Starting /dee2/code/volunteer_pipeline.sh SRR7168844 current disk space = 3092847710208 free memory = 1576615924 SRR7168844 SRAfilesize 693a52a4f44b8a3740bee21fbadebddf SRR7168844.sra SRR7168844.sra file validated SRR7168844 is paired end SRR7168844 is conventional basespace SRR7168844 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7168844_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 32.61975 34.0 33.0 34.0 32.0 34.0 2 33.229 34.0 33.0 34.0 32.0 34.0 3 33.3525 34.0 33.0 34.0 33.0 34.0 4 33.4015 34.0 33.0 34.0 33.0 34.0 5 33.40575 34.0 34.0 34.0 33.0 34.0 6 37.1525 38.0 38.0 38.0 36.0 38.0 7 37.41775 38.0 38.0 38.0 37.0 38.0 8 37.50425 38.0 38.0 38.0 37.0 38.0 9 37.4505 38.0 38.0 38.0 37.0 38.0 10-14 37.5201 38.0 38.0 38.0 38.0 38.0 15-19 37.546800000000005 38.0 38.0 38.0 38.0 38.0 20-24 37.51520000000001 38.0 38.0 38.0 38.0 38.0 25-29 37.50805 38.0 38.0 38.0 38.0 38.0 30-34 37.499900000000004 38.0 38.0 38.0 37.8 38.0 35-39 37.47045 38.0 38.0 38.0 37.6 38.0 40-44 37.346199999999996 38.0 38.0 38.0 37.0 38.0 45-49 37.41345 38.0 38.0 38.0 37.0 38.0 50-54 37.338 38.0 38.0 38.0 37.0 38.0 55-59 37.29655 38.0 38.0 38.0 37.0 38.0 60-64 37.2488 38.0 38.0 38.0 37.0 38.0 65-69 37.26775 38.0 38.0 38.0 37.0 38.0 70-74 37.0794 38.0 38.0 38.0 36.8 38.0 75-79 36.69135 38.0 38.0 38.0 36.0 38.0 80-84 36.634049999999995 38.0 38.0 38.0 36.0 38.0 85-89 36.59994999999999 38.0 38.0 38.0 36.0 38.0 90-94 36.5305 38.0 38.0 38.0 35.4 38.0 95-99 36.399449999999995 38.0 38.0 38.0 35.0 38.0 100-104 36.3481 38.0 38.0 38.0 34.6 38.0 105-109 36.210249999999995 38.0 38.0 38.0 34.0 38.0 110-114 36.11965 38.0 38.0 38.0 34.0 38.0 115-119 36.0327 38.0 38.0 38.0 33.6 38.0 120-124 35.7189 38.0 37.4 38.0 32.6 38.0 125-129 35.464549999999996 38.0 37.0 38.0 31.2 38.0 130-134 35.19175 38.0 36.0 38.0 29.8 38.0 135-139 34.94115 38.0 36.0 38.0 29.4 38.0 140-144 34.5115 38.0 35.0 38.0 28.0 38.0 145-149 34.036649999999995 38.0 34.0 38.0 25.8 38.0 150-151 29.877625 35.5 27.0 38.0 8.5 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 1.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 1.0 11 3.0 12 3.0 13 1.0 14 1.0 15 3.0 16 4.0 17 3.0 18 15.0 19 30.0 20 3.0 21 4.0 22 3.0 23 3.0 24 6.0 25 14.0 26 8.0 27 12.0 28 22.0 29 34.0 30 28.0 31 41.0 32 51.0 33 72.0 34 132.0 35 202.0 36 549.0 37 2751.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 38.43790012804097 13.265044814340591 11.446862996158771 36.850192061459666 2 21.575 17.075000000000003 31.724999999999998 29.625 3 21.2 20.474999999999998 25.674999999999997 32.65 4 22.375 27.750000000000004 22.2 27.675 5 23.974999999999998 32.225 22.575 21.224999999999998 6 19.925 34.475 24.175 21.425 7 14.249999999999998 28.025 39.4 18.325 8 17.75 26.25 31.3 24.7 9 18.3 24.875 32.2 24.625 10-14 18.85 30.654999999999998 26.57 23.925 15-19 19.615 28.634999999999998 26.97 24.779999999999998 20-24 19.814999999999998 28.68 26.740000000000002 24.765 25-29 20.135 28.849999999999998 26.995 24.02 30-34 19.35 28.794999999999998 27.02 24.834999999999997 35-39 20.24 29.09 26.900000000000002 23.77 40-44 20.075000000000003 28.549999999999997 27.215 24.16 45-49 20.49 27.825 27.655 24.03 50-54 20.495 28.000000000000004 26.85 24.654999999999998 55-59 20.605 27.474999999999998 27.83 24.09 60-64 20.465 27.389999999999997 27.97 24.175 65-69 19.994999999999997 28.46 27.439999999999998 24.104999999999997 70-74 20.04 28.904999999999998 27.295 23.76 75-79 20.4 28.349999999999998 26.845000000000002 24.404999999999998 80-84 20.51 27.68 27.73 24.08 85-89 20.200000000000003 27.91 27.415 24.474999999999998 90-94 20.52 27.325 27.07 25.085 95-99 20.424999999999997 27.54 27.150000000000002 24.884999999999998 100-104 20.315 27.935 26.97 24.779999999999998 105-109 20.880000000000003 27.615000000000002 27.229999999999997 24.275 110-114 21.005 27.805000000000003 26.445 24.745 115-119 21.154999999999998 27.6 26.284999999999997 24.959999999999997 120-124 20.935000000000002 27.87 26.19 25.005 125-129 21.11 27.994999999999997 26.119999999999997 24.775 130-134 21.19 27.800000000000004 26.064999999999998 24.945 135-139 21.63 27.685 25.66 25.025 140-144 21.404999999999998 28.005000000000003 25.590000000000003 25.0 145-149 21.2 27.250000000000004 26.015 25.535000000000004 150-151 21.5375 27.925 25.825 24.712500000000002 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.5 3 0.5 4 0.5 5 0.5 6 0.0 7 0.5 8 0.5 9 0.0 10 0.0 11 0.5 12 0.5 13 0.0 14 1.0 15 1.0 16 0.0 17 0.5 18 0.5 19 0.5 20 0.5 21 0.5 22 1.5 23 1.5 24 2.5 25 3.5 26 5.0 27 9.5 28 13.5 29 15.5 30 19.0 31 23.0 32 31.0 33 47.0 34 61.0 35 69.0 36 86.5 37 120.5 38 141.0 39 153.5 40 171.5 41 187.5 42 207.5 43 210.0 44 224.5 45 244.5 46 239.0 47 221.5 48 199.5 49 195.5 50 176.0 51 140.0 52 128.0 53 132.0 54 122.0 55 92.5 56 67.0 57 57.0 58 47.0 59 37.5 60 31.5 61 23.5 62 14.0 63 6.5 64 3.0 65 0.0 66 0.5 67 1.5 68 2.0 69 1.5 70 0.5 71 1.0 72 1.0 73 0.5 74 0.5 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 2.375 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 97.0 #Duplication Level Percentage of deduplicated Percentage of total 1 98.4536082474227 95.5 2 1.2371134020618557 2.4 3 0.2061855670103093 0.6 4 0.025773195876288662 0.1 5 0.025773195876288662 0.125 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.051546391752577324 1.275 >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 fail #Sequence Count Percentage Possible Source GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGGAATATCTCGTATGC 41 1.0250000000000001 TruSeq Adapter, Index 7 (97% over 37bp) GTCGGTTCGGTCCTCCAGTTAGTGTTACCCAACCTTCAACCTGCCCATGG 10 0.25 No Hit CGGAAGAGCACACGTCTGAACTCCAGTCACCGGAATATCTCGTATGCCGT 5 0.125 TruSeq Adapter, Index 7 (97% over 34bp) >>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 0.05 0.0 0.0 0.0 0.0 2 0.05 0.0 0.0 0.0 0.0 3 0.05 0.0 0.0 0.0 0.0 4 0.05 0.0 0.0 0.0 0.0 5 0.05 0.0 0.0 0.0 0.0 6 0.05 0.0 0.0 0.0 0.0 7 0.05 0.0 0.0 0.0 0.0 8 0.05 0.0 0.0 0.0 0.0 9 0.05 0.0 0.0 0.0 0.0 10-11 0.05 0.0 0.0 0.0 0.0 12-13 0.05 0.0 0.0 0.0 0.0 14-15 0.05 0.0 0.0 0.0 0.0 16-17 0.05 0.0 0.0 0.0 0.0 18-19 0.05 0.0 0.0 0.0 0.0 20-21 0.05 0.0 0.0 0.0 0.0 22-23 0.05 0.0 0.0 0.0 0.0 24-25 0.05 0.0 0.0 0.0 0.0 26-27 0.05 0.0 0.0 0.0 0.0 28-29 0.05 0.0 0.0 0.0 0.0 30-31 0.05 0.0 0.0 0.0 0.0 32-33 0.05 0.0 0.0 0.0 0.0 34-35 0.05 0.0 0.0 0.0 0.0 36-37 0.05 0.0 0.0 0.0 0.0 38-39 0.05 0.0 0.0 0.0 0.0 40-41 0.05 0.0 0.0 0.0 0.0 42-43 0.05 0.0 0.0 0.0 0.0 44-45 0.05 0.0 0.0 0.0 0.0 46-47 0.05 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.05 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 0.0625 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 0.075 0.0 0.0 0.0 0.0 70-71 0.075 0.0 0.0 0.0 0.0 72-73 0.075 0.0 0.0 0.0 0.0 74-75 0.1 0.0 0.0 0.0 0.0 76-77 0.1 0.0 0.0 0.0 0.0 78-79 0.1375 0.0 0.0 0.0 0.0 80-81 0.175 0.0 0.0 0.0 0.0 82-83 0.2 0.0 0.0 0.0 0.0 84-85 0.25 0.0 0.0 0.0 0.0 86-87 0.35 0.0 0.0 0.0 0.0 88-89 0.475 0.0 0.0 0.0 0.0 90-91 0.575 0.0 0.0 0.0 0.0 92-93 0.7375 0.0 0.0 0.0 0.0 94-95 0.975 0.0 0.0 0.0 0.0 96-97 1.2 0.0 0.0 0.0 0.0 98-99 1.4125 0.0 0.0 0.0 0.0 100-101 1.7000000000000002 0.0 0.0 0.0 0.0 102-103 1.95 0.0 0.0 0.0 0.0 104-105 2.4124999999999996 0.0 0.0 0.0 0.0 106-107 2.8625 0.0 0.0 0.0 0.0 108-109 3.3875 0.0 0.0 0.0 0.0 110-111 3.9124999999999996 0.0 0.0 0.0 0.0 112-113 4.5375 0.0 0.0 0.0 0.0 114-115 5.3875 0.0 0.0 0.0 0.0 116-117 6.075 0.0 0.0 0.0 0.0 118-119 6.8625 0.0 0.0 0.0 0.0 120-121 7.5625 0.0 0.0 0.0 0.0 122-123 8.325 0.0 0.0 0.0 0.0 124-125 8.9375 0.0 0.0 0.0 0.0 126-127 9.675 0.0 0.0 0.0 0.0 128-129 10.425 0.0 0.0 0.0 0.0 130-131 11.100000000000001 0.0 0.0 0.0 0.0 132-133 11.8 0.0 0.0 0.0 0.0 134-135 12.7625 0.0 0.0 0.0 0.0 136-137 13.587499999999999 0.0 0.0 0.0 0.0 138-139 14.7125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CCGGAAT 40 0.0056290138 54.35625 145 >>END_MODULE SRR7168844 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7168844_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.4855 33.0 33.0 34.0 32.0 34.0 2 32.5085 33.0 33.0 34.0 32.0 34.0 3 32.5045 33.0 33.0 34.0 32.0 34.0 4 32.38175 34.0 33.0 34.0 32.0 34.0 5 32.35075 34.0 33.0 34.0 31.0 34.0 6 36.42725 38.0 38.0 38.0 35.0 38.0 7 36.489 38.0 38.0 38.0 35.0 38.0 8 36.458 38.0 38.0 38.0 35.0 38.0 9 36.492 38.0 38.0 38.0 36.0 38.0 10-14 36.4188 38.0 38.0 38.0 35.2 38.0 15-19 36.393600000000006 38.0 38.0 38.0 35.8 38.0 20-24 36.36335 38.0 38.0 38.0 35.4 38.0 25-29 36.3331 38.0 38.0 38.0 35.4 38.0 30-34 36.267700000000005 38.0 38.0 38.0 35.2 38.0 35-39 36.2582 38.0 38.0 38.0 35.0 38.0 40-44 36.203050000000005 38.0 38.0 38.0 35.0 38.0 45-49 36.19475 38.0 38.0 38.0 34.8 38.0 50-54 36.084649999999996 38.0 38.0 38.0 34.4 38.0 55-59 36.0588 38.0 38.0 38.0 34.2 38.0 60-64 36.12355 38.0 38.0 38.0 34.8 38.0 65-69 35.880649999999996 38.0 38.0 38.0 34.0 38.0 70-74 35.593650000000004 38.0 38.0 38.0 33.2 38.0 75-79 35.4578 38.0 38.0 38.0 33.0 38.0 80-84 35.34725 38.0 38.0 38.0 31.4 38.0 85-89 35.269349999999996 38.0 38.0 38.0 30.6 38.0 90-94 35.16445 38.0 38.0 38.0 30.4 38.0 95-99 35.1481 38.0 38.0 38.0 30.6 38.0 100-104 34.95665 38.0 37.8 38.0 29.0 38.0 105-109 34.80175 38.0 37.0 38.0 28.6 38.0 110-114 34.60875 38.0 37.0 38.0 27.6 38.0 115-119 34.443599999999996 38.0 36.6 38.0 26.0 38.0 120-124 34.2017 38.0 36.0 38.0 23.6 38.0 125-129 33.925050000000006 38.0 35.8 38.0 20.6 38.0 130-134 33.596 38.0 35.0 38.0 16.6 38.0 135-139 33.202799999999996 38.0 34.2 38.0 14.0 38.0 140-144 32.61315 38.0 33.0 38.0 13.0 38.0 145-149 31.42565 38.0 32.6 38.0 4.2 38.0 150-151 26.28225 34.0 16.5 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 44.0 3 10.0 4 11.0 5 5.0 6 4.0 7 3.0 8 8.0 9 3.0 10 10.0 11 3.0 12 5.0 13 14.0 14 13.0 15 14.0 16 22.0 17 27.0 18 6.0 19 9.0 20 4.0 21 12.0 22 16.0 23 15.0 24 13.0 25 17.0 26 12.0 27 23.0 28 30.0 29 38.0 30 40.0 31 45.0 32 55.0 33 80.0 34 138.0 35 201.0 36 613.0 37 2437.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 38.9 18.525 18.625 23.95 2 27.525 24.975 28.675 18.825 3 22.275 27.575 30.7 19.45 4 26.125 31.075000000000003 22.8 20.0 5 26.375 35.699999999999996 20.8 17.125 6 21.725 35.65 22.650000000000002 19.975 7 20.325 22.775000000000002 37.425000000000004 19.475 8 23.825 25.4 25.874999999999996 24.9 9 24.7 26.075 26.674999999999997 22.55 10-14 25.314999999999998 27.800000000000004 25.014999999999997 21.87 15-19 24.91 27.310000000000002 27.155 20.625 20-24 24.72 28.315 26.005 20.96 25-29 25.2 27.685 26.479999999999997 20.635 30-34 25.165 27.455000000000002 26.834999999999997 20.544999999999998 35-39 25.155 26.795 26.995 21.055 40-44 25.785000000000004 27.334999999999997 26.495 20.385 45-49 25.069999999999997 27.339999999999996 26.075 21.515 50-54 24.515 27.785 26.805 20.895 55-59 24.685000000000002 27.515 26.665 21.135 60-64 24.41 28.52 26.085 20.985 65-69 25.014999999999997 28.294999999999998 26.229999999999997 20.46 70-74 24.57 28.17 26.56 20.7 75-79 24.0 27.985 26.55 21.465 80-84 24.645 28.175 26.235000000000003 20.945 85-89 25.465 27.51 26.090000000000003 20.935000000000002 90-94 24.875 28.235 26.515 20.375 95-99 24.327432743274326 28.002800280028 26.472647264726472 21.197119711971197 100-104 24.72370855628344 28.194229134370158 26.77901685252788 20.303045456818523 105-109 24.848727309096365 28.134220133019955 26.71900785117768 20.298044706706005 110-114 25.032503250325032 27.927792779277926 26.797679767976796 20.242024202420243 115-119 25.697569756975696 28.402840284028404 26.237623762376238 19.661966196619662 120-124 25.99129956497825 28.331416570828544 26.31631581579079 19.36096804840242 125-129 26.57132856642832 27.141357067853395 26.511325566278316 19.775988799439972 130-134 26.238935840376055 28.189228384257635 26.133920088013202 19.4379156873531 135-139 27.077707770777078 27.597759775977597 26.247624762476246 19.076907690769076 140-144 26.55 27.93 26.3 19.220000000000002 145-149 27.295 27.6 25.91 19.195 150-151 27.6 28.425 25.374999999999996 18.6 >>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 0.5 18 1.0 19 2.0 20 2.0 21 1.5 22 2.5 23 2.5 24 1.0 25 0.5 26 1.0 27 3.5 28 6.0 29 6.5 30 7.5 31 12.0 32 18.5 33 22.5 34 25.5 35 43.5 36 60.0 37 79.0 38 103.0 39 124.5 40 156.5 41 185.0 42 209.5 43 231.0 44 242.5 45 257.0 46 266.0 47 265.5 48 249.0 49 214.5 50 190.5 51 164.5 52 149.5 53 141.5 54 126.0 55 102.0 56 79.0 57 59.0 58 47.0 59 38.0 60 26.5 61 22.5 62 17.0 63 11.5 64 5.0 65 2.5 66 3.0 67 3.5 68 2.5 69 1.5 70 1.0 71 0.5 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 0.5 81 0.5 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 0.01 100-104 0.015 105-109 0.015 110-114 0.01 115-119 0.01 120-124 0.005 125-129 0.005 130-134 0.015 135-139 0.01 140-144 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 97.425 #Duplication Level Percentage of deduplicated Percentage of total 1 98.5373364126251 96.0 2 1.2317167051578137 2.4 3 0.15396458814472672 0.44999999999999996 4 0.025660764690787787 0.1 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 8 0.025660764690787787 0.2 9 0.0 0.0 >10 0.025660764690787787 0.8500000000000001 >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 GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG 34 0.8500000000000001 Illumina Single End PCR Primer 1 (100% over 50bp) GGTGAGTCGACCCCTAAGGCGAGGCCGAAAGGCGTAGTCGATGGGAAACA 8 0.2 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 0.05 0.0 0.0 0.0 0.0 2 0.05 0.0 0.0 0.0 0.0 3 0.05 0.0 0.0 0.0 0.0 4 0.05 0.0 0.0 0.0 0.0 5 0.05 0.0 0.0 0.0 0.0 6 0.05 0.0 0.0 0.0 0.0 7 0.05 0.0 0.0 0.0 0.0 8 0.05 0.0 0.0 0.0 0.0 9 0.05 0.0 0.0 0.0 0.0 10-11 0.05 0.0 0.0 0.0 0.0 12-13 0.05 0.0 0.0 0.0 0.0 14-15 0.05 0.0 0.0 0.0 0.0 16-17 0.05 0.0 0.0 0.0 0.0 18-19 0.05 0.0 0.0 0.0 0.0 20-21 0.05 0.0 0.0 0.0 0.0 22-23 0.05 0.0 0.0 0.0 0.0 24-25 0.05 0.0 0.0 0.0 0.0 26-27 0.05 0.0 0.0 0.0 0.0 28-29 0.05 0.0 0.0 0.0 0.0 30-31 0.05 0.0 0.0 0.0 0.0 32-33 0.05 0.0 0.0 0.0 0.0 34-35 0.05 0.0 0.0 0.0 0.0 36-37 0.05 0.0 0.0 0.0 0.0 38-39 0.05 0.0 0.0 0.0 0.0 40-41 0.05 0.0 0.0 0.0 0.0 42-43 0.05 0.0 0.0 0.0 0.0 44-45 0.05 0.0 0.0 0.0 0.0 46-47 0.05 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.05 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 0.07500000000000001 0.0 0.0 0.0 0.0 64-65 0.1 0.0 0.0 0.0 0.0 66-67 0.1 0.0 0.0 0.0 0.0 68-69 0.1 0.0 0.0 0.0 0.0 70-71 0.1 0.0 0.0 0.0 0.0 72-73 0.1 0.0 0.0 0.0 0.0 74-75 0.125 0.0 0.0 0.0 0.0 76-77 0.125 0.0 0.0 0.0 0.0 78-79 0.1375 0.0 0.0 0.0 0.0 80-81 0.175 0.0 0.0 0.0 0.0 82-83 0.2 0.0 0.0 0.0 0.0 84-85 0.25 0.0 0.0 0.0 0.0 86-87 0.3625 0.0 0.0 0.0 0.0 88-89 0.5 0.0 0.0 0.0 0.0 90-91 0.6125 0.0 0.0 0.0 0.0 92-93 0.775 0.0 0.0 0.0 0.0 94-95 1.0 0.0 0.0 0.0 0.0 96-97 1.275 0.0 0.0 0.0 0.0 98-99 1.5125 0.0 0.0 0.0 0.0 100-101 1.7999999999999998 0.0 0.0 0.0 0.0 102-103 2.0625 0.0 0.0 0.0 0.0 104-105 2.4875 0.0 0.0 0.0 0.0 106-107 2.95 0.0 0.0 0.0 0.0 108-109 3.5 0.0 0.0 0.0 0.0 110-111 4.0375 0.0 0.0 0.0 0.0 112-113 4.6125 0.0 0.0 0.0 0.0 114-115 5.3875 0.0 0.0 0.0 0.0 116-117 6.1 0.0 0.0 0.0 0.0 118-119 6.95 0.0 0.0 0.0 0.0 120-121 7.6 0.0 0.0 0.0 0.0 122-123 8.3125 0.0 0.0 0.0 0.0 124-125 8.9125 0.0 0.0 0.0 0.0 126-127 9.675 0.0 0.0 0.0 0.0 128-129 10.4875 0.0 0.0 0.0 0.0 130-131 11.149999999999999 0.0 0.0 0.0 0.0 132-133 11.9 0.0 0.0 0.0 0.0 134-135 12.850000000000001 0.0 0.0 0.0 0.0 136-137 13.6 0.0 0.0 0.0 0.0 138-139 14.725000000000001 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AGATCTC 35 0.0033124194 62.14286 145 GTGTAGA 40 0.0076550315 18.125 140-144 AGTGTAG 40 0.0076550315 18.125 140-144 AAAGAGT 50 0.0013298223 17.4 135-139 >>END_MODULE Read 750434 spots for SRR7168844.sra Written 750434 spots for SRR7168844.sra Read 750434 spots for SRR7168844.sra Written 750434 spots for SRR7168844.sra Read 750434 spots for SRR7168844.sra Written 750434 spots for SRR7168844.sra Read 750434 spots for SRR7168844.sra Written 750434 spots for SRR7168844.sra Read 750434 spots for SRR7168844.sra Written 750434 spots for SRR7168844.sra Read 750434 spots for SRR7168844.sra Written 750434 spots for SRR7168844.sra Read 750434 spots for SRR7168844.sra Written 750434 spots for SRR7168844.sra Read 750434 spots for SRR7168844.sra Written 750434 spots for SRR7168844.sra Read 750434 spots for SRR7168844.sra Written 750434 spots for SRR7168844.sra Read 750434 spots for SRR7168844.sra Written 750434 spots for SRR7168844.sra Read 750434 spots for SRR7168844.sra Written 750434 spots for SRR7168844.sra Read 750434 spots for SRR7168844.sra Written 750434 spots for SRR7168844.sra Read 750434 spots for SRR7168844.sra Written 750434 spots for SRR7168844.sra Read 750434 spots for SRR7168844.sra Written 750434 spots for SRR7168844.sra Read 750434 spots for SRR7168844.sra Written 750434 spots for SRR7168844.sra Read 750434 spots for SRR7168844.sra Written 750434 spots for SRR7168844.sra Read 750434 spots for SRR7168844.sra Written 750434 spots for SRR7168844.sra Read 750434 spots for SRR7168844.sra Written 750434 spots for SRR7168844.sra Read 750434 spots for SRR7168844.sra Written 750434 spots for SRR7168844.sra Read 750434 spots for SRR7168844.sra Written 750434 spots for SRR7168844.sra SRR ids: ['SRR7168844.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_t92s5ec2 SRR7168844.sra spots: 15008680 blocks: [[1, 750434], [750435, 1500868], [1500869, 2251302], [2251303, 3001736], [3001737, 3752170], [3752171, 4502604], [4502605, 5253038], [5253039, 6003472], [6003473, 6753906], [6753907, 7504340], [7504341, 8254774], [8254775, 9005208], [9005209, 9755642], [9755643, 10506076], [10506077, 11256510], [11256511, 12006944], [12006945, 12757378], [12757379, 13507812], [13507813, 14258246], [14258247, 15008680]] SRR7168844 file size 5064248 SRR7168844 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 SRR7168844 SRR7168844_1.fastq SRR7168844_2.fastq Input file: SRR7168844_1.fastq Paired file: SRR7168844_2.fastq trimmed: SRR7168844-trimmed-pair1.fastq, SRR7168844-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 Feb 15 07:11:58 2025 >> started Sat Feb 15 07:12:16 2025 >> done (17.673s) 15008680 read pairs processed; of these: 77846 ( 0.52%) short read pairs filtered out after trimming by size control 313174 ( 2.09%) empty read pairs filtered out after trimming by size control 14617660 (97.39%) read pairs available; of these: 8471136 (57.95%) trimmed read pairs available after processing 6146524 (42.05%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 6 0.00% 19 19 0.00% 20 14 0.00% 21 5 0.00% 22 17 0.00% 23 20 0.00% 24 19 0.00% 25 15 0.00% 26 26 0.00% 27 32 0.00% 28 21 0.00% 29 25 0.00% 30 22 0.00% 31 31 0.00% 32 33 0.00% 33 29 0.00% 34 32 0.00% 35 39 0.00% 36 32 0.00% 37 45 0.00% 38 62 0.00% 39 46 0.00% 40 68 0.00% 41 68 0.00% 42 74 0.00% 43 93 0.00% 44 132 0.00% 45 198 0.00% 46 229 0.00% 47 261 0.00% 48 315 0.00% 49 240 0.00% 50 288 0.00% 51 305 0.00% 52 356 0.00% 53 317 0.00% 54 429 0.00% 55 385 0.00% 56 413 0.00% 57 417 0.00% 58 490 0.00% 59 498 0.00% 60 554 0.00% 61 675 0.00% 62 689 0.00% 63 753 0.01% 64 1124 0.01% 65 4649 0.03% 66 1947 0.01% 67 1855 0.01% 68 3933 0.03% 69 20946 0.14% 70 14546 0.10% 71 3955 0.03% 72 2976 0.02% 73 3144 0.02% 74 3247 0.02% 75 3368 0.02% 76 3701 0.03% 77 4020 0.03% 78 4231 0.03% 79 4800 0.03% 80 5243 0.04% 81 6031 0.04% 82 6982 0.05% 83 7990 0.05% 84 11831 0.08% 85 13929 0.10% 86 14525 0.10% 87 15365 0.11% 88 16260 0.11% 89 17099 0.12% 90 17688 0.12% 91 18387 0.13% 92 19458 0.13% 93 21685 0.15% 94 23149 0.16% 95 24994 0.17% 96 26009 0.18% 97 26490 0.18% 98 26763 0.18% 99 28220 0.19% 100 30025 0.21% 101 31097 0.21% 102 33487 0.23% 103 35327 0.24% 104 37399 0.26% 105 40395 0.28% 106 40774 0.28% 107 41849 0.29% 108 43255 0.30% 109 46371 0.32% 110 48034 0.33% 111 47671 0.33% 112 50163 0.34% 113 53714 0.37% 114 54994 0.38% 115 56668 0.39% 116 59296 0.41% 117 59865 0.41% 118 60396 0.41% 119 60977 0.42% 120 62778 0.43% 121 64147 0.44% 122 65687 0.45% 123 68450 0.47% 124 70815 0.48% 125 72585 0.50% 126 75323 0.52% 127 76530 0.52% 128 77974 0.53% 129 78352 0.54% 130 80078 0.55% 131 81802 0.56% 132 83814 0.57% 133 88304 0.60% 134 89516 0.61% 135 94563 0.65% 136 96945 0.66% 137 101515 0.69% 138 104386 0.71% 139 107492 0.74% 140 110684 0.76% 141 116757 0.80% 142 124036 0.85% 143 133874 0.92% 144 149244 1.02% 145 168201 1.15% 146 199587 1.37% 147 253588 1.73% 148 359562 2.46% 149 675749 4.62% 150 3167664 21.67% 151 6146524 42.05% 14617660 reads passed initial QC criterion=sequence-density sequence-density=0.33 sequence-density-rank=1 fanout-score=2.79 fanout-score-rank=28 prefix-density=0.39 prefix-fanout=2.4 sequence=AGTTCCTTCACC criterion=fanout-score sequence-density=0.01 sequence-density-rank=36 fanout-score=40.84 fanout-score-rank=1 prefix-density=0.14 prefix-fanout=1.7 sequence=GTGATCCAACCGCAGGTTCCCCTACGGTTACCTTGTTACGACTTCACCCCAGTCATGAATCACAAAGTGGTAAGCGCCCTCCCGAAGGTTAAGCTACCTACTTCTTTTGCAACCCACTCCCATGGTGTGACGGGCGGTGTGTACAAGGCCCGGGAACGTATTCACCGTGGCATTCTGATCCACGATTACTAGCGATTCCGACTTCATGGAGTCGAGTTGCAGACTCCAATCCGGACTACGACGCACTTTATGAGGTCCGCTTGCTCTCGCGAGGTCGCTTCTCTTTGTATGCGCCATTGTAGCACGTGTGTAGCCCTGGTCGTAAGGGCCATGATGACTTGACGTCATCCCCACCTTCCTCCAGTTTATCACTGGCAGTCTCCTTTGAGTTCCCGGCCGGACCGCTGGCAACAAAGGATAAGGGTTGCGCTCGTTGCGGGACTTAACCCAACATTTCACAACACGAGCTGACGACAGCCATGCAGCACCTGTCTCACGGTTCCCGAAGGCA criterion=sequence-density sequence-density=0.60 sequence-density-rank=1 fanout-score=2.76 fanout-score-rank=24 prefix-density=0.68 prefix-fanout=2.4 sequence=GCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATG criterion=fanout-score sequence-density=0.01 sequence-density-rank=32 fanout-score=37.56 fanout-score-rank=1 prefix-density=0.10 prefix-fanout=3.3 sequence=GCAAAACCACATATAGAGGGTGTAATAGCTAAGTAGCCTGTAAGAGATGGCTTCCTCTGTGATTTCATCGGCGGCCGTTGCCACAGTTAACCGCACCCCGGCACAGGCCAACATGGTTGCACCATTCAACGGCCTCAAGTCTACCTCAGCTTTCCCGGTCACCAGAAAGGCTAA SRR7168844 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 15 07:13:33 Started mapping on | Feb 15 07:13:33 Finished on | Feb 15 07:16:18 Mapping speed, Million of reads per hour | 318.93 Number of input reads | 14617660 Average input read length | 286 UNIQUE READS: Uniquely mapped reads number | 12524639 Uniquely mapped reads % | 85.68% Average mapped length | 287.32 Number of splices: Total | 10953164 Number of splices: Annotated (sjdb) | 10700101 Number of splices: GT/AG | 10748593 Number of splices: GC/AG | 163941 Number of splices: AT/AC | 7248 Number of splices: Non-canonical | 33382 Mismatch rate per base, % | 0.37% Deletion rate per base | 0.03% Deletion average length | 2.58 Insertion rate per base | 0.02% Insertion average length | 2.04 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 350182 % of reads mapped to multiple loci | 2.40% Number of reads mapped to too many loci | 94084 % of reads mapped to too many loci | 0.64% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 11.07% % of reads unmapped: other | 0.21% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1794110 1794110 1794110 N_multimapping 350182 350182 350182 N_noFeature 347715 12205967 478126 N_ambiguous 269223 1293 80251 UnstrandedReadsAssigned:11907701 PositiveStrandReadsAssigned:317379 NegativeStrandReadsAssigned:11966262 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=141 echo kmer=137 SRR7168844 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: SRR7168844-trimmed-pair1.fastq SRR7168844-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 14,617,660 reads, 12,106,224 reads pseudoaligned [quant] estimated average fragment length: 201.428 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,273 rounds 52401 SRR7168844.ke.tsv 34699 SRR7168844.se.tsv 87100 total ==> SRR7168844.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1817.57 581 20.1835 Potri.005G024800.1.v4.1 1035 834.572 313 23.6806 Potri.004G059700.1.v4.1 961 760.587 20 1.66033 Potri.007G009000.2.v4.1 1416 1215.57 0 0 Potri.003G141000.2.v4.1 2943 2742.57 696.395 16.0328 Potri.016G087400.1.v4.1 270 95.1833 787 522.068 Potri.015G069301.1.v4.1 564 364.601 0 0 Potri.010G195200.1.v4.1 1773 1572.57 64 2.5697 Potri.012G127500.1.v4.1 977 776.572 291 23.6605 ==> SRR7168844.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 949 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 315 Potri.001G212900.v4.1 6 Potri.001G182400.v4.1 1 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 7 Potri.001G416900.v4.1 1 Potri.001G452600.v4.1 12 SRR7168844 completed mapping pipeline successfully