Starting /dee2/code/volunteer_pipeline.sh ERR6133352 current disk space = 1548323815424 free memory = 1440205484 ERR6133352 SRAfilesize 9da0282a21d0a1f2807c3014866b9b7d ERR6133352.sra ERR6133352.sra file validated ERR6133352 is single end ERR6133352 is conventional basespace ERR6133352 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133352_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 36.08275 37.0 37.0 37.0 33.0 37.0 2 36.562 37.0 37.0 37.0 37.0 37.0 3 36.542 37.0 37.0 37.0 37.0 37.0 4 36.308 37.0 37.0 37.0 37.0 37.0 5 36.3355 37.0 37.0 37.0 37.0 37.0 6 36.47875 37.0 37.0 37.0 37.0 37.0 7 38.70225 40.0 37.0 40.0 37.0 40.0 8 38.703 40.0 37.0 40.0 37.0 40.0 9 38.75525 40.0 37.0 40.0 37.0 40.0 10-11 38.731875 40.0 37.0 40.0 37.0 40.0 12-13 38.71125 40.0 37.0 40.0 37.0 40.0 14-15 38.7505 40.0 37.0 40.0 37.0 40.0 16-17 38.666 40.0 37.0 40.0 37.0 40.0 18-19 38.63725 40.0 37.0 40.0 37.0 40.0 20-21 38.565625 40.0 37.0 40.0 37.0 40.0 22-23 38.437250000000006 40.0 37.0 40.0 37.0 40.0 24-25 38.390125 40.0 37.0 40.0 37.0 40.0 26-27 38.40675 40.0 37.0 40.0 37.0 40.0 28-29 38.42225 40.0 37.0 40.0 37.0 40.0 30-31 38.39075 40.0 37.0 40.0 37.0 40.0 32-33 38.291875000000005 40.0 37.0 40.0 37.0 40.0 34-35 38.149625 40.0 37.0 40.0 37.0 40.0 36-37 38.070125000000004 40.0 37.0 40.0 37.0 40.0 38-39 38.02575 40.0 37.0 40.0 37.0 40.0 40-41 37.870125 40.0 37.0 40.0 35.0 40.0 42-43 37.83075 37.0 37.0 40.0 37.0 40.0 44-45 37.686875 37.0 37.0 40.0 35.0 40.0 46-47 37.559375 37.0 37.0 40.0 33.0 40.0 48-49 37.4025 37.0 37.0 40.0 33.0 40.0 50-51 37.243875 37.0 37.0 40.0 33.0 40.0 52-53 37.067 37.0 37.0 40.0 33.0 40.0 54-55 36.846125 37.0 37.0 37.0 33.0 40.0 56-57 36.782875000000004 37.0 37.0 37.0 33.0 40.0 58-59 36.5145 37.0 37.0 37.0 33.0 40.0 60-61 36.425 37.0 37.0 37.0 33.0 40.0 62-63 36.2845 37.0 37.0 37.0 33.0 37.0 64-65 36.13725 37.0 37.0 37.0 33.0 37.0 66-67 35.976375000000004 37.0 37.0 37.0 33.0 37.0 68-69 35.1075 35.0 35.0 37.0 33.0 37.0 70-71 35.323315954773875 37.0 33.0 37.0 33.0 37.0 72-73 35.761420621419475 37.0 37.0 37.0 33.0 37.0 74-75 35.73453045546367 37.0 37.0 37.0 33.0 37.0 76-77 35.76546043445101 37.0 37.0 37.0 33.0 37.0 78-79 35.70115724053946 37.0 37.0 37.0 33.0 37.0 80-81 35.6540358780407 37.0 37.0 37.0 33.0 37.0 82-83 35.54725836736136 37.0 35.0 37.0 33.0 37.0 84-85 35.51720300056909 37.0 35.0 37.0 33.0 37.0 86-87 35.44077480490524 37.0 33.0 37.0 33.0 37.0 88-89 35.48397435897436 37.0 33.0 37.0 33.0 37.0 90-91 35.37834448160535 37.0 33.0 37.0 33.0 37.0 92-93 35.32427536231884 37.0 33.0 37.0 33.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 2.0 22 4.0 23 6.0 24 4.0 25 9.0 26 7.0 27 12.0 28 12.0 29 23.0 30 35.0 31 40.0 32 45.0 33 72.0 34 101.0 35 190.0 36 741.0 37 1165.0 38 1459.0 39 73.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 65.975 8.9 7.875 17.25 2 49.7 26.424999999999997 14.725 9.15 3 32.05 38.0 17.275 12.675 4 32.074999999999996 27.1 20.7 20.125 5 26.125 26.55 27.425 19.900000000000002 6 21.224999999999998 34.075 27.0 17.7 7 34.675 25.85 22.650000000000002 16.825000000000003 8 28.375 26.0 26.525 19.1 9 26.400000000000002 27.400000000000002 26.825 19.375 10-11 24.5375 28.4375 27.750000000000004 19.275000000000002 12-13 25.5 28.449999999999996 27.224999999999998 18.825 14-15 21.987499999999997 28.6625 29.9375 19.412499999999998 16-17 25.087500000000002 29.049999999999997 24.525 21.337500000000002 18-19 24.9125 25.4375 30.1375 19.5125 20-21 26.687499999999996 25.662499999999998 27.712500000000002 19.9375 22-23 27.825 24.099999999999998 27.575 20.5 24-25 24.587500000000002 25.5 28.9375 20.974999999999998 26-27 25.575 25.0625 28.15 21.212500000000002 28-29 25.05 27.025 27.1125 20.8125 30-31 26.3 26.887499999999996 26.950000000000003 19.8625 32-33 26.775 25.224999999999998 28.075 19.925 34-35 23.5875 30.062499999999996 26.125 20.225 36-37 25.7125 27.0875 25.224999999999998 21.975 38-39 27.353419177397175 25.353169146143266 26.778347293411674 20.515064383047882 40-41 25.2375 25.412499999999998 28.6625 20.6875 42-43 26.237500000000004 28.3875 26.700000000000003 18.675 44-45 23.674999999999997 27.487499999999997 29.075 19.7625 46-47 26.075 25.825 27.187499999999996 20.9125 48-49 24.925 25.8125 28.512500000000003 20.75 50-51 22.8625 28.0625 28.4 20.674999999999997 52-53 24.1625 28.262500000000003 27.1 20.474999999999998 54-55 24.212500000000002 27.675 28.000000000000004 20.1125 56-57 24.175 28.3625 27.55 19.9125 58-59 23.7875 29.062500000000004 27.750000000000004 19.400000000000002 60-61 27.725 26.625 26.325 19.325 62-63 22.3375 28.037499999999998 30.075000000000003 19.55 64-65 23.118279569892472 31.357839459864966 27.28182045511378 18.242060515128784 66-67 24.575 29.7375 26.825 18.862499999999997 68-69 22.6 27.8625 29.125 20.4125 70-71 24.899749373433583 27.957393483709275 26.654135338345863 20.48872180451128 72-73 25.663492063492065 27.136507936507936 29.26984126984127 17.93015873015873 74-75 24.95814552479073 27.920154539600773 28.023180940115903 19.098518995492594 76-77 23.477240119994782 25.811921220816487 28.081387765749316 22.629450893439415 78-79 26.150793650793652 27.526455026455025 28.04232804232804 18.280423280423282 80-81 23.550676127995715 30.90105770518142 26.79073503815772 18.75753112866515 82-83 23.498161013485902 27.74826317940335 27.244244653316983 21.509331153793763 84-85 22.339246119733925 26.967849223946782 30.238359201773836 20.454545454545457 86-87 21.711259754738016 29.59866220735786 27.77313266443701 20.916945373467115 88-89 21.97603121516165 30.128205128205128 27.91248606465998 19.983277591973245 90-91 23.940914158305464 31.744704570791527 25.571348940914156 18.74303232998885 92-93 21.014492753623188 33.124303232998884 27.0066889632107 18.854515050167226 >>END_MODULE >>Per sequence GC content fail #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 0.5 18 0.5 19 0.5 20 1.0 21 0.5 22 0.0 23 1.0 24 3.5 25 8.0 26 10.5 27 17.0 28 28.0 29 32.0 30 29.5 31 41.0 32 55.5 33 72.0 34 84.5 35 100.0 36 125.5 37 169.0 38 191.5 39 180.5 40 214.0 41 235.5 42 236.5 43 245.0 44 208.5 45 176.5 46 161.5 47 147.5 48 143.0 49 147.5 50 144.5 51 141.5 52 147.5 53 144.0 54 182.0 55 160.5 56 104.0 57 102.5 58 75.0 59 35.5 60 25.0 61 28.0 62 23.5 63 16.0 64 12.5 65 13.5 66 10.0 67 4.0 68 11.0 69 16.5 70 8.0 71 1.0 72 0.5 73 0.5 74 0.5 75 0.5 76 1.0 77 0.5 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 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 0.0125 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 0.025 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 20.0 71 27.0 72 31.0 73 27.0 74 25.0 75 22.0 76 29.0 77 29.0 78 20.0 79 24.0 80 23.0 81 34.0 82 37.0 83 24.0 84 40.0 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 3588.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 78.4 #Duplication Level Percentage of deduplicated Percentage of total 1 92.47448979591837 72.5 2 3.826530612244898 6.0 3 1.1798469387755102 2.775 4 0.6696428571428571 2.1 5 0.47831632653061223 1.875 6 0.1913265306122449 0.8999999999999999 7 0.1913265306122449 1.05 8 0.25510204081632654 1.6 9 0.06377551020408163 0.44999999999999996 >10 0.6377551020408163 8.275 >50 0.03188775510204082 2.475 >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 fail #Sequence Count Percentage Possible Source GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 99 2.475 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 33 0.8250000000000001 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 29 0.7250000000000001 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 26 0.65 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 24 0.6 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 22 0.5499999999999999 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 20 0.5 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 18 0.44999999999999996 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 16 0.4 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 16 0.4 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 15 0.375 No Hit AGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAA 13 0.325 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 12 0.3 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 12 0.3 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 12 0.3 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 12 0.3 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 11 0.27499999999999997 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 10 0.25 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 10 0.25 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 10 0.25 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 10 0.25 No Hit GGAGTACGGTAGGGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCATT 9 0.22499999999999998 No Hit GTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGT 9 0.22499999999999998 No Hit GGAGTTTGGCTGGGGCGGCACATCTGTTAAAAGATAACGCAGGTGTCCTA 8 0.2 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 8 0.2 No Hit GAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTG 8 0.2 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 8 0.2 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 8 0.2 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 8 0.2 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 8 0.2 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 8 0.2 No Hit GGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAG 7 0.17500000000000002 No Hit GGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTG 7 0.17500000000000002 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 7 0.17500000000000002 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 7 0.17500000000000002 No Hit GGAGCAGCCTAAACCGTGAAAACGGGGTTGTGGGAGAGCAATACAAGCGT 7 0.17500000000000002 No Hit GAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCC 7 0.17500000000000002 No Hit GGGCGGAAGACATTGTCAGGTGGGGAGTTTGGCTGGGGCGGCACATCTGT 6 0.15 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 6 0.15 No Hit GGTTGAGTGCCGCACCCTAGATGGCTAAAGTCCAGTAGCCGAAAGCATCA 6 0.15 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 6 0.15 No Hit GGAGATTCCCAAATAGGTCAACCTTTTAAACTGCCTGCTGAATCCATGAG 6 0.15 No Hit GTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTC 6 0.15 No Hit CAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTT 5 0.125 No Hit CGAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTC 5 0.125 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 5 0.125 No Hit GGTCAACCTTTTAAACTGCCTGCTGAATCCATGAGCAGGCAAGAGACAAC 5 0.125 No Hit GTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAA 5 0.125 No Hit GTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATGGA 5 0.125 No Hit AGGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGA 5 0.125 No Hit GTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTA 5 0.125 No Hit TATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAG 5 0.125 No Hit CGGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACC 5 0.125 No Hit GCATGGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAG 5 0.125 No Hit GGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCATAGAT 5 0.125 No Hit GGGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGC 5 0.125 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 5 0.125 No Hit CGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTT 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 0.0125 0.0 0.0 0.0 0.0 14-15 0.025 0.0 0.0 0.0 0.0 16-17 0.025 0.0 0.0 0.0 0.0 18-19 0.05 0.0 0.0 0.0 0.0 20-21 0.05 0.0 0.0 0.0 0.0 22-23 0.05 0.0 0.0 0.0 0.0 24-25 0.05 0.0 0.0 0.0 0.0 26-27 0.05 0.0 0.0 0.0 0.0 28-29 0.05 0.0 0.0 0.0 0.0 30-31 0.05 0.0 0.0 0.0 0.0 32-33 0.05 0.0 0.0 0.0 0.0 34-35 0.05 0.0 0.0 0.0 0.0 36-37 0.05 0.0 0.0 0.0 0.0 38-39 0.05 0.0 0.0 0.0 0.0 40-41 0.05 0.0 0.0 0.0 0.0 42-43 0.05 0.0 0.0 0.0 0.0 44-45 0.05 0.0 0.0 0.0 0.0 46-47 0.05 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.05 0.0 0.0 0.0 0.0 54-55 0.05 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.05 0.0 0.0 0.0 0.0 66-67 0.05 0.0 0.0 0.0 0.0 68-69 0.05 0.0 0.0 0.0 0.0 70-71 0.05 0.0 0.0 0.0 0.0 72-73 0.05 0.0 0.0 0.0 0.0 74-75 0.05 0.0 0.0 0.0 0.0 76-77 0.075 0.0 0.0 0.0 0.0 78-79 0.075 0.0 0.0 0.0 0.0 80-81 0.075 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AAAAGAG 20 0.0029623704 63.918755 3 AAAGAGG 20 0.0029623704 63.918755 4 GCAATAC 25 0.0071682157 51.135 7 GGGAGAG 25 0.0071682157 51.135 1 GAGCAAT 25 0.0071682157 51.135 5 AGAGCAA 25 0.0071682157 51.135 4 GAGAGCA 25 0.0071682157 51.135 3 AGCAATA 25 0.0071682157 51.135 6 AAAAAAA 25 0.0013344004 38.96 86-87 ATGGCTA 25 0.0025936235 34.09 58-59 TGGCTAA 25 0.0025936235 34.09 58-59 AGCATCA 30 0.00326618 32.466667 80-81 >>END_MODULE Rejected 25550 READS because READLEN < 1 Read 25550 spots for ERR6133352.sra Written 25550 spots for ERR6133352.sra Rejected 25550 READS because READLEN < 1 Read 25550 spots for ERR6133352.sra Written 25550 spots for ERR6133352.sra Rejected 25550 READS because READLEN < 1 Read 25550 spots for ERR6133352.sra Written 25550 spots for ERR6133352.sra Rejected 25550 READS because READLEN < 1 Read 25550 spots for ERR6133352.sra Written 25550 spots for ERR6133352.sra Rejected 25550 READS because READLEN < 1 Read 25550 spots for ERR6133352.sra Written 25550 spots for ERR6133352.sra Rejected 25550 READS because READLEN < 1 Read 25550 spots for ERR6133352.sra Written 25550 spots for ERR6133352.sra Rejected 25550 READS because READLEN < 1 Read 25550 spots for ERR6133352.sra Written 25550 spots for ERR6133352.sra Rejected 25550 READS because READLEN < 1 Read 25550 spots for ERR6133352.sra Written 25550 spots for ERR6133352.sra Rejected 25550 READS because READLEN < 1 Read 25550 spots for ERR6133352.sra Written 25550 spots for ERR6133352.sra Rejected 25550 READS because READLEN < 1 Read 25550 spots for ERR6133352.sra Written 25550 spots for ERR6133352.sra Rejected 25550 READS because READLEN < 1 Read 25550 spots for ERR6133352.sra Written 25550 spots for ERR6133352.sra Rejected 25550 READS because READLEN < 1 Read 25550 spots for ERR6133352.sra Written 25550 spots for ERR6133352.sra Rejected 25550 READS because READLEN < 1 Read 25550 spots for ERR6133352.sra Written 25550 spots for ERR6133352.sra Rejected 25550 READS because READLEN < 1 Read 25550 spots for ERR6133352.sra Written 25550 spots for ERR6133352.sra Rejected 25550 READS because READLEN < 1 Read 25550 spots for ERR6133352.sra Written 25550 spots for ERR6133352.sra Rejected 25550 READS because READLEN < 1 Read 25550 spots for ERR6133352.sra Written 25550 spots for ERR6133352.sra Rejected 25569 READS because READLEN < 1 Rejected 25550 READS because READLEN < 1 Read 25569 spots for ERR6133352.sra Written 25569 spots for ERR6133352.sra Read 25550 spots for ERR6133352.sra Written 25550 spots for ERR6133352.sra Rejected 25550 READS because READLEN < 1 Read 25550 spots for ERR6133352.sra Written 25550 spots for ERR6133352.sra Rejected 25550 READS because READLEN < 1 Read 25550 spots for ERR6133352.sra Written 25550 spots for ERR6133352.sra SRR ids: ['ERR6133352.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_lwu9p2la ERR6133352.sra spots: 511019 blocks: [[1, 25550], [25551, 51100], [51101, 76650], [76651, 102200], [102201, 127750], [127751, 153300], [153301, 178850], [178851, 204400], [204401, 229950], [229951, 255500], [255501, 281050], [281051, 306600], [306601, 332150], [332151, 357700], [357701, 383250], [383251, 408800], [408801, 434350], [434351, 459900], [459901, 485450], [485451, 511019]] ERR6133352 file size 111051 ERR6133352 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 ERR6133352 ERR6133352_1.fastq Input file: ERR6133352_1.fastq trimmed: ERR6133352-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 01:16:19 2024 >> started Sat Dec 7 01:16:22 2024 >> done (3.046s) 511019 reads processed; of these: 104 ( 0.02%) short reads filtered out after trimming by size control 5 ( 0.00%) empty reads filtered out after trimming by size control 510910 (99.98%) reads available; of these: 3426 ( 0.67%) trimmed reads available after processing 507484 (99.33%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 7 0.00% 19 15 0.00% 20 8 0.00% 21 8 0.00% 22 7 0.00% 23 11 0.00% 24 2 0.00% 25 6 0.00% 26 6 0.00% 27 4 0.00% 28 4 0.00% 29 122 0.02% 30 5 0.00% 31 6 0.00% 32 12 0.00% 33 7 0.00% 34 6 0.00% 35 12 0.00% 36 3 0.00% 37 3 0.00% 38 7 0.00% 39 18 0.00% 40 22 0.00% 41 6 0.00% 42 4 0.00% 43 8 0.00% 44 9 0.00% 45 5 0.00% 46 3 0.00% 47 4 0.00% 48 0 0.00% 49 2 0.00% 50 7 0.00% 51 24 0.00% 52 4 0.00% 53 4 0.00% 54 1 0.00% 55 4 0.00% 56 4 0.00% 57 5 0.00% 58 5 0.00% 59 7 0.00% 60 5 0.00% 61 5 0.00% 62 2 0.00% 63 2 0.00% 64 1 0.00% 65 4 0.00% 66 5 0.00% 67 5 0.00% 68 8 0.00% 69 31 0.01% 70 3026 0.59% 71 3089 0.60% 72 3152 0.62% 73 3168 0.62% 74 2963 0.58% 75 2926 0.57% 76 2840 0.56% 77 3035 0.59% 78 3106 0.61% 79 3198 0.63% 80 3141 0.61% 81 4003 0.78% 82 4215 0.82% 83 3604 0.71% 84 4337 0.85% 85 18 0.00% 86 25 0.00% 87 43 0.01% 88 65 0.01% 89 108 0.02% 90 209 0.04% 91 453 0.09% 92 1646 0.32% 93 458065 89.66% 510910 reads passed initial QC criterion=sequence-density sequence-density=4.21 sequence-density-rank=1 fanout-score=2.02 fanout-score-rank=17 prefix-density=4.26 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.02 sequence-density-rank=34 fanout-score=213.00 fanout-score-rank=1 prefix-density=4.37 prefix-fanout=1.0 sequence=GAGCAATACCAAGACTACTCCAGGCTGTGATGTGAAGAGGGAAACAACGAGGTCATCATCGACATGATATATTGCTGCTATTTTCCACCAGCGATTAAAAGTTAAAAAATTTAGCTGTAAGCTGTAACTATCTTGAAGAAACTAAACTGGTTGCTGTGCTTGATATGTATAGGGAAAACATAATTTATGAGACAATCATACTGTGCAACTCTTGGCTCCATCGATTAATTAATACTCCTTGTTATTGCT 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 01:16:42 Started mapping on | Dec 07 01:16:42 Finished on | Dec 07 01:16:47 Mapping speed, Million of reads per hour | 367.86 Number of input reads | 510910 Average input read length | 91 UNIQUE READS: Uniquely mapped reads number | 288914 Uniquely mapped reads % | 56.55% Average mapped length | 90.48 Number of splices: Total | 7405 Number of splices: Annotated (sjdb) | 6085 Number of splices: GT/AG | 7074 Number of splices: GC/AG | 168 Number of splices: AT/AC | 6 Number of splices: Non-canonical | 157 Mismatch rate per base, % | 0.28% Deletion rate per base | 0.03% Deletion average length | 1.50 Insertion rate per base | 0.01% Insertion average length | 1.54 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 183900 % of reads mapped to multiple loci | 35.99% Number of reads mapped to too many loci | 24464 % of reads mapped to too many loci | 4.79% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.41% % of reads unmapped: other | 0.26% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 38096 38096 38096 N_multimapping 183900 183900 183900 N_noFeature 20585 23543 276073 N_ambiguous 11149 1277 39 UnstrandedReadsAssigned:257180 PositiveStrandReadsAssigned:264094 NegativeStrandReadsAssigned:12802 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133352 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: ERR6133352-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 510,910 reads, 348,560 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 879 rounds 52973 ERR6133352.ke.tsv 35125 ERR6133352.se.tsv 88098 total ==> ERR6133352.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 13 37.1469 PNS24243 293 194 0 0 KQK14069 1603 1504 11 28.6734 KQK14071 474 375 0 0 ==> ERR6133352.se.tsv <== BRADI_1g14170v3 11 BRADI_1g53295v3 4 BRADI_1g59795v3 1 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 3 BRADI_1g74790v3 5 BRADI_1g09890v3 0 BRADI_1g77505v3 5 BRADI_1g48960v3 0 ERR6133352 completed mapping pipeline successfully