Starting /dee2/code/volunteer_pipeline.sh ERR6133372 current disk space = 1548032569344 free memory = 1387424104 ERR6133372 SRAfilesize ffb0b4d8df41bd99bd5bfbe5d404f2ce ERR6133372.sra ERR6133372.sra file validated ERR6133372 is single end ERR6133372 is conventional basespace ERR6133372 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133372_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 35.5325 37.0 33.0 37.0 33.0 37.0 2 36.52875 37.0 37.0 37.0 37.0 37.0 3 36.09725 37.0 37.0 37.0 33.0 37.0 4 35.56525 37.0 37.0 37.0 33.0 37.0 5 35.393 37.0 37.0 37.0 33.0 37.0 6 35.81325 37.0 37.0 37.0 33.0 37.0 7 37.6345 40.0 37.0 40.0 33.0 40.0 8 37.652 40.0 37.0 40.0 33.0 40.0 9 37.734 40.0 37.0 40.0 33.0 40.0 10-11 37.70325 40.0 37.0 40.0 33.0 40.0 12-13 37.640125 40.0 37.0 40.0 33.0 40.0 14-15 37.64 38.5 37.0 40.0 33.0 40.0 16-17 37.518 38.5 37.0 40.0 33.0 40.0 18-19 37.482 38.5 37.0 40.0 33.0 40.0 20-21 37.404624999999996 37.0 37.0 40.0 33.0 40.0 22-23 37.302625 37.0 37.0 40.0 33.0 40.0 24-25 37.468625 37.0 37.0 40.0 33.0 40.0 26-27 37.43275 37.0 37.0 40.0 33.0 40.0 28-29 37.390125 37.0 37.0 40.0 33.0 40.0 30-31 37.234 37.0 37.0 40.0 33.0 40.0 32-33 37.032250000000005 37.0 37.0 40.0 33.0 40.0 34-35 36.876999999999995 37.0 37.0 40.0 33.0 40.0 36-37 36.802125000000004 37.0 37.0 40.0 33.0 40.0 38-39 36.635625 37.0 37.0 40.0 33.0 40.0 40-41 36.385875 37.0 37.0 40.0 33.0 40.0 42-43 36.296875 37.0 37.0 40.0 33.0 40.0 44-45 36.051874999999995 37.0 35.0 40.0 33.0 40.0 46-47 35.744749999999996 37.0 33.0 38.5 33.0 40.0 48-49 35.6015 37.0 33.0 37.0 33.0 40.0 50-51 35.4715 37.0 33.0 37.0 33.0 40.0 52-53 35.199375 37.0 33.0 37.0 30.0 40.0 54-55 35.208124999999995 37.0 33.0 37.0 33.0 40.0 56-57 35.036125 37.0 33.0 37.0 33.0 38.5 58-59 33.814125000000004 37.0 33.0 37.0 27.0 37.0 60-61 34.426249999999996 37.0 33.0 37.0 27.0 37.0 62-63 34.493375 37.0 33.0 37.0 27.0 37.0 64-65 34.366625 37.0 33.0 37.0 27.0 37.0 66-67 34.525875 37.0 33.0 37.0 30.0 37.0 68-69 33.822375 35.0 33.0 37.0 30.0 37.0 70-71 33.80995344978713 35.0 33.0 37.0 27.0 37.0 72-73 34.13642396547962 37.0 33.0 37.0 27.0 37.0 74-75 33.85355563146558 37.0 33.0 37.0 27.0 37.0 76-77 34.01320594432595 37.0 33.0 37.0 27.0 37.0 78-79 34.07017029722676 37.0 33.0 37.0 27.0 37.0 80-81 33.92138166318212 37.0 33.0 37.0 27.0 37.0 82-83 33.91914322820389 37.0 33.0 37.0 27.0 37.0 84-85 33.961502125462786 37.0 33.0 37.0 27.0 37.0 86-87 33.70762711864407 37.0 33.0 37.0 27.0 37.0 88-89 33.89124293785311 37.0 33.0 37.0 27.0 37.0 90-91 33.55418592706728 37.0 33.0 37.0 27.0 37.0 92-93 33.44889573703133 37.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 7.0 21 13.0 22 15.0 23 17.0 24 22.0 25 30.0 26 36.0 27 46.0 28 48.0 29 53.0 30 77.0 31 122.0 32 131.0 33 157.0 34 244.0 35 399.0 36 934.0 37 980.0 38 657.0 39 12.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 85.02499999999999 4.2 4.8 5.975 2 66.57499999999999 19.575 8.85 5.0 3 33.475 36.15 16.775000000000002 13.600000000000001 4 31.775 28.725 18.5 21.0 5 24.875 30.225 27.150000000000002 17.75 6 18.575 39.425 26.125 15.875 7 35.449999999999996 28.7 20.925 14.924999999999999 8 29.775000000000002 27.6 23.974999999999998 18.65 9 24.775 27.525 26.8 20.9 10-11 24.5 28.3375 28.037499999999998 19.125 12-13 26.8125 26.525 25.85 20.8125 14-15 20.8875 31.424999999999997 28.199999999999996 19.4875 16-17 26.8625 29.012500000000003 24.762500000000003 19.3625 18-19 24.4875 27.025 26.5375 21.95 20-21 26.340792599074884 25.66570821352669 27.778472309038634 20.215026878359797 22-23 27.987499999999997 23.8625 27.325 20.825 24-25 25.206301575393848 25.49387346836709 28.419604901225306 20.880220055013755 26-27 25.7125 25.275 29.099999999999998 19.9125 28-29 25.618904726181547 26.59414853713428 26.59414853713428 21.192798199549888 30-31 27.712500000000002 25.374999999999996 26.650000000000002 20.2625 32-33 25.0125 27.212500000000002 27.1625 20.6125 34-35 25.4625 26.9125 26.937499999999996 20.6875 36-37 25.674999999999997 25.15 26.875 22.3 38-39 27.361441261103465 23.695733767046164 30.251470036281745 18.691354935568622 40-41 26.408715251690456 26.095667417981467 27.548209366391184 19.94740796393689 42-43 25.50956608728273 29.473552582218332 25.734650493935224 19.28223083656371 44-45 24.3 25.8 28.875 21.025 46-47 26.35 23.2375 28.6625 21.75 48-49 25.387500000000003 24.8125 29.1875 20.6125 50-51 23.849999999999998 26.1 28.712500000000002 21.337500000000002 52-53 25.516205731447876 26.667500938555875 26.654986860217743 21.161306469778502 54-55 25.3 25.662499999999998 28.975 20.0625 56-57 26.625 26.737499999999997 26.974999999999998 19.662499999999998 58-59 24.6 25.137500000000003 28.8625 21.4 60-61 27.0125 24.6625 28.5875 19.7375 62-63 23.0 27.8875 30.3 18.8125 64-65 23.6625 29.425 28.025 18.8875 66-67 24.2 28.675 27.3 19.825 68-69 23.275000000000002 26.1 27.962500000000002 22.662499999999998 70-71 25.997748029525837 25.972726135368447 27.4990616789691 20.530464156136617 72-73 26.57035175879397 23.831658291457288 29.032663316582912 20.565326633165828 74-75 24.24357034795764 28.303076147251637 28.303076147251637 19.150277357539082 76-77 23.514538558786345 24.715549936788875 27.686472819216185 24.0834386852086 78-79 26.37725310992638 24.701700939324702 28.99212998222899 19.928915968519927 80-81 24.71037555697008 28.746021642266072 28.809675366008914 17.733927434754936 82-83 24.77627205318333 25.50498593710049 28.72666837126055 20.99207363845564 84-85 23.844969199178646 23.767967145790557 31.558008213552363 20.829055441478438 86-87 21.905495634309194 25.796096558808422 30.76527991782229 21.53312788906009 88-89 22.059578839239858 29.25012840267078 29.006163328197225 19.684129429892142 90-91 26.27118644067797 26.95172059578839 28.261427837699028 18.51566512583462 92-93 23.561890087313817 28.762198253723675 28.09450436569081 19.5814072932717 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 1.0 16 1.5 17 12.5 18 15.5 19 4.0 20 1.0 21 3.0 22 5.0 23 3.5 24 3.0 25 3.5 26 5.5 27 10.0 28 17.5 29 22.0 30 24.0 31 31.0 32 41.0 33 46.0 34 56.0 35 75.5 36 98.5 37 122.0 38 154.5 39 170.5 40 181.5 41 197.5 42 186.0 43 178.0 44 182.5 45 195.5 46 222.5 47 206.0 48 158.0 49 164.0 50 186.5 51 174.5 52 152.5 53 150.5 54 170.5 55 128.0 56 64.0 57 56.5 58 60.0 59 54.5 60 42.0 61 34.5 62 36.0 63 36.0 64 28.5 65 21.0 66 13.5 67 19.0 68 15.5 69 10.0 70 10.0 71 5.0 72 3.5 73 1.5 74 2.0 75 2.5 76 1.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.5 84 0.5 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 0.0125 22-23 0.0 24-25 0.025 26-27 0.0 28-29 0.025 30-31 0.0 32-33 0.0 34-35 0.0 36-37 0.0 38-39 0.08750000000000001 40-41 0.17500000000000002 42-43 0.0375 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.11249999999999999 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 7.0 71 9.0 72 8.0 73 7.0 74 6.0 75 4.0 76 8.0 77 7.0 78 10.0 79 4.0 80 5.0 81 10.0 82 8.0 83 9.0 84 4.0 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 3894.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 80.30000000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 94.33374844333748 75.75 2 3.3935242839352426 5.45 3 0.684931506849315 1.6500000000000001 4 0.24906600249066002 0.8 5 0.28019925280199254 1.125 6 0.21793275217932753 1.05 7 0.12453300124533001 0.7000000000000001 8 0.09339975093399751 0.6 9 0.062266500622665005 0.44999999999999996 >10 0.49813200498132004 8.450000000000001 >50 0.062266500622665005 3.975 >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 93 2.325 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 66 1.6500000000000001 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 47 1.175 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 28 0.7000000000000001 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 27 0.675 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 25 0.625 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 25 0.625 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 22 0.5499999999999999 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 22 0.5499999999999999 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 22 0.5499999999999999 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 21 0.525 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 21 0.525 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 20 0.5 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 13 0.325 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 13 0.325 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 12 0.3 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 10 0.25 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 10 0.25 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 9 0.22499999999999998 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 9 0.22499999999999998 No Hit GGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTA 8 0.2 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 8 0.2 No Hit GGCATATGCCAGCTCTGACCGAAATCTTTGGGGATGATTCTGTATTACAA 8 0.2 No Hit GACCACAGCGCATTCCCAATTAGCATCTAAGCTCTCGTTGACATTTCCTT 7 0.17500000000000002 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 7 0.17500000000000002 No Hit CTGAGCCGTGCTCTCTTCTGTGTACATCTCATGTCATTTTAGCGATTCTC 7 0.17500000000000002 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 7 0.17500000000000002 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 6 0.15 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 6 0.15 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 6 0.15 No Hit GAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGG 6 0.15 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 6 0.15 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 6 0.15 No Hit GGAGCAGCCTAAACCGTGAAAACGGGGTTGTGGGAGAGCAATACAAGCGT 6 0.15 No Hit GGAGAGAGTGAGCATATATATTTATACGACGAATAAAAGGCTGCCACGTG 5 0.125 No Hit GGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAA 5 0.125 No Hit GGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGT 5 0.125 No Hit AACAGTAAAGCTTCATAGGGTCTTTCTGTCCAGGTGCAGGTAGTCCGCAT 5 0.125 No Hit GATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGC 5 0.125 No Hit GGGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAA 5 0.125 No Hit GGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTG 5 0.125 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 5 0.125 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 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 0.025 0.0 0.0 0.0 0.0 12-13 0.025 0.0 0.0 0.0 0.0 14-15 0.025 0.0 0.0 0.0 0.0 16-17 0.037500000000000006 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 0.0625 0.0 0.0 0.0 0.0 38-39 0.1 0.0 0.0 0.0 0.0 40-41 0.1 0.0 0.0 0.0 0.0 42-43 0.1 0.0 0.0 0.0 0.0 44-45 0.1 0.0 0.0 0.0 0.0 46-47 0.1 0.0 0.0 0.0 0.0 48-49 0.1 0.0 0.0 0.0 0.0 50-51 0.1 0.0 0.0 0.0 0.0 52-53 0.1 0.0 0.0 0.0 0.0 54-55 0.1 0.0 0.0 0.0 0.0 56-57 0.1 0.0 0.0 0.0 0.0 58-59 0.1 0.0 0.0 0.0 0.0 60-61 0.1 0.0 0.0 0.0 0.0 62-63 0.1 0.0 0.0 0.0 0.0 64-65 0.1 0.0 0.0 0.0 0.0 66-67 0.1 0.0 0.0 0.0 0.0 68-69 0.1 0.0 0.0 0.0 0.0 70-71 0.1 0.0 0.0 0.0 0.0 72-73 0.1 0.0 0.0 0.0 0.0 74-75 0.1 0.0 0.0 0.0 0.0 76-77 0.1 0.0 0.0 0.0 0.0 78-79 0.1 0.0 0.0 0.0 0.0 80-81 0.1 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GCAATAC 20 2.4392648E-5 86.5875 7 CAATACA 20 2.4392648E-5 86.5875 8 GAGCAAT 20 2.4392648E-5 86.5875 5 AGAGCAA 20 2.4392648E-5 86.5875 4 GAGAGCA 20 2.4392648E-5 86.5875 3 GGAGAGC 25 7.377222E-5 69.270004 2 GGGAGAG 25 7.377222E-5 69.270004 1 AGCAATA 25 7.377222E-5 69.270004 6 AATACAA 30 1.8192135E-4 57.725002 9 CATCACT 20 7.0598087E-4 44.403847 82-83 ATCACTA 20 7.0598087E-4 44.403847 84-85 CGAAAGC 20 7.0598087E-4 44.403847 76-77 AGCATCA 20 7.0598087E-4 44.403847 80-81 CACTAGC 20 7.0598087E-4 44.403847 86-87 TCACTAG 20 7.0598087E-4 44.403847 84-85 ACTAGCT 20 7.0598087E-4 44.403847 86-87 AAAGCAT 20 7.0598087E-4 44.403847 78-79 GCATCAC 20 7.0598087E-4 44.403847 82-83 GAAAGCA 20 7.0598087E-4 44.403847 78-79 AAGCATC 20 7.0598087E-4 44.403847 80-81 >>END_MODULE Rejected 186597 READS because READLEN < 1 Read 186597 spots for ERR6133372.sra Written 186597 spots for ERR6133372.sra Rejected 186597 READS because READLEN < 1 Read 186597 spots for ERR6133372.sra Written 186597 spots for ERR6133372.sra Rejected 186597 READS because READLEN < 1 Read 186597 spots for ERR6133372.sra Written 186597 spots for ERR6133372.sra Rejected 186597 READS because READLEN < 1 Read 186597 spots for ERR6133372.sra Written 186597 spots for ERR6133372.sra Rejected 186597 READS because READLEN < 1 Read 186597 spots for ERR6133372.sra Written 186597 spots for ERR6133372.sra Rejected 186597 READS because READLEN < 1 Read 186597 spots for ERR6133372.sra Written 186597 spots for ERR6133372.sra Rejected 186597 READS because READLEN < 1 Read 186597 spots for ERR6133372.sra Written 186597 spots for ERR6133372.sra Rejected 186597 READS because READLEN < 1 Read 186597 spots for ERR6133372.sra Written 186597 spots for ERR6133372.sra Rejected 186610 READS because READLEN < 1 Read 186610 spots for ERR6133372.sra Written 186610 spots for ERR6133372.sra Rejected 186597 READS because READLEN < 1 Read 186597 spots for ERR6133372.sra Written 186597 spots for ERR6133372.sra Rejected 186597 READS because READLEN < 1 Read 186597 spots for ERR6133372.sra Written 186597 spots for ERR6133372.sra Rejected 186597 READS because READLEN < 1 Read 186597 spots for ERR6133372.sra Written 186597 spots for ERR6133372.sra Rejected 186597 READS because READLEN < 1 Read 186597 spots for ERR6133372.sra Written 186597 spots for ERR6133372.sra Rejected 186597 READS because READLEN < 1 Read 186597 spots for ERR6133372.sra Written 186597 spots for ERR6133372.sra Rejected 186597 READS because READLEN < 1 Read 186597 spots for ERR6133372.sra Written 186597 spots for ERR6133372.sra Rejected 186597 READS because READLEN < 1 Read 186597 spots for ERR6133372.sra Written 186597 spots for ERR6133372.sra Rejected 186597 READS because READLEN < 1 Read 186597 spots for ERR6133372.sra Written 186597 spots for ERR6133372.sra Rejected 186597 READS because READLEN < 1 Read 186597 spots for ERR6133372.sra Written 186597 spots for ERR6133372.sra Rejected 186597 READS because READLEN < 1 Read 186597 spots for ERR6133372.sra Written 186597 spots for ERR6133372.sra Rejected 186597 READS because READLEN < 1 Read 186597 spots for ERR6133372.sra Written 186597 spots for ERR6133372.sra SRR ids: ['ERR6133372.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_6ywl41e7 ERR6133372.sra spots: 3731953 blocks: [[1, 186597], [186598, 373194], [373195, 559791], [559792, 746388], [746389, 932985], [932986, 1119582], [1119583, 1306179], [1306180, 1492776], [1492777, 1679373], [1679374, 1865970], [1865971, 2052567], [2052568, 2239164], [2239165, 2425761], [2425762, 2612358], [2612359, 2798955], [2798956, 2985552], [2985553, 3172149], [3172150, 3358746], [3358747, 3545343], [3545344, 3731953]] ERR6133372 file size 825730 ERR6133372 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 ERR6133372 ERR6133372_1.fastq Input file: ERR6133372_1.fastq trimmed: ERR6133372-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 01:53:32 2024 >> started Sat Dec 7 01:53:34 2024 >> done (2.186s) 3731953 reads processed; of these: 308 ( 0.01%) short reads filtered out after trimming by size control 50 ( 0.00%) empty reads filtered out after trimming by size control 3731595 (99.99%) reads available; of these: 74679 ( 2.00%) trimmed reads available after processing 3656916 (98.00%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 29 0.00% 19 84 0.00% 20 52 0.00% 21 79 0.00% 22 57 0.00% 23 16 0.00% 24 25 0.00% 25 9 0.00% 26 15 0.00% 27 22 0.00% 28 43 0.00% 29 30 0.00% 30 31 0.00% 31 51 0.00% 32 27 0.00% 33 35 0.00% 34 42 0.00% 35 546 0.01% 36 395 0.01% 37 36 0.00% 38 46 0.00% 39 233 0.01% 40 121 0.00% 41 90 0.00% 42 14 0.00% 43 12 0.00% 44 11 0.00% 45 9 0.00% 46 13 0.00% 47 12 0.00% 48 13 0.00% 49 13 0.00% 50 8 0.00% 51 38 0.00% 52 10 0.00% 53 6 0.00% 54 10 0.00% 55 13 0.00% 56 8 0.00% 57 10 0.00% 58 2 0.00% 59 7 0.00% 60 14 0.00% 61 9 0.00% 62 4 0.00% 63 5 0.00% 64 8 0.00% 65 3 0.00% 66 10 0.00% 67 6 0.00% 68 20 0.00% 69 79 0.00% 70 6382 0.17% 71 6077 0.16% 72 7087 0.19% 73 6121 0.16% 74 6218 0.17% 75 6381 0.17% 76 5594 0.15% 77 5892 0.16% 78 6265 0.17% 79 7031 0.19% 80 6549 0.18% 81 6837 0.18% 82 7751 0.21% 83 7875 0.21% 84 6728 0.18% 85 164 0.00% 86 291 0.01% 87 508 0.01% 88 832 0.02% 89 1574 0.04% 90 3284 0.09% 91 9757 0.26% 92 54488 1.46% 93 3559428 95.39% 3731595 reads passed initial QC criterion=sequence-density sequence-density=0.59 sequence-density-rank=1 fanout-score=1.47 fanout-score-rank=32 prefix-density=0.04 prefix-fanout=1.5 sequence=GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAAAAATTCTTCCTGGGTCGATGCCCGAGCGGTTAATGGGGACGGACTGTAAATTCGTTGACAAAATGTCTACGCTGGTTCAAATCCAGCTCGGCCCAAAAATCTGGGGCTTCGTGAATATGAACTAAATCTT criterion=fanout-score sequence-density=0.01 sequence-density-rank=25 fanout-score=93.38 fanout-score-rank=1 prefix-density=0.17 prefix-fanout=8.2 sequence=TGAAGAAGAATTGGAAGAAGAAAAGTTTTCTCAACATGGGGAGGAAGTCCCTCCGAAATTTGATTTGTTATTGTATTGTAAGGGGCTTTTTTAGTATTTATCTAAAGGAAGGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCAAGTGGGATATATGGCATACTATTCTTTCCATTTTCATCTTTTTTTCTATTCCACTCCATCTAGATATAAGAAAGAACCCAATGCAATGAAATTCCACTAATATACAATACAAAAAAGAAGAA Started job on | Dec 07 01:53:50 Started mapping on | Dec 07 01:53:50 Finished on | Dec 07 01:53:57 Mapping speed, Million of reads per hour | 1919.11 Number of input reads | 3731595 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 2531002 Uniquely mapped reads % | 67.83% Average mapped length | 92.08 Number of splices: Total | 141944 Number of splices: Annotated (sjdb) | 118920 Number of splices: GT/AG | 137143 Number of splices: GC/AG | 2831 Number of splices: AT/AC | 63 Number of splices: Non-canonical | 1907 Mismatch rate per base, % | 0.44% Deletion rate per base | 0.05% Deletion average length | 1.70 Insertion rate per base | 0.02% Insertion average length | 1.62 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1114907 % of reads mapped to multiple loci | 29.88% Number of reads mapped to too many loci | 29290 % of reads mapped to too many loci | 0.78% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.45% % of reads unmapped: other | 0.06% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 85686 85686 85686 N_multimapping 1114907 1114907 1114907 N_noFeature 147607 177130 2414005 N_ambiguous 98345 10914 278 UnstrandedReadsAssigned:2285050 PositiveStrandReadsAssigned:2342958 NegativeStrandReadsAssigned:116719 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133372 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: ERR6133372-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,731,595 reads, 3,024,815 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,027 rounds 52973 ERR6133372.ke.tsv 35125 ERR6133372.se.tsv 88098 total ==> ERR6133372.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 64 20.3481 PNS24243 293 194 0 0 KQK14069 1603 1504 49 14.2117 KQK14071 474 375 0 0 ==> ERR6133372.se.tsv <== BRADI_1g14170v3 49 BRADI_1g53295v3 94 BRADI_1g59795v3 11 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 35 BRADI_1g74790v3 41 BRADI_1g09890v3 0 BRADI_1g77505v3 70 BRADI_1g48960v3 0 ERR6133372 completed mapping pipeline successfully