Starting /dee2/code/volunteer_pipeline.sh SRR7166172 current disk space = 3110323818496 free memory = 1448131488 SRR7166172 SRAfilesize 943ed1bb66cd03b7a4dce1e8a0a5412e SRR7166172.sra SRR7166172.sra file validated SRR7166172 is paired end SRR7166172 is conventional basespace SRR7166172 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7166172_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 43 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.3535 33.0 32.0 34.0 18.0 34.0 2 32.2615 33.0 31.0 34.0 29.0 34.0 3 32.31675 33.0 33.0 34.0 29.0 34.0 4 32.7655 33.0 33.0 34.0 32.0 34.0 5 32.977 33.0 33.0 34.0 32.0 34.0 6 36.4825 38.0 36.0 38.0 34.0 38.0 7 37.01975 38.0 38.0 38.0 35.0 38.0 8 37.448 38.0 38.0 38.0 37.0 38.0 9 37.547 38.0 38.0 38.0 37.0 38.0 10-14 37.6255 38.0 38.0 38.0 38.0 38.0 15-19 37.5724 38.0 38.0 38.0 38.0 38.0 20-24 37.6031 38.0 38.0 38.0 38.0 38.0 25-29 37.576350000000005 38.0 38.0 38.0 38.0 38.0 30-34 37.5312 38.0 38.0 38.0 38.0 38.0 35-39 37.490249999999996 38.0 38.0 38.0 37.6 38.0 40-44 37.48745 38.0 38.0 38.0 37.2 38.0 45-49 37.4784 38.0 38.0 38.0 37.4 38.0 50-54 37.40985 38.0 38.0 38.0 37.0 38.0 55-59 37.08255 38.0 38.0 38.0 37.0 38.0 60-64 37.20195 38.0 38.0 38.0 36.6 38.0 65-69 37.258 38.0 38.0 38.0 37.0 38.0 70-74 37.13065 38.0 38.0 38.0 36.2 38.0 75-79 37.09125 38.0 38.0 38.0 36.0 38.0 80-84 36.9819 38.0 38.0 38.0 36.0 38.0 85-89 36.890550000000005 38.0 38.0 38.0 36.0 38.0 90-94 36.791 38.0 38.0 38.0 35.0 38.0 95-99 36.740750000000006 38.0 38.0 38.0 35.0 38.0 100-104 36.6364 38.0 38.0 38.0 34.8 38.0 105-109 36.51005 38.0 38.0 38.0 34.0 38.0 110-114 36.5022 38.0 38.0 38.0 34.0 38.0 115-119 36.237 38.0 38.0 38.0 33.8 38.0 120-124 36.08645 38.0 37.6 38.0 33.6 38.0 125-129 35.8878 38.0 37.0 38.0 32.2 38.0 130-134 35.7236 38.0 36.8 38.0 31.8 38.0 135-139 35.4979 38.0 36.0 38.0 31.0 38.0 140-144 35.1654 38.0 35.8 38.0 29.8 38.0 145-149 34.68675 38.0 35.6 38.0 28.0 38.0 150-151 31.320125 36.5 31.0 38.0 13.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 10 1.0 11 1.0 12 2.0 13 1.0 14 1.0 15 0.0 16 0.0 17 4.0 18 3.0 19 3.0 20 2.0 21 2.0 22 3.0 23 5.0 24 12.0 25 9.0 26 10.0 27 13.0 28 17.0 29 20.0 30 30.0 31 37.0 32 70.0 33 95.0 34 130.0 35 242.0 36 595.0 37 2692.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 41.159938681655596 17.39908022483393 11.573837506387328 29.867143587123145 2 19.775000000000002 23.425 37.875 18.925 3 17.45 30.65 27.0 24.9 4 20.674999999999997 38.475 21.6 19.25 5 20.445445445445447 38.713713713713716 23.44844844844845 17.39239239239239 6 16.425 37.8 24.975 20.8 7 12.3 21.075 46.45 20.175 8 18.15 21.9 27.675 32.275 9 17.599999999999998 23.9 30.525000000000002 27.975 10-14 20.044999999999998 30.65 26.375 22.93 15-19 19.93 29.025000000000002 27.755000000000003 23.29 20-24 19.955000000000002 28.715000000000003 28.185 23.145 25-29 19.845 29.395 27.52 23.24 30-34 19.634999999999998 29.43 28.305000000000003 22.63 35-39 20.135 28.875 27.584999999999997 23.405 40-44 19.675 29.695 27.639999999999997 22.99 45-49 20.325 29.349999999999998 27.71 22.615 50-54 19.895 29.104999999999997 27.985 23.015 55-59 20.0372739636327 29.189543142094394 27.446733491160025 23.32644940311288 60-64 19.841865585747886 29.264875143872292 27.843667117049492 23.04959215333033 65-69 19.81 29.275000000000002 27.525 23.39 70-74 20.025000000000002 29.134999999999998 27.48 23.36 75-79 20.165 29.39 27.785 22.66 80-84 20.28 28.24 27.775 23.705000000000002 85-89 20.03 28.615000000000002 27.894999999999996 23.46 90-94 19.875 29.294999999999998 27.345000000000002 23.485 95-99 20.215 28.515 28.04 23.23 100-104 20.544381066746723 28.690083058140697 27.704393075152606 23.06114279995997 105-109 20.65979175010012 29.26011213456147 27.197637164597516 22.88245895074089 110-114 21.02 28.325 27.355 23.3 115-119 20.505000000000003 28.21 27.689999999999998 23.595 120-124 20.71 28.57 27.095000000000002 23.625 125-129 21.11 28.32 27.255000000000003 23.315 130-134 20.775 28.804999999999996 26.52 23.9 135-139 21.005 28.07 26.99 23.935000000000002 140-144 21.145 28.22 26.32 24.315 145-149 20.96 28.310000000000002 26.795 23.935000000000002 150-151 20.761809297080568 28.480140333291565 26.575617090590153 24.182433279037717 >>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 0.0 13 0.0 14 0.0 15 0.0 16 0.5 17 0.5 18 0.0 19 0.0 20 0.0 21 1.0 22 3.5 23 4.0 24 4.0 25 6.5 26 6.5 27 7.5 28 15.0 29 23.0 30 31.5 31 38.0 32 44.0 33 55.5 34 74.5 35 97.0 36 114.0 37 121.0 38 136.0 39 163.0 40 197.0 41 240.0 42 249.0 43 263.0 44 297.0 45 272.0 46 238.5 47 244.0 48 215.5 49 174.0 50 145.0 51 121.5 52 103.5 53 74.5 54 52.5 55 38.5 56 28.5 57 21.0 58 15.5 59 9.5 60 8.5 61 9.5 62 9.5 63 6.0 64 4.0 65 6.0 66 3.5 67 2.5 68 2.0 69 0.5 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 0.0 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 2.15 2 0.0 3 0.0 4 0.0 5 0.1 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 0.735 60-64 0.08499999999999999 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 0.06999999999999999 105-109 0.12 110-114 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 0.2375 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.575 #Duplication Level Percentage of deduplicated Percentage of total 1 99.64850615114236 99.225 2 0.2761737383881496 0.5499999999999999 3 0.07532011046949535 0.22499999999999998 4 0.0 0.0 5 0.0 0.0 6 0.0 0.0 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 pass >>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 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.025 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.0625 0.0 0.0 0.0 0.0 80-81 0.075 0.0 0.0 0.0 0.0 82-83 0.1125 0.0 0.0 0.0 0.0 84-85 0.25 0.0 0.0 0.0 0.0 86-87 0.3875 0.0 0.0 0.0 0.0 88-89 0.4625 0.0 0.0 0.0 0.0 90-91 0.525 0.0 0.0 0.0 0.0 92-93 0.575 0.0 0.0 0.0 0.0 94-95 0.7375 0.0 0.0 0.0 0.0 96-97 0.9125 0.0 0.0 0.0 0.0 98-99 1.1625 0.0 0.0 0.0 0.0 100-101 1.4500000000000002 0.0 0.0 0.0 0.0 102-103 1.7125 0.0 0.0 0.0 0.0 104-105 2.0 0.0 0.0 0.0 0.0 106-107 2.3 0.0 0.0 0.0 0.0 108-109 2.6500000000000004 0.0 0.0 0.0 0.0 110-111 2.9000000000000004 0.0 0.0 0.0 0.0 112-113 3.25 0.0 0.0 0.0 0.0 114-115 3.525 0.0 0.0 0.0 0.0 116-117 4.0125 0.0 0.0 0.0 0.0 118-119 4.5375 0.0 0.0 0.0 0.0 120-121 4.9875 0.0 0.0 0.0 0.0 122-123 5.35 0.0 0.0 0.0 0.0 124-125 6.0375 0.0 0.0 0.0 0.0 126-127 6.75 0.0 0.0 0.0 0.0 128-129 7.2875 0.0 0.0 0.0 0.0 130-131 8.0625 0.0 0.0 0.0 0.0 132-133 8.6625 0.0 0.0 0.0 0.0 134-135 9.2875 0.0 0.0 0.0 0.0 136-137 9.8875 0.0 0.0 0.0 0.0 138-139 10.55 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TCAGCAT 10 0.006892826 144.5625 8 CAAATCC 10 0.006892826 144.5625 3 >>END_MODULE SRR7166172 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7166172_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 43 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.0325 33.0 33.0 34.0 32.0 34.0 2 33.13125 34.0 33.0 34.0 32.0 34.0 3 33.16275 34.0 33.0 34.0 33.0 34.0 4 33.16775 34.0 33.0 34.0 33.0 34.0 5 33.1275 34.0 33.0 34.0 33.0 34.0 6 37.352 38.0 38.0 38.0 37.0 38.0 7 37.3575 38.0 38.0 38.0 37.0 38.0 8 37.2985 38.0 38.0 38.0 37.0 38.0 9 37.389 38.0 38.0 38.0 37.0 38.0 10-14 37.3469 38.0 38.0 38.0 37.0 38.0 15-19 37.3427 38.0 38.0 38.0 37.0 38.0 20-24 37.32000000000001 38.0 38.0 38.0 37.0 38.0 25-29 37.26105 38.0 38.0 38.0 37.0 38.0 30-34 37.214749999999995 38.0 38.0 38.0 37.0 38.0 35-39 37.181149999999995 38.0 38.0 38.0 37.0 38.0 40-44 37.099000000000004 38.0 38.0 38.0 36.6 38.0 45-49 36.9821 38.0 38.0 38.0 36.0 38.0 50-54 36.92015 38.0 38.0 38.0 36.0 38.0 55-59 36.8555 38.0 38.0 38.0 35.8 38.0 60-64 36.80649999999999 38.0 38.0 38.0 35.4 38.0 65-69 36.74865 38.0 38.0 38.0 35.2 38.0 70-74 36.64135 38.0 38.0 38.0 35.0 38.0 75-79 36.544650000000004 38.0 38.0 38.0 34.8 38.0 80-84 36.398700000000005 38.0 38.0 38.0 34.0 38.0 85-89 36.279199999999996 38.0 37.8 38.0 33.8 38.0 90-94 36.078649999999996 38.0 37.0 38.0 33.2 38.0 95-99 35.89135 38.0 37.2 38.0 32.2 38.0 100-104 35.782450000000004 38.0 37.0 38.0 32.0 38.0 105-109 35.51655 38.0 37.0 38.0 30.6 38.0 110-114 35.25895 38.0 36.0 38.0 29.0 38.0 115-119 35.0788 38.0 36.0 38.0 28.6 38.0 120-124 34.7505 38.0 35.4 38.0 27.2 38.0 125-129 34.52515000000001 38.0 35.0 38.0 26.4 38.0 130-134 33.88735 38.0 34.4 38.0 22.8 38.0 135-139 33.4716 38.0 34.0 38.0 19.0 38.0 140-144 32.49995 38.0 33.2 38.0 14.2 38.0 145-149 31.2922 37.2 31.0 38.0 8.6 38.0 150-151 26.652375 33.5 16.5 37.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 5.0 3 2.0 4 1.0 5 1.0 6 0.0 7 2.0 8 0.0 9 3.0 10 1.0 11 5.0 12 1.0 13 3.0 14 1.0 15 1.0 16 1.0 17 3.0 18 5.0 19 11.0 20 9.0 21 9.0 22 15.0 23 14.0 24 15.0 25 10.0 26 20.0 27 22.0 28 32.0 29 31.0 30 53.0 31 61.0 32 90.0 33 139.0 34 205.0 35 375.0 36 911.0 37 1943.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 43.0 16.275000000000002 13.925 26.8 2 23.425 23.825 35.65 17.1 3 19.75 27.3 33.225 19.725 4 23.575 35.449999999999996 22.175 18.8 5 23.125 38.1 22.275 16.5 6 18.7 38.15 23.3 19.85 7 17.474999999999998 14.924999999999999 45.4 22.2 8 20.75 22.650000000000002 27.175 29.425 9 23.45 23.425 28.000000000000004 25.124999999999996 10-14 23.005 28.965000000000003 26.255 21.775 15-19 22.939999999999998 27.87 28.54 20.65 20-24 22.37 29.435 27.750000000000004 20.445 25-29 22.27 28.57 27.950000000000003 21.21 30-34 22.965 28.33 28.485 20.22 35-39 22.935 28.075 27.845 21.145 40-44 23.09 28.884999999999998 28.035 19.99 45-49 23.02 28.485 28.08 20.415 50-54 22.745 28.21 28.325 20.72 55-59 23.23 28.515 27.985 20.27 60-64 23.03 28.199999999999996 27.99 20.78 65-69 23.77 27.889999999999997 28.110000000000003 20.23 70-74 23.400000000000002 28.060000000000002 28.04 20.5 75-79 23.395 27.855 28.189999999999998 20.560000000000002 80-84 23.48 27.965 28.000000000000004 20.555 85-89 23.72 28.255000000000003 28.134999999999998 19.89 90-94 23.325000000000003 28.28 27.779999999999998 20.615 95-99 23.375 27.894999999999996 28.71 20.02 100-104 23.84 28.294999999999998 27.700000000000003 20.165 105-109 23.615 28.215 28.105000000000004 20.064999999999998 110-114 24.165 28.1 27.72 20.015 115-119 23.95 27.79 28.255000000000003 20.005 120-124 24.415 28.26 27.815 19.509999999999998 125-129 24.265 28.415000000000003 27.650000000000002 19.67 130-134 24.515 28.58 27.474999999999998 19.43 135-139 25.235000000000003 27.88 27.815 19.07 140-144 24.97 28.48 27.465 19.085 145-149 25.89 27.975 27.165 18.970000000000002 150-151 25.781836377282964 28.646484863647736 26.632474355766828 18.939204403302476 >>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 0.5 12 0.5 13 0.0 14 0.5 15 0.5 16 0.0 17 0.0 18 0.0 19 0.0 20 0.5 21 2.0 22 1.5 23 2.0 24 4.0 25 4.0 26 3.0 27 4.5 28 9.5 29 11.5 30 16.5 31 25.0 32 32.0 33 48.0 34 61.0 35 73.0 36 87.0 37 102.0 38 130.0 39 168.5 40 204.0 41 224.0 42 243.0 43 281.5 44 301.0 45 298.0 46 273.0 47 244.0 48 228.0 49 196.5 50 169.0 51 133.0 52 94.5 53 72.5 54 58.0 55 43.5 56 32.0 57 26.0 58 21.0 59 13.0 60 7.5 61 11.5 62 13.5 63 8.5 64 5.0 65 2.5 66 1.5 67 3.0 68 2.0 69 0.0 70 0.5 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 0.0 100-104 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 0.075 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.1 #Duplication Level Percentage of deduplicated Percentage of total 1 99.34409687184662 98.45 2 0.5297679112008072 1.05 3 0.050454086781029264 0.15 4 0.025227043390514632 0.1 5 0.050454086781029264 0.25 6 0.0 0.0 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 GCAAATTCAGTTTCTAAGCAAAAGCTTTCCAGGCCCCTTTATCCTATTTT 5 0.125 No Hit AGCAAATTCAGTTTCTAAGCAAAAGCTTTCCAGGCCCCTTTATCCTATTT 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 0.0 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 0.025 0.0 56-57 0.0 0.0 0.0 0.025 0.0 58-59 0.0 0.0 0.0 0.025 0.0 60-61 0.0 0.0 0.0 0.025 0.0 62-63 0.0 0.0 0.0 0.025 0.0 64-65 0.0 0.0 0.0 0.025 0.0 66-67 0.0 0.0 0.0 0.025 0.0 68-69 0.0 0.0 0.0 0.025 0.0 70-71 0.0 0.0 0.0 0.025 0.0 72-73 0.0 0.0 0.0 0.025 0.0 74-75 0.025 0.0 0.0 0.025 0.0 76-77 0.025 0.0 0.0 0.025 0.0 78-79 0.0625 0.0 0.0 0.025 0.0 80-81 0.075 0.0 0.0 0.025 0.0 82-83 0.1125 0.0 0.0 0.025 0.0 84-85 0.25 0.0 0.0 0.025 0.0 86-87 0.3875 0.0 0.0 0.025 0.0 88-89 0.4625 0.0 0.0 0.025 0.0 90-91 0.525 0.0 0.0 0.025 0.0 92-93 0.5625 0.0 0.0 0.025 0.0 94-95 0.7125 0.0 0.0 0.025 0.0 96-97 0.8875 0.0 0.0 0.025 0.0 98-99 1.1375 0.0 0.0 0.025 0.0 100-101 1.4125 0.0 0.0 0.025 0.0 102-103 1.6625 0.0 0.0 0.025 0.0 104-105 1.95 0.0 0.0 0.025 0.0 106-107 2.25 0.0 0.0 0.025 0.0 108-109 2.5999999999999996 0.0 0.0 0.025 0.0 110-111 2.8499999999999996 0.0 0.0 0.025 0.0 112-113 3.2 0.0 0.0 0.025 0.0 114-115 3.4625000000000004 0.0 0.0 0.025 0.0 116-117 3.9749999999999996 0.0 0.0 0.025 0.0 118-119 4.4875 0.0 0.0 0.025 0.0 120-121 4.975 0.0 0.0 0.025 0.0 122-123 5.35 0.0 0.0 0.025 0.0 124-125 5.9625 0.0 0.0 0.025 0.0 126-127 6.65 0.0 0.0 0.025 0.0 128-129 7.2 0.0 0.0 0.025 0.0 130-131 7.9625 0.0 0.0 0.025 0.0 132-133 8.55 0.0 0.0 0.025 0.0 134-135 9.2 0.0 0.0 0.025 0.0 136-137 9.787500000000001 0.0 0.0 0.025 0.0 138-139 10.425 0.0 0.0 0.025 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AAAACAA 10 0.006830828 145.0 2 AGATCCA 10 0.006830828 145.0 4 >>END_MODULE Read 709176 spots for SRR7166172.sra Written 709176 spots for SRR7166172.sra Read 709176 spots for SRR7166172.sra Written 709176 spots for SRR7166172.sra Read 709176 spots for SRR7166172.sra Written 709176 spots for SRR7166172.sra Read 709176 spots for SRR7166172.sra Written 709176 spots for SRR7166172.sra Read 709176 spots for SRR7166172.sra Written 709176 spots for SRR7166172.sra Read 709176 spots for SRR7166172.sra Written 709176 spots for SRR7166172.sra Read 709181 spots for SRR7166172.sra Written 709181 spots for SRR7166172.sra Read 709176 spots for SRR7166172.sra Written 709176 spots for SRR7166172.sra Read 709176 spots for SRR7166172.sra Written 709176 spots for SRR7166172.sra Read 709176 spots for SRR7166172.sra Written 709176 spots for SRR7166172.sra Read 709176 spots for SRR7166172.sra Written 709176 spots for SRR7166172.sra Read 709176 spots for SRR7166172.sra Written 709176 spots for SRR7166172.sra Read 709176 spots for SRR7166172.sra Written 709176 spots for SRR7166172.sra Read 709176 spots for SRR7166172.sra Written 709176 spots for SRR7166172.sra Read 709176 spots for SRR7166172.sra Written 709176 spots for SRR7166172.sra Read 709176 spots for SRR7166172.sra Written 709176 spots for SRR7166172.sra Read 709176 spots for SRR7166172.sra Written 709176 spots for SRR7166172.sra Read 709176 spots for SRR7166172.sra Written 709176 spots for SRR7166172.sra Read 709176 spots for SRR7166172.sra Written 709176 spots for SRR7166172.sra Read 709176 spots for SRR7166172.sra Written 709176 spots for SRR7166172.sra SRR ids: ['SRR7166172.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_hnm6sbnk SRR7166172.sra spots: 14183525 blocks: [[1, 709176], [709177, 1418352], [1418353, 2127528], [2127529, 2836704], [2836705, 3545880], [3545881, 4255056], [4255057, 4964232], [4964233, 5673408], [5673409, 6382584], [6382585, 7091760], [7091761, 7800936], [7800937, 8510112], [8510113, 9219288], [9219289, 9928464], [9928465, 10637640], [10637641, 11346816], [11346817, 12055992], [12055993, 12765168], [12765169, 13474344], [13474345, 14183525]] SRR7166172 file size 4784630 SRR7166172 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 SRR7166172 SRR7166172_1.fastq SRR7166172_2.fastq Input file: SRR7166172_1.fastq Paired file: SRR7166172_2.fastq trimmed: SRR7166172-trimmed-pair1.fastq, SRR7166172-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 Fri Feb 14 19:30:06 2025 >> started Fri Feb 14 19:30:32 2025 >> done (26.002s) 14183525 read pairs processed; of these: 9405 ( 0.07%) short read pairs filtered out after trimming by size control 8490 ( 0.06%) empty read pairs filtered out after trimming by size control 14165630 (99.87%) read pairs available; of these: 7204816 (50.86%) trimmed read pairs available after processing 6960814 (49.14%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 4 0.00% 19 11 0.00% 20 7 0.00% 21 6 0.00% 22 5 0.00% 23 6 0.00% 24 3 0.00% 25 6 0.00% 26 5 0.00% 27 5 0.00% 28 7 0.00% 29 7 0.00% 30 5 0.00% 31 2 0.00% 32 6 0.00% 33 3 0.00% 34 10 0.00% 35 7 0.00% 36 10 0.00% 37 14 0.00% 38 10 0.00% 39 12 0.00% 40 10 0.00% 41 13 0.00% 42 18 0.00% 43 15 0.00% 44 26 0.00% 45 29 0.00% 46 29 0.00% 47 28 0.00% 48 44 0.00% 49 39 0.00% 50 39 0.00% 51 73 0.00% 52 57 0.00% 53 71 0.00% 54 77 0.00% 55 103 0.00% 56 99 0.00% 57 144 0.00% 58 154 0.00% 59 153 0.00% 60 171 0.00% 61 205 0.00% 62 203 0.00% 63 249 0.00% 64 321 0.00% 65 359 0.00% 66 352 0.00% 67 400 0.00% 68 534 0.00% 69 614 0.00% 70 780 0.01% 71 866 0.01% 72 926 0.01% 73 1073 0.01% 74 1193 0.01% 75 1335 0.01% 76 1620 0.01% 77 1691 0.01% 78 1989 0.01% 79 2163 0.02% 80 2531 0.02% 81 2967 0.02% 82 3394 0.02% 83 3844 0.03% 84 4815 0.03% 85 5283 0.04% 86 5789 0.04% 87 6298 0.04% 88 6728 0.05% 89 7485 0.05% 90 8181 0.06% 91 8835 0.06% 92 9766 0.07% 93 10808 0.08% 94 11719 0.08% 95 12555 0.09% 96 13232 0.09% 97 13735 0.10% 98 15087 0.11% 99 16146 0.11% 100 16725 0.12% 101 17943 0.13% 102 19200 0.14% 103 20620 0.15% 104 22059 0.16% 105 23377 0.17% 106 24125 0.17% 107 24904 0.18% 108 25844 0.18% 109 27011 0.19% 110 28197 0.20% 111 29839 0.21% 112 31440 0.22% 113 32871 0.23% 114 34192 0.24% 115 35874 0.25% 116 37751 0.27% 117 38253 0.27% 118 39012 0.28% 119 40577 0.29% 120 41440 0.29% 121 43175 0.30% 122 44903 0.32% 123 47059 0.33% 124 49469 0.35% 125 50852 0.36% 126 52695 0.37% 127 53686 0.38% 128 55003 0.39% 129 57057 0.40% 130 59015 0.42% 131 60646 0.43% 132 64036 0.45% 133 66790 0.47% 134 70251 0.50% 135 73057 0.52% 136 76427 0.54% 137 79900 0.56% 138 83143 0.59% 139 87481 0.62% 140 92895 0.66% 141 100388 0.71% 142 108691 0.77% 143 119448 0.84% 144 136558 0.96% 145 158828 1.12% 146 191211 1.35% 147 248646 1.76% 148 361651 2.55% 149 676125 4.77% 150 3036862 21.44% 151 6960814 49.14% 14165630 reads passed initial QC criterion=sequence-density sequence-density=0.42 sequence-density-rank=1 fanout-score=2.83 fanout-score-rank=27 prefix-density=0.54 prefix-fanout=2.2 sequence=CATCTCAGACCTCTCATAGAACATCTTAACTGGTGCAACACCTGCAATGATTGTCTCAGTTGTGGTGTTCTCTGAGAAACCTAAGTCAGGGTACATGCCACATTTGCA criterion=fanout-score sequence-density=0.02 sequence-density-rank=34 fanout-score=132.32 fanout-score-rank=1 prefix-density=0.18 prefix-fanout=14.1 sequence=CTCCTTCCTCTAAATGATAAGGTTCAGTGGACTTCTCGCGACGTCGCCGGCGGCGAACCGCCCACGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAGACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAA criterion=sequence-density sequence-density=0.52 sequence-density-rank=1 fanout-score=3.05 fanout-score-rank=24 prefix-density=0.64 prefix-fanout=2.5 sequence=GGTTTCTCAGAGA criterion=fanout-score sequence-density=0.09 sequence-density-rank=33 fanout-score=27.80 fanout-score-rank=1 prefix-density=0.28 prefix-fanout=9.1 sequence=AAGGCCAAGATCCAGGACAAGGA SRR7166172 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 14 19:31:59 Started mapping on | Feb 14 19:32:00 Finished on | Feb 14 19:34:09 Mapping speed, Million of reads per hour | 395.32 Number of input reads | 14165630 Average input read length | 292 UNIQUE READS: Uniquely mapped reads number | 13118380 Uniquely mapped reads % | 92.61% Average mapped length | 291.25 Number of splices: Total | 12088728 Number of splices: Annotated (sjdb) | 11822670 Number of splices: GT/AG | 11883631 Number of splices: GC/AG | 153089 Number of splices: AT/AC | 11585 Number of splices: Non-canonical | 40423 Mismatch rate per base, % | 0.37% Deletion rate per base | 0.04% Deletion average length | 2.21 Insertion rate per base | 0.02% Insertion average length | 2.14 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 394771 % of reads mapped to multiple loci | 2.79% Number of reads mapped to too many loci | 88994 % of reads mapped to too many loci | 0.63% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.82% % of reads unmapped: other | 0.15% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 661927 661927 661927 N_multimapping 394771 394771 394771 N_noFeature 523184 12961491 609772 N_ambiguous 145429 1303 74320 UnstrandedReadsAssigned:12449767 PositiveStrandReadsAssigned:155586 NegativeStrandReadsAssigned:12434288 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=149 echo kmer=145 SRR7166172 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: SRR7166172-trimmed-pair1.fastq SRR7166172-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 14,165,630 reads, 12,412,872 reads pseudoaligned [quant] estimated average fragment length: 222.783 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,075 rounds 52401 SRR7166172.ke.tsv 34699 SRR7166172.se.tsv 87100 total ==> SRR7166172.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1796.22 1250 49.1528 Potri.005G024800.1.v4.1 1035 813.217 448 38.9107 Potri.004G059700.1.v4.1 961 739.227 54 5.15957 Potri.007G009000.2.v4.1 1416 1194.22 0 0 Potri.003G141000.2.v4.1 2943 2721.22 443.198 11.5036 Potri.016G087400.1.v4.1 270 90.5958 914 712.583 Potri.015G069301.1.v4.1 564 345.854 0 0 Potri.010G195200.1.v4.1 1773 1551.22 444 20.2166 Potri.012G127500.1.v4.1 977 755.222 7326 685.157 ==> SRR7166172.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 13 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 410 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 3 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 618 SRR7166172 completed mapping pipeline successfully