Starting /dee2/code/volunteer_pipeline.sh SRR18694365 current disk space = 1525801832448 free memory = 1557845320 SRR18694365 SRAfilesize 9203547ae2d0a0cef5c39fdcf16ed478 SRR18694365.sra SRR18694365.sra file validated SRR18694365 is paired end SRR18694365 is conventional basespace SRR18694365 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR18694365_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 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.993 37.0 37.0 37.0 37.0 37.0 2 36.08625 37.0 37.0 37.0 37.0 37.0 3 36.4205 37.0 37.0 37.0 37.0 37.0 4 36.523 37.0 37.0 37.0 37.0 37.0 5 36.4905 37.0 37.0 37.0 37.0 37.0 6 36.445 37.0 37.0 37.0 37.0 37.0 7 36.5905 37.0 37.0 37.0 37.0 37.0 8 36.564 37.0 37.0 37.0 37.0 37.0 9 36.628 37.0 37.0 37.0 37.0 37.0 10-14 36.60189999999999 37.0 37.0 37.0 37.0 37.0 15-19 36.56179999999999 37.0 37.0 37.0 37.0 37.0 20-24 36.608999999999995 37.0 37.0 37.0 37.0 37.0 25-29 36.5457 37.0 37.0 37.0 37.0 37.0 30-34 36.4913 37.0 37.0 37.0 37.0 37.0 35-39 36.6264 37.0 37.0 37.0 37.0 37.0 40-44 36.551 37.0 37.0 37.0 37.0 37.0 45-49 36.3656 37.0 37.0 37.0 37.0 37.0 50-54 36.4781 37.0 37.0 37.0 37.0 37.0 55-59 36.4656 37.0 37.0 37.0 37.0 37.0 60-64 36.46410000000001 37.0 37.0 37.0 37.0 37.0 65-69 36.2784 37.0 37.0 37.0 37.0 37.0 70-74 36.3491 37.0 37.0 37.0 37.0 37.0 75-79 36.497 37.0 37.0 37.0 37.0 37.0 80-84 36.341899999999995 37.0 37.0 37.0 37.0 37.0 85-89 36.0989 37.0 37.0 37.0 37.0 37.0 90-94 35.4002 37.0 37.0 37.0 29.8 37.0 95-99 36.1128 37.0 37.0 37.0 37.0 37.0 100-104 36.15 37.0 37.0 37.0 37.0 37.0 105-109 36.0986 37.0 37.0 37.0 37.0 37.0 110-114 36.228300000000004 37.0 37.0 37.0 37.0 37.0 115-119 36.4403 37.0 37.0 37.0 37.0 37.0 120-124 36.5449 37.0 37.0 37.0 37.0 37.0 125-129 36.4945 37.0 37.0 37.0 37.0 37.0 130-134 36.472 37.0 37.0 37.0 37.0 37.0 135-139 36.3951 37.0 37.0 37.0 37.0 37.0 140-144 36.19539999999999 37.0 37.0 37.0 37.0 37.0 145-149 36.120799999999996 37.0 37.0 37.0 37.0 37.0 150-151 33.79925 37.0 31.0 37.0 24.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 25 2.0 26 5.0 27 1.0 28 3.0 29 5.0 30 15.0 31 22.0 32 35.0 33 60.0 34 107.0 35 348.0 36 3198.0 37 199.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 46.475 12.025 4.375 37.125 2 21.333667585861118 10.729506141890198 35.87365254449737 32.06317372775131 3 19.3 13.975000000000001 25.924999999999997 40.8 4 24.825 22.125 22.525000000000002 30.525000000000002 5 27.125 26.25 24.474999999999998 22.15 6 24.075 29.2 22.5 24.224999999999998 7 18.075 24.224999999999998 39.275 18.425 8 18.95 23.525 31.324999999999996 26.200000000000003 9 19.675 20.325 33.275 26.724999999999998 10-14 23.474999999999998 26.340000000000003 25.71 24.474999999999998 15-19 22.97 24.93 25.724999999999998 26.375 20-24 22.665 25.495 25.900000000000002 25.94 25-29 23.155 25.415 25.905 25.525 30-34 22.725 25.545 25.685000000000002 26.045 35-39 23.105 25.39 25.825 25.679999999999996 40-44 23.305 24.255 26.715 25.724999999999998 45-49 22.939999999999998 25.035 25.445 26.58 50-54 22.855 25.430000000000003 26.085 25.629999999999995 55-59 23.28 25.445 25.679999999999996 25.595000000000002 60-64 23.36 24.59 25.324999999999996 26.724999999999998 65-69 23.244999999999997 25.96 25.11 25.685000000000002 70-74 23.25 24.759999999999998 26.14 25.85 75-79 23.599999999999998 24.955 25.405 26.040000000000003 80-84 23.86 24.79 25.564999999999998 25.785000000000004 85-89 23.119999999999997 25.380000000000003 24.965 26.534999999999997 90-94 23.435 25.295 24.97 26.3 95-99 23.215 24.615000000000002 25.615 26.555 100-104 23.169999999999998 25.365 25.545 25.919999999999998 105-109 23.97 25.335 25.1 25.595000000000002 110-114 23.849999999999998 25.0 25.765 25.385 115-119 24.26 24.6 25.27 25.869999999999997 120-124 23.595 25.130000000000003 25.019999999999996 26.255 125-129 23.799999999999997 25.080000000000002 24.36 26.76 130-134 23.974999999999998 24.8 25.180000000000003 26.045 135-139 23.505000000000003 25.895000000000003 24.529999999999998 26.07 140-144 23.855 25.445 24.55 26.150000000000002 145-149 23.555 26.650000000000002 24.11 25.685000000000002 150-151 23.45 25.112499999999997 24.7375 26.700000000000003 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.5 2 0.5 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 0.0 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 0.0 23 1.0 24 1.0 25 1.0 26 2.0 27 2.5 28 3.5 29 6.0 30 9.0 31 10.5 32 17.0 33 27.0 34 32.0 35 38.0 36 50.0 37 68.0 38 77.0 39 88.5 40 106.0 41 131.0 42 161.5 43 184.0 44 196.5 45 197.0 46 205.0 47 201.0 48 188.0 49 178.0 50 171.5 51 153.0 52 119.5 53 105.5 54 96.0 55 92.0 56 102.0 57 93.5 58 95.5 59 86.5 60 70.5 61 75.0 62 72.0 63 67.0 64 61.5 65 57.5 66 54.0 67 51.5 68 37.5 69 27.5 70 30.5 71 27.0 72 19.0 73 12.5 74 11.5 75 13.0 76 8.0 77 3.0 78 1.0 79 1.5 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 0.0 2 0.27499999999999997 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 86.1 #Duplication Level Percentage of deduplicated Percentage of total 1 86.46922183507549 74.45 2 11.29500580720093 19.45 3 1.9163763066202089 4.95 4 0.29036004645760743 1.0 5 0.0 0.0 6 0.029036004645760744 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 CACAACTTCATGTCGCTCTGCACGGACGGATCGGAGAAACGCCTGCCGAT 6 0.15 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 0.0 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 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.025 0.0 0.0 0.0 0.0 68-69 0.025 0.0 0.0 0.0 0.0 70-71 0.037500000000000006 0.0 0.0 0.0 0.0 72-73 0.15 0.0 0.0 0.0 0.0 74-75 0.2 0.0 0.0 0.0 0.0 76-77 0.2 0.0 0.0 0.0 0.0 78-79 0.2875 0.0 0.0 0.0 0.0 80-81 0.4 0.0 0.0 0.0 0.0 82-83 0.425 0.0 0.0 0.0 0.0 84-85 0.45 0.0 0.0 0.0 0.0 86-87 0.45 0.0 0.0 0.0 0.0 88-89 0.45 0.0 0.0 0.0 0.0 90-91 0.5375 0.0 0.0 0.0 0.0 92-93 0.7 0.0 0.0 0.0 0.0 94-95 0.8 0.0 0.0 0.0 0.0 96-97 1.0499999999999998 0.0 0.0 0.0 0.0 98-99 1.25 0.0 0.0 0.0 0.0 100-101 1.5125000000000002 0.0 0.0 0.0 0.0 102-103 1.6875 0.0 0.0 0.0 0.0 104-105 1.9375 0.0 0.0 0.0 0.0 106-107 2.325 0.0 0.0 0.0 0.0 108-109 2.6375 0.0 0.0 0.0 0.0 110-111 3.1625 0.0 0.0 0.0 0.0 112-113 3.55 0.0 0.0 0.0 0.0 114-115 3.8375 0.0 0.0 0.0 0.0 116-117 4.300000000000001 0.0 0.0 0.0 0.0 118-119 4.8125 0.0 0.0 0.0 0.0 120-121 5.2875 0.0 0.0 0.0 0.0 122-123 5.887499999999999 0.0 0.0 0.0 0.0 124-125 6.4875 0.0 0.0 0.0 0.0 126-127 6.987500000000001 0.0 0.0 0.0 0.0 128-129 7.7875 0.0 0.0 0.0 0.0 130-131 8.2125 0.0 0.0 0.0 0.0 132-133 8.7 0.0 0.0 0.0 0.0 134-135 9.4125 0.0 0.0 0.0 0.0 136-137 10.2625 0.0 0.0 0.0 0.0 138-139 10.9625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GCCACTA 10 0.006830828 145.0 1 >>END_MODULE SRR18694365 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR18694365_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 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 34.221 37.0 37.0 37.0 25.0 37.0 2 35.1495 37.0 37.0 37.0 25.0 37.0 3 35.295 37.0 37.0 37.0 25.0 37.0 4 35.4655 37.0 37.0 37.0 37.0 37.0 5 35.256 37.0 37.0 37.0 25.0 37.0 6 35.258 37.0 37.0 37.0 25.0 37.0 7 35.345 37.0 37.0 37.0 37.0 37.0 8 35.6355 37.0 37.0 37.0 37.0 37.0 9 35.531 37.0 37.0 37.0 37.0 37.0 10-14 35.6097 37.0 37.0 37.0 37.0 37.0 15-19 35.6419 37.0 37.0 37.0 37.0 37.0 20-24 35.4754 37.0 37.0 37.0 34.6 37.0 25-29 35.6283 37.0 37.0 37.0 34.6 37.0 30-34 35.813900000000004 37.0 37.0 37.0 37.0 37.0 35-39 35.6777 37.0 37.0 37.0 37.0 37.0 40-44 35.316700000000004 37.0 37.0 37.0 29.8 37.0 45-49 35.5512 37.0 37.0 37.0 37.0 37.0 50-54 35.0227 37.0 37.0 37.0 32.2 37.0 55-59 34.37749999999999 37.0 37.0 37.0 25.0 37.0 60-64 35.045399999999994 37.0 37.0 37.0 27.4 37.0 65-69 34.262100000000004 37.0 34.6 37.0 27.4 37.0 70-74 33.0413 37.0 29.8 37.0 22.2 37.0 75-79 33.6125 37.0 34.6 37.0 22.2 37.0 80-84 34.59439999999999 37.0 37.0 37.0 25.0 37.0 85-89 32.662400000000005 37.0 32.2 37.0 19.4 37.0 90-94 34.1777 37.0 37.0 37.0 25.0 37.0 95-99 33.923500000000004 37.0 37.0 37.0 25.0 37.0 100-104 33.5077 37.0 37.0 37.0 25.0 37.0 105-109 34.239799999999995 37.0 37.0 37.0 25.0 37.0 110-114 34.607299999999995 37.0 37.0 37.0 25.0 37.0 115-119 34.56349999999999 37.0 37.0 37.0 25.0 37.0 120-124 33.9895 37.0 37.0 37.0 25.0 37.0 125-129 34.028800000000004 37.0 37.0 37.0 25.0 37.0 130-134 33.7211 37.0 34.6 37.0 25.0 37.0 135-139 32.17059999999999 37.0 25.0 37.0 13.8 37.0 140-144 31.6887 37.0 25.0 37.0 11.0 37.0 145-149 31.1693 37.0 25.0 37.0 13.8 37.0 150-151 30.849249999999998 37.0 25.0 37.0 18.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 14 1.0 15 1.0 16 0.0 17 2.0 18 2.0 19 9.0 20 0.0 21 2.0 22 5.0 23 4.0 24 7.0 25 8.0 26 5.0 27 15.0 28 28.0 29 48.0 30 86.0 31 146.0 32 247.0 33 551.0 34 1113.0 35 1481.0 36 239.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 44.4 21.825 7.475 26.3 2 31.525 22.1 28.325 18.05 3 22.15 24.65 30.65 22.55 4 26.0 31.1 20.25 22.650000000000002 5 29.049999999999997 32.6 18.15 20.200000000000003 6 23.65 35.625 18.725 22.0 7 22.625 20.7 34.675 22.0 8 22.650000000000002 24.2 24.925 28.225 9 23.35 22.05 27.700000000000003 26.900000000000002 10-14 26.674999999999997 25.55 23.34 24.435000000000002 15-19 25.75 24.64 25.11 24.5 20-24 25.650000000000002 25.505 24.755 24.09 25-29 26.419999999999998 25.745 23.755000000000003 24.08 30-34 25.814999999999998 25.540000000000003 24.22 24.425 35-39 27.195000000000004 25.495 23.84 23.47 40-44 26.179999999999996 25.695 24.36 23.765 45-49 27.07 26.125 23.61 23.195 50-54 24.93 25.919999999999998 26.08 23.07 55-59 25.729999999999997 25.874999999999996 24.825 23.57 60-64 26.179999999999996 25.509999999999998 24.395 23.915 65-69 26.405 25.735000000000003 24.355 23.505000000000003 70-74 26.229999999999997 25.22 24.205 24.345 75-79 27.515 23.345 25.069999999999997 24.07 80-84 25.929999999999996 25.81 24.235 24.025 85-89 23.549999999999997 27.750000000000004 24.91 23.79 90-94 26.44 26.075 24.55 22.935 95-99 26.11 25.990000000000002 24.575 23.325000000000003 100-104 26.095000000000002 25.990000000000002 24.335 23.580000000000002 105-109 26.61 26.02 24.37 23.0 110-114 26.56 25.885 24.044999999999998 23.51 115-119 27.075 26.240000000000002 23.82 22.865 120-124 26.56 25.314999999999998 25.145 22.98 125-129 27.150000000000002 25.929999999999996 23.810000000000002 23.11 130-134 28.105000000000004 25.845000000000002 23.93 22.12 135-139 27.33 26.185000000000002 24.09 22.395 140-144 27.884999999999998 26.435 23.825 21.855 145-149 27.96 26.779999999999998 23.494999999999997 21.765 150-151 26.9125 25.8625 25.1 22.125 >>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 0.5 9 1.0 10 0.5 11 0.5 12 0.5 13 0.0 14 0.0 15 1.0 16 1.0 17 0.0 18 0.0 19 0.0 20 0.5 21 1.0 22 1.0 23 1.5 24 2.5 25 3.0 26 1.5 27 4.5 28 8.0 29 6.5 30 9.0 31 12.0 32 15.5 33 24.0 34 34.5 35 39.0 36 44.5 37 57.0 38 72.5 39 98.5 40 122.5 41 136.0 42 148.0 43 160.0 44 172.0 45 179.0 46 172.5 47 166.0 48 183.0 49 178.0 50 150.5 51 135.0 52 117.5 53 120.5 54 129.5 55 125.5 56 114.5 57 104.5 58 100.5 59 90.5 60 77.5 61 76.0 62 73.0 63 65.5 64 63.0 65 57.5 66 60.0 67 56.5 68 50.5 69 45.5 70 37.0 71 27.0 72 14.5 73 11.0 74 11.0 75 8.0 76 5.0 77 3.0 78 2.5 79 3.0 80 1.5 81 0.5 82 0.0 83 0.0 84 0.0 85 0.5 86 0.5 87 0.0 88 0.0 89 0.0 90 0.5 91 0.5 92 0.0 93 0.0 94 0.5 95 0.5 96 0.0 97 0.0 98 0.0 99 0.0 100 0.5 >>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 87.2 #Duplication Level Percentage of deduplicated Percentage of total 1 87.70068807339449 76.47500000000001 2 10.263761467889907 17.9 3 1.7488532110091741 4.575 4 0.25802752293577985 0.8999999999999999 5 0.0 0.0 6 0.028669724770642203 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 AGCACGACCGCGTCGAGATCATCGCCAATGACCAGGGGAACCGGACCACG 6 0.15 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 0.0 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 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.025 0.0 0.0 0.0 0.0 68-69 0.025 0.0 0.0 0.0 0.0 70-71 0.037500000000000006 0.0 0.0 0.0 0.0 72-73 0.15 0.0 0.0 0.0 0.0 74-75 0.2 0.0 0.0 0.0 0.0 76-77 0.2 0.0 0.0 0.0 0.0 78-79 0.2875 0.0 0.0 0.0 0.0 80-81 0.3875 0.0 0.0 0.0 0.0 82-83 0.425 0.0 0.0 0.0 0.0 84-85 0.45 0.0 0.0 0.0 0.0 86-87 0.45 0.0 0.0 0.0 0.0 88-89 0.45 0.0 0.0 0.0 0.0 90-91 0.5375 0.0 0.0 0.0 0.0 92-93 0.7 0.0 0.0 0.0 0.0 94-95 0.8 0.0 0.0 0.0 0.0 96-97 0.95 0.0 0.0 0.0 0.0 98-99 1.15 0.0 0.0 0.0 0.0 100-101 1.4125 0.0 0.0 0.0 0.0 102-103 1.5625 0.0 0.0 0.0 0.0 104-105 1.8125 0.0 0.0 0.0 0.0 106-107 2.2 0.0 0.0 0.0 0.0 108-109 2.5125 0.0 0.0 0.0 0.0 110-111 3.0125 0.0 0.0 0.0 0.0 112-113 3.375 0.0 0.0 0.0 0.0 114-115 3.6375 0.0 0.0 0.0 0.0 116-117 4.125 0.0 0.0 0.0 0.0 118-119 4.6375 0.0 0.0 0.0 0.0 120-121 5.1125 0.0 0.0 0.0 0.0 122-123 5.699999999999999 0.0 0.0 0.0 0.0 124-125 6.2875 0.0 0.0 0.0 0.0 126-127 6.7875 0.0 0.0 0.0 0.0 128-129 7.5625 0.0 0.0 0.0 0.0 130-131 8.0 0.0 0.0 0.0 0.0 132-133 8.475 0.0 0.0 0.0 0.0 134-135 9.1625 0.0 0.0 0.0 0.0 136-137 9.9875 0.0 0.0 0.0 0.0 138-139 10.6625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTTTTTT 80 0.0020131238 12.6875 120-124 >>END_MODULE Read 604203 spots for SRR18694365.sra Written 604203 spots for SRR18694365.sra Read 604203 spots for SRR18694365.sra Written 604203 spots for SRR18694365.sra Read 604203 spots for SRR18694365.sra Written 604203 spots for SRR18694365.sra Read 604203 spots for SRR18694365.sra Written 604203 spots for SRR18694365.sra Read 604203 spots for SRR18694365.sra Written 604203 spots for SRR18694365.sra Read 604203 spots for SRR18694365.sra Written 604203 spots for SRR18694365.sra Read 604203 spots for SRR18694365.sra Written 604203 spots for SRR18694365.sra Read 604203 spots for SRR18694365.sra Written 604203 spots for SRR18694365.sra Read 604203 spots for SRR18694365.sra Written 604203 spots for SRR18694365.sra Read 604203 spots for SRR18694365.sra Written 604203 spots for SRR18694365.sra Read 604203 spots for SRR18694365.sra Written 604203 spots for SRR18694365.sra Read 604203 spots for SRR18694365.sra Written 604203 spots for SRR18694365.sra Read 604203 spots for SRR18694365.sra Written 604203 spots for SRR18694365.sra Read 604203 spots for SRR18694365.sra Written 604203 spots for SRR18694365.sra Read 604203 spots for SRR18694365.sra Written 604203 spots for SRR18694365.sra Read 604203 spots for SRR18694365.sra Written 604203 spots for SRR18694365.sra Read 604203 spots for SRR18694365.sra Written 604203 spots for SRR18694365.sra Read 604203 spots for SRR18694365.sra Written 604203 spots for SRR18694365.sra Read 604203 spots for SRR18694365.sra Written 604203 spots for SRR18694365.sra Read 604203 spots for SRR18694365.sra Written 604203 spots for SRR18694365.sra SRR ids: ['SRR18694365.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_aead4cb3 SRR18694365.sra spots: 12084060 blocks: [[1, 604203], [604204, 1208406], [1208407, 1812609], [1812610, 2416812], [2416813, 3021015], [3021016, 3625218], [3625219, 4229421], [4229422, 4833624], [4833625, 5437827], [5437828, 6042030], [6042031, 6646233], [6646234, 7250436], [7250437, 7854639], [7854640, 8458842], [8458843, 9063045], [9063046, 9667248], [9667249, 10271451], [10271452, 10875654], [10875655, 11479857], [11479858, 12084060]] SRR18694365 file size 4084991 SRR18694365 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 SRR18694365 SRR18694365_1.fastq SRR18694365_2.fastq Input file: SRR18694365_1.fastq Paired file: SRR18694365_2.fastq trimmed: SRR18694365-trimmed-pair1.fastq, SRR18694365-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 Dec 10 05:59:38 2024 >> started Tue Dec 10 05:59:52 2024 >> done (13.951s) 12084060 read pairs processed; of these: 141 ( 0.00%) short read pairs filtered out after trimming by size control 3288 ( 0.03%) empty read pairs filtered out after trimming by size control 12080631 (99.97%) read pairs available; of these: 1711951 (14.17%) trimmed read pairs available after processing 10368680 (85.83%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 10 0.00% 19 10 0.00% 20 12 0.00% 21 21 0.00% 22 18 0.00% 23 14 0.00% 24 26 0.00% 25 23 0.00% 26 11 0.00% 27 20 0.00% 28 21 0.00% 29 31 0.00% 30 33 0.00% 31 37 0.00% 32 37 0.00% 33 30 0.00% 34 29 0.00% 35 35 0.00% 36 39 0.00% 37 38 0.00% 38 33 0.00% 39 35 0.00% 40 53 0.00% 41 53 0.00% 42 49 0.00% 43 43 0.00% 44 68 0.00% 45 63 0.00% 46 75 0.00% 47 77 0.00% 48 95 0.00% 49 120 0.00% 50 103 0.00% 51 135 0.00% 52 120 0.00% 53 148 0.00% 54 155 0.00% 55 207 0.00% 56 208 0.00% 57 252 0.00% 58 246 0.00% 59 292 0.00% 60 348 0.00% 61 424 0.00% 62 453 0.00% 63 459 0.00% 64 534 0.00% 65 579 0.00% 66 648 0.01% 67 719 0.01% 68 832 0.01% 69 1015 0.01% 70 1128 0.01% 71 1361 0.01% 72 1481 0.01% 73 1627 0.01% 74 1827 0.02% 75 2092 0.02% 76 2266 0.02% 77 2526 0.02% 78 2722 0.02% 79 3163 0.03% 80 3375 0.03% 81 3903 0.03% 82 4277 0.04% 83 4790 0.04% 84 5123 0.04% 85 5757 0.05% 86 5803 0.05% 87 6281 0.05% 88 7195 0.06% 89 7312 0.06% 90 7967 0.07% 91 8586 0.07% 92 9089 0.08% 93 9736 0.08% 94 10419 0.09% 95 11077 0.09% 96 11681 0.10% 97 12093 0.10% 98 12533 0.10% 99 13304 0.11% 100 13958 0.12% 101 14463 0.12% 102 15251 0.13% 103 16241 0.13% 104 16580 0.14% 105 16903 0.14% 106 17663 0.15% 107 18179 0.15% 108 18785 0.16% 109 19449 0.16% 110 20200 0.17% 111 20741 0.17% 112 21977 0.18% 113 22375 0.19% 114 23324 0.19% 115 24327 0.20% 116 24693 0.20% 117 24654 0.20% 118 25334 0.21% 119 25677 0.21% 120 26719 0.22% 121 27318 0.23% 122 27605 0.23% 123 29098 0.24% 124 29963 0.25% 125 30664 0.25% 126 31216 0.26% 127 31380 0.26% 128 31789 0.26% 129 33300 0.28% 130 32749 0.27% 131 33443 0.28% 132 34445 0.29% 133 35341 0.29% 134 35473 0.29% 135 36602 0.30% 136 37823 0.31% 137 37450 0.31% 138 37821 0.31% 139 38464 0.32% 140 38326 0.32% 141 39750 0.33% 142 40218 0.33% 143 41318 0.34% 144 41927 0.35% 145 42704 0.35% 146 42524 0.35% 147 44497 0.37% 148 43740 0.36% 149 44064 0.36% 150 43816 0.36% 151 10368680 85.83% 12080631 reads passed initial QC criterion=sequence-density sequence-density=0.33 sequence-density-rank=1 fanout-score=3.34 fanout-score-rank=22 prefix-density=0.37 prefix-fanout=3.0 sequence=GGTGTTGTCGAAG criterion=fanout-score sequence-density=0.03 sequence-density-rank=32 fanout-score=173.99 fanout-score-rank=1 prefix-density=0.45 prefix-fanout=10.1 sequence=CGCCGCCGCCACCACGGGACTGCGCTTCGTTGACGGTGATGTTGCGGCCATCCAGGTCCTTGCCGTTCATGCCCTCGATGGCGTCGCGCATCGACTGCTCGCTGGCGAAGGTGACGAAGCCGAACCCGCGGGAACGGCCAGTCTCCCTGTCGTTGATGATCTTGGAGTCGATGATCTCGCCGAAGGAGGAGAAGGCATCCTGGAGACCACGGTCGTCGGTAGCCCAGGCGAGGCCGCCCACG criterion=sequence-density sequence-density=0.29 sequence-density-rank=1 fanout-score=3.73 fanout-score-rank=15 prefix-density=0.50 prefix-fanout=2.1 sequence=TGGTGCATGGCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGTTAACGAACGAGACCTCAGCCTGCTAACTAGCTATGCGGAGCCATCCCTCCGCAGCTAGCTTCTTAGAGGGACTATCGCCGTTTAGGCGACGGAAGTTTGAGGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCACGCGCGCTACACTGATGTATTCAACGAGTATATAGCCTTGGCCGACAGGCCCGGGTAATCTTGGGAAATTTCATCGTGATGGGGATAGATCATTGCAATTGTTGGTCTTCAACGAGGAATGCCTAGTAAGCGCGAGTCATCAGCTCGCGTTGACTACGTCCCTGCCCTTTGTACACACCGCCCGTC criterion=fanout-score sequence-density=0.21 sequence-density-rank=10 fanout-score=26.06 fanout-score-rank=1 prefix-density=0.54 prefix-fanout=10.3 sequence=CAAGAAGGAGTACCC SRR18694365 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 10 06:00:45 Started mapping on | Dec 10 06:00:45 Finished on | Dec 10 06:02:51 Mapping speed, Million of reads per hour | 345.16 Number of input reads | 12080631 Average input read length | 294 UNIQUE READS: Uniquely mapped reads number | 10732687 Uniquely mapped reads % | 88.84% Average mapped length | 293.12 Number of splices: Total | 10331196 Number of splices: Annotated (sjdb) | 9664306 Number of splices: GT/AG | 10190377 Number of splices: GC/AG | 116338 Number of splices: AT/AC | 5103 Number of splices: Non-canonical | 19378 Mismatch rate per base, % | 0.41% Deletion rate per base | 0.01% Deletion average length | 2.34 Insertion rate per base | 0.01% Insertion average length | 2.48 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 347965 % of reads mapped to multiple loci | 2.88% Number of reads mapped to too many loci | 51222 % of reads mapped to too many loci | 0.42% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.58% % of reads unmapped: other | 3.27% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 999979 999979 999979 N_multimapping 347965 347965 347965 N_noFeature 757678 10410670 890909 N_ambiguous 231036 1615 42357 UnstrandedReadsAssigned:9743973 PositiveStrandReadsAssigned:320402 NegativeStrandReadsAssigned:9799421 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR18694365 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: SRR18694365-trimmed-pair1.fastq SRR18694365-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 12,080,631 reads, 10,008,143 reads pseudoaligned [quant] estimated average fragment length: 248.624 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,080 rounds 52973 SRR18694365.ke.tsv 35125 SRR18694365.se.tsv 88098 total ==> SRR18694365.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 688.958 0 0 PNS24247 1044 796.376 45.9512 8.44718 PNS24249 1928 1680.38 20.955 1.82563 PNS24246 1044 796.376 45.9512 8.44718 PNS24248 1044 796.376 45.9512 8.44718 PNS24244 1471 1223.38 86.1913 10.3142 PNS24243 293 101.756 0 0 KQK14069 1603 1355.38 487.141 52.6172 KQK14071 474 246.519 0 0 ==> SRR18694365.se.tsv <== BRADI_1g14170v3 533 BRADI_1g53295v3 1264 BRADI_1g59795v3 343 BRADI_1g07683v3 0 BRADI_1g00485v3 3 BRADI_1g20270v3 220 BRADI_1g74790v3 172 BRADI_1g09890v3 0 BRADI_1g77505v3 112 BRADI_1g48960v3 2 SRR18694365 completed mapping pipeline successfully