Starting /dee2/code/volunteer_pipeline.sh SRR17234931 current disk space = 3049155346432 free memory = 1319128260 SRR17234931 SRAfilesize 0ea5df0c14831990ace7d84f5b95217e SRR17234931.sra SRR17234931.sra file validated SRR17234931 is paired end SRR17234931 is conventional basespace SRR17234931 read1 length is 92-141 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR17234931_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 92-141 %GC 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.7205 37.0 37.0 37.0 37.0 37.0 2 36.57 37.0 37.0 37.0 37.0 37.0 3 36.637 37.0 37.0 37.0 37.0 37.0 4 36.483 37.0 37.0 37.0 37.0 37.0 5 36.6 37.0 37.0 37.0 37.0 37.0 6 36.596 37.0 37.0 37.0 37.0 37.0 7 36.5635 37.0 37.0 37.0 37.0 37.0 8 36.57075 37.0 37.0 37.0 37.0 37.0 9 36.566 37.0 37.0 37.0 37.0 37.0 10-14 36.5622 37.0 37.0 37.0 37.0 37.0 15-19 36.520700000000005 37.0 37.0 37.0 37.0 37.0 20-24 36.5137 37.0 37.0 37.0 37.0 37.0 25-29 36.467600000000004 37.0 37.0 37.0 37.0 37.0 30-34 36.5024 37.0 37.0 37.0 37.0 37.0 35-39 36.4666 37.0 37.0 37.0 37.0 37.0 40-44 36.4713 37.0 37.0 37.0 37.0 37.0 45-49 36.499 37.0 37.0 37.0 37.0 37.0 50-54 36.467400000000005 37.0 37.0 37.0 37.0 37.0 55-59 36.46399999999999 37.0 37.0 37.0 37.0 37.0 60-64 36.4552 37.0 37.0 37.0 37.0 37.0 65-69 36.4237 37.0 37.0 37.0 37.0 37.0 70-74 36.409000000000006 37.0 37.0 37.0 37.0 37.0 75-79 36.363299999999995 37.0 37.0 37.0 37.0 37.0 80-84 36.3709 37.0 37.0 37.0 37.0 37.0 85-89 36.307 37.0 37.0 37.0 37.0 37.0 90-94 36.27511690506249 37.0 37.0 37.0 37.0 37.0 95-99 36.2490792308621 37.0 37.0 37.0 37.0 37.0 100-104 36.16048847712234 37.0 37.0 37.0 37.0 37.0 105-109 36.17092812206505 37.0 37.0 37.0 37.0 37.0 110-114 36.16272826049411 37.0 37.0 37.0 37.0 37.0 115-119 36.11469330171433 37.0 37.0 37.0 37.0 37.0 120-124 36.127785061326115 37.0 37.0 37.0 37.0 37.0 125-129 36.15322455920874 37.0 37.0 37.0 37.0 37.0 130-134 36.00266370699224 37.0 37.0 37.0 37.0 37.0 135-139 35.985238623751385 37.0 37.0 37.0 37.0 37.0 140-141 35.74916759156493 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 22 1.0 23 0.0 24 2.0 25 2.0 26 5.0 27 7.0 28 18.0 29 13.0 30 23.0 31 31.0 32 46.0 33 50.0 34 119.0 35 257.0 36 2691.0 37 735.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 49.875 7.825 5.2749999999999995 37.025000000000006 2 18.375 10.2 41.949999999999996 29.475 3 19.325 16.05 25.75 38.875 4 25.624999999999996 23.025000000000002 23.474999999999998 27.875 5 21.85 29.45 25.825 22.875 6 18.575 30.575000000000003 28.475 22.375 7 14.625 26.25 41.4 17.724999999999998 8 15.928982245561391 23.080770192548137 36.98424606151538 24.006001500375092 9 17.025000000000002 21.2 36.75 25.025 10-14 19.925 28.78 27.735 23.56 15-19 20.43 27.544999999999998 28.225 23.799999999999997 20-24 20.345 27.74 27.625 24.29 25-29 20.32 27.725 28.175 23.78 30-34 19.88 27.395000000000003 27.955000000000002 24.77 35-39 20.474999999999998 26.939999999999998 27.915 24.67 40-44 20.235 28.275 27.134999999999998 24.355 45-49 20.97 27.534999999999997 27.169999999999998 24.325 50-54 21.025 26.93 28.255000000000003 23.79 55-59 20.815 27.47 27.715 24.0 60-64 20.165 26.939999999999998 28.000000000000004 24.895 65-69 21.47 27.060000000000002 27.495000000000005 23.974999999999998 70-74 20.474999999999998 27.544999999999998 28.035 23.945 75-79 21.15 26.8 27.55 24.5 80-84 20.925 27.295 27.700000000000003 24.08 85-89 20.605 27.47 27.85 24.075 90-94 21.230307576894223 27.576894223555886 26.561640410102527 24.63115778944736 95-99 20.805974637862764 28.063756202696606 27.081349305799208 24.048919853641422 100-104 20.6731012178483 28.217696700186973 27.237354085603112 23.871847996361613 105-109 20.991000204540804 27.63346287584373 27.137451421558602 24.238085498056865 110-114 21.25719023682438 28.019899466238275 27.28403378763538 23.438876509301963 115-119 20.97453167754157 27.557356346032414 27.531046095558832 23.937065880867188 120-124 20.53068882337175 27.735191637630663 27.63870276065398 24.095416778343605 125-129 20.659798334064007 27.065979833406402 27.964708461201226 24.309513371328364 130-134 20.9322974472808 27.7968923418424 27.508324084350722 23.762486126526085 135-139 20.86015538290788 27.46392896781354 27.36958934517203 24.30632630410655 140-141 20.491120976692564 27.538845726970035 27.62208657047725 24.347946725860155 >>END_MODULE >>Per sequence GC content pass #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 1.0 13 1.0 14 0.0 15 0.0 16 0.5 17 0.5 18 0.0 19 0.0 20 0.5 21 1.5 22 2.0 23 1.5 24 1.0 25 1.5 26 5.5 27 8.0 28 6.0 29 8.0 30 12.0 31 22.5 32 34.0 33 36.5 34 42.5 35 53.5 36 82.5 37 104.0 38 107.0 39 138.0 40 171.5 41 182.0 42 203.5 43 207.0 44 234.0 45 269.0 46 272.0 47 261.5 48 236.0 49 223.0 50 190.5 51 153.0 52 132.0 53 128.5 54 112.5 55 78.5 56 55.5 57 47.5 58 35.0 59 28.5 60 28.0 61 17.5 62 12.5 63 9.0 64 6.0 65 5.5 66 6.5 67 4.5 68 2.5 69 3.0 70 2.5 71 1.0 72 2.0 73 4.0 74 3.0 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 0.025 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-141 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 92-93 3.0 94-95 1.0 96-97 10.0 98-99 14.0 100-101 13.0 102-103 19.0 104-105 17.0 106-107 25.0 108-109 18.0 110-111 19.0 112-113 25.0 114-115 25.0 116-117 19.0 118-119 29.0 120-121 34.0 122-123 32.0 124-125 27.0 126-127 35.0 128-129 31.0 130-131 0.0 132-133 0.0 134-135 0.0 136-137 0.0 138-139 0.0 140-141 3604.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 82.625 #Duplication Level Percentage of deduplicated Percentage of total 1 83.32829046898638 68.85 2 13.464447806354011 22.25 3 2.2995461422087744 5.7 4 0.6656580937972768 2.1999999999999997 5 0.2420574886535552 1.0 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >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 GGCGCCAGTAAGGTCCATAGGGTGCCCAAGCGAGATCGGAATACTCATAA 5 0.125 No Hit TGGATAAATGCCACCTGGTGGAATGGGTTTGGAACGTTGCCTCCAGTCCT 5 0.125 No Hit CTCTGCAACCAAGGAGCAGGATCCGGATGTCGCCGACTCATTCTCCCCAG 5 0.125 No Hit CCTGGAAGTTGGAAGCTATAGACTTCTCAAGTGCTTCTTGGAAATGTCTG 5 0.125 No Hit GCGGCAATAAAGCTGATGCACTGCACTTGACGCGTGTTGTCGAATCCGAT 5 0.125 No Hit CACAAGAATGTGCTTAAATTGCCGAAGGTTATAATTTTTACAAGAAGACA 5 0.125 No Hit CTCTATTGTTTTCGACAACAATCTCTTCTACATGACTTCTTAGAGAAAGC 5 0.125 No Hit GTTTCTGCCATGGTTTATCTGGCGTGCCAGGGCTCCCTGAGCTTTTGTTC 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 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 82-83 0.0 0.0 0.0 0.0 0.0 84-85 0.0 0.0 0.0 0.0 0.0 86-87 0.0 0.0 0.0 0.0 0.0 88-89 0.0 0.0 0.0 0.0 0.0 90-91 0.0 0.0 0.0 0.0 0.0 92-93 0.0 0.0 0.0 0.0 0.0 94-95 0.0 0.0 0.0 0.0 0.0 96-97 0.0 0.0 0.0 0.0 0.0 98-99 0.0 0.0 0.0 0.0 0.0 100-101 0.0 0.0 0.0 0.0 0.0 102-103 0.0 0.0 0.0 0.0 0.0 104-105 0.0 0.0 0.0 0.0 0.0 106-107 0.0 0.0 0.0 0.0 0.0 108-109 0.0 0.0 0.0 0.0 0.0 110-111 0.0 0.0 0.0 0.0 0.0 112-113 0.0 0.0 0.0 0.0 0.0 114-115 0.0 0.0 0.0 0.0 0.0 116-117 0.0 0.0 0.0 0.0 0.0 118-119 0.0 0.0 0.0 0.0 0.0 120-121 0.0 0.0 0.0 0.0 0.0 122-123 0.0 0.0 0.0 0.0 0.0 124-125 0.0 0.0 0.0 0.0 0.0 126-127 0.0 0.0 0.0 0.0 0.0 128-129 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ATCTCAA 10 0.0089136 132.65001 2 CATCTCA 10 0.0089136 132.65001 1 ATTGGGC 10 0.0089136 132.65001 8 TCTCAAT 10 0.0089136 132.65001 3 CTCAATT 10 0.0089136 132.65001 4 AATTGGG 10 0.0089136 132.65001 7 TAGATCA 20 0.008296993 49.74375 82-83 >>END_MODULE SRR17234931 read2 length is 92-141 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR17234931_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 92-141 %GC 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.6035 37.0 37.0 37.0 37.0 37.0 2 36.4965 37.0 37.0 37.0 37.0 37.0 3 36.4525 37.0 37.0 37.0 37.0 37.0 4 36.484 37.0 37.0 37.0 37.0 37.0 5 36.538 37.0 37.0 37.0 37.0 37.0 6 36.4375 37.0 37.0 37.0 37.0 37.0 7 36.4585 37.0 37.0 37.0 37.0 37.0 8 36.513 37.0 37.0 37.0 37.0 37.0 9 36.4975 37.0 37.0 37.0 37.0 37.0 10-14 36.5004 37.0 37.0 37.0 37.0 37.0 15-19 36.4626 37.0 37.0 37.0 37.0 37.0 20-24 36.4568 37.0 37.0 37.0 37.0 37.0 25-29 36.4165 37.0 37.0 37.0 37.0 37.0 30-34 36.4288 37.0 37.0 37.0 37.0 37.0 35-39 36.356100000000005 37.0 37.0 37.0 37.0 37.0 40-44 36.4043 37.0 37.0 37.0 37.0 37.0 45-49 36.2975 37.0 37.0 37.0 37.0 37.0 50-54 36.33399999999999 37.0 37.0 37.0 37.0 37.0 55-59 36.349199999999996 37.0 37.0 37.0 37.0 37.0 60-64 36.283899999999996 37.0 37.0 37.0 37.0 37.0 65-69 36.2496 37.0 37.0 37.0 37.0 37.0 70-74 36.233000000000004 37.0 37.0 37.0 37.0 37.0 75-79 36.185500000000005 37.0 37.0 37.0 37.0 37.0 80-84 36.187 37.0 37.0 37.0 37.0 37.0 85-89 36.1092 37.0 37.0 37.0 37.0 37.0 90-94 36.15838756379691 37.0 37.0 37.0 37.0 37.0 95-99 36.07534169807706 37.0 37.0 37.0 37.0 37.0 100-104 36.05585417084864 37.0 37.0 37.0 37.0 37.0 105-109 35.99252776772026 37.0 37.0 37.0 37.0 37.0 110-114 36.03500625278036 37.0 37.0 37.0 37.0 37.0 115-119 35.910193467167986 37.0 37.0 37.0 37.0 37.0 120-124 35.87459799997663 37.0 37.0 37.0 37.0 37.0 125-129 35.816628527032165 37.0 37.0 37.0 37.0 37.0 130-134 35.7454394233435 37.0 37.0 37.0 37.0 37.0 135-139 35.65406154699197 37.0 37.0 37.0 37.0 37.0 140-141 35.596894926531746 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 11 1.0 12 1.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 1.0 19 0.0 20 0.0 21 0.0 22 2.0 23 1.0 24 5.0 25 5.0 26 7.0 27 10.0 28 11.0 29 10.0 30 21.0 31 21.0 32 37.0 33 85.0 34 142.0 35 363.0 36 2901.0 37 376.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 55.325 21.925 7.324999999999999 15.425 2 21.875 27.975 33.074999999999996 17.075000000000003 3 20.825 28.349999999999998 30.3 20.525 4 26.0 34.025 20.775 19.2 5 24.975 36.975 22.5 15.55 6 20.175 36.6 25.4 17.825 7 22.275 22.25 35.9 19.575 8 21.475 25.3 28.825 24.4 9 23.5 26.05 28.825 21.625 10-14 24.595 28.71 25.759999999999998 20.935000000000002 15-19 24.22 28.025 27.16 20.595 20-24 24.07 27.694999999999997 27.250000000000004 20.985 25-29 24.7 28.355000000000004 26.715 20.23 30-34 23.95 28.249999999999996 26.884999999999998 20.915 35-39 23.165 28.23 27.634999999999998 20.97 40-44 24.245 27.98 27.185 20.59 45-49 23.755000000000003 28.134999999999998 27.26 20.849999999999998 50-54 23.595 28.050000000000004 27.215 21.14 55-59 24.625 27.310000000000002 27.089999999999996 20.974999999999998 60-64 24.25 27.82 26.875 21.055 65-69 23.735 27.139999999999997 27.68 21.445 70-74 23.599999999999998 28.15 27.43 20.82 75-79 24.03 28.175 26.240000000000002 21.555 80-84 23.935000000000002 27.605 26.85 21.61 85-89 24.975 27.1 27.284999999999997 20.64 90-94 24.016004001000248 27.571892973243312 26.971742935733932 21.440360090022505 95-99 23.82718524458701 27.325581395348834 27.064955894145946 21.782277465918202 100-104 24.093159543295947 28.048903708194402 27.28604627664949 20.57189047186016 105-109 23.914932774398036 28.336997086038547 26.782884310618066 20.96518582894535 110-114 23.540684725747138 28.424923602838348 26.720878437872276 21.31351323354224 115-119 23.987588092984115 27.90049437256758 26.848637845797835 21.263279688650467 120-124 24.33851098018211 28.344938403856457 27.059453668987683 20.257096946973753 125-129 24.9233464739378 27.819754708716598 26.33048620236531 20.92641261498029 130-134 24.202938730246743 28.965899639589686 25.827557527030777 21.003604103132798 135-139 24.779595231494316 28.36706404214028 26.154699196007762 20.698641530357637 140-141 23.23260327141669 28.26448572220682 27.280288328250624 21.222622678125866 >>END_MODULE >>Per sequence GC content pass #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 0.5 13 0.5 14 0.0 15 0.5 16 0.5 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.5 24 1.5 25 4.0 26 4.0 27 5.0 28 8.0 29 10.5 30 16.5 31 19.0 32 19.5 33 36.5 34 47.5 35 50.0 36 66.0 37 82.5 38 100.0 39 137.0 40 174.0 41 188.5 42 213.5 43 256.5 44 277.0 45 270.0 46 260.5 47 256.5 48 267.5 49 234.5 50 175.0 51 159.0 52 140.0 53 118.0 54 100.5 55 74.0 56 51.0 57 35.5 58 26.5 59 23.0 60 22.5 61 16.0 62 9.5 63 10.5 64 11.0 65 7.0 66 2.5 67 0.0 68 1.5 69 2.0 70 2.0 71 1.5 72 0.5 73 0.5 74 0.5 75 0.5 76 0.5 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 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-141 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 92-93 3.0 94-95 1.0 96-97 10.0 98-99 13.0 100-101 13.0 102-103 19.0 104-105 17.0 106-107 25.0 108-109 17.0 110-111 19.0 112-113 25.0 114-115 25.0 116-117 19.0 118-119 28.0 120-121 34.0 122-123 32.0 124-125 25.0 126-127 39.0 128-129 29.0 130-131 0.0 132-133 0.0 134-135 0.0 136-137 0.0 138-139 0.0 140-141 3607.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 82.775 #Duplication Level Percentage of deduplicated Percentage of total 1 83.50951374207189 69.125 2 13.2890365448505 22.0 3 2.3557837511325883 5.8500000000000005 4 0.6040471156750227 2.0 5 0.21141649048625794 0.8750000000000001 6 0.030202355783751134 0.15 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >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 ACCACATATAGAGGGTGTAATAGCTAAGTAGCCTGTAAGAGATGGCTTCC 6 0.15 No Hit AGGAGGTCAAGAAGTGATGCAGATAAAAGAATTTCCCCTTGCGATACCGA 5 0.125 No Hit GAGATCAAGCACGCTCGCCTTGCCATGGTTGCCTTCCTTGGCTTTGCAGT 5 0.125 No Hit GGTGTAATAGCTAAGTAGCCTGTAAGAGATGGCTTCCTCTGTGATTTCAT 5 0.125 No Hit GCTCTCACTACCAATCATTTCCTCATCATCTTCTTCTTCGAACTCCAATT 5 0.125 No Hit AAGCAAATTACCAGCTAAACGAAGAAGCGATGGAGGAACTGGGGGAGAGG 5 0.125 No Hit TAGATTTGCTCTTTTTATAATTAATAACATGTTCATTTTCCTTTTCGAAT 5 0.125 No Hit GGTAAAACGATGCAGCTCCAATTTGGGTCCTACCCAGTTTTTGTTACCTC 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 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 82-83 0.0 0.0 0.0 0.0 0.0 84-85 0.0 0.0 0.0 0.0 0.0 86-87 0.0 0.0 0.0 0.0 0.0 88-89 0.0 0.0 0.0 0.0 0.0 90-91 0.0 0.0 0.0 0.0 0.0 92-93 0.0 0.0 0.0 0.0 0.0 94-95 0.0 0.0 0.0 0.0 0.0 96-97 0.0 0.0 0.0 0.0 0.0 98-99 0.0 0.0 0.0 0.0 0.0 100-101 0.0 0.0 0.0 0.0 0.0 102-103 0.0 0.0 0.0 0.0 0.0 104-105 0.0 0.0 0.0 0.0 0.0 106-107 0.0 0.0 0.0 0.0 0.0 108-109 0.0 0.0 0.0 0.0 0.0 110-111 0.0 0.0 0.0 0.0 0.0 112-113 0.0 0.0 0.0 0.0 0.0 114-115 0.0 0.0 0.0 0.0 0.0 116-117 0.0 0.0 0.0 0.0 0.0 118-119 0.0 0.0 0.0 0.0 0.0 120-121 0.0 0.0 0.0 0.0 0.0 122-123 0.0 0.0 0.0 0.0 0.0 124-125 0.0 0.0 0.0 0.0 0.0 126-127 0.0 0.0 0.0 0.0 0.0 128-129 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GATATGC 15 1.6268379E-4 132.65001 7 TATGCGT 10 0.0089136 132.65001 9 CCAGATA 10 0.0089136 132.65001 4 ATATGCG 10 0.0089136 132.65001 8 AGATATG 10 0.0089136 132.65001 6 >>END_MODULE Read 1251075 spots for SRR17234931.sra Written 1251075 spots for SRR17234931.sra Read 1251075 spots for SRR17234931.sra Written 1251075 spots for SRR17234931.sra Read 1251075 spots for SRR17234931.sra Written 1251075 spots for SRR17234931.sra Read 1251075 spots for SRR17234931.sra Written 1251075 spots for SRR17234931.sra Read 1251075 spots for SRR17234931.sra Written 1251075 spots for SRR17234931.sra Read 1251075 spots for SRR17234931.sra Written 1251075 spots for SRR17234931.sra Read 1251075 spots for SRR17234931.sra Written 1251075 spots for SRR17234931.sra Read 1251075 spots for SRR17234931.sra Written 1251075 spots for SRR17234931.sra Read 1251075 spots for SRR17234931.sra Written 1251075 spots for SRR17234931.sra Read 1251075 spots for SRR17234931.sra Written 1251075 spots for SRR17234931.sra Read 1251075 spots for SRR17234931.sra Written 1251075 spots for SRR17234931.sra Read 1251075 spots for SRR17234931.sra Written 1251075 spots for SRR17234931.sra Read 1251075 spots for SRR17234931.sra Written 1251075 spots for SRR17234931.sra Read 1251075 spots for SRR17234931.sra Written 1251075 spots for SRR17234931.sra Read 1251075 spots for SRR17234931.sra Written 1251075 spots for SRR17234931.sra Read 1251075 spots for SRR17234931.sra Written 1251075 spots for SRR17234931.sra Read 1251075 spots for SRR17234931.sra Written 1251075 spots for SRR17234931.sra Read 1251083 spots for SRR17234931.sra Written 1251083 spots for SRR17234931.sra Read 1251075 spots for SRR17234931.sra Written 1251075 spots for SRR17234931.sra Read 1251075 spots for SRR17234931.sra Written 1251075 spots for SRR17234931.sra SRR ids: ['SRR17234931.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_j_r28b2s SRR17234931.sra spots: 25021508 blocks: [[1, 1251075], [1251076, 2502150], [2502151, 3753225], [3753226, 5004300], [5004301, 6255375], [6255376, 7506450], [7506451, 8757525], [8757526, 10008600], [10008601, 11259675], [11259676, 12510750], [12510751, 13761825], [13761826, 15012900], [15012901, 16263975], [16263976, 17515050], [17515051, 18766125], [18766126, 20017200], [20017201, 21268275], [21268276, 22519350], [22519351, 23770425], [23770426, 25021508]] SRR17234931 file size 7878888 SRR17234931 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 SRR17234931 SRR17234931_1.fastq SRR17234931_2.fastq Input file: SRR17234931_1.fastq Paired file: SRR17234931_2.fastq trimmed: SRR17234931-trimmed-pair1.fastq, SRR17234931-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 Wed Feb 12 04:54:20 2025 >> started Wed Feb 12 04:54:46 2025 >> done (26.735s) 25021508 read pairs processed; of these: 0 ( 0.00%) short read pairs filtered out after trimming by size control 0 ( 0.00%) empty read pairs filtered out after trimming by size control 25021508 (100.00%) read pairs available; of these: 1006274 ( 4.02%) trimmed read pairs available after processing 24015234 (95.98%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 90 3904 0.02% 91 4446 0.02% 92 12843 0.05% 93 14314 0.06% 94 16078 0.06% 95 17896 0.07% 96 19742 0.08% 97 21654 0.09% 98 24343 0.10% 99 26168 0.10% 100 28275 0.11% 101 31289 0.13% 102 33967 0.14% 103 37639 0.15% 104 40700 0.16% 105 43503 0.17% 106 46852 0.19% 107 50047 0.20% 108 52759 0.21% 109 56124 0.22% 110 59131 0.24% 111 64465 0.26% 112 66985 0.27% 113 72708 0.29% 114 76756 0.31% 115 80672 0.32% 116 85574 0.34% 117 90280 0.36% 118 92310 0.37% 119 96770 0.39% 120 99796 0.40% 121 103331 0.41% 122 109048 0.44% 123 113931 0.46% 124 117596 0.47% 125 121587 0.49% 126 129120 0.52% 127 87302 0.35% 128 92559 0.37% 129 2007 0.01% 130 2429 0.01% 131 2301 0.01% 132 7384 0.03% 133 8208 0.03% 134 25553 0.10% 135 0 0.00% 136 1617 0.01% 137 3472 0.01% 138 24961 0.10% 139 53577 0.21% 140 167457 0.67% 141 22380078 89.44% 25021508 reads passed initial QC criterion=sequence-density sequence-density=0.99 sequence-density-rank=1 fanout-score=2.04 fanout-score-rank=16 prefix-density=1.01 prefix-fanout=2.0 sequence=CGGTAGACCCAACCTTTCTCCAACTCGAATTCCAAGCAAGGAACCCACTT criterion=fanout-score sequence-density=0.02 sequence-density-rank=23 fanout-score=58.02 fanout-score-rank=1 prefix-density=0.70 prefix-fanout=1.8 sequence=TGAATGGTGCACATTACGGGTCCATGGCACAAAATCAGAGGATAACAATATCCATTCAAGACTATGCAACAATATAATTTGATTATCCTTAGAAAGTGCTTCTCCTTACACACCCACAAGCCTAGAAAAGGAATTAGAATTTGTAAGTGCAGCTTCCATCATCACTCCTTGCAGTTGGATCAAAGTTTGCTGCATTTGGATCAGTACAGCCTTCAGCGACAGGCACCTTTACTTGCTGTGCCGCTTGGCC criterion=sequence-density sequence-density=0.83 sequence-density-rank=1 fanout-score=2.01 fanout-score-rank=22 prefix-density=0.80 prefix-fanout=2.0 sequence=TACCTTCTTCGC criterion=fanout-score sequence-density=0.03 sequence-density-rank=23 fanout-score=132.89 fanout-score-rank=1 prefix-density=0.26 prefix-fanout=12.9 sequence=AGAGAGAGAGACAGAGAGAATGGCCACCACAGCAGCCCTCTCCAGCGCCATGGTCAGCACATCGTTTACTCGCCGGGTGCCAGTGACAAGCCTACGGGCACTTCCCAACGTGGGGGAGTCTCTTCTTGGCTTGAAAGCCAGTCGAGGAGGACGTGTTAAAGCAATGGCAG SRR17234931 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 12 04:55:31 Started mapping on | Feb 12 04:55:31 Finished on | Feb 12 04:57:22 Mapping speed, Million of reads per hour | 811.51 Number of input reads | 25021508 Average input read length | 277 UNIQUE READS: Uniquely mapped reads number | 21849009 Uniquely mapped reads % | 87.32% Average mapped length | 275.71 Number of splices: Total | 20186121 Number of splices: Annotated (sjdb) | 19895326 Number of splices: GT/AG | 19779484 Number of splices: GC/AG | 359077 Number of splices: AT/AC | 11750 Number of splices: Non-canonical | 35810 Mismatch rate per base, % | 0.23% Deletion rate per base | 0.02% Deletion average length | 1.99 Insertion rate per base | 0.01% Insertion average length | 2.30 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 588174 % of reads mapped to multiple loci | 2.35% Number of reads mapped to too many loci | 543336 % of reads mapped to too many loci | 2.17% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 7.86% % of reads unmapped: other | 0.30% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 2584325 2584325 2584325 N_multimapping 588174 588174 588174 N_noFeature 688813 21638338 736518 N_ambiguous 321922 952 158533 UnstrandedReadsAssigned:20838274 PositiveStrandReadsAssigned:209719 NegativeStrandReadsAssigned:20953958 Dataset is classified negative stranded MeadianReadLen=141 20thPercentileLength=141 echo kmer=137 SRR17234931 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: 52,400 [index] number of k-mers: 62,057,036 [index] number of equivalence classes: 130,681 [quant] running in paired-end mode [quant] will process pair 1: SRR17234931-trimmed-pair1.fastq SRR17234931-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 25,021,508 reads, 23,042,430 reads pseudoaligned [quant] estimated average fragment length: 183.84 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,096 rounds 52401 SRR17234931.ke.tsv 34699 SRR17234931.se.tsv 87100 total ==> SRR17234931.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1835.16 429 10.4287 Potri.005G024800.1.v4.1 1035 852.16 136 7.11978 Potri.004G059700.1.v4.1 961 778.16 52 2.98114 Potri.007G009000.2.v4.1 1416 1233.16 15 0.542651 Potri.003G141000.2.v4.1 2943 2760.16 651 10.5219 Potri.016G087400.1.v4.1 270 99.5248 749 335.737 Potri.015G069301.1.v4.1 564 381.219 0 0 Potri.010G195200.1.v4.1 1773 1590.16 2 0.0561097 Potri.012G127500.1.v4.1 977 794.16 439 24.6607 ==> SRR17234931.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 390 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 263 Potri.001G212900.v4.1 91 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 189 Potri.001G416900.v4.1 2 Potri.001G452600.v4.1 6 SRR17234931 completed mapping pipeline successfully