Starting /dee2/code/volunteer_pipeline.sh ERR6133347 current disk space = 1548435525632 free memory = 1601972504 ERR6133347 SRAfilesize bbfbb2bfee1676ff37e31b36d00661be ERR6133347.sra ERR6133347.sra file validated ERR6133347 is single end ERR6133347 is conventional basespace ERR6133347 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133347_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 70-93 %GC 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.996 37.0 37.0 37.0 33.0 37.0 2 36.5865 37.0 37.0 37.0 37.0 37.0 3 36.54975 37.0 37.0 37.0 37.0 37.0 4 36.31125 37.0 37.0 37.0 37.0 37.0 5 36.292 37.0 37.0 37.0 33.0 37.0 6 36.44775 37.0 37.0 37.0 37.0 37.0 7 38.65875 40.0 37.0 40.0 37.0 40.0 8 38.6465 40.0 37.0 40.0 37.0 40.0 9 38.6895 40.0 37.0 40.0 37.0 40.0 10-11 38.688500000000005 40.0 37.0 40.0 37.0 40.0 12-13 38.659125 40.0 37.0 40.0 37.0 40.0 14-15 38.6685 40.0 37.0 40.0 37.0 40.0 16-17 38.59025 40.0 37.0 40.0 37.0 40.0 18-19 38.508 40.0 37.0 40.0 37.0 40.0 20-21 38.454 40.0 37.0 40.0 37.0 40.0 22-23 38.379125 40.0 37.0 40.0 37.0 40.0 24-25 38.278 40.0 37.0 40.0 37.0 40.0 26-27 38.284000000000006 40.0 37.0 40.0 37.0 40.0 28-29 38.342124999999996 40.0 37.0 40.0 37.0 40.0 30-31 38.28075 40.0 37.0 40.0 37.0 40.0 32-33 38.195499999999996 40.0 37.0 40.0 37.0 40.0 34-35 38.022625000000005 40.0 37.0 40.0 35.0 40.0 36-37 37.99325 40.0 37.0 40.0 37.0 40.0 38-39 37.933125000000004 40.0 37.0 40.0 37.0 40.0 40-41 37.765625 38.5 37.0 40.0 35.0 40.0 42-43 37.70625 37.0 37.0 40.0 35.0 40.0 44-45 37.49725 37.0 37.0 40.0 33.0 40.0 46-47 37.450375 37.0 37.0 40.0 33.0 40.0 48-49 37.222750000000005 37.0 37.0 40.0 33.0 40.0 50-51 37.068 37.0 37.0 40.0 33.0 40.0 52-53 36.986125 37.0 37.0 40.0 33.0 40.0 54-55 36.822500000000005 37.0 37.0 37.0 33.0 40.0 56-57 36.643249999999995 37.0 37.0 37.0 33.0 40.0 58-59 36.462125 37.0 37.0 37.0 33.0 40.0 60-61 36.292500000000004 37.0 37.0 37.0 33.0 40.0 62-63 36.102875 37.0 37.0 37.0 33.0 37.0 64-65 35.970875 37.0 37.0 37.0 33.0 37.0 66-67 35.841125 37.0 37.0 37.0 33.0 37.0 68-69 34.97075 35.0 35.0 37.0 33.0 37.0 70-71 35.17511178553364 37.0 33.0 37.0 33.0 37.0 72-73 35.605161895688155 37.0 37.0 37.0 33.0 37.0 74-75 35.53545545586813 37.0 37.0 37.0 33.0 37.0 76-77 35.506997018663476 37.0 37.0 37.0 33.0 37.0 78-79 35.52511345473228 37.0 37.0 37.0 33.0 37.0 80-81 35.54497010180086 37.0 37.0 37.0 33.0 37.0 82-83 35.423951207311745 37.0 33.0 37.0 33.0 37.0 84-85 35.348548506303175 37.0 33.0 37.0 33.0 37.0 86-87 35.25029815146094 37.0 33.0 37.0 33.0 37.0 88-89 35.30813953488372 37.0 33.0 37.0 33.0 37.0 90-91 35.2443351222421 37.0 33.0 37.0 33.0 37.0 92-93 35.10957066189624 37.0 33.0 37.0 33.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 5.0 22 2.0 23 5.0 24 5.0 25 14.0 26 10.0 27 17.0 28 13.0 29 23.0 30 30.0 31 39.0 32 65.0 33 74.0 34 107.0 35 210.0 36 785.0 37 1086.0 38 1400.0 39 109.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 66.05 8.4 8.6 16.950000000000003 2 48.15 25.5 15.825 10.525 3 31.8 37.375 16.625 14.2 4 32.025 25.7 21.349999999999998 20.925 5 24.75 28.225 26.6 20.424999999999997 6 21.025 34.5 26.875 17.599999999999998 7 33.2 26.3 22.3 18.2 8 28.875 28.349999999999998 25.900000000000002 16.875 9 26.325 26.05 28.775000000000002 18.85 10-11 26.1125 27.55 26.987499999999997 19.35 12-13 24.9875 28.6375 27.6625 18.712500000000002 14-15 22.0625 29.037499999999998 28.975 19.925 16-17 24.462500000000002 30.325000000000003 24.4375 20.775 18-19 25.124999999999996 25.374999999999996 28.325 21.175 20-21 26.0 26.025 27.3375 20.6375 22-23 27.474999999999998 25.825 25.4375 21.2625 24-25 24.7875 27.0 27.762500000000003 20.45 26-27 25.624999999999996 25.2125 27.900000000000002 21.2625 28-29 25.55 26.950000000000003 26.1 21.4 30-31 25.9875 26.674999999999997 26.825 20.5125 32-33 25.624999999999996 26.187500000000004 27.9375 20.25 34-35 23.9875 29.549999999999997 26.0375 20.424999999999997 36-37 24.474999999999998 28.537499999999998 25.0375 21.95 38-39 25.900000000000002 25.587500000000002 26.825 21.6875 40-41 25.7625 26.2625 25.825 22.15 42-43 26.487500000000004 28.7 25.7625 19.05 44-45 22.2625 29.425 28.287499999999998 20.025000000000002 46-47 25.474999999999998 28.0625 25.95 20.5125 48-49 24.0 26.950000000000003 27.4125 21.637500000000003 50-51 22.7 27.650000000000002 28.8625 20.7875 52-53 25.074999999999996 29.0875 26.4125 19.425 54-55 24.55 29.049999999999997 27.0 19.400000000000002 56-57 23.275000000000002 29.525000000000002 26.987499999999997 20.2125 58-59 24.325 28.599999999999998 26.724999999999998 20.349999999999998 60-61 26.2875 27.487499999999997 26.7625 19.4625 62-63 22.162499999999998 30.2625 28.4125 19.162499999999998 64-65 23.4125 31.5375 27.275 17.775 66-67 23.6375 28.975 27.200000000000003 20.1875 68-69 22.675 29.1375 26.7125 21.475 70-71 24.70455116922303 29.909479507166203 26.82926829268293 18.556701030927837 72-73 24.69910371318822 29.078104993597954 27.195902688860436 19.026888604353392 74-75 24.102228047182177 28.1389252948886 27.680209698558322 20.078636959370904 76-77 23.924659364146407 27.464600587763826 27.117285599786268 21.4934544483035 78-79 24.959105779716467 29.15757906215922 26.131406761177757 19.751908396946565 80-81 23.863162286191073 31.09442358503685 25.295508274231675 19.746905854540397 82-83 23.490606625555717 28.524308045317653 26.258425354940485 21.72665997418615 84-85 23.8391008577344 25.850340136054424 28.098195800059155 22.212363206152023 86-87 21.31782945736434 30.20274299344067 26.34168157423971 22.137745974955276 88-89 22.137745974955276 32.72212283840191 26.013714967203338 19.126416219439477 90-91 22.06320810971974 33.49731663685152 25.178890876565298 19.260584376863445 92-93 20.945140131186644 35.3309481216458 24.776386404293383 18.94752534287418 >>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 0.5 15 0.5 16 0.5 17 2.0 18 1.5 19 0.5 20 1.5 21 2.0 22 4.0 23 4.5 24 5.5 25 7.5 26 13.5 27 20.0 28 23.0 29 28.5 30 32.0 31 41.5 32 58.5 33 73.0 34 89.5 35 107.0 36 125.0 37 163.5 38 184.0 39 172.0 40 205.5 41 223.5 42 228.5 43 246.5 44 206.5 45 178.5 46 179.0 47 167.5 48 157.0 49 152.0 50 154.0 51 150.5 52 141.5 53 156.5 54 155.5 55 113.5 56 106.0 57 119.5 58 90.0 59 47.5 60 28.0 61 26.5 62 21.5 63 16.5 64 16.0 65 13.0 66 6.5 67 6.0 68 14.0 69 19.0 70 13.0 71 5.0 72 2.5 73 1.0 74 1.5 75 1.0 76 1.0 77 0.5 78 0.5 79 0.5 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 0.0 7 0.0 8 0.0 9 0.0 10-11 0.0 12-13 0.0 14-15 0.0 16-17 0.0 18-19 0.0 20-21 0.0 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.0 30-31 0.0 32-33 0.0 34-35 0.0 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 76-77 0.0 78-79 0.0 80-81 0.0 82-83 0.0 84-85 0.0 86-87 0.0 88-89 0.0 90-91 0.0 92-93 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 70 46.0 71 28.0 72 42.0 73 49.0 74 40.0 75 37.0 76 30.0 77 40.0 78 40.0 79 32.0 80 41.0 81 57.0 82 63.0 83 47.0 84 54.0 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 3354.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 74.35000000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 89.94620040349697 66.875 2 5.144586415601883 7.6499999999999995 3 1.6139878950907869 3.5999999999999996 4 0.9078681909885675 2.7 5 0.4371217215870881 1.625 6 0.4371217215870881 1.95 7 0.3026227303295225 1.575 8 0.13449899125756556 0.8 9 0.10087424344317418 0.675 >10 0.9751176866173503 12.55 >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 GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 38 0.95 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 35 0.8750000000000001 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 29 0.7250000000000001 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 29 0.7250000000000001 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 29 0.7250000000000001 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 28 0.7000000000000001 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 28 0.7000000000000001 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 20 0.5 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 20 0.5 No Hit GTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTC 19 0.475 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 19 0.475 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 15 0.375 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 14 0.35000000000000003 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 14 0.35000000000000003 No Hit GGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAG 13 0.325 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 13 0.325 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 13 0.325 No Hit GTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTA 12 0.3 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 12 0.3 No Hit GCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAA 11 0.27499999999999997 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 11 0.27499999999999997 No Hit GGAGTTTGGCTGGGGCGGCACATCTGTTAAAAGATAACGCAGGTGTCCTA 10 0.25 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 10 0.25 No Hit CAACGAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCC 10 0.25 No Hit GTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAA 10 0.25 No Hit CGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAG 10 0.25 No Hit GGAAGACATTGTCAGGTGGGGAGTTTGGCTGGGGCGGCACATCTGTTAAA 10 0.25 No Hit GGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAA 10 0.25 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 10 0.25 No Hit GTCAACGAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACT 9 0.22499999999999998 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 9 0.22499999999999998 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 9 0.22499999999999998 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 8 0.2 No Hit AACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCCC 8 0.2 No Hit GGGAATTTCCGGTGGAGCGGTGAAATGCATTGAGATCGGAAAGAACACCA 8 0.2 No Hit GTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGT 8 0.2 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 7 0.17500000000000002 No Hit GCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 7 0.17500000000000002 No Hit GGGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCATTGAGATCGGAAA 7 0.17500000000000002 No Hit GGTCAACCTTTTAAACTGCCTGCTGAATCCATGAGCAGGCAAGAGACAAC 7 0.17500000000000002 No Hit GCAGCTTGTGAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGA 7 0.17500000000000002 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 7 0.17500000000000002 No Hit GAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTG 7 0.17500000000000002 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 7 0.17500000000000002 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 7 0.17500000000000002 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 6 0.15 No Hit CAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAGGCGAGAGACCGATAGCGAACAAGTACCGCGAGGG 6 0.15 No Hit GAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGA 6 0.15 No Hit GGACCCTGTCGCCCCACGAGGCGCCGTCAACGAGTCGGGTTGTTTGGGAA 6 0.15 No Hit CAACCTTTTAAACTGCCTGCTGAATCCATGAGCAGGCAAGAGACAACCTG 6 0.15 No Hit TCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCAT 6 0.15 No Hit CGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGG 6 0.15 No Hit GGAGCAGCCTAAACCGTGAAAACGGGGTTGTGGGAGAGCAATACAAGCGT 6 0.15 No Hit GGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGG 6 0.15 No Hit GGCCCGGACCCTGTCGCCCCACGAGGCGCCGTCAACGAGTCGGGTTGTTT 6 0.15 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 6 0.15 No Hit TCAGTGTCGGCCCAGCAGAGTGCTTTCGCCGTTGGTGTTCTTTCCGATCT 6 0.15 No Hit CACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGT 6 0.15 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 5 0.125 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 5 0.125 No Hit CAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTT 5 0.125 No Hit GGGTGAGTAACGCGTAAGAACCTGCCCTTGGGAGGGGAACAACAACTGGA 5 0.125 No Hit GGGCTCGAGGAGCATATGTACATTTGAACCCTGACTACACATATACACAC 5 0.125 No Hit CGAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTC 5 0.125 No Hit GGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCAT 5 0.125 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 5 0.125 No Hit GGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTG 5 0.125 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 5 0.125 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 5 0.125 No Hit GGGGAGTTTGGCTGGGGCGGCACATCTGTTAAAAGATAACGCAGGTGTCC 5 0.125 No Hit GGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAA 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 0.05 0.0 0.0 0.0 0.0 32-33 0.0625 0.0 0.0 0.0 0.0 34-35 0.4 0.0 0.0 0.0 0.0 36-37 0.4 0.0 0.0 0.0 0.0 38-39 0.4125 0.0 0.0 0.0 0.0 40-41 0.44999999999999996 0.0 0.0 0.0 0.0 42-43 0.4875 0.0 0.0 0.0 0.0 44-45 0.5 0.0 0.0 0.0 0.0 46-47 0.5125 0.0 0.0 0.0 0.0 48-49 0.525 0.0 0.0 0.0 0.0 50-51 0.525 0.0 0.0 0.0 0.0 52-53 0.525 0.0 0.0 0.0 0.0 54-55 0.55 0.0 0.0 0.0 0.0 56-57 0.55 0.0 0.0 0.0 0.0 58-59 0.55 0.0 0.0 0.0 0.0 60-61 0.55 0.0 0.0 0.0 0.0 62-63 0.55 0.0 0.0 0.0 0.0 64-65 0.55 0.0 0.0 0.0 0.0 66-67 0.5625 0.0 0.0 0.0 0.0 68-69 0.575 0.0 0.0 0.0 0.0 70-71 0.575 0.0 0.0 0.0 0.0 72-73 0.575 0.0 0.0 0.0 0.0 74-75 0.575 0.0 0.0 0.0 0.0 76-77 0.575 0.0 0.0 0.0 0.0 78-79 0.575 0.0 0.0 0.0 0.0 80-81 0.5874999999999999 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CATCACT 15 0.006951726 51.907692 82-83 AGCATCA 15 0.006951726 51.907692 80-81 TCACTAG 15 0.006951726 51.907692 84-85 ACTAGCT 15 0.006951726 51.907692 86-87 AAAGCAT 15 0.007389513 51.121212 78-79 >>END_MODULE Rejected 48021 READS because READLEN < 1 Read 48021 spots for ERR6133347.sra Written 48021 spots for ERR6133347.sra Rejected 48021 READS because READLEN < 1 Read 48021 spots for ERR6133347.sra Written 48021 spots for ERR6133347.sra Rejected 48021 READS because READLEN < 1 Read 48021 spots for ERR6133347.sra Written 48021 spots for ERR6133347.sra Rejected 48021 READS because READLEN < 1 Read 48021 spots for ERR6133347.sra Written 48021 spots for ERR6133347.sra Rejected 48021 READS because READLEN < 1 Read 48021 spots for ERR6133347.sra Written 48021 spots for ERR6133347.sra Rejected 48021 READS because READLEN < 1 Read 48021 spots for ERR6133347.sra Written 48021 spots for ERR6133347.sra Rejected 48021 READS because READLEN < 1 Read 48021 spots for ERR6133347.sra Written 48021 spots for ERR6133347.sra Rejected 48021 READS because READLEN < 1 Read 48021 spots for ERR6133347.sra Written 48021 spots for ERR6133347.sra Rejected 48021 READS because READLEN < 1 Read 48021 spots for ERR6133347.sra Written 48021 spots for ERR6133347.sra Rejected 48021 READS because READLEN < 1 Read 48021 spots for ERR6133347.sra Written 48021 spots for ERR6133347.sra Rejected 48021 READS because READLEN < 1 Read 48021 spots for ERR6133347.sra Written 48021 spots for ERR6133347.sra Rejected 48021 READS because READLEN < 1 Read 48021 spots for ERR6133347.sra Written 48021 spots for ERR6133347.sra Rejected 48021 READS because READLEN < 1 Read 48021 spots for ERR6133347.sra Written 48021 spots for ERR6133347.sra Rejected 48021 READS because READLEN < 1 Read 48021 spots for ERR6133347.sra Written 48021 spots for ERR6133347.sra Rejected 48021 READS because READLEN < 1 Read 48021 spots for ERR6133347.sra Written 48021 spots for ERR6133347.sra Rejected 48021 READS because READLEN < 1 Read 48021 spots for ERR6133347.sra Written 48021 spots for ERR6133347.sra Rejected 48021 READS because READLEN < 1 Read 48021 spots for ERR6133347.sra Written 48021 spots for ERR6133347.sra Rejected 48021 READS because READLEN < 1 Read 48021 spots for ERR6133347.sra Written 48021 spots for ERR6133347.sra Rejected 48036 READS because READLEN < 1 Read 48036 spots for ERR6133347.sra Written 48036 spots for ERR6133347.sra Rejected 48021 READS because READLEN < 1 Read 48021 spots for ERR6133347.sra Written 48021 spots for ERR6133347.sra SRR ids: ['ERR6133347.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_2sgtnmrt ERR6133347.sra spots: 960435 blocks: [[1, 48021], [48022, 96042], [96043, 144063], [144064, 192084], [192085, 240105], [240106, 288126], [288127, 336147], [336148, 384168], [384169, 432189], [432190, 480210], [480211, 528231], [528232, 576252], [576253, 624273], [624274, 672294], [672295, 720315], [720316, 768336], [768337, 816357], [816358, 864378], [864379, 912399], [912400, 960435]] ERR6133347 file size 207159 ERR6133347 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 ERR6133347 ERR6133347_1.fastq Input file: ERR6133347_1.fastq trimmed: ERR6133347-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 01:09:48 2024 >> started Sat Dec 7 01:09:49 2024 >> done (0.663s) 960435 reads processed; of these: 268 ( 0.03%) short reads filtered out after trimming by size control 10 ( 0.00%) empty reads filtered out after trimming by size control 960157 (99.97%) reads available; of these: 9480 ( 0.99%) trimmed reads available after processing 950677 (99.01%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 22 0.00% 19 58 0.01% 20 31 0.00% 21 17 0.00% 22 31 0.00% 23 13 0.00% 24 30 0.00% 25 11 0.00% 26 16 0.00% 27 21 0.00% 28 24 0.00% 29 191 0.02% 30 17 0.00% 31 26 0.00% 32 63 0.01% 33 1871 0.19% 34 13 0.00% 35 50 0.01% 36 19 0.00% 37 17 0.00% 38 44 0.00% 39 64 0.01% 40 113 0.01% 41 31 0.00% 42 24 0.00% 43 34 0.00% 44 32 0.00% 45 24 0.00% 46 16 0.00% 47 12 0.00% 48 16 0.00% 49 13 0.00% 50 21 0.00% 51 82 0.01% 52 24 0.00% 53 7 0.00% 54 11 0.00% 55 10 0.00% 56 11 0.00% 57 37 0.00% 58 18 0.00% 59 20 0.00% 60 23 0.00% 61 19 0.00% 62 2 0.00% 63 5 0.00% 64 5 0.00% 65 7 0.00% 66 14 0.00% 67 11 0.00% 68 34 0.00% 69 54 0.01% 70 10261 1.07% 71 9424 0.98% 72 10090 1.05% 73 9455 0.98% 74 8999 0.94% 75 8791 0.92% 76 8449 0.88% 77 8964 0.93% 78 9099 0.95% 79 9325 0.97% 80 9423 0.98% 81 11822 1.23% 82 12165 1.27% 83 10518 1.10% 84 13016 1.36% 85 39 0.00% 86 58 0.01% 87 79 0.01% 88 103 0.01% 89 224 0.02% 90 406 0.04% 91 956 0.10% 92 3156 0.33% 93 801956 83.52% 960157 reads passed initial QC criterion=sequence-density sequence-density=6.76 sequence-density-rank=1 fanout-score=2.02 fanout-score-rank=24 prefix-density=6.84 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.03 sequence-density-rank=19 fanout-score=73.87 fanout-score-rank=1 prefix-density=1.26 prefix-fanout=1.6 sequence=TTAAAAGATTTATTAGATAATCGAAAACAGAGGATCTTGAGTACTATTCGAAATTCGGAAGAATTGCGTAGAGGGACCTTTGAGCAGCTCGAAAAAGCTCGGATTCGATTACAGAAAGTCGAACTAGAAGCGGATGAGTATCGAATGAATGGATACTCTGAGATAGAACGAG Potential 3prime adapter identified. Now checking if in reference sequence Warning: gzbuffer added in zlib v1.2.3.5. Unable to change buffer size from default of 8192. 1 reads; of these: 1 (100.00%) were unpaired; of these: 0 (0.00%) aligned 0 times 0 (0.00%) aligned exactly 1 time 1 (100.00%) aligned >1 times 100.00% overall alignment rate Potential adapter found in reference sequence. Continuing without clipping. Started job on | Dec 07 01:10:05 Started mapping on | Dec 07 01:10:06 Finished on | Dec 07 01:10:11 Mapping speed, Million of reads per hour | 691.31 Number of input reads | 960157 Average input read length | 90 UNIQUE READS: Uniquely mapped reads number | 472290 Uniquely mapped reads % | 49.19% Average mapped length | 88.95 Number of splices: Total | 13208 Number of splices: Annotated (sjdb) | 10316 Number of splices: GT/AG | 12000 Number of splices: GC/AG | 312 Number of splices: AT/AC | 14 Number of splices: Non-canonical | 882 Mismatch rate per base, % | 0.53% Deletion rate per base | 0.05% Deletion average length | 1.75 Insertion rate per base | 0.03% Insertion average length | 1.68 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 370657 % of reads mapped to multiple loci | 38.60% Number of reads mapped to too many loci | 69752 % of reads mapped to too many loci | 7.26% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.60% % of reads unmapped: other | 0.34% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 117210 117210 117210 N_multimapping 370657 370657 370657 N_noFeature 41452 46451 450671 N_ambiguous 19669 3044 106 UnstrandedReadsAssigned:411169 PositiveStrandReadsAssigned:422795 NegativeStrandReadsAssigned:21513 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133347 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: ERR6133347-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 960,157 reads, 602,938 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 858 rounds 52973 ERR6133347.ke.tsv 35125 ERR6133347.se.tsv 88098 total ==> ERR6133347.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 0 0 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 8 13.334 PNS24243 293 194 0 0 KQK14069 1603 1504 15 22.807 KQK14071 474 375 0 0 ==> ERR6133347.se.tsv <== BRADI_1g14170v3 15 BRADI_1g53295v3 4 BRADI_1g59795v3 1 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 2 BRADI_1g74790v3 2 BRADI_1g09890v3 0 BRADI_1g77505v3 3 BRADI_1g48960v3 0 ERR6133347 completed mapping pipeline successfully