Starting /dee2/code/volunteer_pipeline.sh SRR7170807 current disk space = 3088737722368 free memory = 1449650052 SRR7170807 SRAfilesize 2223f3a4bd969f4310613a837f6bcac5 SRR7170807.sra SRR7170807.sra file validated SRR7170807 is paired end SRR7170807 is conventional basespace SRR7170807 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7170807_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 42 >>END_MODULE >>Per base sequence quality warn #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.557 34.0 33.0 34.0 32.0 34.0 2 33.15875 34.0 33.0 34.0 32.0 34.0 3 33.18225 34.0 33.0 34.0 32.0 34.0 4 33.24375 34.0 33.0 34.0 32.0 34.0 5 33.25875 34.0 33.0 34.0 33.0 34.0 6 36.75675 38.0 37.0 38.0 34.0 38.0 7 37.128 38.0 38.0 38.0 36.0 38.0 8 37.336 38.0 38.0 38.0 37.0 38.0 9 37.4365 38.0 38.0 38.0 37.0 38.0 10-14 37.3755 38.0 38.0 38.0 37.0 38.0 15-19 37.255700000000004 38.0 38.0 38.0 36.8 38.0 20-24 37.1885 38.0 38.0 38.0 36.4 38.0 25-29 37.1823 38.0 38.0 38.0 36.0 38.0 30-34 37.07785 38.0 38.0 38.0 36.0 38.0 35-39 37.00065 38.0 38.0 38.0 36.0 38.0 40-44 36.7822 38.0 38.0 38.0 35.2 38.0 45-49 36.86815 38.0 38.0 38.0 35.6 38.0 50-54 36.717600000000004 38.0 38.0 38.0 35.0 38.0 55-59 36.6029 38.0 38.0 38.0 34.4 38.0 60-64 36.56195 38.0 38.0 38.0 34.2 38.0 65-69 36.45975 38.0 38.0 38.0 34.0 38.0 70-74 36.367 38.0 38.0 38.0 34.0 38.0 75-79 35.5129 38.0 37.2 38.0 31.6 38.0 80-84 35.2312 38.0 37.0 38.0 29.8 38.0 85-89 35.25705000000001 38.0 37.0 38.0 31.0 38.0 90-94 34.97715 38.0 36.6 38.0 29.2 38.0 95-99 34.745999999999995 38.0 36.2 38.0 27.8 38.0 100-104 34.618900000000004 38.0 36.0 38.0 27.0 38.0 105-109 34.29065 38.0 35.4 38.0 25.0 38.0 110-114 34.14235000000001 38.0 35.0 38.0 23.8 38.0 115-119 33.805400000000006 38.0 34.4 38.0 21.8 38.0 120-124 33.3014 38.0 33.0 38.0 16.2 38.0 125-129 32.83295 38.0 33.0 38.0 14.8 38.0 130-134 32.267649999999996 38.0 32.0 38.0 13.8 38.0 135-139 31.661900000000003 37.8 30.6 38.0 13.0 38.0 140-144 30.754749999999994 37.0 28.8 38.0 9.8 38.0 145-149 29.27715 36.0 27.6 38.0 2.0 38.0 150-151 23.437875 29.5 7.5 36.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 6 2.0 7 0.0 8 4.0 9 0.0 10 1.0 11 2.0 12 2.0 13 5.0 14 10.0 15 6.0 16 10.0 17 7.0 18 17.0 19 65.0 20 19.0 21 10.0 22 9.0 23 17.0 24 21.0 25 22.0 26 36.0 27 25.0 28 40.0 29 51.0 30 63.0 31 87.0 32 136.0 33 164.0 34 238.0 35 417.0 36 1062.0 37 1452.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 35.801838610827375 17.23697650663943 13.866189989785497 33.09499489274771 2 18.099999999999998 22.7 36.8 22.400000000000002 3 14.549999999999999 27.575 32.25 25.624999999999996 4 18.475 33.5 25.0 23.025000000000002 5 20.875 37.05 25.3 16.775000000000002 6 18.075 38.2 26.625 17.1 7 12.625 27.525 42.575 17.275 8 16.05 28.499999999999996 30.7 24.75 9 17.724999999999998 24.125 33.225 24.925 10-14 18.035 32.82 26.33 22.814999999999998 15-19 18.509999999999998 31.169999999999998 27.644999999999996 22.675 20-24 18.395 32.05 27.355 22.2 25-29 18.215 31.34 27.589999999999996 22.855 30-34 17.8 31.2 27.825 23.175 35-39 19.375 31.924999999999997 27.075 21.625 40-44 18.12 31.814999999999998 27.46 22.605 45-49 18.875 30.615 27.800000000000004 22.71 50-54 19.36 31.005 27.045 22.59 55-59 18.310000000000002 30.17 28.025 23.494999999999997 60-64 19.25 30.275000000000002 27.900000000000002 22.575 65-69 19.265 32.9 25.955000000000002 21.88 70-74 18.29 32.62 26.525 22.564999999999998 75-79 18.545 32.269999999999996 26.740000000000002 22.445 80-84 18.44 31.59 27.384999999999998 22.585 85-89 18.98 30.740000000000002 27.105 23.175 90-94 19.009999999999998 30.03 27.3 23.66 95-99 18.69 30.680000000000003 27.405 23.225 100-104 19.46 30.39 27.084999999999997 23.064999999999998 105-109 20.23 29.4 27.439999999999998 22.93 110-114 20.255000000000003 29.78 26.590000000000003 23.375 115-119 20.605 30.294999999999998 25.88 23.22 120-124 20.13 29.805 25.955000000000002 24.11 125-129 20.085 29.7 25.825 24.39 130-134 20.625 29.609999999999996 25.540000000000003 24.224999999999998 135-139 20.555 29.304999999999996 26.085 24.055 140-144 20.25 29.615000000000002 25.515 24.62 145-149 20.995 29.37 25.2 24.435000000000002 150-151 20.4875 28.9 26.3625 24.25 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 4.0 1 4.0 2 2.5 3 0.5 4 0.0 5 1.0 6 1.0 7 0.5 8 2.0 9 1.5 10 0.5 11 0.5 12 0.0 13 0.0 14 0.5 15 0.5 16 0.0 17 1.0 18 1.0 19 1.0 20 3.0 21 4.0 22 3.5 23 3.5 24 5.0 25 11.5 26 15.0 27 15.5 28 27.5 29 51.5 30 52.5 31 61.5 32 84.5 33 101.5 34 123.0 35 144.0 36 170.5 37 182.0 38 184.5 39 200.0 40 202.5 41 217.0 42 226.5 43 215.0 44 215.5 45 196.5 46 180.0 47 180.0 48 169.5 49 144.5 50 121.5 51 104.5 52 86.0 53 67.0 54 56.5 55 52.5 56 40.0 57 20.0 58 10.0 59 7.5 60 7.0 61 7.0 62 4.5 63 2.0 64 1.0 65 0.5 66 0.5 67 0.0 68 0.5 69 0.5 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 2.1 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 95.35 #Duplication Level Percentage of deduplicated Percentage of total 1 98.42684845306765 93.85 2 1.1798636601992658 2.25 3 0.13109596224436287 0.375 4 0.13109596224436287 0.5 5 0.026219192448872573 0.125 6 0.026219192448872573 0.15 7 0.026219192448872573 0.17500000000000002 8 0.026219192448872573 0.2 9 0.0 0.0 >10 0.0 0.0 >50 0.026219192448872573 2.375 >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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACCTGAAGCTATCTCGTAT 95 2.375 TruSeq Adapter, Index 19 (97% over 38bp) TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 8 0.2 No Hit GGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGA 7 0.17500000000000002 No Hit CGGAAGAGCACACGTCTGAACTCCAGTCACCTGAAGCTATCTCGTATGCC 6 0.15 TruSeq Adapter, Index 19 (97% over 35bp) CTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAAC 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 0.025 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 0.037500000000000006 0.0 0.0 0.0 0.0 58-59 0.1 0.0 0.0 0.0 0.0 60-61 0.1625 0.0 0.0 0.0 0.0 62-63 0.225 0.0 0.0 0.0 0.0 64-65 0.25 0.0 0.0 0.0 0.0 66-67 0.275 0.0 0.0 0.0 0.0 68-69 0.3125 0.0 0.0 0.0 0.0 70-71 0.4 0.0 0.0 0.0 0.0 72-73 0.525 0.0 0.0 0.0 0.0 74-75 0.5874999999999999 0.0 0.0 0.0 0.0 76-77 0.65 0.0 0.0 0.0 0.0 78-79 0.7 0.0 0.0 0.0 0.0 80-81 0.8875 0.0 0.0 0.0 0.0 82-83 1.125 0.0 0.0 0.0 0.0 84-85 1.2875 0.0 0.0 0.0 0.0 86-87 1.5 0.0 0.0 0.0 0.0 88-89 1.7125 0.0 0.0 0.0 0.0 90-91 1.925 0.0 0.0 0.0 0.0 92-93 2.325 0.0 0.0 0.0 0.0 94-95 2.6500000000000004 0.0 0.0 0.0 0.0 96-97 2.975 0.0 0.0 0.0 0.0 98-99 3.3 0.0 0.0 0.0 0.0 100-101 3.825 0.0 0.0 0.0 0.0 102-103 4.4875 0.0 0.0 0.0 0.0 104-105 5.05 0.0 0.0 0.0 0.0 106-107 5.7125 0.0 0.0 0.0 0.0 108-109 6.3 0.0 0.0 0.0 0.0 110-111 7.15 0.0 0.0 0.0 0.0 112-113 7.800000000000001 0.0 0.0 0.0 0.0 114-115 8.4875 0.0 0.0 0.0 0.0 116-117 9.2625 0.0 0.0 0.0 0.0 118-119 10.175 0.0 0.0 0.0 0.0 120-121 11.1 0.0 0.0 0.0 0.0 122-123 11.8875 0.0 0.0 0.0 0.0 124-125 12.7 0.0 0.0 0.0 0.0 126-127 13.3875 0.0 0.0 0.0 0.0 128-129 14.3625 0.0 0.0 0.0 0.0 130-131 14.9875 0.0 0.0 0.0 0.0 132-133 15.862499999999999 0.0 0.0 0.0 0.0 134-135 16.762500000000003 0.0 0.0 0.0 0.0 136-137 17.7 0.0 0.0 0.0 0.0 138-139 18.5875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CATTCAG 10 0.006832588 144.9875 5 CCATTCA 10 0.006832588 144.9875 4 AGTTCAA 10 0.006832588 144.9875 5 >>END_MODULE SRR7170807 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7170807_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 32.77625 33.0 33.0 34.0 32.0 34.0 2 32.93025 33.0 33.0 34.0 32.0 34.0 3 32.9855 34.0 33.0 34.0 32.0 34.0 4 32.99475 34.0 33.0 34.0 33.0 34.0 5 33.0385 34.0 33.0 34.0 32.0 34.0 6 37.21375 38.0 38.0 38.0 37.0 38.0 7 37.19275 38.0 38.0 38.0 37.0 38.0 8 37.06775 38.0 38.0 38.0 37.0 38.0 9 37.03875 38.0 38.0 38.0 37.0 38.0 10-14 37.09845 38.0 38.0 38.0 37.0 38.0 15-19 37.08975 38.0 38.0 38.0 37.0 38.0 20-24 37.05929999999999 38.0 38.0 38.0 37.0 38.0 25-29 37.0102 38.0 38.0 38.0 36.6 38.0 30-34 36.9645 38.0 38.0 38.0 36.4 38.0 35-39 36.9071 38.0 38.0 38.0 36.2 38.0 40-44 36.95805000000001 38.0 38.0 38.0 36.6 38.0 45-49 36.896699999999996 38.0 38.0 38.0 36.0 38.0 50-54 36.833549999999995 38.0 38.0 38.0 36.0 38.0 55-59 36.7162 38.0 38.0 38.0 35.6 38.0 60-64 36.6101 38.0 38.0 38.0 35.0 38.0 65-69 36.62135 38.0 38.0 38.0 35.2 38.0 70-74 36.6591 38.0 38.0 38.0 35.0 38.0 75-79 36.601499999999994 38.0 38.0 38.0 35.0 38.0 80-84 35.6926 38.0 38.0 38.0 33.4 38.0 85-89 35.54905 38.0 38.0 38.0 33.0 38.0 90-94 35.37384999999999 38.0 37.8 38.0 32.2 38.0 95-99 35.29455 38.0 37.8 38.0 31.0 38.0 100-104 35.0535 38.0 37.0 38.0 29.4 38.0 105-109 34.903600000000004 38.0 37.0 38.0 28.4 38.0 110-114 34.62665 38.0 36.4 38.0 27.4 38.0 115-119 34.3807 38.0 36.0 38.0 25.8 38.0 120-124 34.1369 38.0 35.8 38.0 23.6 38.0 125-129 33.7242 38.0 34.8 38.0 20.2 38.0 130-134 33.341899999999995 38.0 33.8 38.0 16.2 38.0 135-139 32.82315 38.0 33.0 38.0 13.8 38.0 140-144 31.8947 38.0 32.6 38.0 12.4 38.0 145-149 30.331199999999995 37.6 29.8 38.0 2.0 38.0 150-151 24.33725 31.0 14.0 36.5 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 8.0 3 4.0 4 3.0 5 1.0 6 1.0 7 1.0 8 0.0 9 3.0 10 3.0 11 3.0 12 4.0 13 6.0 14 4.0 15 2.0 16 4.0 17 15.0 18 17.0 19 36.0 20 51.0 21 9.0 22 13.0 23 22.0 24 18.0 25 15.0 26 27.0 27 31.0 28 21.0 29 36.0 30 36.0 31 43.0 32 81.0 33 132.0 34 185.0 35 283.0 36 731.0 37 2151.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 38.800000000000004 20.724999999999998 15.625 24.85 2 25.374999999999996 25.924999999999997 31.974999999999998 16.725 3 19.950000000000003 26.025 35.325 18.7 4 23.724999999999998 32.85 23.175 20.25 5 27.3 35.55 21.175 15.975 6 23.75 35.175 23.625 17.45 7 18.925 21.75 39.825 19.5 8 21.85 25.275 27.55 25.324999999999996 9 24.925 24.45 28.625 22.0 10-14 24.235 27.725 27.355 20.685000000000002 15-19 24.025 27.08 28.89 20.005 20-24 24.925 28.9 26.985 19.189999999999998 25-29 23.62 29.515 27.265 19.6 30-34 23.44 27.794999999999998 29.220000000000002 19.545 35-39 23.29 27.67 28.965000000000003 20.075000000000003 40-44 24.065 27.345000000000002 28.665000000000003 19.925 45-49 23.14 28.515 28.845 19.5 50-54 24.37 26.715 29.13 19.785 55-59 24.755 26.745 28.99 19.509999999999998 60-64 23.474999999999998 27.395000000000003 29.21 19.919999999999998 65-69 22.49 27.834999999999997 29.830000000000002 19.845 70-74 22.525000000000002 29.74 28.410000000000004 19.325 75-79 22.575 28.975 28.73 19.72 80-84 22.97 29.285 28.185 19.56 85-89 23.215 28.78 28.810000000000002 19.195 90-94 23.585 28.71 28.735 18.970000000000002 95-99 23.43 28.83 29.060000000000002 18.68 100-104 24.279999999999998 28.04 28.675 19.005 105-109 24.325 28.335 28.64 18.7 110-114 24.55 28.255000000000003 28.505000000000003 18.69 115-119 24.745 28.645 28.205000000000002 18.404999999999998 120-124 25.095 28.305000000000003 27.58 19.02 125-129 25.255 28.815 28.349999999999998 17.580000000000002 130-134 25.86 27.900000000000002 28.349999999999998 17.89 135-139 26.119999999999997 28.315 27.229999999999997 18.335 140-144 26.165 28.050000000000004 27.900000000000002 17.885 145-149 26.384999999999998 28.57 27.845 17.2 150-151 27.5125 27.474999999999998 27.3625 17.65 >>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 0.0 14 0.0 15 0.5 16 0.5 17 1.0 18 3.0 19 2.0 20 1.0 21 3.0 22 3.0 23 2.5 24 4.0 25 5.5 26 5.5 27 6.5 28 12.5 29 16.5 30 17.5 31 32.5 32 43.0 33 59.0 34 79.5 35 91.5 36 112.5 37 128.5 38 152.5 39 182.0 40 196.5 41 215.0 42 251.5 43 263.5 44 259.5 45 264.5 46 253.0 47 222.5 48 186.5 49 167.0 50 153.0 51 126.0 52 112.5 53 97.0 54 74.0 55 56.5 56 35.0 57 26.5 58 20.5 59 15.0 60 10.5 61 6.5 62 7.0 63 3.0 64 1.5 65 2.5 66 2.5 67 1.5 68 0.5 69 1.0 70 0.5 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 0.0 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 96.2 #Duplication Level Percentage of deduplicated Percentage of total 1 98.93451143451144 95.175 2 0.8056133056133057 1.55 3 0.12993762993762994 0.375 4 0.05197505197505198 0.2 5 0.0 0.0 6 0.02598752598752599 0.15 7 0.0 0.0 8 0.0 0.0 9 0.02598752598752599 0.22499999999999998 >10 0.0 0.0 >50 0.02598752598752599 2.325 >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 GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTGTCAGTACGTGTAGATCT 93 2.325 Illumina Single End PCR Primer 1 (96% over 32bp) AGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATC 9 0.22499999999999998 No Hit AACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAA 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 0.025 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 0.037500000000000006 0.0 0.0 0.0 0.0 58-59 0.1 0.0 0.0 0.0 0.0 60-61 0.1625 0.0 0.0 0.0 0.0 62-63 0.225 0.0 0.0 0.0 0.0 64-65 0.225 0.0 0.0 0.0 0.0 66-67 0.25 0.0 0.0 0.0 0.0 68-69 0.2875 0.0 0.0 0.0 0.0 70-71 0.375 0.0 0.0 0.0 0.0 72-73 0.5 0.0 0.0 0.0 0.0 74-75 0.5625 0.0 0.0 0.0 0.0 76-77 0.625 0.0 0.0 0.0 0.0 78-79 0.675 0.0 0.0 0.0 0.0 80-81 0.8625 0.0 0.0 0.0 0.0 82-83 1.0750000000000002 0.0 0.0 0.0 0.0 84-85 1.2374999999999998 0.0 0.0 0.0 0.0 86-87 1.45 0.0 0.0 0.0 0.0 88-89 1.6625 0.0 0.0 0.0 0.0 90-91 1.875 0.0 0.0 0.0 0.0 92-93 2.275 0.0 0.0 0.0 0.0 94-95 2.5999999999999996 0.0 0.0 0.0 0.0 96-97 2.925 0.0 0.0 0.0 0.0 98-99 3.25 0.0 0.0 0.0 0.0 100-101 3.7625 0.0 0.0 0.0 0.0 102-103 4.35 0.0 0.0 0.0 0.0 104-105 4.9 0.0 0.0 0.0 0.0 106-107 5.5625 0.0 0.0 0.0 0.0 108-109 6.137499999999999 0.0 0.0 0.0 0.0 110-111 6.975 0.0 0.0 0.0 0.0 112-113 7.6 0.0 0.0 0.0 0.0 114-115 8.3 0.0 0.0 0.0 0.0 116-117 9.0625 0.0 0.0 0.0 0.0 118-119 9.95 0.0 0.0 0.0 0.0 120-121 10.8875 0.0 0.0 0.0 0.0 122-123 11.65 0.0 0.0 0.0 0.0 124-125 12.475 0.0 0.0 0.0 0.0 126-127 13.1875 0.0 0.0 0.0 0.0 128-129 14.175 0.0 0.0 0.0 0.0 130-131 14.7625 0.0 0.0 0.0 0.0 132-133 15.65 0.0 0.0 0.0 0.0 134-135 16.549999999999997 0.0 0.0 0.0 0.0 136-137 17.5375 0.0 0.0 0.0 0.0 138-139 18.487499999999997 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AAGGCTA 10 0.006830828 145.0 5 AGGCTAG 10 0.006830828 145.0 6 >>END_MODULE Read 790836 spots for SRR7170807.sra Written 790836 spots for SRR7170807.sra Read 790836 spots for SRR7170807.sra Written 790836 spots for SRR7170807.sra Read 790836 spots for SRR7170807.sra Written 790836 spots for SRR7170807.sra Read 790836 spots for SRR7170807.sra Written 790836 spots for SRR7170807.sra Read 790836 spots for SRR7170807.sra Written 790836 spots for SRR7170807.sra Read 790836 spots for SRR7170807.sra Written 790836 spots for SRR7170807.sra Read 790836 spots for SRR7170807.sra Written 790836 spots for SRR7170807.sra Read 790836 spots for SRR7170807.sra Written 790836 spots for SRR7170807.sra Read 790851 spots for SRR7170807.sra Written 790851 spots for SRR7170807.sra Read 790836 spots for SRR7170807.sra Written 790836 spots for SRR7170807.sra Read 790836 spots for SRR7170807.sra Written 790836 spots for SRR7170807.sra Read 790836 spots for SRR7170807.sra Written 790836 spots for SRR7170807.sra Read 790836 spots for SRR7170807.sra Written 790836 spots for SRR7170807.sra Read 790836 spots for SRR7170807.sra Written 790836 spots for SRR7170807.sra Read 790836 spots for SRR7170807.sra Written 790836 spots for SRR7170807.sra Read 790836 spots for SRR7170807.sra Written 790836 spots for SRR7170807.sra Read 790836 spots for SRR7170807.sra Written 790836 spots for SRR7170807.sra Read 790836 spots for SRR7170807.sra Written 790836 spots for SRR7170807.sra Read 790836 spots for SRR7170807.sra Written 790836 spots for SRR7170807.sra Read 790836 spots for SRR7170807.sra Written 790836 spots for SRR7170807.sra SRR ids: ['SRR7170807.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_fjbbq4n0 SRR7170807.sra spots: 15816735 blocks: [[1, 790836], [790837, 1581672], [1581673, 2372508], [2372509, 3163344], [3163345, 3954180], [3954181, 4745016], [4745017, 5535852], [5535853, 6326688], [6326689, 7117524], [7117525, 7908360], [7908361, 8699196], [8699197, 9490032], [9490033, 10280868], [10280869, 11071704], [11071705, 11862540], [11862541, 12653376], [12653377, 13444212], [13444213, 14235048], [14235049, 15025884], [15025885, 15816735]] SRR7170807 file size 5338072 SRR7170807 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 SRR7170807 SRR7170807_1.fastq SRR7170807_2.fastq Input file: SRR7170807_1.fastq Paired file: SRR7170807_2.fastq trimmed: SRR7170807-trimmed-pair1.fastq, SRR7170807-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 Thu Feb 13 16:27:37 2025 >> started Thu Feb 13 16:28:03 2025 >> done (25.756s) 15816735 read pairs processed; of these: 29126 ( 0.18%) short read pairs filtered out after trimming by size control 384987 ( 2.43%) empty read pairs filtered out after trimming by size control 15402622 (97.38%) read pairs available; of these: 11271240 (73.18%) trimmed read pairs available after processing 4131382 (26.82%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 31 0.00% 19 31 0.00% 20 41 0.00% 21 41 0.00% 22 36 0.00% 23 51 0.00% 24 50 0.00% 25 44 0.00% 26 51 0.00% 27 81 0.00% 28 65 0.00% 29 70 0.00% 30 69 0.00% 31 107 0.00% 32 71 0.00% 33 78 0.00% 34 118 0.00% 35 95 0.00% 36 97 0.00% 37 113 0.00% 38 164 0.00% 39 171 0.00% 40 221 0.00% 41 240 0.00% 42 251 0.00% 43 269 0.00% 44 321 0.00% 45 341 0.00% 46 449 0.00% 47 499 0.00% 48 599 0.00% 49 697 0.00% 50 849 0.01% 51 902 0.01% 52 1040 0.01% 53 1004 0.01% 54 1070 0.01% 55 1174 0.01% 56 1291 0.01% 57 1464 0.01% 58 1706 0.01% 59 1919 0.01% 60 2269 0.01% 61 2603 0.02% 62 2852 0.02% 63 3225 0.02% 64 3394 0.02% 65 3315 0.02% 66 3588 0.02% 67 3698 0.02% 68 4235 0.03% 69 4799 0.03% 70 5416 0.04% 71 6731 0.04% 72 8397 0.05% 73 9434 0.06% 74 10546 0.07% 75 14044 0.09% 76 31672 0.21% 77 30187 0.20% 78 16272 0.11% 79 13773 0.09% 80 14646 0.10% 81 16917 0.11% 82 18453 0.12% 83 20539 0.13% 84 22802 0.15% 85 23470 0.15% 86 24760 0.16% 87 25952 0.17% 88 26664 0.17% 89 28137 0.18% 90 29869 0.19% 91 32690 0.21% 92 35237 0.23% 93 38691 0.25% 94 40097 0.26% 95 41371 0.27% 96 42297 0.27% 97 42492 0.28% 98 42808 0.28% 99 43953 0.29% 100 46077 0.30% 101 48296 0.31% 102 52191 0.34% 103 55726 0.36% 104 57753 0.37% 105 59084 0.38% 106 60155 0.39% 107 59774 0.39% 108 60166 0.39% 109 60823 0.39% 110 62247 0.40% 111 63720 0.41% 112 67714 0.44% 113 69756 0.45% 114 73085 0.47% 115 75623 0.49% 116 76837 0.50% 117 77042 0.50% 118 76601 0.50% 119 76397 0.50% 120 78006 0.51% 121 80475 0.52% 122 82354 0.53% 123 86211 0.56% 124 89903 0.58% 125 92314 0.60% 126 95412 0.62% 127 95933 0.62% 128 96570 0.63% 129 97502 0.63% 130 100036 0.65% 131 102435 0.67% 132 105737 0.69% 133 111592 0.72% 134 117142 0.76% 135 124011 0.81% 136 130485 0.85% 137 135975 0.88% 138 143271 0.93% 139 149010 0.97% 140 157842 1.02% 141 168795 1.10% 142 184737 1.20% 143 205043 1.33% 144 233279 1.51% 145 269848 1.75% 146 331162 2.15% 147 429626 2.79% 148 616469 4.00% 149 1067033 6.93% 150 3403689 22.10% 151 4131382 26.82% 15402622 reads passed initial QC criterion=sequence-density sequence-density=0.31 sequence-density-rank=1 fanout-score=2.77 fanout-score-rank=37 prefix-density=0.34 prefix-fanout=2.6 sequence=TTGCTTGCTTCTTCTAATCCACTGGAGAACTTT criterion=fanout-score sequence-density=0.01 sequence-density-rank=44 fanout-score=86.41 fanout-score-rank=1 prefix-density=0.08 prefix-fanout=7.6 sequence=TGAAACAATGTTGGGCTCTCATAAACCGAGCCAGAAGATCTTTAAACAAGTACGAAACTGAAAGTACAATTCACTAATTAGGGCAATATCTGCCTGCAAACATCACGAGAGAGCTACAGAGAGAGATCTCTTGTTTATGCAAAAGGAAATGACAGAAACACAACAATAGATGAACATTGAATTCAATTTCTAAATTGCTCCATTCAGCTAATTCATTTGTTCATGCCAGTTGCCTTCTTAACTCCTTCAACAGCTCCCTGTGCCGTAGACATCACCTGTTGACCAGCCCCTTGCACTGATTCCTTTGCATATTGAGCAGCAGTACCAGCTTTGTCCATCATGGTAGGACTGGTCTTCTCCCCTACGACTGATTCCTT criterion=sequence-density sequence-density=0.27 sequence-density-rank=1 fanout-score=3.43 fanout-score-rank=24 prefix-density=0.31 prefix-fanout=3.0 sequence=TGCAAGTGCGGCAGTGGCTGCAATGGATGCAGCATGTACCCAGACTTGAGTTTCTCCGAGACCACCACAAGTCAGACAATCATTGCTGGTGTAGCTCCAGTTAGGATGTTCTACGAGAGCTCTGAGATGAACTTTGGTGCTGAGAATGGCTGCAAATGTGGATCAAACTGCACCTGTGATCCATGCTCCTGCAAATGAGAAAACGTCGCCGCATGGCTCCAACCAAGCAGTTTTATGGAACTATAATAAATAAAAAGAAGAAGTCTGGTCACTCCATGTTTGTCTAATATAGTATTTGCTGTAAATTAAAGTACAGTTAGCTAGCCATGGCCTCCTCAAATCCTTTCTACAGGATCTCATTTGATGGCTAGTAATCTGTAAGTGTCTTGTATTTCCTGCTGCTTTGTTGGTTCCATTCCATGGAATTATGTATCTTTAATCGGAAGCTTGATTCTGCTTTTATG criterion=fanout-score sequence-density=0.01 sequence-density-rank=40 fanout-score=76.77 fanout-score-rank=1 prefix-density=0.07 prefix-fanout=7.9 sequence=CAAAACCACATATAGAGGGTGTAATAGCTAAGTAGCCTGTAAGAGATGGCTTCCTCTGTGATTTCATCGGCGGCCGTTGCCACAGTTAACCGCACCCCTGCACAGGCCAACATGGTTGCACCATTCAACGGCCTCAAGTCTACCTCAGCTTTCCCGGTCACCAGAAAGGCTAACAATGACATTACTTCCATTGCAAGCAATGGCGGAAGAGTTCAATGCATGCAGGTGTGGCCTCCAACTGGATTGAAGAAGTTCGAGACTCTTTCTTACCTTCCAGATCTCACTACTGAGCAATTGGCCCAGGAAATTGAGTACCTTCTTCGCAACAAGTGGGTTCCTTGCTTGGAATTCGAGTTGGAGAAAGGTTGGGTCTACCGCGAGCACCACCAGTCCCCAGGGTACTATGATGGACGCTACTGGACTATGTGGAAACTACCCATGTTTGGATGCACTGAGGCATCTCAGGTGCTGATTGAGCTCGAGGAGGCGAAGAAAGCTTACCCTAACTCCT SRR7170807 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 13 16:28:44 Started mapping on | Feb 13 16:28:44 Finished on | Feb 13 16:30:13 Mapping speed, Million of reads per hour | 623.03 Number of input reads | 15402622 Average input read length | 280 UNIQUE READS: Uniquely mapped reads number | 14536566 Uniquely mapped reads % | 94.38% Average mapped length | 280.01 Number of splices: Total | 9449549 Number of splices: Annotated (sjdb) | 9187148 Number of splices: GT/AG | 9249647 Number of splices: GC/AG | 140083 Number of splices: AT/AC | 9553 Number of splices: Non-canonical | 50266 Mismatch rate per base, % | 0.42% Deletion rate per base | 0.04% Deletion average length | 2.51 Insertion rate per base | 0.03% Insertion average length | 2.20 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 389702 % of reads mapped to multiple loci | 2.53% Number of reads mapped to too many loci | 24043 % of reads mapped to too many loci | 0.16% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.87% % of reads unmapped: other | 0.07% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 502720 502720 502720 N_multimapping 389702 389702 389702 N_noFeature 497779 13968233 695571 N_ambiguous 474192 1236 103450 UnstrandedReadsAssigned:13564595 PositiveStrandReadsAssigned:567097 NegativeStrandReadsAssigned:13737545 Dataset is classified negative stranded MeadianReadLen=150 20thPercentileLength=130 echo kmer=125 SRR7170807 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: SRR7170807-trimmed-pair1.fastq SRR7170807-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 15,402,622 reads, 13,662,264 reads pseudoaligned [quant] estimated average fragment length: 192.482 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,142 rounds 52401 SRR7170807.ke.tsv 34699 SRR7170807.se.tsv 87100 total ==> SRR7170807.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1826.52 410 11.9606 Potri.005G024800.1.v4.1 1035 843.518 372 23.4986 Potri.004G059700.1.v4.1 961 769.531 6 0.41545 Potri.007G009000.2.v4.1 1416 1224.52 0 0 Potri.003G141000.2.v4.1 2943 2751.52 746 14.4464 Potri.016G087400.1.v4.1 270 103.845 718.733 368.788 Potri.015G069301.1.v4.1 564 373.619 0 0 Potri.010G195200.1.v4.1 1773 1581.52 113 3.80713 Potri.012G127500.1.v4.1 977 785.531 209 14.1767 ==> SRR7170807.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 541 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 615 Potri.001G212900.v4.1 20 Potri.001G182400.v4.1 5 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 131 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 5 SRR7170807 completed mapping pipeline successfully