Starting /dee2/code/volunteer_pipeline.sh SRR12670099 current disk space = 3057659637760 free memory = 1576519160 SRR12670099 SRAfilesize f8d72419fe5a3fa68d0c40081549a557 SRR12670099.sra SRR12670099.sra file validated SRR12670099 is paired end SRR12670099 is conventional basespace SRR12670099 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670099_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.6455 37.0 37.0 37.0 37.0 37.0 2 36.4235 37.0 37.0 37.0 37.0 37.0 3 36.646 37.0 37.0 37.0 37.0 37.0 4 36.6495 37.0 37.0 37.0 37.0 37.0 5 36.712 37.0 37.0 37.0 37.0 37.0 6 36.672 37.0 37.0 37.0 37.0 37.0 7 36.6725 37.0 37.0 37.0 37.0 37.0 8 36.696 37.0 37.0 37.0 37.0 37.0 9 36.5755 37.0 37.0 37.0 37.0 37.0 10-14 36.5903 37.0 37.0 37.0 37.0 37.0 15-19 36.6109 37.0 37.0 37.0 37.0 37.0 20-24 36.568799999999996 37.0 37.0 37.0 37.0 37.0 25-29 36.5315 37.0 37.0 37.0 37.0 37.0 30-34 36.516400000000004 37.0 37.0 37.0 37.0 37.0 35-39 36.503 37.0 37.0 37.0 37.0 37.0 40-44 36.462599999999995 37.0 37.0 37.0 37.0 37.0 45-49 36.3965 37.0 37.0 37.0 37.0 37.0 50-54 36.378699999999995 37.0 37.0 37.0 37.0 37.0 55-59 36.326 37.0 37.0 37.0 37.0 37.0 60-64 36.3493 37.0 37.0 37.0 37.0 37.0 65-69 36.306200000000004 37.0 37.0 37.0 37.0 37.0 70-74 36.273399999999995 37.0 37.0 37.0 37.0 37.0 75-79 36.3115 37.0 37.0 37.0 37.0 37.0 80-84 36.3493 37.0 37.0 37.0 37.0 37.0 85-89 36.3055 37.0 37.0 37.0 37.0 37.0 90-94 36.2553 37.0 37.0 37.0 37.0 37.0 95-99 36.2432 37.0 37.0 37.0 37.0 37.0 100-104 36.281699999999994 37.0 37.0 37.0 37.0 37.0 105-109 36.2898 37.0 37.0 37.0 37.0 37.0 110-114 36.193799999999996 37.0 37.0 37.0 37.0 37.0 115-119 36.166900000000005 37.0 37.0 37.0 37.0 37.0 120-124 36.0759 37.0 37.0 37.0 37.0 37.0 125-129 35.9921 37.0 37.0 37.0 37.0 37.0 130-134 35.8793 37.0 37.0 37.0 37.0 37.0 135-139 35.7614 37.0 37.0 37.0 37.0 37.0 140-144 35.62779999999999 37.0 37.0 37.0 37.0 37.0 145-149 35.4233 37.0 37.0 37.0 37.0 37.0 150-151 35.31175 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 1.0 22 0.0 23 1.0 24 3.0 25 6.0 26 3.0 27 7.0 28 9.0 29 18.0 30 21.0 31 31.0 32 59.0 33 75.0 34 127.0 35 291.0 36 2925.0 37 422.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 36.975 11.75 8.7 42.575 2 20.356425702811247 13.177710843373495 34.964859437751 31.501004016064254 3 18.25 16.625 27.725 37.4 4 23.599999999999998 22.3 23.625 30.475 5 23.525 30.099999999999998 24.075 22.3 6 21.95 33.675 22.650000000000002 21.725 7 15.6 27.650000000000002 39.6 17.150000000000002 8 18.875 26.424999999999997 30.65 24.05 9 18.275 24.975 33.825 22.925 10-14 20.175 28.95 27.744999999999997 23.13 15-19 20.575 27.97 27.634999999999998 23.82 20-24 20.244999999999997 27.955000000000002 27.935 23.865 25-29 21.335 27.750000000000004 27.33 23.585 30-34 20.57 27.975 27.42 24.035 35-39 20.915 28.225 27.224999999999998 23.635 40-44 20.695 28.205000000000002 27.055 24.044999999999998 45-49 21.21 27.955000000000002 27.02 23.815 50-54 20.23 26.700000000000003 28.025 25.045 55-59 20.315 27.939999999999998 27.38 24.365000000000002 60-64 21.335 27.35 27.71 23.605 65-69 20.845 27.884999999999998 27.455000000000002 23.815 70-74 22.06 26.93 27.12 23.89 75-79 21.34 27.48 27.195000000000004 23.985 80-84 21.325 27.810000000000002 27.54 23.325000000000003 85-89 20.34 28.395 27.275 23.990000000000002 90-94 22.400000000000002 27.169999999999998 26.66 23.77 95-99 22.215 27.61 26.865 23.31 100-104 22.085 27.92 26.55 23.445 105-109 22.18 27.63 26.174999999999997 24.015 110-114 22.33 27.894999999999996 25.580000000000002 24.195 115-119 22.7 27.455000000000002 25.735000000000003 24.11 120-124 21.445 27.839999999999996 26.424999999999997 24.29 125-129 21.915000000000003 27.034999999999997 26.584999999999997 24.465 130-134 21.83 27.095000000000002 26.265 24.81 135-139 22.23 27.255000000000003 25.735000000000003 24.779999999999998 140-144 21.7 27.21 26.16 24.93 145-149 22.185 26.174999999999997 26.775 24.865000000000002 150-151 22.5125 25.95 26.5875 24.95 >>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 0.5 6 0.5 7 0.0 8 0.0 9 0.5 10 0.5 11 0.0 12 0.0 13 0.5 14 0.5 15 0.0 16 0.0 17 0.0 18 0.0 19 1.0 20 1.5 21 0.5 22 0.0 23 1.5 24 3.0 25 4.0 26 3.5 27 4.0 28 6.5 29 12.0 30 18.5 31 17.5 32 18.0 33 21.5 34 31.0 35 45.5 36 64.0 37 85.5 38 113.0 39 136.0 40 149.5 41 181.5 42 232.5 43 253.0 44 248.5 45 252.0 46 254.0 47 264.5 48 267.5 49 249.0 50 229.0 51 182.0 52 130.5 53 116.0 54 96.5 55 63.5 56 49.5 57 47.5 58 36.5 59 26.5 60 21.0 61 13.5 62 9.0 63 8.5 64 5.5 65 4.5 66 7.0 67 6.5 68 3.0 69 1.0 70 0.0 71 0.0 72 0.0 73 0.0 74 0.0 75 0.0 76 0.0 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 0.4 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 80.77499999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 82.29650263076446 66.475 2 13.587124729186009 21.95 3 2.971216341689879 7.199999999999999 4 0.7118539151965335 2.3 5 0.2785515320334262 1.125 6 0.12380068090374496 0.6 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.03095017022593624 0.35000000000000003 >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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTGCCACTATCTCGTAT 14 0.35000000000000003 TruSeq Adapter, Index 10 (97% over 37bp) ACAAAATTAAGTCTTTCTATTGCCTTGGGCATACTTCTACTACTAGAGCT 6 0.15 No Hit CCTGACGTTCAAAGTGCTTGGCCATGATGGAGAACTCAATTGGACCCCAC 6 0.15 No Hit GGGGAATTAGAACAACTGCCCGATTTGAAGGGCAGCTGCTATTGAACCGG 6 0.15 No Hit CCTCCTTGAGACCCAATGCTGCCCTGAAGCTTTTTCCTGGAGGGATCACA 6 0.15 No Hit GCCTTTTCAACTTGCATCCTGCGTCTTTGAAGAGCCTCAGCTCTCTTCAA 5 0.125 No Hit TTCACGCTTTTGCAGTCTGTGGAAGGACTGATTTTGTAGGAGATGGATAC 5 0.125 No Hit CTACTTGTAAAACCACCTCTCAACTCTTGTTGTTACTAGCACCAATGCTC 5 0.125 No Hit GGGGTCGTGAATACCCAGATTAGTGCCCCAGTGTAAGCTCTTCAAGGGTT 5 0.125 No Hit CCAACGTAGAGCATCAGAAACTAACTACTGCCGTTCTGCTAGTACAAAAT 5 0.125 No Hit GTCCATCATAGTACCCTGGTGAGCTGTGGTGCTCACGGTAGACCCAACCT 5 0.125 No Hit GCCCCAAATGGTCGAGACATGGATTCTTCATCACCTTCACCAAATCGCAG 5 0.125 No Hit GCAATGATCCAAGGTCAAGGTGGTTAGAAAATTCTTCACCATCAGTCTGC 5 0.125 No Hit GCCGGTTACAGAGAAAACCCGAAGAAAAAAAACTTAATCAGGGAAGTTTC 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 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.075 0.0 0.0 0.0 0.0 58-59 0.1375 0.0 0.0 0.0 0.0 60-61 0.15 0.0 0.0 0.0 0.0 62-63 0.15 0.0 0.0 0.0 0.0 64-65 0.225 0.0 0.0 0.0 0.0 66-67 0.275 0.0 0.0 0.0 0.0 68-69 0.32499999999999996 0.0 0.0 0.0 0.0 70-71 0.3625 0.0 0.0 0.0 0.0 72-73 0.425 0.0 0.0 0.0 0.0 74-75 0.575 0.0 0.0 0.0 0.0 76-77 0.7250000000000001 0.0 0.0 0.0 0.0 78-79 0.875 0.0 0.0 0.0 0.0 80-81 1.2374999999999998 0.0 0.0 0.0 0.0 82-83 1.4 0.0 0.0 0.0 0.0 84-85 1.7875 0.0 0.0 0.0 0.0 86-87 2.4 0.0 0.0 0.0 0.0 88-89 2.7249999999999996 0.0 0.0 0.0 0.0 90-91 3.225 0.0 0.0 0.0 0.0 92-93 3.8 0.0 0.0 0.0 0.0 94-95 4.4 0.0 0.0 0.0 0.0 96-97 4.75 0.0 0.0 0.0 0.0 98-99 5.275 0.0 0.0 0.0 0.0 100-101 6.35 0.0 0.0 0.0 0.0 102-103 7.025 0.0 0.0 0.0 0.0 104-105 7.85 0.0 0.0 0.0 0.0 106-107 8.6625 0.0 0.0 0.0 0.0 108-109 9.3625 0.0 0.0 0.0 0.0 110-111 10.3 0.0 0.0 0.0 0.0 112-113 10.925 0.0 0.0 0.0 0.0 114-115 11.725 0.0 0.0 0.0 0.0 116-117 12.5875 0.0 0.0 0.0 0.0 118-119 13.3125 0.0 0.0 0.0 0.0 120-121 14.2375 0.0 0.0 0.0 0.0 122-123 15.1125 0.0 0.0 0.0 0.0 124-125 16.175 0.0 0.0 0.0 0.0 126-127 17.4625 0.0 0.0 0.0 0.0 128-129 18.575000000000003 0.0 0.0 0.0 0.0 130-131 19.725 0.0 0.0 0.0 0.0 132-133 20.5875 0.0 0.0 0.0 0.0 134-135 21.35 0.0 0.0 0.0 0.0 136-137 22.15 0.0 0.0 0.0 0.0 138-139 23.112499999999997 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TGTCTGC 10 0.006830828 145.0 9 CTGTCTG 10 0.006830828 145.0 8 >>END_MODULE SRR12670099 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670099_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 46 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.251 37.0 37.0 37.0 37.0 37.0 2 36.029 37.0 37.0 37.0 37.0 37.0 3 35.9675 37.0 37.0 37.0 37.0 37.0 4 36.0925 37.0 37.0 37.0 37.0 37.0 5 36.305 37.0 37.0 37.0 37.0 37.0 6 36.144 37.0 37.0 37.0 37.0 37.0 7 36.2985 37.0 37.0 37.0 37.0 37.0 8 36.1865 37.0 37.0 37.0 37.0 37.0 9 36.0415 37.0 37.0 37.0 37.0 37.0 10-14 36.276599999999995 37.0 37.0 37.0 37.0 37.0 15-19 36.2462 37.0 37.0 37.0 37.0 37.0 20-24 36.1318 37.0 37.0 37.0 37.0 37.0 25-29 36.137 37.0 37.0 37.0 37.0 37.0 30-34 36.082100000000004 37.0 37.0 37.0 37.0 37.0 35-39 36.028999999999996 37.0 37.0 37.0 37.0 37.0 40-44 36.0552 37.0 37.0 37.0 37.0 37.0 45-49 36.021100000000004 37.0 37.0 37.0 37.0 37.0 50-54 35.9396 37.0 37.0 37.0 37.0 37.0 55-59 35.9324 37.0 37.0 37.0 37.0 37.0 60-64 35.96300000000001 37.0 37.0 37.0 37.0 37.0 65-69 35.9187 37.0 37.0 37.0 37.0 37.0 70-74 35.8836 37.0 37.0 37.0 37.0 37.0 75-79 35.8352 37.0 37.0 37.0 37.0 37.0 80-84 35.8138 37.0 37.0 37.0 37.0 37.0 85-89 35.8279 37.0 37.0 37.0 37.0 37.0 90-94 35.911500000000004 37.0 37.0 37.0 37.0 37.0 95-99 35.835300000000004 37.0 37.0 37.0 37.0 37.0 100-104 35.8449 37.0 37.0 37.0 37.0 37.0 105-109 35.7407 37.0 37.0 37.0 37.0 37.0 110-114 35.674400000000006 37.0 37.0 37.0 37.0 37.0 115-119 35.7436 37.0 37.0 37.0 37.0 37.0 120-124 35.5934 37.0 37.0 37.0 37.0 37.0 125-129 35.5109 37.0 37.0 37.0 37.0 37.0 130-134 35.3286 37.0 37.0 37.0 34.6 37.0 135-139 35.207499999999996 37.0 37.0 37.0 32.2 37.0 140-144 35.09779999999999 37.0 37.0 37.0 27.4 37.0 145-149 34.7833 37.0 37.0 37.0 25.0 37.0 150-151 34.28874999999999 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 4.0 14 4.0 15 2.0 16 2.0 17 1.0 18 0.0 19 1.0 20 1.0 21 4.0 22 6.0 23 7.0 24 12.0 25 16.0 26 12.0 27 11.0 28 10.0 29 19.0 30 20.0 31 30.0 32 65.0 33 105.0 34 214.0 35 598.0 36 2586.0 37 269.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 36.375 22.900000000000002 12.275 28.449999999999996 2 27.85 26.325 27.500000000000004 18.325 3 22.400000000000002 29.725 28.799999999999997 19.075 4 24.75 35.65 21.3 18.3 5 25.275 36.25 21.675 16.8 6 21.625 38.375 20.75 19.25 7 21.4 22.875 37.325 18.4 8 22.1 25.374999999999996 27.200000000000003 25.324999999999996 9 23.875 24.775 28.825 22.525000000000002 10-14 24.68 29.735 24.605 20.979999999999997 15-19 24.39 28.000000000000004 26.245 21.365000000000002 20-24 24.535 27.794999999999998 26.325 21.345 25-29 24.37 28.265 26.1 21.265 30-34 23.565 28.58 26.169999999999998 21.685 35-39 24.615000000000002 27.805000000000003 26.174999999999997 21.404999999999998 40-44 23.96 27.965 26.85 21.224999999999998 45-49 24.645 28.299999999999997 26.215 20.84 50-54 24.465 28.04 26.26 21.235 55-59 24.535 28.244999999999997 26.395000000000003 20.825 60-64 24.23 27.779999999999998 26.52 21.47 65-69 24.05 27.685 26.97 21.295 70-74 24.12 27.794999999999998 26.85 21.235 75-79 23.895 28.060000000000002 26.275 21.77 80-84 24.365000000000002 27.900000000000002 26.334999999999997 21.4 85-89 24.79 27.305 26.240000000000002 21.665 90-94 25.255 27.6 26.200000000000003 20.945 95-99 25.264999999999997 26.935 26.14 21.66 100-104 25.580000000000002 28.115000000000002 25.869999999999997 20.435 105-109 26.090000000000003 27.345000000000002 25.905 20.66 110-114 25.72 27.925 25.97 20.385 115-119 26.715 27.98 25.290000000000003 20.015 120-124 26.465 27.445000000000004 26.08 20.01 125-129 27.250000000000004 27.305 25.66 19.785 130-134 27.54 27.389999999999997 25.77 19.3 135-139 27.900000000000002 26.97 26.13 19.0 140-144 28.28 26.009999999999998 26.095000000000002 19.615 145-149 28.854999999999997 26.245 26.36 18.54 150-151 30.2875 26.5 24.9375 18.275 >>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 0.5 6 0.5 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 1.0 13 2.0 14 1.5 15 0.5 16 0.0 17 0.0 18 0.0 19 0.0 20 1.0 21 1.5 22 1.5 23 1.5 24 0.5 25 1.0 26 1.0 27 1.5 28 3.0 29 2.0 30 6.5 31 12.5 32 10.5 33 13.0 34 25.5 35 42.0 36 58.0 37 75.0 38 94.0 39 121.0 40 148.5 41 203.0 42 257.0 43 277.0 44 278.5 45 271.0 46 264.0 47 267.0 48 274.5 49 230.0 50 196.0 51 180.5 52 149.5 53 129.0 54 91.5 55 68.0 56 61.0 57 47.5 58 34.5 59 24.5 60 17.5 61 7.5 62 4.0 63 3.0 64 1.5 65 1.5 66 1.0 67 1.0 68 1.5 69 1.0 70 0.5 71 0.0 72 0.0 73 0.0 74 0.0 75 0.5 76 1.0 77 0.5 78 0.0 79 1.0 80 1.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.5 87 0.5 88 0.0 89 0.5 90 0.5 91 0.0 92 0.5 93 1.5 94 3.0 95 2.0 96 1.0 97 3.0 98 2.5 99 1.5 100 4.5 >>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 0.0 140-144 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 80.825 #Duplication Level Percentage of deduplicated Percentage of total 1 82.43117847200743 66.625 2 13.362202288895764 21.6 3 2.9384472626043925 7.124999999999999 4 0.9279307145066501 3.0 5 0.18558614290133002 0.75 6 0.12372409526755336 0.6 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.03093102381688834 0.3 >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 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 12 0.3 No Hit CCAAATAGCAGAAAGTTGAGATACATTCAGTCGATAAGGTCTCATAGACA 6 0.15 No Hit GCAAAAATAAGTGCCTACGTGACTCATGGGATTTTTCCAAATAGATCGTG 6 0.15 No Hit AGAGACTGGAATTCCCATTTACGAAGCAGAACCACTTCTTCTTTTCTTCA 6 0.15 No Hit CCACTAAGTTATATAAAGCTGCACTTGGCAATTGCTTTGAAGCGGAGGAG 6 0.15 No Hit CTTGGCACAATGTATAACCTACCTCCAGAAGGGTGGGGCTGTGCCTGCAG 5 0.125 No Hit GATAATGTGGGATTGTCGAGCAGGAATATTGGGACTTTGAGGATGTTGAC 5 0.125 No Hit TAATCATGGGCACTATGTGAGCCTTGTGAAAAGCCACAACCACTGGTTAT 5 0.125 No Hit GTGGAACAGCGGAAGATATCGAGAGTATTGAAGAGAAATGTTGATGGTCT 5 0.125 No Hit TGTTAAAGCATTTTAGATCCAATCAAAGATGTTTCTCACAAGGACTGAGT 5 0.125 No Hit CAAAGGCAGTGAAGCACACTCTATTCGTCAAGTTCAAAGATGACGTTACC 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 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.075 0.0 0.0 0.0 0.0 58-59 0.1375 0.0 0.0 0.0 0.0 60-61 0.15 0.0 0.0 0.0 0.0 62-63 0.15 0.0 0.0 0.0 0.0 64-65 0.225 0.0 0.0 0.0 0.0 66-67 0.275 0.0 0.0 0.0 0.0 68-69 0.32499999999999996 0.0 0.0 0.0 0.0 70-71 0.3625 0.0 0.0 0.0 0.0 72-73 0.425 0.0 0.0 0.0 0.0 74-75 0.575 0.0 0.0 0.0 0.0 76-77 0.7250000000000001 0.0 0.0 0.0 0.0 78-79 0.8875 0.0 0.0 0.0 0.0 80-81 1.25 0.0 0.0 0.0 0.0 82-83 1.4 0.0 0.0 0.0 0.0 84-85 1.8 0.0 0.0 0.0 0.0 86-87 2.425 0.0 0.0 0.0 0.0 88-89 2.75 0.0 0.0 0.0 0.0 90-91 3.25 0.0 0.0 0.0 0.0 92-93 3.825 0.0 0.0 0.0 0.0 94-95 4.425 0.0 0.0 0.0 0.0 96-97 4.775 0.0 0.0 0.0 0.0 98-99 5.2875 0.0 0.0 0.0 0.0 100-101 6.35 0.0 0.0 0.0 0.0 102-103 7.025 0.0 0.0 0.0 0.0 104-105 7.85 0.0 0.0 0.0 0.0 106-107 8.6375 0.0 0.0 0.0 0.0 108-109 9.3375 0.0 0.0 0.0 0.0 110-111 10.275 0.0 0.0 0.0 0.0 112-113 10.875 0.0 0.0 0.0 0.0 114-115 11.7 0.0 0.0 0.0 0.0 116-117 12.5875 0.0 0.0 0.0 0.0 118-119 13.3 0.0 0.0 0.0 0.0 120-121 14.1875 0.0 0.0 0.0 0.0 122-123 15.1 0.0 0.0 0.0 0.0 124-125 16.1625 0.0 0.0 0.0 0.0 126-127 17.3875 0.0 0.0 0.0 0.0 128-129 18.4625 0.0 0.0 0.0 0.0 130-131 19.625 0.0 0.0 0.0 0.0 132-133 20.4375 0.0 0.0 0.0 0.0 134-135 21.1875 0.0 0.0 0.0 0.0 136-137 21.95 0.0 0.0 0.0 0.0 138-139 22.924999999999997 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 677760 spots for SRR12670099.sra Written 677760 spots for SRR12670099.sra Read 677760 spots for SRR12670099.sra Written 677760 spots for SRR12670099.sra Read 677760 spots for SRR12670099.sra Written 677760 spots for SRR12670099.sra Read 677760 spots for SRR12670099.sra Written 677760 spots for SRR12670099.sra Read 677760 spots for SRR12670099.sra Written 677760 spots for SRR12670099.sra Read 677760 spots for SRR12670099.sra Written 677760 spots for SRR12670099.sra Read 677760 spots for SRR12670099.sra Written 677760 spots for SRR12670099.sra Read 677760 spots for SRR12670099.sra Written 677760 spots for SRR12670099.sra Read 677760 spots for SRR12670099.sra Written 677760 spots for SRR12670099.sra Read 677760 spots for SRR12670099.sra Written 677760 spots for SRR12670099.sra Read 677760 spots for SRR12670099.sra Written 677760 spots for SRR12670099.sra Read 677760 spots for SRR12670099.sra Written 677760 spots for SRR12670099.sra Read 677760 spots for SRR12670099.sra Written 677760 spots for SRR12670099.sra Read 677760 spots for SRR12670099.sra Written 677760 spots for SRR12670099.sra Read 677760 spots for SRR12670099.sra Written 677760 spots for SRR12670099.sra Read 677760 spots for SRR12670099.sra Written 677760 spots for SRR12670099.sra Read 677767 spots for SRR12670099.sra Written 677767 spots for SRR12670099.sra Read 677760 spots for SRR12670099.sra Written 677760 spots for SRR12670099.sra Read 677760 spots for SRR12670099.sra Written 677760 spots for SRR12670099.sra Read 677760 spots for SRR12670099.sra Written 677760 spots for SRR12670099.sra SRR ids: ['SRR12670099.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_fv2a9us_ SRR12670099.sra spots: 13555207 blocks: [[1, 677760], [677761, 1355520], [1355521, 2033280], [2033281, 2711040], [2711041, 3388800], [3388801, 4066560], [4066561, 4744320], [4744321, 5422080], [5422081, 6099840], [6099841, 6777600], [6777601, 7455360], [7455361, 8133120], [8133121, 8810880], [8810881, 9488640], [9488641, 10166400], [10166401, 10844160], [10844161, 11521920], [11521921, 12199680], [12199681, 12877440], [12877441, 13555207]] SRR12670099 file size 4584952 SRR12670099 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 SRR12670099 SRR12670099_1.fastq SRR12670099_2.fastq Input file: SRR12670099_1.fastq Paired file: SRR12670099_2.fastq trimmed: SRR12670099-trimmed-pair1.fastq, SRR12670099-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 Mon Feb 10 23:22:39 2025 >> started Mon Feb 10 23:22:54 2025 >> done (14.176s) 13555207 read pairs processed; of these: 82 ( 0.00%) short read pairs filtered out after trimming by size control 37411 ( 0.28%) empty read pairs filtered out after trimming by size control 13517714 (99.72%) read pairs available; of these: 3767024 (27.87%) trimmed read pairs available after processing 9750690 (72.13%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 6 0.00% 19 6 0.00% 20 9 0.00% 21 9 0.00% 22 17 0.00% 23 35 0.00% 24 35 0.00% 25 40 0.00% 26 32 0.00% 27 48 0.00% 28 59 0.00% 29 67 0.00% 30 66 0.00% 31 84 0.00% 32 94 0.00% 33 97 0.00% 34 105 0.00% 35 119 0.00% 36 130 0.00% 37 141 0.00% 38 164 0.00% 39 165 0.00% 40 197 0.00% 41 239 0.00% 42 246 0.00% 43 241 0.00% 44 228 0.00% 45 234 0.00% 46 314 0.00% 47 310 0.00% 48 361 0.00% 49 469 0.00% 50 539 0.00% 51 654 0.00% 52 701 0.01% 53 689 0.01% 54 776 0.01% 55 877 0.01% 56 899 0.01% 57 1043 0.01% 58 1213 0.01% 59 1402 0.01% 60 1675 0.01% 61 2026 0.01% 62 2241 0.02% 63 2575 0.02% 64 2688 0.02% 65 2938 0.02% 66 3091 0.02% 67 3385 0.03% 68 3875 0.03% 69 4383 0.03% 70 5067 0.04% 71 5527 0.04% 72 6547 0.05% 73 7456 0.06% 74 8084 0.06% 75 8807 0.07% 76 9500 0.07% 77 10120 0.07% 78 11162 0.08% 79 12380 0.09% 80 13276 0.10% 81 15122 0.11% 82 17061 0.13% 83 18508 0.14% 84 20401 0.15% 85 21940 0.16% 86 23127 0.17% 87 24119 0.18% 88 25139 0.19% 89 26134 0.19% 90 28221 0.21% 91 29869 0.22% 92 32072 0.24% 93 34759 0.26% 94 37016 0.27% 95 39308 0.29% 96 39978 0.30% 97 40521 0.30% 98 41540 0.31% 99 41925 0.31% 100 43758 0.32% 101 44670 0.33% 102 46138 0.34% 103 48417 0.36% 104 49894 0.37% 105 51792 0.38% 106 52550 0.39% 107 52968 0.39% 108 52759 0.39% 109 53460 0.40% 110 53619 0.40% 111 54354 0.40% 112 55990 0.41% 113 56909 0.42% 114 58396 0.43% 115 59241 0.44% 116 60319 0.45% 117 60723 0.45% 118 61076 0.45% 119 60603 0.45% 120 59951 0.44% 121 60949 0.45% 122 60632 0.45% 123 61859 0.46% 124 63055 0.47% 125 63314 0.47% 126 64422 0.48% 127 65272 0.48% 128 64802 0.48% 129 63682 0.47% 130 63039 0.47% 131 63522 0.47% 132 63336 0.47% 133 63773 0.47% 134 65037 0.48% 135 65076 0.48% 136 65728 0.49% 137 66202 0.49% 138 65289 0.48% 139 66276 0.49% 140 64595 0.48% 141 64615 0.48% 142 64569 0.48% 143 65017 0.48% 144 65150 0.48% 145 65505 0.48% 146 66434 0.49% 147 65572 0.49% 148 66019 0.49% 149 64883 0.48% 150 65090 0.48% 151 9750690 72.13% 13517714 reads passed initial QC criterion=sequence-density sequence-density=0.83 sequence-density-rank=1 fanout-score=2.01 fanout-score-rank=17 prefix-density=0.83 prefix-fanout=2.0 sequence=CGGTAGACCCAACCTTTCTCCAACTCGAATTCCAAGCAAGGAACCCACTT criterion=fanout-score sequence-density=0.01 sequence-density-rank=23 fanout-score=184.51 fanout-score-rank=1 prefix-density=0.25 prefix-fanout=10.3 sequence=TGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGTTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGGAGTATGAATGTGTTCTCTG criterion=sequence-density sequence-density=0.81 sequence-density-rank=1 fanout-score=1.96 fanout-score-rank=23 prefix-density=0.80 prefix-fanout=2.0 sequence=TGTAAGAGATGGCTTCCTC criterion=fanout-score sequence-density=0.01 sequence-density-rank=23 fanout-score=26.73 fanout-score-rank=1 prefix-density=0.16 prefix-fanout=1.0 sequence=GCTACACAGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAATCAATCATCATGTCTAGCACCTGCGACAACTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCA SRR12670099 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 10 23:23:35 Started mapping on | Feb 10 23:23:35 Finished on | Feb 10 23:24:47 Mapping speed, Million of reads per hour | 675.89 Number of input reads | 13517714 Average input read length | 284 UNIQUE READS: Uniquely mapped reads number | 12866110 Uniquely mapped reads % | 95.18% Average mapped length | 283.05 Number of splices: Total | 12174499 Number of splices: Annotated (sjdb) | 11957555 Number of splices: GT/AG | 11920790 Number of splices: GC/AG | 216750 Number of splices: AT/AC | 7517 Number of splices: Non-canonical | 29442 Mismatch rate per base, % | 0.34% Deletion rate per base | 0.02% Deletion average length | 2.96 Insertion rate per base | 0.02% Insertion average length | 2.38 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 317337 % of reads mapped to multiple loci | 2.35% Number of reads mapped to too many loci | 17793 % of reads mapped to too many loci | 0.13% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.22% % of reads unmapped: other | 0.12% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 334267 334267 334267 N_multimapping 317337 317337 317337 N_noFeature 246481 12690876 302974 N_ambiguous 204178 700 85105 UnstrandedReadsAssigned:12415451 PositiveStrandReadsAssigned:174534 NegativeStrandReadsAssigned:12478031 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=134 echo kmer=129 SRR12670099 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: SRR12670099-trimmed-pair1.fastq SRR12670099-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 13,517,714 reads, 12,583,184 reads pseudoaligned [quant] estimated average fragment length: 198.712 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,119 rounds 52401 SRR12670099.ke.tsv 34699 SRR12670099.se.tsv 87100 total ==> SRR12670099.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1820.29 354 14.4224 Potri.005G024800.1.v4.1 1035 837.288 138 12.223 Potri.004G059700.1.v4.1 961 763.303 21 2.04031 Potri.007G009000.2.v4.1 1416 1218.29 0 0 Potri.003G141000.2.v4.1 2943 2745.29 468 12.6425 Potri.016G087400.1.v4.1 270 109.267 706 479.168 Potri.015G069301.1.v4.1 564 370.038 0 0 Potri.010G195200.1.v4.1 1773 1575.29 39 1.83602 Potri.012G127500.1.v4.1 977 779.296 198 18.8424 ==> SRR12670099.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 474 Potri.001G233950.v4.1 1 Potri.001G122700.v4.1 227 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 2 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 11 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 2 SRR12670099 completed mapping pipeline successfully