NegativeStrandReadsAssigned:7859850 Dataset is classified negative stranded MeadianReadLen=76 20thPercentileLength=75 echo kmer=71 SRR11389840 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: SRR11389840-trimmed-pair1.fastq SRR11389840-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 10,011,996 reads, 8,885,803 reads pseudoaligned [quant] estimated average fragment length: 186.841 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,066 rounds 52973 SRR11389840.ke.tsv 35125 SRR11389840.se.tsv 88098 total ==> SRR11389840.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 750.349 0 0 PNS24247 1044 858.159 6.51153 1.16358 PNS24249 1928 1742.16 63.6478 5.60243 PNS24246 1044 858.159 6.51153 1.16358 PNS24248 1044 858.159 6.51153 1.16358 PNS24244 1471 1285.16 21.8176 2.60334 PNS24243 293 125.932 0 0 KQK14069 1603 1417.16 882.275 95.4698 KQK14071 474 290.702 43.2886 22.8353 ==> SRR11389840.se.tsv <== BRADI_1g14170v3 983 BRADI_1g53295v3 3 BRADI_1g59795v3 144 BRADI_1g07683v3 0 BRADI_1g00485v3 1 BRADI_1g20270v3 45 BRADI_1g74790v3 156 BRADI_1g09890v3 0 BRADI_1g77505v3 118 BRADI_1g48960v3 0 SRR11389840 completed mapping pipeline successfully