Starting /dee2/code/volunteer_pipeline.sh SRR18274411 current disk space = 3056948535296 free memory = 1484190060 SRR18274411 SRAfilesize 1cd30ed63c3b25dc16f5111d86278c15 SRR18274411.sra SRR18274411.sra file validated SRR18274411 is paired end SRR18274411 is conventional basespace SRR18274411 read1 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR18274411_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.14 32.0 32.0 32.0 32.0 32.0 2 30.63625 32.0 32.0 32.0 32.0 32.0 3 34.8925 37.0 32.0 37.0 32.0 37.0 4 35.87375 37.0 37.0 37.0 32.0 37.0 5 35.97875 37.0 37.0 37.0 32.0 37.0 6 39.40725 41.0 41.0 41.0 37.0 41.0 7 39.56475 41.0 41.0 41.0 37.0 41.0 8 39.59625 41.0 41.0 41.0 37.0 41.0 9 39.664 41.0 41.0 41.0 37.0 41.0 10-14 39.6378 41.0 41.0 41.0 37.0 41.0 15-19 39.592400000000005 41.0 41.0 41.0 37.0 41.0 20-24 39.435050000000004 41.0 41.0 41.0 37.0 41.0 25-29 39.357150000000004 41.0 41.0 41.0 37.0 41.0 30-34 39.324400000000004 41.0 41.0 41.0 37.0 41.0 35-39 39.272450000000006 41.0 41.0 41.0 37.0 41.0 40-44 39.0499 41.0 41.0 41.0 37.0 41.0 45-49 39.0023 41.0 41.0 41.0 36.0 41.0 50-54 39.04745 41.0 41.0 41.0 37.0 41.0 55-59 38.95655000000001 41.0 41.0 41.0 36.0 41.0 60-64 38.8554 41.0 41.0 41.0 33.0 41.0 65-69 38.851549999999996 41.0 41.0 41.0 33.0 41.0 70-74 38.79245 41.0 41.0 41.0 33.0 41.0 75-79 38.646049999999995 41.0 40.2 41.0 33.0 41.0 80-84 38.8922 41.0 41.0 41.0 34.0 41.0 85-89 38.9724 41.0 41.0 41.0 34.0 41.0 90-94 38.955650000000006 41.0 41.0 41.0 32.0 41.0 95-99 38.919549999999994 41.0 41.0 41.0 33.0 41.0 100-104 38.7534 41.0 41.0 41.0 32.0 41.0 105-109 38.7866 41.0 41.0 41.0 32.0 41.0 110-114 38.65095 41.0 41.0 41.0 32.0 41.0 115-119 38.381550000000004 41.0 41.0 41.0 32.0 41.0 120-124 38.45865 41.0 41.0 41.0 32.0 41.0 125-129 38.409299999999995 41.0 41.0 41.0 32.0 41.0 130-134 37.9923 41.0 37.8 41.0 31.0 41.0 135-139 38.065099999999994 41.0 39.4 41.0 31.0 41.0 140-144 37.8885 41.0 37.0 41.0 30.0 41.0 145-149 37.7093 41.0 37.0 41.0 27.0 41.0 150 37.481 41.0 37.0 41.0 27.0 41.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 1101 1 0.13139106691049562 1101 2 -0.8198476915754433 1101 3 0.10571407099376273 1101 4 -0.001753550940655657 1101 5 0.28845912973772414 1101 6 0.3356547007690551 1101 7 0.6368897016458348 1101 8 0.16840351712217227 1101 9 0.28815852100503747 1101 10-14 -0.013742829229194342 1101 15-19 0.09250231719230584 1101 20-24 0.13598537037501046 1101 25-29 0.21443673438713517 1101 30-34 0.21282096244895854 1101 35-39 0.19618727924046198 1101 40-44 0.18611688669555804 1101 45-49 0.17584859340163916 1101 50-54 0.025867381447433502 1101 55-59 -0.005027681054137645 1101 60-64 0.10070893559458227 1101 65-69 0.16487136451313944 1101 70-74 0.10621508554823578 1101 75-79 -0.044933490317895064 1101 80-84 -0.14778426313284143 1101 85-89 0.1390966707582848 1101 90-94 0.268558831634067 1101 95-99 -0.10603973045417092 1101 100-104 0.03713018863198414 1101 105-109 0.0955960820661872 1101 110-114 -0.07679050076404792 1101 115-119 0.06743655903203916 1101 120-124 0.09190360479971105 1101 125-129 -0.10440892807935853 1101 130-134 -0.12523610310879718 1101 135-139 -0.20670357473885304 1101 140-144 -0.01377289010245164 1101 145-149 0.0532002304666932 1101 150 0.14836293494325759 1102 1 -0.13139106691049207 1102 2 0.8198476915754398 1102 3 -0.10571407099376273 1102 4 0.001753550940655657 1102 5 -0.28845912973771703 1102 6 -0.33565470076906223 1102 7 -0.6368897016458277 1102 8 -0.16840351712217227 1102 9 -0.28815852100503037 1102 10-14 0.013742829229187237 1102 15-19 -0.09250231719231294 1102 20-24 -0.13598537037501046 1102 25-29 -0.21443673438712807 1102 30-34 -0.21282096244896564 1102 35-39 -0.19618727924046198 1102 40-44 -0.18611688669555804 1102 45-49 -0.17584859340163916 1102 50-54 -0.025867381447426396 1102 55-59 0.005027681054137645 1102 60-64 -0.10070893559457517 1102 65-69 -0.16487136451313944 1102 70-74 -0.10621508554823578 1102 75-79 0.044933490317895064 1102 80-84 0.14778426313284143 1102 85-89 -0.1390966707582777 1102 90-94 -0.2685588316340599 1102 95-99 0.10603973045417092 1102 100-104 -0.037130188631977035 1102 105-109 -0.0955960820661872 1102 110-114 0.07679050076404792 1102 115-119 -0.06743655903203916 1102 120-124 -0.09190360479971815 1102 125-129 0.10440892807936564 1102 130-134 0.12523610310879008 1102 135-139 0.20670357473884593 1102 140-144 0.013772890102458746 1102 145-149 -0.0532002304666932 1102 150 -0.14836293494325759 >>END_MODULE >>Per sequence quality scores pass #Quality Count 17 4.0 18 4.0 19 4.0 20 11.0 21 12.0 22 18.0 23 18.0 24 12.0 25 15.0 26 20.0 27 24.0 28 26.0 29 29.0 30 54.0 31 64.0 32 42.0 33 64.0 34 92.0 35 100.0 36 118.0 37 175.0 38 221.0 39 407.0 40 2466.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 17.05719324766944 27.513227513227513 15.99899218946838 39.43058704963467 2 22.0277920741122 24.98713329902213 33.86515697375193 19.119917653113742 3 19.3 26.174999999999997 29.325000000000003 25.2 4 21.3 23.5 28.275 26.924999999999997 5 25.900000000000002 24.7 26.724999999999998 22.675 6 23.925 25.575 24.9 25.6 7 24.224999999999998 26.25 25.025 24.5 8 20.65 22.825 29.799999999999997 26.724999999999998 9 24.275 22.6 29.549999999999997 23.575 10-14 24.01 24.95 25.665 25.374999999999996 15-19 24.605 24.925 24.834999999999997 25.635 20-24 24.62 24.355 25.36 25.665 25-29 24.425 24.265 25.34 25.97 30-34 24.95 24.565 24.535 25.95 35-39 25.169999999999998 24.715 24.315 25.8 40-44 25.15 24.505 24.505 25.840000000000003 45-49 24.490000000000002 24.665 24.86 25.985000000000003 50-54 25.205 24.46 24.625 25.71 55-59 25.437543754375437 24.327432743274326 24.70747074707471 25.52755275527553 60-64 25.03 23.794999999999998 25.415 25.759999999999998 65-69 25.085 23.945 25.145 25.825 70-74 25.21 24.26 25.215 25.314999999999998 75-79 25.790000000000003 24.205 24.12 25.885 80-84 25.335 24.62 24.23 25.814999999999998 85-89 25.135 25.019999999999996 24.115000000000002 25.729999999999997 90-94 25.77 24.285 24.34 25.605 95-99 25.88 23.485 25.28 25.355 100-104 26.013902085312797 24.378656798519778 24.138620793118967 25.468820323048458 105-109 24.88 24.52 24.575 26.025 110-114 25.682568256825682 24.457445744574457 24.71247124712471 25.147514751475146 115-119 25.2737910686603 24.733710056508475 24.16862529379407 25.823873581037155 120-124 25.998899834975248 24.218632794919237 24.558683802570386 25.22378356753513 125-129 26.105 24.235 25.09 24.57 130-134 25.705 24.595 24.485 25.215 135-139 25.485000000000003 24.635 24.315 25.564999999999998 140-144 25.31 25.405 24.38 24.905 145-149 26.150000000000002 25.845000000000002 23.494999999999997 24.51 150 25.825 28.125 22.575 23.474999999999998 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 1.0 1 1.0 2 1.0 3 2.0 4 3.0 5 1.5 6 0.0 7 0.0 8 0.0 9 0.5 10 0.5 11 0.5 12 0.5 13 0.0 14 1.0 15 1.0 16 0.5 17 1.5 18 1.0 19 0.0 20 0.5 21 1.0 22 0.5 23 0.0 24 2.0 25 4.5 26 4.0 27 2.5 28 6.5 29 7.5 30 8.0 31 12.0 32 15.5 33 20.5 34 25.0 35 29.0 36 33.0 37 40.5 38 40.0 39 55.5 40 87.0 41 109.0 42 124.5 43 142.0 44 170.5 45 193.5 46 182.5 47 160.0 48 169.5 49 172.5 50 164.5 51 161.0 52 169.5 53 173.5 54 143.5 55 132.5 56 139.0 57 122.5 58 116.0 59 132.5 60 121.5 61 81.0 62 64.5 63 75.0 64 60.5 65 37.0 66 24.5 67 29.5 68 42.5 69 36.5 70 27.5 71 21.0 72 14.0 73 13.5 74 11.0 75 7.5 76 10.5 77 13.5 78 13.0 79 5.5 80 1.0 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 0.775 2 2.85 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 0.01 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 0.015 105-109 0.0 110-114 0.01 115-119 0.015 120-124 0.015 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 86.3 #Duplication Level Percentage of deduplicated Percentage of total 1 87.97798377752028 75.925 2 9.125144843568945 15.75 3 2.172653534183082 5.625 4 0.5214368482039398 1.7999999999999998 5 0.17381228273464658 0.75 6 0.028968713789107762 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 CCCTCTTTTTGGACCCAAGGCCGCTTCGGCGGCCGATCCGGGCGGAAGAC 6 0.15 No Hit TTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGCAGTTGTTCGTC 5 0.125 No Hit CTCTTAGGATCGACTAACCCATGTGCAAGTGCCGTTCACATGGAACCTTT 5 0.125 No Hit AACGTTATTTTACTTATTCCGTGAATCGGAGGCGGGGCGCTGCCCCTCTT 5 0.125 No Hit TACTGGAAATCAGAATCAAACGAGCTTTTACCCTTTTGTTCCACACGAGA 5 0.125 No Hit CGGAAGACATTGTCAGGTGGGGAGTTTGGCTGGGGCGGCACATCTGTTAA 5 0.125 No Hit AAACGAGCTTTTACCCTTTTGTTCCACACGAGATTTCTGTTCTCGTTGAG 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 0.0 130-131 0.0 0.0 0.0 0.0 0.0 132-133 0.0 0.0 0.0 0.0 0.0 134-135 0.0 0.0 0.0 0.0 0.0 136-137 0.0 0.0 0.0 0.0 0.0 138 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 CTCTTAG 10 0.0062209954 149.53246 1 CTTAGGA 30 0.0018512175 71.9625 3 >>END_MODULE SRR18274411 read2 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR18274411_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 25.91125 32.0 27.0 32.0 2.0 32.0 2 30.43125 32.0 32.0 32.0 27.0 32.0 3 32.795 32.0 32.0 37.0 27.0 37.0 4 34.30625 37.0 32.0 37.0 27.0 37.0 5 34.32375 37.0 37.0 37.0 27.0 37.0 6 36.88375 41.0 37.0 41.0 27.0 41.0 7 37.55625 41.0 37.0 41.0 32.0 41.0 8 37.86575 41.0 37.0 41.0 32.0 41.0 9 37.5565 41.0 37.0 41.0 27.0 41.0 10-14 38.0527 41.0 37.8 41.0 31.0 41.0 15-19 37.90709999999999 41.0 38.6 41.0 28.0 41.0 20-24 37.8688 41.0 37.0 41.0 28.0 41.0 25-29 37.900099999999995 41.0 38.6 41.0 28.0 41.0 30-34 37.7275 41.0 37.0 41.0 27.0 41.0 35-39 37.82645 41.0 37.0 41.0 27.0 41.0 40-44 37.7114 41.0 37.0 41.0 27.0 41.0 45-49 37.73905 41.0 37.0 41.0 27.0 41.0 50-54 37.6174 41.0 37.0 41.0 27.0 41.0 55-59 37.57475 41.0 37.0 41.0 27.0 41.0 60-64 37.356 41.0 37.0 41.0 27.0 41.0 65-69 37.75595 41.0 38.6 41.0 29.0 41.0 70-74 38.401849999999996 41.0 41.0 41.0 32.0 41.0 75-79 37.66065 41.0 38.6 41.0 30.0 41.0 80-84 38.08325 41.0 40.2 41.0 30.0 41.0 85-89 38.02865 41.0 40.2 41.0 30.0 41.0 90-94 38.17375 41.0 41.0 41.0 32.0 41.0 95-99 38.17345 41.0 41.0 41.0 32.0 41.0 100-104 37.90875 41.0 40.2 41.0 29.0 41.0 105-109 38.028949999999995 41.0 38.6 41.0 30.0 41.0 110-114 37.89565 41.0 37.0 41.0 29.0 41.0 115-119 37.62735 41.0 37.0 41.0 28.0 41.0 120-124 37.181650000000005 41.0 37.0 41.0 26.0 41.0 125-129 37.11165 41.0 37.0 41.0 27.0 41.0 130-134 37.12395 41.0 37.0 41.0 27.0 41.0 135-139 36.7958 41.0 37.0 41.0 25.0 41.0 140-144 36.439350000000005 41.0 37.0 41.0 23.0 41.0 145-149 35.927800000000005 41.0 33.0 41.0 22.0 41.0 150 36.125 41.0 32.0 41.0 22.0 41.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 1101 1 -3.8088378967409007 1101 2 0.09030787344372371 1101 3 -0.5680878779528555 1101 4 -0.03757609158545705 1101 5 0.10302111776346834 1101 6 -0.1406097347127968 1101 7 0.282697462361277 1101 8 -0.21165359853703336 1101 9 0.14245096320047423 1101 10-14 0.1106841353741288 1101 15-19 0.26228863448483253 1101 20-24 0.3286981136802041 1101 25-29 -0.05849344923470312 1101 30-34 -0.04494601568175227 1101 35-39 0.11926651469225646 1101 40-44 0.06859139758010713 1101 45-49 0.07155489866980247 1101 50-54 0.2557078083118256 1101 55-59 0.11042110273303507 1101 60-64 0.008186577820083585 1101 65-69 0.4132493298930342 1101 70-74 0.0753776397204291 1101 75-79 -0.46617400235476936 1101 80-84 -0.20311631052882007 1101 85-89 -0.268801823692975 1101 90-94 -0.1443823743079733 1101 95-99 -0.13312958741451553 1101 100-104 -0.21577193817480378 1101 105-109 -0.0657957363661481 1101 110-114 -0.05815275933765918 1101 115-119 -0.06979132743806105 1101 120-124 -0.3645231593977769 1101 125-129 -0.45469325383902515 1101 130-134 -0.24610586437535176 1101 135-139 -0.3103434454770948 1101 140-144 -0.37130689646534165 1101 145-149 -0.13289912071945764 1101 150 -0.523961021067656 1102 1 3.8088378967409007 1102 2 -0.09030787344372371 1102 3 0.5680878779528555 1102 4 0.037576091585464155 1102 5 -0.10302111776347544 1102 6 0.1406097347127897 1102 7 -0.2826974623612841 1102 8 0.21165359853704047 1102 9 -0.14245096320048134 1102 10-14 -0.1106841353741359 1102 15-19 -0.26228863448483253 1102 20-24 -0.32869811368019697 1102 25-29 0.058493449234696016 1102 30-34 0.04494601568175227 1102 35-39 -0.11926651469225646 1102 40-44 -0.06859139758010713 1102 45-49 -0.07155489866980247 1102 50-54 -0.2557078083118256 1102 55-59 -0.11042110273303507 1102 60-64 -0.00818657782009069 1102 65-69 -0.4132493298930271 1102 70-74 -0.0753776397204291 1102 75-79 0.46617400235476225 1102 80-84 0.20311631052881296 1102 85-89 0.268801823692975 1102 90-94 0.1443823743079733 1102 95-99 0.13312958741450842 1102 100-104 0.21577193817481088 1102 105-109 0.065795736366141 1102 110-114 0.05815275933765207 1102 115-119 0.06979132743806815 1102 120-124 0.364523159397784 1102 125-129 0.45469325383902515 1102 130-134 0.24610586437535886 1102 135-139 0.3103434454770948 1102 140-144 0.37130689646534876 1102 145-149 0.13289912071945764 1102 150 0.5239610210676631 >>END_MODULE >>Per sequence quality scores pass #Quality Count 14 1.0 15 0.0 16 0.0 17 6.0 18 6.0 19 14.0 20 9.0 21 21.0 22 22.0 23 26.0 24 49.0 25 35.0 26 37.0 27 48.0 28 65.0 29 64.0 30 72.0 31 81.0 32 89.0 33 90.0 34 116.0 35 159.0 36 157.0 37 182.0 38 284.0 39 517.0 40 1850.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 16.1395211350872 27.78598876736624 16.08040201005025 39.9940880874963 2 22.325 23.525 34.675 19.475 3 19.85 25.874999999999996 28.325 25.95 4 21.025 23.425 27.800000000000004 27.750000000000004 5 26.150000000000002 23.974999999999998 25.8 24.075 6 24.625 25.624999999999996 25.324999999999996 24.425 7 24.3 25.874999999999996 24.65 25.174999999999997 8 20.65 22.875 30.275000000000002 26.200000000000003 9 23.200000000000003 23.35 29.975 23.474999999999998 10-14 24.63 25.095 25.069999999999997 25.205 15-19 25.275 24.635 24.709999999999997 25.380000000000003 20-24 24.65 24.435000000000002 24.91 26.005 25-29 24.4 24.455 24.990000000000002 26.155 30-34 24.98 24.575 24.265 26.179999999999996 35-39 24.575 24.565 24.87 25.990000000000002 40-44 24.224999999999998 24.895 24.89 25.990000000000002 45-49 25.205 24.77 24.635 25.39 50-54 24.95747022916041 24.362053437406182 25.06254378064645 25.617932552786947 55-59 25.3 24.33 24.4 25.97 60-64 25.69 24.05 24.565 25.695 65-69 25.490000000000002 24.54 24.33 25.64 70-74 25.130000000000003 24.425 24.779999999999998 25.665 75-79 25.424999999999997 25.005 24.175 25.395 80-84 24.75 24.55 24.525 26.174999999999997 85-89 25.36 24.905 24.015 25.72 90-94 25.369999999999997 25.580000000000002 24.075 24.975 95-99 25.505 24.75 24.099999999999998 25.645 100-104 25.619999999999997 24.725 24.26 25.395 105-109 25.580000000000002 24.295 24.265 25.86 110-114 25.805 24.15 24.805 25.240000000000002 115-119 25.740000000000002 24.88 24.425 24.955 120-124 25.835 24.92 24.26 24.985 125-129 25.85 24.77 24.41 24.97 130-134 26.035000000000004 24.45 24.57 24.945 135-139 25.005 24.63 24.435000000000002 25.929999999999996 140-144 25.845000000000002 25.790000000000003 24.255 24.11 145-149 25.674999999999997 26.400000000000002 24.12 23.805 150 26.224999999999998 26.625 24.4 22.75 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.5 2 0.5 3 1.0 4 1.5 5 0.5 6 0.0 7 0.5 8 0.5 9 0.5 10 0.5 11 0.5 12 0.5 13 1.0 14 1.0 15 0.5 16 1.5 17 2.0 18 2.0 19 1.5 20 1.0 21 1.0 22 1.5 23 3.5 24 3.0 25 2.5 26 3.5 27 3.0 28 4.0 29 5.0 30 6.0 31 8.5 32 13.0 33 19.5 34 27.5 35 31.5 36 40.0 37 47.0 38 50.0 39 58.0 40 81.0 41 117.5 42 129.5 43 141.0 44 179.0 45 193.0 46 180.0 47 183.5 48 178.0 49 162.5 50 143.5 51 146.5 52 164.5 53 157.0 54 148.5 55 126.0 56 124.5 57 135.0 58 126.5 59 122.5 60 111.5 61 78.5 62 60.5 63 72.0 64 65.0 65 44.5 66 30.0 67 34.5 68 39.5 69 36.5 70 33.5 71 20.5 72 14.0 73 16.0 74 9.5 75 7.5 76 12.0 77 14.0 78 9.0 79 3.5 80 3.0 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 warn #Base N-Count 1 15.425 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 0.06999999999999999 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 0.0 140-144 0.0 145-149 0.0 150 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 90.375 #Duplication Level Percentage of deduplicated Percentage of total 1 91.56293222683264 82.75 2 6.721991701244813 12.15 3 1.3831258644536653 3.75 4 0.19363762102351315 0.7000000000000001 5 0.11065006915629322 0.5 6 0.027662517289073305 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 CTCTGACTATGAAATACGAATGCCCCCGACTGTCCCTGTTAATCATTACT 6 0.15 No Hit CAAAGCAAGCCTACGCTCTGGATACATTAGCATGGGATAACATCATAGGA 5 0.125 No Hit CTGCGTTATCTTTTAACAGATGTGCCGCCCCAGCCAAACTCCCCACCTGA 5 0.125 No Hit ATTCGTACTGGAAATCAGAATCAAACGAGCTTTTACCCTTTTGTTCCACA 5 0.125 No Hit CAACCCAAAGTCCAACTACGAGCTTTTTAACTGCAACAACTTAAATATAC 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 0.0 130-131 0.0 0.0 0.0 0.0 0.0 132-133 0.0 0.0 0.0 0.0 0.0 134-135 0.0 0.0 0.0 0.0 0.0 136-137 0.0 0.0 0.0 0.0 0.0 138 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 993023 spots for SRR18274411.sra Written 993023 spots for SRR18274411.sra Read 993015 spots for SRR18274411.sra Written 993015 spots for SRR18274411.sra Read 993015 spots for SRR18274411.sra Written 993015 spots for SRR18274411.sra Read 993015 spots for SRR18274411.sra Written 993015 spots for SRR18274411.sra Read 993015 spots for SRR18274411.sra Written 993015 spots for SRR18274411.sra Read 993015 spots for SRR18274411.sra Written 993015 spots for SRR18274411.sra Read 993015 spots for SRR18274411.sra Written 993015 spots for SRR18274411.sra Read 993015 spots for SRR18274411.sra Written 993015 spots for SRR18274411.sra Read 993015 spots for SRR18274411.sra Written 993015 spots for SRR18274411.sra Read 993015 spots for SRR18274411.sra Written 993015 spots for SRR18274411.sra Read 993015 spots for SRR18274411.sra Written 993015 spots for SRR18274411.sra Read 993015 spots for SRR18274411.sra Written 993015 spots for SRR18274411.sra Read 993015 spots for SRR18274411.sra Written 993015 spots for SRR18274411.sra Read 993015 spots for SRR18274411.sra Written 993015 spots for SRR18274411.sra Read 993015 spots for SRR18274411.sra Written 993015 spots for SRR18274411.sra Read 993015 spots for SRR18274411.sra Written 993015 spots for SRR18274411.sra Read 993015 spots for SRR18274411.sra Written 993015 spots for SRR18274411.sra Read 993015 spots for SRR18274411.sra Written 993015 spots for SRR18274411.sra Read 993015 spots for SRR18274411.sra Written 993015 spots for SRR18274411.sra Read 993015 spots for SRR18274411.sra Written 993015 spots for SRR18274411.sra SRR ids: ['SRR18274411.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_5tkz1403 SRR18274411.sra spots: 19860308 blocks: [[1, 993015], [993016, 1986030], [1986031, 2979045], [2979046, 3972060], [3972061, 4965075], [4965076, 5958090], [5958091, 6951105], [6951106, 7944120], [7944121, 8937135], [8937136, 9930150], [9930151, 10923165], [10923166, 11916180], [11916181, 12909195], [12909196, 13902210], [13902211, 14895225], [14895226, 15888240], [15888241, 16881255], [16881256, 17874270], [17874271, 18867285], [18867286, 19860308]] SRR18274411 file size 7292185 SRR18274411 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 SRR18274411 SRR18274411_1.fastq SRR18274411_2.fastq Input file: SRR18274411_1.fastq Paired file: SRR18274411_2.fastq trimmed: SRR18274411-trimmed-pair1.fastq, SRR18274411-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 Tue Feb 11 03:46:54 2025 >> started Tue Feb 11 03:52:13 2025 >> done (319.355s) 19860308 read pairs processed; of these: 0 ( 0.00%) short read pairs filtered out after trimming by size control 1 ( 0.00%) empty read pairs filtered out after trimming by size control 19860307 (100.00%) read pairs available; of these: 2879559 (14.50%) trimmed read pairs available after processing 16980748 (85.50%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 28 1 0.00% 29 0 0.00% 30 0 0.00% 31 0 0.00% 32 0 0.00% 33 0 0.00% 34 0 0.00% 35 0 0.00% 36 0 0.00% 37 0 0.00% 38 0 0.00% 39 0 0.00% 40 0 0.00% 41 0 0.00% 42 0 0.00% 43 0 0.00% 44 0 0.00% 45 0 0.00% 46 1 0.00% 47 0 0.00% 48 0 0.00% 49 0 0.00% 50 0 0.00% 51 0 0.00% 52 0 0.00% 53 0 0.00% 54 0 0.00% 55 0 0.00% 56 0 0.00% 57 0 0.00% 58 0 0.00% 59 0 0.00% 60 0 0.00% 61 0 0.00% 62 0 0.00% 63 0 0.00% 64 1 0.00% 65 0 0.00% 66 0 0.00% 67 0 0.00% 68 0 0.00% 69 0 0.00% 70 0 0.00% 71 0 0.00% 72 0 0.00% 73 0 0.00% 74 0 0.00% 75 0 0.00% 76 0 0.00% 77 0 0.00% 78 0 0.00% 79 0 0.00% 80 0 0.00% 81 0 0.00% 82 0 0.00% 83 0 0.00% 84 0 0.00% 85 0 0.00% 86 1 0.00% 87 0 0.00% 88 0 0.00% 89 0 0.00% 90 0 0.00% 91 0 0.00% 92 0 0.00% 93 0 0.00% 94 0 0.00% 95 0 0.00% 96 0 0.00% 97 0 0.00% 98 0 0.00% 99 0 0.00% 100 1 0.00% 101 0 0.00% 102 0 0.00% 103 0 0.00% 104 0 0.00% 105 0 0.00% 106 2 0.00% 107 0 0.00% 108 0 0.00% 109 1 0.00% 110 0 0.00% 111 0 0.00% 112 1 0.00% 113 0 0.00% 114 0 0.00% 115 0 0.00% 116 1 0.00% 117 0 0.00% 118 0 0.00% 119 0 0.00% 120 0 0.00% 121 0 0.00% 122 0 0.00% 123 1 0.00% 124 2 0.00% 125 2 0.00% 126 2 0.00% 127 1 0.00% 128 6 0.00% 129 3 0.00% 130 5 0.00% 131 2 0.00% 132 2 0.00% 133 0 0.00% 134 0 0.00% 135 0 0.00% 136 2 0.00% 137 1 0.00% 138 14 0.00% 139 159 0.00% 140 2850 0.01% 141 259648 1.31% 142 259093 1.30% 143 260199 1.31% 144 260176 1.31% 145 262763 1.32% 146 264729 1.33% 147 269924 1.36% 148 300841 1.51% 149 739124 3.72% 150 16980748 85.50% 19860307 reads passed initial QC criterion=sequence-density sequence-density=0.76 sequence-density-rank=1 fanout-score=1.46 fanout-score-rank=38 prefix-density=0.17 prefix-fanout=1.5 sequence=TTTGTGTTTGAG criterion=fanout-score sequence-density=0.03 sequence-density-rank=40 fanout-score=152.91 fanout-score-rank=1 prefix-density=2.54 prefix-fanout=1.6 sequence=CGCATCGCCGGCCCCCATCCACTTCCCTCCCGACAATTTCAAGCACTCTTTGACTCTCTTTTCAAAGTCCTTTTCATCTTTCCCTCGCGGTACTTGTTTGCTATCGGTCTCTCGCCCGTATTTAGCCTTGGACGGAATTTACCGCCCGATTGGGGCTGCATTCCCAAACAACCCGACTCGCAGACAGCGCCTCGTGGTGCGGCAGGGTCCAGCCACGACGGGGCTCTCACCCTCTCCGGCGCCCCTTTCCAGGGGACTTGGGCCTGGTCCGCCGCTGAGGACGCTTCTCCAGACTACAATTCGGACGCCGCAGGCGCCAGATTCTCAAGCTGGGCATTTCCCGGTTCGCTCGCCGTTACTAGGGGAATCCTTGTAAGTTTCTTTTCCTCCGCTT criterion=sequence-density sequence-density=1.31 sequence-density-rank=1 fanout-score=2.23 fanout-score-rank=36 prefix-density=1.26 prefix-fanout=2.2 sequence=TTTGTGTTTGAG criterion=fanout-score sequence-density=0.04 sequence-density-rank=43 fanout-score=108.40 fanout-score-rank=1 prefix-density=2.43 prefix-fanout=1.6 sequence=CGCATCGCCGGCCCCCATCCACTTCCCTCCCGACAATTTCAAGCACTCTTTGACTCTCTTTTCAAAGTCCTTTTCATCTTTCCCTCGCGGTACTTGTTTGCTATCGGTCTCTCGCCCGTATTTAGCCTTGGACGGAATTTACCGCCCGATTGGGGCTGCATTCCCAAACAACCCGACTCGCAGACAGCGCCTCGTGGTGCGGCAGGGTCCAGCCACGACGGGGCTCTCACCCTCTCCGGCGCCCCTTTCCAGGGGACTTGGGCCTGGTCCGCCGCTGAGGACGCTTCTCCAGACTACAATTCGGACGCCGCAGGCGCCAGATTCTCAAGCTGGGCATTTCCCGGTTCGCTCGCCGTTACTAGGGGAATCCTTGTAAGTTTCTTTTCCTCCGCTT SRR18274411 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 04:26:30 Started mapping on | Feb 11 04:26:45 Finished on | Feb 11 06:20:05 Mapping speed, Million of reads per hour | 10.51 Number of input reads | 19860307 Average input read length | 290 UNIQUE READS: Uniquely mapped reads number | 4711444 Uniquely mapped reads % | 23.72% Average mapped length | 280.97 Number of splices: Total | 2329129 Number of splices: Annotated (sjdb) | 2254114 Number of splices: GT/AG | 2268766 Number of splices: GC/AG | 29931 Number of splices: AT/AC | 2618 Number of splices: Non-canonical | 27814 Mismatch rate per base, % | 0.72% Deletion rate per base | 0.01% Deletion average length | 2.11 Insertion rate per base | 0.03% Insertion average length | 3.73 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 452767 % of reads mapped to multiple loci | 2.28% Number of reads mapped to too many loci | 9998662 % of reads mapped to too many loci | 50.34% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 11.34% % of reads unmapped: other | 12.31% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 14696096 14696096 14696096 N_multimapping 452767 452767 452767 N_noFeature 1554644 3100252 3110331 N_ambiguous 82131 13141 13649 UnstrandedReadsAssigned:3074669 PositiveStrandReadsAssigned:1598051 NegativeStrandReadsAssigned:1587464 Dataset is classified unstranded MeadianReadLen=142 20thPercentileLength=142 echo kmer=137 SRR18274411 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: SRR18274411-trimmed-pair1.fastq SRR18274411-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 19,860,307 reads, 16,039,643 reads pseudoaligned [quant] estimated average fragment length: 180.8 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,008 rounds 52401 SRR18274411.ke.tsv 34699 SRR18274411.se.tsv 87100 total ==> SRR18274411.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1838.2 139 2.8299 Potri.005G024800.1.v4.1 1035 855.2 82 3.58835 Potri.004G059700.1.v4.1 961 781.2 1 0.0479056 Potri.007G009000.2.v4.1 1416 1236.2 0 0 Potri.003G141000.2.v4.1 2943 2763.2 69.1149 0.936068 Potri.016G087400.1.v4.1 270 97.3301 180 69.2108 Potri.015G069301.1.v4.1 564 384.247 0 0 Potri.010G195200.1.v4.1 1773 1593.2 13 0.305366 Potri.012G127500.1.v4.1 977 797.2 16 0.751105 ==> SRR18274411.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 99 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 114 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 3 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 0 SRR18274411 completed mapping pipeline successfully