Starting /dee2/code/volunteer_pipeline.sh ERR6133550 current disk space = 1544525852672 free memory = 1469300008 ERR6133550 SRAfilesize a52df16e9f9422facd8d38a24ee7c795 ERR6133550.sra ERR6133550.sra file validated ERR6133550 is single end ERR6133550 is conventional basespace ERR6133550 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133550_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 46 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.7285 33.0 33.0 37.0 27.0 37.0 2 35.85625 37.0 37.0 37.0 33.0 37.0 3 35.2035 37.0 33.0 37.0 33.0 37.0 4 35.39325 37.0 37.0 37.0 33.0 37.0 5 35.3345 37.0 37.0 37.0 33.0 37.0 6 35.62825 37.0 37.0 37.0 33.0 37.0 7 37.382 37.0 37.0 40.0 33.0 40.0 8 37.45625 37.0 37.0 40.0 33.0 40.0 9 37.551 37.0 37.0 40.0 33.0 40.0 10-11 37.551125 37.0 37.0 40.0 33.0 40.0 12-13 37.509625 37.0 37.0 40.0 33.0 40.0 14-15 37.461625 37.0 37.0 40.0 33.0 40.0 16-17 37.283 37.0 37.0 40.0 33.0 40.0 18-19 37.277 37.0 37.0 40.0 33.0 40.0 20-21 37.15725 37.0 37.0 40.0 33.0 40.0 22-23 37.11625 37.0 37.0 40.0 33.0 40.0 24-25 37.20225 37.0 37.0 40.0 33.0 40.0 26-27 37.207 37.0 37.0 40.0 33.0 40.0 28-29 37.129125 37.0 37.0 40.0 33.0 40.0 30-31 37.053875 37.0 37.0 40.0 33.0 40.0 32-33 36.892624999999995 37.0 37.0 40.0 33.0 40.0 34-35 36.727375 37.0 37.0 40.0 33.0 40.0 36-37 36.459625 37.0 37.0 40.0 33.0 40.0 38-39 36.4965 37.0 37.0 40.0 33.0 40.0 40-41 36.221999999999994 37.0 37.0 40.0 33.0 40.0 42-43 36.162125 37.0 37.0 40.0 33.0 40.0 44-45 35.831875 37.0 35.0 40.0 33.0 40.0 46-47 35.491625 37.0 33.0 37.0 30.0 40.0 48-49 35.568 37.0 33.0 37.0 33.0 40.0 50-51 35.58175 37.0 33.0 37.0 33.0 40.0 52-53 35.248125 37.0 33.0 37.0 30.0 40.0 54-55 35.265125 37.0 33.0 37.0 33.0 40.0 56-57 35.017375 37.0 33.0 37.0 33.0 40.0 58-59 34.358875 37.0 33.0 37.0 27.0 37.0 60-61 34.599375 37.0 33.0 37.0 27.0 37.0 62-63 34.552499999999995 37.0 33.0 37.0 30.0 37.0 64-65 34.60425 37.0 33.0 37.0 27.0 37.0 66-67 34.57125 37.0 33.0 37.0 27.0 37.0 68-69 33.672125 35.0 33.0 37.0 27.0 37.0 70-71 33.74527331995988 35.0 33.0 37.0 27.0 37.0 72-73 34.12077389770387 37.0 33.0 37.0 27.0 37.0 74-75 34.122657543483456 37.0 33.0 37.0 27.0 37.0 76-77 34.0505769481613 37.0 33.0 37.0 27.0 37.0 78-79 34.0174742296888 37.0 33.0 37.0 27.0 37.0 80-81 33.88380152299557 37.0 33.0 37.0 27.0 37.0 82-83 33.81788300947938 37.0 33.0 37.0 27.0 37.0 84-85 33.72373474293433 37.0 33.0 37.0 27.0 37.0 86-87 33.69498170412964 37.0 33.0 37.0 27.0 37.0 88-89 33.709618400418194 37.0 33.0 37.0 27.0 37.0 90-91 33.54351803450078 37.0 33.0 37.0 27.0 37.0 92-93 33.55828541557763 37.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 12.0 21 10.0 22 20.0 23 15.0 24 39.0 25 29.0 26 37.0 27 42.0 28 60.0 29 60.0 30 81.0 31 123.0 32 121.0 33 156.0 34 254.0 35 406.0 36 925.0 37 885.0 38 705.0 39 20.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 84.775 4.3 4.375 6.550000000000001 2 66.60000000000001 18.25 8.875 6.275 3 36.275 35.325 15.1 13.3 4 30.825000000000003 29.825000000000003 18.875 20.474999999999998 5 28.075 28.775000000000002 25.924999999999997 17.224999999999998 6 19.525000000000002 39.074999999999996 25.374999999999996 16.025 7 37.15 27.200000000000003 20.125 15.525 8 28.125 26.55 23.75 21.575 9 24.4 29.9 27.3 18.4 10-11 23.1875 28.799999999999997 29.049999999999997 18.9625 12-13 25.775 27.250000000000004 26.2125 20.7625 14-15 20.974999999999998 33.5 27.825 17.7 16-17 26.0375 29.0875 24.5125 20.3625 18-19 24.40305038129766 25.61570196274534 29.641205150643827 20.340042505313164 20-21 26.056514128532132 24.90622655663916 29.34483620905226 19.692423105776445 22-23 28.349999999999998 22.400000000000002 29.299999999999997 19.950000000000003 24-25 24.95 24.099999999999998 29.099999999999998 21.85 26-27 27.3625 23.9375 28.549999999999997 20.150000000000002 28-29 24.775 28.15 28.1625 18.912499999999998 30-31 30.425 23.7875 26.237500000000004 19.55 32-33 25.5625 26.6625 26.474999999999998 21.3 34-35 23.776748842447752 30.384182204980604 26.11688149167814 19.722187460893505 36-37 27.425 23.4125 26.200000000000003 22.9625 38-39 29.525000000000002 24.3875 28.575 17.5125 40-41 24.530898173630224 24.10557918438829 30.810607955966972 20.55291468601451 42-43 27.07237665915352 29.939894815927875 24.442774855997996 18.54495366892061 44-45 24.818613960470355 24.74355766825119 30.485364023017265 19.952464348261195 46-47 26.25 22.1875 27.725 23.8375 48-49 25.378172271533945 23.27790973871734 30.103762970371296 21.240155019377422 50-51 23.849999999999998 27.3625 26.8625 21.925 52-53 23.71778834125594 26.99524643482612 24.69352014010508 24.59344508381286 54-55 23.200000000000003 26.6625 29.799999999999997 20.3375 56-57 26.5375 28.3875 26.487500000000004 18.587500000000002 58-59 22.6 26.437500000000004 31.0125 19.950000000000003 60-61 29.062500000000004 25.124999999999996 26.674999999999997 19.1375 62-63 21.637500000000003 26.625 32.3625 19.375 64-65 22.175 31.887500000000003 27.325 18.6125 66-67 25.7 30.099999999999998 26.200000000000003 18.0 68-69 21.2 25.85 29.45 23.5 70-71 23.798197295943915 26.74011016524787 27.12819228843265 22.33350025037556 72-73 27.179939516129032 24.508568548387096 28.95665322580645 19.35483870967742 74-75 24.245880861850445 29.340937896070972 28.39036755386565 18.022813688212928 76-77 22.15004458030824 24.404534454209657 27.55063049293084 25.894790472551264 78-79 25.556123753515724 25.96522628483764 29.570442342111992 18.908207619534643 80-81 22.85053335046909 31.821102686030073 27.528595296234414 17.79976866726642 82-83 24.66037003493337 25.268469400957432 27.59736058998577 22.47379997412343 84-85 22.829917765304792 24.722621067745727 32.17595614149589 20.271505025453596 86-87 21.19707266074229 27.49607945635128 29.312598013591217 21.99424986931521 88-89 20.386826973340302 27.65290120230005 31.129116570831155 20.83115525352849 90-91 26.110820700470466 27.83585990590695 28.084161003659176 17.969158389963408 92-93 22.138003136434918 28.410872974385782 28.998954521693676 20.452169367485627 >>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 1.0 17 7.5 18 9.5 19 4.0 20 1.0 21 0.5 22 0.5 23 3.0 24 6.0 25 4.5 26 9.0 27 16.0 28 15.5 29 14.5 30 22.0 31 31.5 32 46.5 33 64.5 34 68.5 35 84.0 36 106.5 37 133.0 38 165.0 39 174.0 40 173.0 41 194.0 42 214.0 43 214.5 44 210.5 45 186.0 46 190.5 47 188.5 48 149.5 49 158.0 50 178.5 51 163.5 52 140.0 53 153.0 54 221.0 55 174.5 56 67.5 57 53.0 58 49.5 59 34.0 60 29.5 61 35.0 62 24.5 63 20.5 64 24.5 65 22.0 66 18.0 67 14.5 68 12.0 69 11.0 70 7.5 71 4.0 72 3.0 73 1.5 74 1.0 75 1.0 76 0.5 77 0.0 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 0.0125 20-21 0.025 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 0.11249999999999999 36-37 0.0 38-39 0.0 40-41 0.075 42-43 0.17500000000000002 44-45 0.075 46-47 0.0 48-49 0.0125 50-51 0.0 52-53 0.075 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 12.0 71 13.0 72 14.0 73 10.0 74 12.0 75 9.0 76 9.0 77 5.0 78 10.0 79 10.0 80 11.0 81 13.0 82 15.0 83 22.0 84 9.0 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 3826.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 76.775 #Duplication Level Percentage of deduplicated Percentage of total 1 93.58515141647672 71.85000000000001 2 3.321393682839466 5.1 3 1.0420058612829697 2.4 4 0.5861282969716705 1.7999999999999998 5 0.4233148811462064 1.625 6 0.19537609899055683 0.8999999999999999 7 0.09768804949527841 0.525 8 0.09768804949527841 0.6 9 0.0651253663301856 0.44999999999999996 >10 0.5535656138065776 9.5 >50 0.0 0.0 >100 0.0325626831650928 5.25 >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 210 5.25 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 49 1.225 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 46 1.15 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 30 0.75 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 29 0.7250000000000001 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 27 0.675 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 26 0.65 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 23 0.575 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 22 0.5499999999999999 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 19 0.475 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 18 0.44999999999999996 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 16 0.4 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 14 0.35000000000000003 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 14 0.35000000000000003 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 13 0.325 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 12 0.3 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 11 0.27499999999999997 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 11 0.27499999999999997 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 9 0.22499999999999998 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 9 0.22499999999999998 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 8 0.2 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 8 0.2 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 8 0.2 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 7 0.17500000000000002 No Hit GGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCG 7 0.17500000000000002 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 7 0.17500000000000002 No Hit GGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 6 0.15 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 6 0.15 No Hit GAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAAT 6 0.15 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 6 0.15 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 6 0.15 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 6 0.15 No Hit CAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGG 5 0.125 No Hit GCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 5 0.125 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 5 0.125 No Hit GTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCA 5 0.125 No Hit GCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGA 5 0.125 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 5 0.125 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 5 0.125 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 5 0.125 No Hit GATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGC 5 0.125 No Hit GGGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAA 5 0.125 No Hit GAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTG 5 0.125 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 5 0.125 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 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 0.0125 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.025 0.0 0.0 0.0 0.0 68-69 0.025 0.0 0.0 0.0 0.0 70-71 0.025 0.0 0.0 0.0 0.0 72-73 0.025 0.0 0.0 0.0 0.0 74-75 0.025 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.025 0.0 0.0 0.0 0.0 80-81 0.025 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GCAATAC 25 7.205523E-5 69.6 7 CAATACA 25 7.205523E-5 69.6 8 GAGCAAT 25 7.205523E-5 69.6 5 AGCAATA 25 7.205523E-5 69.6 6 GGAGAGC 30 1.7769479E-4 58.0 2 GGGAGAG 30 1.7769479E-4 58.0 1 AGAGCAA 30 1.7769479E-4 58.0 4 GAGAGCA 30 1.7769479E-4 58.0 3 AATACAA 30 1.7769479E-4 58.0 9 GGCACCC 25 0.006606883 52.2 7 CACCCAG 25 0.006606883 52.2 9 GCACCCA 25 0.006606883 52.2 8 GATGGCT 20 7.824886E-4 43.5 56-57 GTTGAGT 25 4.3413726E-5 43.5 38-39 CCAGTAG 25 4.3413726E-5 43.5 68-69 AGTAGCC 25 4.3413726E-5 43.5 70-71 TGCCGCA 25 4.3413726E-5 43.5 44-45 GAAGCGG 25 4.3413726E-5 43.5 32-33 TAGCCGA 25 4.3413726E-5 43.5 72-73 GCGAAGC 25 4.3413726E-5 43.5 30-31 >>END_MODULE Rejected 263510 READS because READLEN < 1 Read 263510 spots for ERR6133550.sra Written 263510 spots for ERR6133550.sra Rejected 263510 READS because READLEN < 1 Read 263510 spots for ERR6133550.sra Written 263510 spots for ERR6133550.sra Rejected 263510 READS because READLEN < 1 Read 263510 spots for ERR6133550.sra Written 263510 spots for ERR6133550.sra Rejected 263510 READS because READLEN < 1 Read 263510 spots for ERR6133550.sra Written 263510 spots for ERR6133550.sra Rejected 263510 READS because READLEN < 1 Read 263510 spots for ERR6133550.sra Written 263510 spots for ERR6133550.sra Rejected 263510 READS because READLEN < 1 Read 263510 spots for ERR6133550.sra Written 263510 spots for ERR6133550.sra Rejected 263510 READS because READLEN < 1 Read 263510 spots for ERR6133550.sra Written 263510 spots for ERR6133550.sra Rejected 263510 READS because READLEN < 1 Read 263510 spots for ERR6133550.sra Written 263510 spots for ERR6133550.sra Rejected 263510 READS because READLEN < 1 Read 263510 spots for ERR6133550.sra Written 263510 spots for ERR6133550.sra Rejected 263510 READS because READLEN < 1 Read 263510 spots for ERR6133550.sra Written 263510 spots for ERR6133550.sra Rejected 263510 READS because READLEN < 1 Read 263510 spots for ERR6133550.sra Written 263510 spots for ERR6133550.sra Rejected 263510 READS because READLEN < 1 Read 263510 spots for ERR6133550.sra Written 263510 spots for ERR6133550.sra Rejected 263510 READS because READLEN < 1 Read 263510 spots for ERR6133550.sra Written 263510 spots for ERR6133550.sra Rejected 263510 READS because READLEN < 1 Read 263510 spots for ERR6133550.sra Written 263510 spots for ERR6133550.sra Rejected 263510 READS because READLEN < 1 Read 263510 spots for ERR6133550.sra Written 263510 spots for ERR6133550.sra Rejected 263510 READS because READLEN < 1 Read 263510 spots for ERR6133550.sra Written 263510 spots for ERR6133550.sra Rejected 263510 READS because READLEN < 1 Read 263510 spots for ERR6133550.sra Written 263510 spots for ERR6133550.sra Rejected 263510 READS because READLEN < 1 Read 263510 spots for ERR6133550.sra Written 263510 spots for ERR6133550.sra Rejected 263510 READS because READLEN < 1 Read 263510 spots for ERR6133550.sra Written 263510 spots for ERR6133550.sra Rejected 263527 READS because READLEN < 1 Read 263527 spots for ERR6133550.sra Written 263527 spots for ERR6133550.sra SRR ids: ['ERR6133550.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_i7y4xt50 ERR6133550.sra spots: 5270217 blocks: [[1, 263510], [263511, 527020], [527021, 790530], [790531, 1054040], [1054041, 1317550], [1317551, 1581060], [1581061, 1844570], [1844571, 2108080], [2108081, 2371590], [2371591, 2635100], [2635101, 2898610], [2898611, 3162120], [3162121, 3425630], [3425631, 3689140], [3689141, 3952650], [3952651, 4216160], [4216161, 4479670], [4479671, 4743180], [4743181, 5006690], [5006691, 5270217]] ERR6133550 file size 1164530 ERR6133550 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 ERR6133550 ERR6133550_1.fastq Input file: ERR6133550_1.fastq trimmed: ERR6133550-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 08:27:35 2024 >> started Sat Dec 7 08:27:50 2024 >> done (15.431s) 5270217 reads processed; of these: 374 ( 0.01%) short reads filtered out after trimming by size control 59 ( 0.00%) empty reads filtered out after trimming by size control 5269784 (99.99%) reads available; of these: 93607 ( 1.78%) trimmed reads available after processing 5176177 (98.22%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 37 0.00% 19 59 0.00% 20 34 0.00% 21 30 0.00% 22 30 0.00% 23 10 0.00% 24 22 0.00% 25 15 0.00% 26 13 0.00% 27 16 0.00% 28 37 0.00% 29 37 0.00% 30 20 0.00% 31 38 0.00% 32 36 0.00% 33 42 0.00% 34 72 0.00% 35 701 0.01% 36 594 0.01% 37 40 0.00% 38 37 0.00% 39 110 0.00% 40 87 0.00% 41 41 0.00% 42 15 0.00% 43 17 0.00% 44 11 0.00% 45 14 0.00% 46 13 0.00% 47 11 0.00% 48 13 0.00% 49 17 0.00% 50 16 0.00% 51 64 0.00% 52 19 0.00% 53 12 0.00% 54 14 0.00% 55 9 0.00% 56 13 0.00% 57 10 0.00% 58 19 0.00% 59 10 0.00% 60 13 0.00% 61 15 0.00% 62 1 0.00% 63 3 0.00% 64 4 0.00% 65 9 0.00% 66 9 0.00% 67 13 0.00% 68 41 0.00% 69 186 0.00% 70 13931 0.26% 71 12806 0.24% 72 14896 0.28% 73 13477 0.26% 74 13934 0.26% 75 13994 0.27% 76 12301 0.23% 77 12720 0.24% 78 14556 0.28% 79 16311 0.31% 80 14665 0.28% 81 16197 0.31% 82 17014 0.32% 83 18582 0.35% 84 15059 0.29% 85 193 0.00% 86 388 0.01% 87 636 0.01% 88 1148 0.02% 89 2328 0.04% 90 5008 0.10% 91 15093 0.29% 92 63142 1.20% 93 4958656 94.10% 5269784 reads passed initial QC criterion=sequence-density sequence-density=0.47 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=34 prefix-density=0.47 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=37 fanout-score=84.67 fanout-score-rank=1 prefix-density=0.11 prefix-fanout=6.2 sequence=AAAAGAAGGGGTGTTCCATCTCCGGACGACGATCCTGCCTGCGGAGGAAGACATGCCGGCGATCATGTCGAGCTTCAAGAAGTTCAACGACTCATTCATGGAGCAATACCAAGACTACTCCAGGCTGTGATGTGAAGAGGGAAACAACGACGTCATCATCGACATGATATATTGCTGCTATTTTCCACCAGCGATTAAAAGTTAAAAAATTTAGCTGTAAGCTGTAACTATCTTGAAGAAACTAAACTGGTTGCTGTGCTTGATATGTATAGGGAAAACATAATTTATGAGACAATCATACTGTGCAACTCTTGGCTCCATCGATTAATTAATACTCCTTGTTATTGC Started job on | Dec 07 08:29:35 Started mapping on | Dec 07 08:29:36 Finished on | Dec 07 08:30:26 Mapping speed, Million of reads per hour | 379.42 Number of input reads | 5269784 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 3385933 Uniquely mapped reads % | 64.25% Average mapped length | 91.79 Number of splices: Total | 161106 Number of splices: Annotated (sjdb) | 131085 Number of splices: GT/AG | 153399 Number of splices: GC/AG | 3389 Number of splices: AT/AC | 114 Number of splices: Non-canonical | 4204 Mismatch rate per base, % | 0.44% Deletion rate per base | 0.05% Deletion average length | 1.64 Insertion rate per base | 0.02% Insertion average length | 1.93 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1760069 % of reads mapped to multiple loci | 33.40% Number of reads mapped to too many loci | 41845 % of reads mapped to too many loci | 0.79% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.49% % of reads unmapped: other | 0.06% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 123782 123782 123782 N_multimapping 1760069 1760069 1760069 N_noFeature 223266 258824 3231328 N_ambiguous 134631 15479 542 UnstrandedReadsAssigned:3028036 PositiveStrandReadsAssigned:3111630 NegativeStrandReadsAssigned:154063 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133550 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: ERR6133550-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 5,269,784 reads, 4,162,735 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,079 rounds 52973 ERR6133550.ke.tsv 35125 ERR6133550.se.tsv 88098 total ==> ERR6133550.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 124 29.1421 PNS24243 293 194 0 0 KQK14069 1603 1504 54 11.5771 KQK14071 474 375 1 0.859848 ==> ERR6133550.se.tsv <== BRADI_1g14170v3 55 BRADI_1g53295v3 45 BRADI_1g59795v3 34 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 46 BRADI_1g74790v3 33 BRADI_1g09890v3 2 BRADI_1g77505v3 102 BRADI_1g48960v3 1 ERR6133550 completed mapping pipeline successfully