Starting /dee2/code/volunteer_pipeline.sh SRR13165348 current disk space = 1542252625920 free memory = 1600038032 SRR13165348 SRAfilesize b7a8892e9ca85f9649561e38613fc181 SRR13165348.sra SRR13165348.sra file validated SRR13165348 is paired end SRR13165348 is conventional basespace SRR13165348 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR13165348_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.6275 37.0 37.0 37.0 37.0 37.0 2 36.13475 37.0 37.0 37.0 37.0 37.0 3 36.547 37.0 37.0 37.0 37.0 37.0 4 36.5445 37.0 37.0 37.0 37.0 37.0 5 36.584 37.0 37.0 37.0 37.0 37.0 6 36.574 37.0 37.0 37.0 37.0 37.0 7 36.5075 37.0 37.0 37.0 37.0 37.0 8 36.5035 37.0 37.0 37.0 37.0 37.0 9 36.4775 37.0 37.0 37.0 37.0 37.0 10-14 36.5062 37.0 37.0 37.0 37.0 37.0 15-19 36.499 37.0 37.0 37.0 37.0 37.0 20-24 36.485699999999994 37.0 37.0 37.0 37.0 37.0 25-29 36.4383 37.0 37.0 37.0 37.0 37.0 30-34 36.440200000000004 37.0 37.0 37.0 37.0 37.0 35-39 36.397800000000004 37.0 37.0 37.0 37.0 37.0 40-44 36.3758 37.0 37.0 37.0 37.0 37.0 45-49 36.282399999999996 37.0 37.0 37.0 37.0 37.0 50-54 36.275099999999995 37.0 37.0 37.0 37.0 37.0 55-59 36.2528 37.0 37.0 37.0 37.0 37.0 60-64 36.2158 37.0 37.0 37.0 37.0 37.0 65-69 36.1875 37.0 37.0 37.0 37.0 37.0 70-74 36.193 37.0 37.0 37.0 37.0 37.0 75-79 36.253499999999995 37.0 37.0 37.0 37.0 37.0 80-84 36.1464 37.0 37.0 37.0 37.0 37.0 85-89 36.190400000000004 37.0 37.0 37.0 37.0 37.0 90-94 36.106199999999994 37.0 37.0 37.0 37.0 37.0 95-99 36.101 37.0 37.0 37.0 37.0 37.0 100-104 36.089600000000004 37.0 37.0 37.0 37.0 37.0 105-109 36.0791 37.0 37.0 37.0 37.0 37.0 110-114 36.025 37.0 37.0 37.0 37.0 37.0 115-119 35.9967 37.0 37.0 37.0 37.0 37.0 120-124 35.9404 37.0 37.0 37.0 37.0 37.0 125-129 35.86149999999999 37.0 37.0 37.0 37.0 37.0 130-134 35.804500000000004 37.0 37.0 37.0 37.0 37.0 135-139 35.6987 37.0 37.0 37.0 37.0 37.0 140-144 35.5154 37.0 37.0 37.0 37.0 37.0 145-149 35.1662 37.0 37.0 37.0 37.0 37.0 150-151 34.9095 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 22 1.0 23 3.0 24 3.0 25 6.0 26 7.0 27 12.0 28 14.0 29 18.0 30 32.0 31 46.0 32 72.0 33 104.0 34 135.0 35 321.0 36 2786.0 37 440.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 53.175 9.725 6.25 30.85 2 23.850213621512943 11.108318673033425 32.77205327971852 32.26941442573511 3 21.075 15.024999999999999 26.325 37.574999999999996 4 27.025 20.275000000000002 21.85 30.85 5 30.225 26.0 22.125 21.65 6 24.2 30.9 21.625 23.275000000000002 7 20.075000000000003 25.624999999999996 35.725 18.575 8 20.525 25.174999999999997 27.150000000000002 27.150000000000002 9 19.15 22.125 31.95 26.775 10-14 23.419999999999998 26.815 25.165 24.6 15-19 23.01 25.965 25.21 25.814999999999998 20-24 24.05 26.35 24.52 25.080000000000002 25-29 23.315 25.465 25.650000000000002 25.569999999999997 30-34 23.455000000000002 25.665 25.540000000000003 25.34 35-39 23.935000000000002 25.77 24.84 25.455 40-44 23.47 26.21 24.875 25.445 45-49 24.035 25.35 24.099999999999998 26.515 50-54 24.145 24.875 25.624999999999996 25.355 55-59 23.885 25.345000000000002 25.180000000000003 25.590000000000003 60-64 24.065 25.88 24.395 25.66 65-69 24.709999999999997 24.975 25.055 25.259999999999998 70-74 24.310000000000002 26.075 24.474999999999998 25.14 75-79 24.325 25.235000000000003 25.005 25.435000000000002 80-84 24.5 25.025 24.85 25.624999999999996 85-89 24.46 25.480000000000004 24.51 25.55 90-94 24.535 24.81 24.995 25.66 95-99 23.955000000000002 25.445 24.525 26.075 100-104 24.560000000000002 25.05 24.315 26.075 105-109 25.11 25.319999999999997 23.919999999999998 25.650000000000002 110-114 24.385 25.590000000000003 24.11 25.915 115-119 24.779999999999998 25.22 23.995 26.005 120-124 25.014999999999997 25.305 23.955000000000002 25.724999999999998 125-129 24.905 25.069999999999997 23.46 26.565 130-134 24.47 25.259999999999998 24.08 26.19 135-139 25.290000000000003 24.67 23.51 26.529999999999998 140-144 24.945 24.535 23.82 26.700000000000003 145-149 25.41 24.805 23.89 25.895000000000003 150-151 24.175 25.4375 24.45 25.937500000000004 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 2.0 2 2.0 3 0.0 4 0.5 5 0.5 6 0.0 7 1.0 8 1.5 9 0.5 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.5 23 0.5 24 0.0 25 0.5 26 4.0 27 7.5 28 6.0 29 5.0 30 7.0 31 11.0 32 13.0 33 20.0 34 34.5 35 37.0 36 45.0 37 67.0 38 82.0 39 109.5 40 132.5 41 145.5 42 159.0 43 164.0 44 175.0 45 177.5 46 175.0 47 177.0 48 181.0 49 170.5 50 148.0 51 140.0 52 126.0 53 114.5 54 115.0 55 116.5 56 110.0 57 93.5 58 84.5 59 78.5 60 70.5 61 59.5 62 63.0 63 65.5 64 58.5 65 51.0 66 45.5 67 49.0 68 41.0 69 43.5 70 44.5 71 32.5 72 27.5 73 23.5 74 26.0 75 18.5 76 12.5 77 11.0 78 3.0 79 2.5 80 2.5 81 2.0 82 2.0 83 1.0 84 1.0 85 1.0 86 0.5 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 0.525 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 0.0 140-144 0.0 145-149 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 75.75 #Duplication Level Percentage of deduplicated Percentage of total 1 76.93069306930693 58.275 2 17.02970297029703 25.8 3 3.762376237623762 8.55 4 1.7161716171617163 5.2 5 0.49504950495049505 1.875 6 0.066006600660066 0.3 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 TGGCCCCTCGATCTCGTCCAGCGTGTAGGTGAGCCGGGTCATGAGCTTGG 6 0.15 No Hit GTTCCTCTCGGTGGGTTTTCCAGAAGAAGCTTTGTATACAGGCGGCTGCG 6 0.15 No Hit ACCAGACTTGCCCTCCAATGGATCCTCGTTAAGGGATTTAGATTGTACTC 5 0.125 No Hit CCCATTTCCCGGGTGTAACAACACTGAATTTGATCCAAGTATTGCACAAG 5 0.125 No Hit AGGGATTTGATGATTTTGCATCGTGGTATCTCATAATTACTATTCTTTCT 5 0.125 No Hit GGGGCCTACTAGCGTTTCCAAATTTTTATTTTGCGCTGGAAAACCTAGTT 5 0.125 No Hit GTCCAGTCTAGCAGAAACAGTGGTAGCACGTCGGTGGTCAGAGCCCTTCA 5 0.125 No Hit GATACTGACACCGTACAACGTCTCTTCATTCCTTGTGTGCCCCCTTCGAC 5 0.125 No Hit CTCGAGCCCGCCCATGTCTGACGACGGCGGCGGCGCGCGGCGGTGCGGTG 5 0.125 No Hit GACGTTGATACGCTCGAGCTGGAGGTCGGAGTCGCCGGCGTACTTGCCCG 5 0.125 No Hit CGTGTAAACAAAAACATACTATATTAAATATTGAAATTGTGTAAGTATAG 5 0.125 No Hit CCTGTCCTTCAGCACATACTTGTGCTCATTGTTGTCAACATCACTGTACA 5 0.125 No Hit CCCATAGCAAGAATTTTGACAGTGTACAAATCCAGCAGAATATACTAAAA 5 0.125 No Hit ATGCAGCCATGACCGAAAGGGTCACAATGGTACCCTTGATCGACAATCTA 5 0.125 No Hit GTTCAGACTACCACTGTGTACTGATACAGGATGGTAGGATTACATTATGA 5 0.125 No Hit GGCACATGATAAATAGCAACTATAACGAATAATAATAACAAGCTGGGCCT 5 0.125 No Hit GTACCGGTCCCCCAAGCGTGGGTCTATAAGCTCATCAATTGCATGCTCCT 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #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 0.025 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 0.037500000000000006 0.0 0.0 0.0 0.0 54-55 0.05 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.075 0.0 0.0 0.0 0.0 66-67 0.075 0.0 0.0 0.0 0.0 68-69 0.1 0.0 0.0 0.0 0.0 70-71 0.125 0.0 0.0 0.0 0.0 72-73 0.1375 0.0 0.0 0.0 0.0 74-75 0.225 0.0 0.0 0.0 0.0 76-77 0.2625 0.0 0.0 0.0 0.0 78-79 0.42500000000000004 0.0 0.0 0.0 0.0 80-81 0.5625 0.0 0.0 0.0 0.0 82-83 0.7250000000000001 0.0 0.0 0.0 0.0 84-85 0.875 0.0 0.0 0.0 0.0 86-87 1.15 0.0 0.0 0.0 0.0 88-89 1.2625000000000002 0.0 0.0 0.0 0.0 90-91 1.6375 0.0 0.0 0.0 0.0 92-93 1.8375 0.0 0.0 0.0 0.0 94-95 2.1624999999999996 0.0 0.0 0.0 0.0 96-97 2.5250000000000004 0.0 0.0 0.0 0.0 98-99 2.7625 0.0 0.0 0.0 0.0 100-101 3.4000000000000004 0.0 0.0 0.0 0.0 102-103 3.8375000000000004 0.0 0.0 0.0 0.0 104-105 4.4125 0.0 0.0 0.0 0.0 106-107 5.0 0.0 0.0 0.0 0.0 108-109 5.4625 0.0 0.0 0.0 0.0 110-111 5.925 0.0 0.0 0.0 0.0 112-113 6.5375 0.0 0.0 0.0 0.0 114-115 7.15 0.0 0.0 0.0 0.0 116-117 7.825 0.0 0.0 0.0 0.0 118-119 8.725 0.0 0.0 0.0 0.0 120-121 9.5125 0.0 0.0 0.0 0.0 122-123 10.0625 0.0 0.0 0.0 0.0 124-125 10.6625 0.0 0.0 0.0 0.0 126-127 11.3 0.0 0.0 0.0 0.0 128-129 12.1 0.0 0.0 0.0 0.0 130-131 12.7875 0.0 0.0 0.0 0.0 132-133 13.25 0.0 0.0 0.0 0.0 134-135 13.825 0.0 0.0 0.0 0.0 136-137 14.575 0.0 0.0 0.0 0.0 138-139 15.4875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR13165348 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR13165348_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.12175 37.0 37.0 37.0 37.0 37.0 2 36.1305 37.0 37.0 37.0 37.0 37.0 3 36.0815 37.0 37.0 37.0 37.0 37.0 4 36.239 37.0 37.0 37.0 37.0 37.0 5 36.296 37.0 37.0 37.0 37.0 37.0 6 36.2225 37.0 37.0 37.0 37.0 37.0 7 36.2645 37.0 37.0 37.0 37.0 37.0 8 36.214 37.0 37.0 37.0 37.0 37.0 9 36.2555 37.0 37.0 37.0 37.0 37.0 10-14 36.224599999999995 37.0 37.0 37.0 37.0 37.0 15-19 36.220299999999995 37.0 37.0 37.0 37.0 37.0 20-24 36.190749999999994 37.0 37.0 37.0 37.0 37.0 25-29 36.12575 37.0 37.0 37.0 37.0 37.0 30-34 36.07084999999999 37.0 37.0 37.0 37.0 37.0 35-39 36.052350000000004 37.0 37.0 37.0 37.0 37.0 40-44 36.03685 37.0 37.0 37.0 37.0 37.0 45-49 36.06925 37.0 37.0 37.0 37.0 37.0 50-54 36.008950000000006 37.0 37.0 37.0 37.0 37.0 55-59 36.00795 37.0 37.0 37.0 37.0 37.0 60-64 35.95485 37.0 37.0 37.0 37.0 37.0 65-69 35.911 37.0 37.0 37.0 37.0 37.0 70-74 35.89625 37.0 37.0 37.0 37.0 37.0 75-79 35.88815 37.0 37.0 37.0 37.0 37.0 80-84 35.86864999999999 37.0 37.0 37.0 37.0 37.0 85-89 35.875949999999996 37.0 37.0 37.0 37.0 37.0 90-94 35.87545 37.0 37.0 37.0 37.0 37.0 95-99 35.87885 37.0 37.0 37.0 37.0 37.0 100-104 35.80375 37.0 37.0 37.0 37.0 37.0 105-109 35.79795 37.0 37.0 37.0 37.0 37.0 110-114 35.70535 37.0 37.0 37.0 37.0 37.0 115-119 35.59785000000001 37.0 37.0 37.0 37.0 37.0 120-124 35.57215 37.0 37.0 37.0 37.0 37.0 125-129 35.638149999999996 37.0 37.0 37.0 37.0 37.0 130-134 35.44435 37.0 37.0 37.0 37.0 37.0 135-139 35.3329 37.0 37.0 37.0 37.0 37.0 140-144 35.08735 37.0 37.0 37.0 29.8 37.0 145-149 35.02595 37.0 37.0 37.0 27.4 37.0 150-151 34.579875 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 5 1.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 3.0 14 3.0 15 2.0 16 2.0 17 2.0 18 0.0 19 1.0 20 2.0 21 6.0 22 5.0 23 4.0 24 8.0 25 9.0 26 10.0 27 16.0 28 16.0 29 22.0 30 21.0 31 38.0 32 66.0 33 111.0 34 206.0 35 543.0 36 2623.0 37 280.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 45.926297317623465 21.20832288794184 8.022060666833793 24.843319127600903 2 30.725 21.075 26.724999999999998 21.475 3 23.325000000000003 25.1 29.799999999999997 21.775 4 27.224999999999998 29.25 21.525 22.0 5 29.325000000000003 29.599999999999998 18.125 22.95 6 21.55 35.05 20.075000000000003 23.325000000000003 7 22.55 21.575 32.225 23.65 8 22.125 23.7 23.5 30.675 9 24.6 22.3 25.974999999999998 27.125 10-14 26.369999999999997 25.564999999999998 23.28 24.785 15-19 26.435 24.26 23.65 25.655 20-24 25.52638159539885 25.1262815703926 23.220805201300326 26.12653163290823 25-29 26.446611652913226 24.626156539134783 23.565891472868216 25.36134033508377 30-34 26.096524131032755 24.63615903975994 23.725931482870717 25.541385346336583 35-39 26.176544136034007 24.991247811952988 23.360840210052515 25.47136784196049 40-44 26.38159539884971 24.63115778944736 24.20105026256564 24.786196549137284 45-49 26.006501625406354 24.626156539134783 23.320830207551886 26.046511627906977 50-54 26.426606651662915 24.9662415603901 24.0960240060015 24.511127781945486 55-59 26.866716679169794 24.296074018504626 23.845961490372595 24.991247811952988 60-64 26.376594148537137 24.85621405351338 23.870967741935484 24.896224056014006 65-69 25.49009801960392 24.1498299659932 25.470094018803763 24.889977995599118 70-74 26.936734183545884 24.621155288822205 24.191047761940485 24.251062765691422 75-79 25.926481620405102 24.521130282570645 24.296074018504626 25.256314078519633 80-84 26.576644161040257 24.87621905476369 23.85596399099775 24.691172793198298 85-89 27.336834208552137 24.601150287571894 23.725931482870717 24.336084021005252 90-94 26.291572893223307 25.406351587896975 24.16104026006502 24.141035258814703 95-99 26.9567391847962 24.601150287571894 24.18104526131533 24.261065266316578 100-104 27.12678169542386 24.38609652413103 24.50112528132033 23.98599649912478 105-109 26.666666666666668 25.136284071017755 24.0960240060015 24.10102525631408 110-114 27.406851712928233 25.101275318829707 24.051012753188296 23.440860215053764 115-119 27.09677419354839 24.571142785696424 24.246061515378845 24.086021505376344 120-124 28.162040510127532 25.18129532383096 23.78094523630908 22.875718929732432 125-129 28.322080520130033 24.93123280820205 24.166041510377596 22.58064516129032 130-134 28.459960986345223 25.198819586855397 23.688290901815638 22.652928524983746 135-139 28.503551065319595 24.832449734920477 23.71711513454036 22.946884065219567 140-144 29.387346836709177 25.14128532133033 23.980995248812203 21.490372593148287 145-149 29.612403100775193 24.93123280820205 23.44586146536634 22.010502625656414 150-151 28.898336876328624 24.684256596223584 22.70851569338502 23.708890834062775 >>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 0.5 11 0.5 12 0.5 13 0.5 14 0.5 15 0.5 16 0.5 17 0.5 18 1.5 19 2.0 20 0.5 21 0.0 22 0.5 23 1.5 24 1.0 25 0.0 26 1.0 27 1.0 28 1.5 29 2.5 30 2.5 31 4.0 32 7.5 33 13.0 34 25.5 35 28.5 36 27.0 37 46.0 38 65.0 39 87.5 40 106.0 41 136.0 42 148.5 43 148.0 44 173.5 45 193.0 46 187.0 47 182.0 48 182.0 49 160.5 50 139.5 51 132.5 52 136.5 53 131.0 54 110.5 55 102.5 56 102.0 57 93.0 58 83.0 59 82.0 60 86.5 61 85.0 62 79.0 63 68.5 64 67.5 65 67.0 66 61.0 67 72.5 68 61.5 69 51.0 70 47.5 71 34.0 72 38.5 73 29.5 74 17.0 75 14.5 76 15.0 77 12.0 78 9.0 79 7.0 80 5.0 81 2.0 82 1.0 83 1.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.5 89 0.5 90 0.5 91 0.5 92 0.0 93 2.0 94 3.0 95 1.0 96 0.5 97 1.5 98 1.5 99 0.5 100 1.5 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.27499999999999997 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 0.025 25-29 0.025 30-34 0.025 35-39 0.025 40-44 0.025 45-49 0.025 50-54 0.025 55-59 0.025 60-64 0.025 65-69 0.02 70-74 0.025 75-79 0.025 80-84 0.025 85-89 0.025 90-94 0.025 95-99 0.025 100-104 0.025 105-109 0.025 110-114 0.025 115-119 0.025 120-124 0.025 125-129 0.025 130-134 0.034999999999999996 135-139 0.03 140-144 0.025 145-149 0.025 150-151 0.0375 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 75.825 #Duplication Level Percentage of deduplicated Percentage of total 1 77.25024727992087 58.575 2 16.584240026376527 25.15 3 3.824596109462578 8.7 4 1.8463567424991758 5.6000000000000005 5 0.3626772172766238 1.375 6 0.13188262446422683 0.6 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 GGGAGATTGGCTTCATTGTCTACTCCATTGGCAAGCCACTTGATGCTTGG 6 0.15 No Hit CCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGCAA 6 0.15 No Hit AGCAAAGGCCCTTGAACAGATAAAGCAACTATCAGACAGGGCAAGTGCTG 6 0.15 No Hit GGAGGTCAAGGGGACGGGGACAGCCAACCAGTGCCCGACCATCGACGGCG 6 0.15 No Hit GTGGGACAAGAGCAGCGCCGCGGACTGGGACGTCGAGTCCGCCGCCGCCC 5 0.125 No Hit CAGCCACTTCACATTCAGTCTTGCCTGTATCCAGAGGTATGCATCGTGCT 5 0.125 No Hit CCTCCACACTCCCTTCCCCTCTCTCCTCCTAAACCTCGCCGGAACCCTAT 5 0.125 No Hit CTCATACATGGATATATAGGAAGCAGATTGAAGCTAGAAGGAAGGTAGTT 5 0.125 No Hit ACTACTATTTCCTGGACTACTGCAAACCTGAGGCGATTAAGAATAGTGCT 5 0.125 No Hit ACCAACTCCTAGTACAAATGTATGCATGGCATTACCTTCAAAATGCTACT 5 0.125 No Hit GTGACAATAAATAACAATACCGGGCACATTAGTGTCTGGTAATTGGAATG 5 0.125 No Hit CGAATCTCACATGGCATTCACAATGCCTGGAATGTACCGTGTTGTCCACG 5 0.125 No Hit GTGACAACTACATCAAGGCAATGCGGCTCTTCGTGGGTGAGCCTGTCTGG 5 0.125 No Hit CCTTGACAATGATTTTATGCTGTACTATATCTGCCCCATGCATACCCTAT 5 0.125 No Hit GAGTACATTTGCAACGGATCCTTGGATTCACATCTTTATGGTCGTAATAA 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #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 0.025 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 0.037500000000000006 0.0 0.0 0.0 0.0 54-55 0.05 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.075 0.0 0.0 0.0 0.0 66-67 0.075 0.0 0.0 0.0 0.0 68-69 0.1 0.0 0.0 0.0 0.0 70-71 0.1375 0.0 0.0 0.0 0.0 72-73 0.16249999999999998 0.0 0.0 0.0 0.0 74-75 0.225 0.0 0.0 0.0 0.0 76-77 0.2625 0.0 0.0 0.0 0.0 78-79 0.42500000000000004 0.0 0.0 0.0 0.0 80-81 0.5625 0.0 0.0 0.0 0.0 82-83 0.7250000000000001 0.0 0.0 0.0 0.0 84-85 0.875 0.0 0.0 0.0 0.0 86-87 1.15 0.0 0.0 0.0 0.0 88-89 1.2625000000000002 0.0 0.0 0.0 0.0 90-91 1.65 0.0 0.0 0.0 0.0 92-93 1.8875 0.0 0.0 0.0 0.0 94-95 2.2125000000000004 0.0 0.0 0.0 0.0 96-97 2.5999999999999996 0.0 0.0 0.0 0.0 98-99 2.8125 0.0 0.0 0.0 0.0 100-101 3.4749999999999996 0.0 0.0 0.0 0.0 102-103 3.8875 0.0 0.0 0.0 0.0 104-105 4.4625 0.0 0.0 0.0 0.0 106-107 5.05 0.0 0.0 0.0 0.0 108-109 5.512499999999999 0.0 0.0 0.0 0.0 110-111 5.9875 0.0 0.0 0.0 0.0 112-113 6.6125 0.0 0.0 0.0 0.0 114-115 7.3 0.0 0.0 0.0 0.0 116-117 7.975 0.0 0.0 0.0 0.0 118-119 8.925 0.0 0.0 0.0 0.0 120-121 9.7125 0.0 0.0 0.0 0.0 122-123 10.275 0.0 0.0 0.0 0.0 124-125 10.8875 0.0 0.0 0.0 0.0 126-127 11.524999999999999 0.0 0.0 0.0 0.0 128-129 12.337499999999999 0.0 0.0 0.0 0.0 130-131 13.05 0.0 0.0 0.0 0.0 132-133 13.524999999999999 0.0 0.0 0.0 0.0 134-135 14.0875 0.0 0.0 0.0 0.0 136-137 14.85 0.0 0.0 0.0 0.0 138-139 15.8125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AAAAAAA 40 0.0076550315 18.125 15-19 >>END_MODULE Read 1324428 spots for SRR13165348.sra Written 1324428 spots for SRR13165348.sra Read 1324428 spots for SRR13165348.sra Written 1324428 spots for SRR13165348.sra Read 1324428 spots for SRR13165348.sra Written 1324428 spots for SRR13165348.sra Read 1324428 spots for SRR13165348.sra Written 1324428 spots for SRR13165348.sra Read 1324428 spots for SRR13165348.sra Written 1324428 spots for SRR13165348.sra Read 1324428 spots for SRR13165348.sra Written 1324428 spots for SRR13165348.sra Read 1324428 spots for SRR13165348.sra Written 1324428 spots for SRR13165348.sra Read 1324428 spots for SRR13165348.sra Written 1324428 spots for SRR13165348.sra Read 1324428 spots for SRR13165348.sra Written 1324428 spots for SRR13165348.sra Read 1324428 spots for SRR13165348.sra Written 1324428 spots for SRR13165348.sra Read 1324428 spots for SRR13165348.sra Written 1324428 spots for SRR13165348.sra Read 1324428 spots for SRR13165348.sra Written 1324428 spots for SRR13165348.sra Read 1324428 spots for SRR13165348.sra Written 1324428 spots for SRR13165348.sra Read 1324428 spots for SRR13165348.sra Written 1324428 spots for SRR13165348.sra Read 1324428 spots for SRR13165348.sra Written 1324428 spots for SRR13165348.sra Read 1324428 spots for SRR13165348.sra Written 1324428 spots for SRR13165348.sra Read 1324428 spots for SRR13165348.sra Read 1324428 spots for SRR13165348.sra Written 1324428 spots for SRR13165348.sra Written 1324428 spots for SRR13165348.sra Read 1324428 spots for SRR13165348.sra Written 1324428 spots for SRR13165348.sra Read 1324446 spots for SRR13165348.sra Written 1324446 spots for SRR13165348.sra SRR ids: ['SRR13165348.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_cgzeky4b SRR13165348.sra spots: 26488578 blocks: [[1, 1324428], [1324429, 2648856], [2648857, 3973284], [3973285, 5297712], [5297713, 6622140], [6622141, 7946568], [7946569, 9270996], [9270997, 10595424], [10595425, 11919852], [11919853, 13244280], [13244281, 14568708], [14568709, 15893136], [15893137, 17217564], [17217565, 18541992], [18541993, 19866420], [19866421, 21190848], [21190849, 22515276], [22515277, 23839704], [23839705, 25164132], [25164133, 26488578]] SRR13165348 file size 8980277 SRR13165348 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 SRR13165348 SRR13165348_1.fastq SRR13165348_2.fastq Input file: SRR13165348_1.fastq Paired file: SRR13165348_2.fastq trimmed: SRR13165348-trimmed-pair1.fastq, SRR13165348-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 Sat Dec 7 15:44:06 2024 >> started Sat Dec 7 15:44:47 2024 >> done (41.841s) 26488578 read pairs processed; of these: 643 ( 0.00%) short read pairs filtered out after trimming by size control 32443 ( 0.12%) empty read pairs filtered out after trimming by size control 26455492 (99.88%) read pairs available; of these: 5418559 (20.48%) trimmed read pairs available after processing 21036933 (79.52%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 27 0.00% 19 37 0.00% 20 40 0.00% 21 38 0.00% 22 46 0.00% 23 74 0.00% 24 82 0.00% 25 80 0.00% 26 87 0.00% 27 102 0.00% 28 136 0.00% 29 141 0.00% 30 136 0.00% 31 150 0.00% 32 129 0.00% 33 158 0.00% 34 159 0.00% 35 164 0.00% 36 164 0.00% 37 210 0.00% 38 217 0.00% 39 235 0.00% 40 238 0.00% 41 290 0.00% 42 325 0.00% 43 319 0.00% 44 315 0.00% 45 389 0.00% 46 383 0.00% 47 422 0.00% 48 462 0.00% 49 563 0.00% 50 649 0.00% 51 759 0.00% 52 861 0.00% 53 925 0.00% 54 974 0.00% 55 1039 0.00% 56 1076 0.00% 57 1207 0.00% 58 1464 0.01% 59 1609 0.01% 60 2016 0.01% 61 2204 0.01% 62 2513 0.01% 63 2745 0.01% 64 3013 0.01% 65 3281 0.01% 66 3759 0.01% 67 4146 0.02% 68 4478 0.02% 69 5132 0.02% 70 5763 0.02% 71 6379 0.02% 72 7277 0.03% 73 8313 0.03% 74 9149 0.03% 75 10379 0.04% 76 11146 0.04% 77 11967 0.05% 78 13103 0.05% 79 14570 0.06% 80 15818 0.06% 81 17511 0.07% 82 19380 0.07% 83 21002 0.08% 84 23643 0.09% 85 25700 0.10% 86 26788 0.10% 87 28649 0.11% 88 30306 0.11% 89 32090 0.12% 90 34562 0.13% 91 36505 0.14% 92 38861 0.15% 93 41438 0.16% 94 44080 0.17% 95 46927 0.18% 96 49302 0.19% 97 51547 0.19% 98 52494 0.20% 99 54279 0.21% 100 55839 0.21% 101 57416 0.22% 102 59057 0.22% 103 61700 0.23% 104 63903 0.24% 105 66710 0.25% 106 68869 0.26% 107 70540 0.27% 108 71651 0.27% 109 73895 0.28% 110 73323 0.28% 111 75574 0.29% 112 77022 0.29% 113 78046 0.30% 114 79871 0.30% 115 81997 0.31% 116 83843 0.32% 117 84768 0.32% 118 86326 0.33% 119 87746 0.33% 120 88786 0.34% 121 89127 0.34% 122 89364 0.34% 123 91351 0.35% 124 93019 0.35% 125 93949 0.36% 126 94913 0.36% 127 96034 0.36% 128 96307 0.36% 129 97624 0.37% 130 97870 0.37% 131 98730 0.37% 132 99293 0.38% 133 101200 0.38% 134 100138 0.38% 135 100851 0.38% 136 101987 0.39% 137 102202 0.39% 138 103841 0.39% 139 104045 0.39% 140 105545 0.40% 141 105393 0.40% 142 106099 0.40% 143 106506 0.40% 144 107726 0.41% 145 108107 0.41% 146 107041 0.40% 147 108553 0.41% 148 108334 0.41% 149 107846 0.41% 150 109586 0.41% 151 21036933 79.52% 26455492 reads passed initial QC criterion=sequence-density sequence-density=0.23 sequence-density-rank=1 fanout-score=6.07 fanout-score-rank=16 prefix-density=0.33 prefix-fanout=4.2 sequence=GGTGTTGTCGAAGCCGATGATGCGGAC criterion=fanout-score sequence-density=0.03 sequence-density-rank=41 fanout-score=320.90 fanout-score-rank=1 prefix-density=0.53 prefix-fanout=17.5 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.21 sequence-density-rank=1 fanout-score=6.72 fanout-score-rank=16 prefix-density=0.28 prefix-fanout=5.1 sequence=GAGGAGATTGCTGACCGCGTCAACAAGATGCT criterion=fanout-score sequence-density=0.01 sequence-density-rank=46 fanout-score=50.04 fanout-score-rank=1 prefix-density=0.06 prefix-fanout=4.8 sequence=TCTCCTCTCAGTCGCTCACTCACACCAAGAAGGCAAGAACACACCTACCAAGCAGAAAGAAGAAGCAGCCAGCAACCCCCAGCAGCAATTCGATCCATGGGTTCCACGGCGGCGGACATGGCCGCGACGGCGGACGAGGAGGCCTGCATGTTCGCGCTGCAGCTGGCGTCGTCCTCGATCCTGCCCATGACGCTCAAGAACGCCATCGAGCTGGGCCTCCTGGACACCCTCGTCCAGGCCTCCGGCAAGTCCCTGACCCCGGCCGAGGTCGCCGCCAAGCT SRR13165348 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 15:46:05 Started mapping on | Dec 07 15:46:06 Finished on | Dec 07 15:48:12 Mapping speed, Million of reads per hour | 755.87 Number of input reads | 26455492 Average input read length | 289 UNIQUE READS: Uniquely mapped reads number | 25216283 Uniquely mapped reads % | 95.32% Average mapped length | 288.67 Number of splices: Total | 21765967 Number of splices: Annotated (sjdb) | 20454545 Number of splices: GT/AG | 21496982 Number of splices: GC/AG | 219782 Number of splices: AT/AC | 12154 Number of splices: Non-canonical | 37049 Mismatch rate per base, % | 0.22% Deletion rate per base | 0.01% Deletion average length | 2.90 Insertion rate per base | 0.01% Insertion average length | 2.31 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 211456 % of reads mapped to multiple loci | 0.80% Number of reads mapped to too many loci | 51343 % of reads mapped to too many loci | 0.19% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.83% % of reads unmapped: other | 0.86% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1028038 1028038 1028038 N_multimapping 211456 211456 211456 N_noFeature 828485 24518453 1058236 N_ambiguous 523424 3385 55810 UnstrandedReadsAssigned:23864374 PositiveStrandReadsAssigned:694445 NegativeStrandReadsAssigned:24102237 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=150 echo kmer=145 SRR13165348 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: 52,972 [index] number of k-mers: 66,720,672 [index] number of equivalence classes: 111,837 [quant] running in paired-end mode [quant] will process pair 1: SRR13165348-trimmed-pair1.fastq SRR13165348-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 26,455,492 reads, 24,371,715 reads pseudoaligned [quant] estimated average fragment length: 236.578 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,216 rounds 52973 SRR13165348.ke.tsv 35125 SRR13165348.se.tsv 88098 total ==> SRR13165348.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 700.877 0 0 PNS24247 1044 808.422 20.8953 1.64871 PNS24249 1928 1692.42 82.1709 3.09701 PNS24246 1044 808.422 20.8953 1.64871 PNS24248 1044 808.422 20.8953 1.64871 PNS24244 1471 1235.42 92.1433 4.75753 PNS24243 293 112.345 0 0 KQK14069 1603 1367.42 4 0.186591 KQK14071 474 256.4 0 0 ==> SRR13165348.se.tsv <== BRADI_1g14170v3 4 BRADI_1g53295v3 56 BRADI_1g59795v3 334 BRADI_1g07683v3 0 BRADI_1g00485v3 64 BRADI_1g20270v3 4250 BRADI_1g74790v3 152 BRADI_1g09890v3 55 BRADI_1g77505v3 189 BRADI_1g48960v3 0 SRR13165348 completed mapping pipeline successfully