Starting /dee2/code/volunteer_pipeline.sh SRR13165362 current disk space = 1541979598848 free memory = 1599157436 SRR13165362 SRAfilesize 094de5ee9e9ef12f9dcf028348d148be SRR13165362.sra SRR13165362.sra file validated SRR13165362 is paired end SRR13165362 is conventional basespace SRR13165362 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR13165362_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 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.5965 37.0 37.0 37.0 37.0 37.0 2 36.07275 37.0 37.0 37.0 37.0 37.0 3 36.472 37.0 37.0 37.0 37.0 37.0 4 36.4425 37.0 37.0 37.0 37.0 37.0 5 36.562 37.0 37.0 37.0 37.0 37.0 6 36.6165 37.0 37.0 37.0 37.0 37.0 7 36.514 37.0 37.0 37.0 37.0 37.0 8 36.481 37.0 37.0 37.0 37.0 37.0 9 36.555 37.0 37.0 37.0 37.0 37.0 10-14 36.5835 37.0 37.0 37.0 37.0 37.0 15-19 36.501400000000004 37.0 37.0 37.0 37.0 37.0 20-24 36.51049999999999 37.0 37.0 37.0 37.0 37.0 25-29 36.4764 37.0 37.0 37.0 37.0 37.0 30-34 36.406400000000005 37.0 37.0 37.0 37.0 37.0 35-39 36.470000000000006 37.0 37.0 37.0 37.0 37.0 40-44 36.4646 37.0 37.0 37.0 37.0 37.0 45-49 36.3244 37.0 37.0 37.0 37.0 37.0 50-54 36.3534 37.0 37.0 37.0 37.0 37.0 55-59 36.304500000000004 37.0 37.0 37.0 37.0 37.0 60-64 36.3343 37.0 37.0 37.0 37.0 37.0 65-69 36.292699999999996 37.0 37.0 37.0 37.0 37.0 70-74 36.24679999999999 37.0 37.0 37.0 37.0 37.0 75-79 36.290200000000006 37.0 37.0 37.0 37.0 37.0 80-84 36.1868 37.0 37.0 37.0 37.0 37.0 85-89 36.20739999999999 37.0 37.0 37.0 37.0 37.0 90-94 36.1192 37.0 37.0 37.0 37.0 37.0 95-99 36.161500000000004 37.0 37.0 37.0 37.0 37.0 100-104 36.0702 37.0 37.0 37.0 37.0 37.0 105-109 36.1612 37.0 37.0 37.0 37.0 37.0 110-114 36.103500000000004 37.0 37.0 37.0 37.0 37.0 115-119 35.9908 37.0 37.0 37.0 37.0 37.0 120-124 35.989999999999995 37.0 37.0 37.0 37.0 37.0 125-129 35.9832 37.0 37.0 37.0 37.0 37.0 130-134 35.925 37.0 37.0 37.0 37.0 37.0 135-139 35.8662 37.0 37.0 37.0 37.0 37.0 140-144 35.6618 37.0 37.0 37.0 37.0 37.0 145-149 35.35119999999999 37.0 37.0 37.0 37.0 37.0 150-151 35.126999999999995 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 22 1.0 23 2.0 24 0.0 25 5.0 26 3.0 27 7.0 28 14.0 29 25.0 30 26.0 31 37.0 32 50.0 33 92.0 34 148.0 35 340.0 36 2847.0 37 403.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 51.849999999999994 9.5 5.675 32.975 2 22.788001008318627 10.637761532644316 35.29115200403328 31.28308545500378 3 21.05 13.675 26.200000000000003 39.074999999999996 4 26.174999999999997 21.425 21.099999999999998 31.3 5 29.2 26.424999999999997 22.525000000000002 21.85 6 25.95 30.475 21.65 21.925 7 19.275000000000002 24.925 36.1 19.7 8 20.599999999999998 23.25 30.425 25.724999999999998 9 20.025000000000002 19.950000000000003 34.300000000000004 25.724999999999998 10-14 23.34 25.430000000000003 25.905 25.324999999999996 15-19 23.810000000000002 24.69 25.580000000000002 25.919999999999998 20-24 24.145 25.345000000000002 25.624999999999996 24.884999999999998 25-29 24.175 24.279999999999998 25.430000000000003 26.115 30-34 23.84 24.735 24.86 26.565 35-39 23.535 25.005 25.590000000000003 25.869999999999997 40-44 24.474999999999998 25.095 24.654999999999998 25.775 45-49 23.56 24.779999999999998 24.38 27.279999999999998 50-54 23.810000000000002 25.395 24.985 25.81 55-59 23.75 24.529999999999998 25.46 26.26 60-64 24.08 24.474999999999998 24.965 26.479999999999997 65-69 23.685000000000002 25.445 24.635 26.235000000000003 70-74 25.314999999999998 24.86 24.445 25.380000000000003 75-79 24.75 25.040000000000003 24.23 25.979999999999997 80-84 24.765 24.224999999999998 25.19 25.82 85-89 24.495 24.29 25.34 25.874999999999996 90-94 24.67 25.330000000000002 24.52 25.480000000000004 95-99 24.39 24.46 24.9 26.25 100-104 24.785 24.735 24.675 25.805 105-109 24.635 24.965 23.86 26.540000000000003 110-114 25.224999999999998 25.230000000000004 24.18 25.365 115-119 25.0 25.005 24.085 25.91 120-124 24.65 25.490000000000002 23.755000000000003 26.105 125-129 24.37 25.52 23.635 26.474999999999998 130-134 24.654999999999998 24.525 24.32 26.5 135-139 25.314999999999998 25.165 23.455000000000002 26.064999999999998 140-144 24.37 24.7 24.22 26.71 145-149 25.509999999999998 25.35 23.54 25.6 150-151 25.55 24.975 24.1625 25.3125 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.5 5 0.5 6 0.5 7 0.5 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 0.0 24 0.0 25 0.0 26 2.0 27 3.0 28 2.5 29 6.0 30 9.5 31 15.0 32 14.5 33 18.0 34 28.0 35 30.0 36 42.0 37 57.5 38 75.5 39 91.5 40 115.0 41 130.5 42 155.5 43 179.5 44 163.5 45 168.0 46 192.0 47 184.5 48 170.5 49 171.5 50 171.5 51 147.0 52 132.0 53 127.5 54 110.0 55 102.5 56 90.5 57 86.5 58 81.0 59 86.5 60 93.0 61 77.0 62 54.0 63 57.5 64 66.5 65 57.5 66 58.0 67 64.0 68 64.0 69 51.5 70 39.5 71 33.5 72 28.5 73 20.0 74 22.0 75 23.0 76 13.5 77 6.5 78 2.5 79 2.0 80 1.5 81 1.0 82 0.5 83 0.5 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 0.8250000000000001 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 74.1 #Duplication Level Percentage of deduplicated Percentage of total 1 75.10121457489879 55.65 2 17.88124156545209 26.5 3 4.824561403508771 10.725 4 1.5519568151147098 4.6 5 0.47233468286099867 1.7500000000000002 6 0.1349527665317139 0.6 7 0.033738191632928474 0.17500000000000002 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 GTTTGGGTGCGTGCTAGGGTTTCGTGGTGCGAATCAGGCCAAGAGAGGAG 7 0.17500000000000002 No Hit GTCTCTTTCTCGAACCCAATTGTTGGGAACTGTTTCGCATATTCCTCCAC 6 0.15 No Hit CCCAAATCGCACATTGTATTCAATAAGCTTAGGTAGCCCAGATTTCTTCT 6 0.15 No Hit GGATGTAGTGCATCTCGGCCGGGCTGAGCTCGGCCTGGGCCTGGGCCTGC 6 0.15 No Hit CGGCTTCCCACGCATCATCTCCTCCCGAGCTGGATCTTTAATGCTACCAC 6 0.15 No Hit CTGAGGGCGCCGATTTTATACAGTTTTTCTTATGCTGCAACAACAAAGCA 5 0.125 No Hit GCTACCTCATCAATCGGTTCAATAAGGTAGAGAACTTCAATATCTTTCTG 5 0.125 No Hit ATCACCAACAACCACTAGCCCTCTATCGCCAATCACATTCCTCACCTCAA 5 0.125 No Hit CGGCGGCGCGTCCATGGAGGCGAACGGCGATGCGGACCGATCGGCGGAGG 5 0.125 No Hit GTGGCGTTGGGGTCTTTGGGCATGAGCATCTCCTTGCCGACAGGTCCTGT 5 0.125 No Hit AAGTGCTTTCAGTTCTCTTTTATCTGTAAATGATTCCGCTAAATATCCAC 5 0.125 No Hit GTCCGGTAGATGAGGCTGTAGTTCACCTGGTTCGCCGCCAGCGGCACCCT 5 0.125 No Hit CAGCTTTCCTCAACTCCTCAATGTTAATGTTACCTTTGGAATCAGTTCCA 5 0.125 No Hit AGATCGAGTAGCTATATGTAGATGGTCGTTGCATGCGTCCCTGGCATGCA 5 0.125 No Hit TGCCGGCGCGCCACCGCGTGGAGCGCGTCGTCCATGTCGATCTGCTCCTG 5 0.125 No Hit GCCGCACTTGCAGGTGCTGCAGCCGCAGCCGCCGTTCTCCGCGGCCATCT 5 0.125 No Hit CTGTATTCTTTCTTCAAGCCCTGGACAGTAGTCAGACTCTTTCTTCCGTT 5 0.125 No Hit GTTACTAGTAGTGTAGTACGGGTAGAGGCATCAGAGGCTGCTGCTTCAGT 5 0.125 No Hit CCTGTTTGTTGGTCTGGGCATTGTTTAATTGCTGATGCCGGATGCCCGTG 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 0.05 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 0.05 0.0 0.0 0.0 0.0 64-65 0.05 0.0 0.0 0.0 0.0 66-67 0.05 0.0 0.0 0.0 0.0 68-69 0.075 0.0 0.0 0.0 0.0 70-71 0.11249999999999999 0.0 0.0 0.0 0.0 72-73 0.16249999999999998 0.0 0.0 0.0 0.0 74-75 0.1875 0.0 0.0 0.0 0.0 76-77 0.325 0.0 0.0 0.0 0.0 78-79 0.4625 0.0 0.0 0.0 0.0 80-81 0.575 0.0 0.0 0.0 0.0 82-83 0.7124999999999999 0.0 0.0 0.0 0.0 84-85 0.8125 0.0 0.0 0.0 0.0 86-87 1.0 0.0 0.0 0.0 0.0 88-89 1.125 0.0 0.0 0.0 0.0 90-91 1.4125 0.0 0.0 0.0 0.0 92-93 1.7625 0.0 0.0 0.0 0.0 94-95 2.125 0.0 0.0 0.0 0.0 96-97 2.55 0.0 0.0 0.0 0.0 98-99 2.8375 0.0 0.0 0.0 0.0 100-101 3.15 0.0 0.0 0.0 0.0 102-103 3.7875 0.0 0.0 0.0 0.0 104-105 4.3 0.0 0.0 0.0 0.0 106-107 4.9125 0.0 0.0 0.0 0.0 108-109 5.5375 0.0 0.0 0.0 0.0 110-111 6.2625 0.0 0.0 0.0 0.0 112-113 7.025 0.0 0.0 0.0 0.0 114-115 7.6875 0.0 0.0 0.0 0.0 116-117 8.2125 0.0 0.0 0.0 0.0 118-119 8.837499999999999 0.0 0.0 0.0 0.0 120-121 9.7125 0.0 0.0 0.0 0.0 122-123 10.3125 0.0 0.0 0.0 0.0 124-125 10.9 0.0 0.0 0.0 0.0 126-127 11.6875 0.0 0.0 0.0 0.0 128-129 12.55 0.0 0.0 0.0 0.0 130-131 12.975 0.0 0.0 0.0 0.0 132-133 13.4375 0.0 0.0 0.0 0.0 134-135 14.1875 0.0 0.0 0.0 0.0 136-137 15.1375 0.0 0.0 0.0 0.0 138-139 16.1 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GATCTCG 20 3.5877043E-4 108.75 145 >>END_MODULE SRR13165362 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR13165362_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 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.99925 37.0 37.0 37.0 37.0 37.0 2 36.1015 37.0 37.0 37.0 37.0 37.0 3 36.12 37.0 37.0 37.0 37.0 37.0 4 36.171 37.0 37.0 37.0 37.0 37.0 5 36.242 37.0 37.0 37.0 37.0 37.0 6 36.15 37.0 37.0 37.0 37.0 37.0 7 36.2335 37.0 37.0 37.0 37.0 37.0 8 36.2295 37.0 37.0 37.0 37.0 37.0 9 36.12 37.0 37.0 37.0 37.0 37.0 10-14 36.221000000000004 37.0 37.0 37.0 37.0 37.0 15-19 36.203599999999994 37.0 37.0 37.0 37.0 37.0 20-24 36.1626 37.0 37.0 37.0 37.0 37.0 25-29 36.041 37.0 37.0 37.0 37.0 37.0 30-34 36.024300000000004 37.0 37.0 37.0 37.0 37.0 35-39 35.986200000000004 37.0 37.0 37.0 37.0 37.0 40-44 35.9859 37.0 37.0 37.0 37.0 37.0 45-49 36.04045 37.0 37.0 37.0 37.0 37.0 50-54 35.9961 37.0 37.0 37.0 37.0 37.0 55-59 35.9893 37.0 37.0 37.0 37.0 37.0 60-64 35.929500000000004 37.0 37.0 37.0 37.0 37.0 65-69 35.897450000000006 37.0 37.0 37.0 37.0 37.0 70-74 35.81 37.0 37.0 37.0 37.0 37.0 75-79 35.84585 37.0 37.0 37.0 37.0 37.0 80-84 35.89375 37.0 37.0 37.0 37.0 37.0 85-89 35.7241 37.0 37.0 37.0 37.0 37.0 90-94 35.79755 37.0 37.0 37.0 37.0 37.0 95-99 35.7138 37.0 37.0 37.0 37.0 37.0 100-104 35.7664 37.0 37.0 37.0 37.0 37.0 105-109 35.703 37.0 37.0 37.0 37.0 37.0 110-114 35.5449 37.0 37.0 37.0 37.0 37.0 115-119 35.5755 37.0 37.0 37.0 37.0 37.0 120-124 35.470099999999995 37.0 37.0 37.0 37.0 37.0 125-129 35.47435 37.0 37.0 37.0 37.0 37.0 130-134 35.2614 37.0 37.0 37.0 34.6 37.0 135-139 35.21635 37.0 37.0 37.0 32.2 37.0 140-144 34.9871 37.0 37.0 37.0 27.4 37.0 145-149 34.8274 37.0 37.0 37.0 25.0 37.0 150-151 34.555875 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 6 1.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 3.0 14 6.0 15 2.0 16 1.0 17 2.0 18 2.0 19 3.0 20 4.0 21 5.0 22 6.0 23 9.0 24 4.0 25 10.0 26 7.0 27 10.0 28 13.0 29 19.0 30 34.0 31 32.0 32 73.0 33 101.0 34 225.0 35 590.0 36 2639.0 37 199.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 45.834382079033475 20.9161842436446 6.821042033727662 26.428391643594264 2 30.475 22.0 26.5 21.025 3 23.200000000000003 26.1 27.1 23.599999999999998 4 26.275 32.65 18.775 22.3 5 27.250000000000004 33.025 17.65 22.075 6 21.925 37.425000000000004 17.375 23.275000000000002 7 24.425 18.925 33.6 23.05 8 23.625 22.45 24.875 29.049999999999997 9 23.825 21.775 25.75 28.65 10-14 26.279999999999998 25.88 22.62 25.22 15-19 25.455 26.125 23.695 24.725 20-24 24.83745123537061 26.067820346103833 23.186956086826047 25.90777233169951 25-29 26.513256628314156 24.88744372186093 23.551775887943972 25.047523761880942 30-34 25.770308123249297 25.755302120848338 23.81452581032413 24.65986394557823 35-39 25.48264479343803 24.74742422726818 24.267280184055217 25.502650795238573 40-44 25.930372148859544 24.704881952781115 23.954581832733094 25.41016406562625 45-49 25.834041914670138 24.383534236982943 24.718651528034812 25.06377232031211 50-54 25.772731819545864 24.967490247074124 24.03220966289887 25.227568270481143 55-59 26.578289144572288 24.647323661830917 23.80190095047524 24.972486243121562 60-64 26.74302290687206 24.427328198459538 23.862158647594278 24.967490247074124 65-69 27.029054358153726 24.693704055608343 23.07846176926539 25.198779816972543 70-74 26.928464232116056 24.89744872436218 23.5967983991996 24.577288644322163 75-79 26.476914611575207 25.351408133660147 23.265469461257567 24.90620779350708 80-84 26.451612903225808 24.88122030507627 23.845961490372595 24.82120530132533 85-89 26.108054027013505 24.927463731865934 24.372186093046526 24.592296148074038 90-94 27.20452158255389 24.34352023208123 24.168458960636222 24.283499224728654 95-99 27.108132439731918 24.612383715114532 23.85215564669401 24.427328198459538 100-104 27.293646823411706 25.23261630815408 23.246623311655828 24.22711355677839 105-109 26.97848924462231 24.947473736868435 23.60680340170085 24.467233616808404 110-114 27.738321496448936 24.83745123537061 23.512053616084824 23.91217365209563 115-119 28.37418709354677 25.717858929464732 22.591295647823912 23.316658329164582 120-124 28.659329664832416 25.41270635317659 22.95647823911956 22.971485742871437 125-129 27.93757190735831 25.716572457605924 23.10539742884298 23.240458206192788 130-134 29.287572543526114 24.939963978387034 22.798679207524515 22.973784270562337 135-139 29.286107359047474 25.183851118114966 23.863124718595227 21.666916804242334 140-144 30.039011703511054 25.687706311893564 22.77183154946484 21.50145043513054 145-149 30.200100050025014 25.212606303151574 22.976488244122063 21.61080540270135 150-151 30.481550969355848 25.89118198874296 22.689180737961227 20.93808630393996 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.5 4 0.5 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.5 11 0.5 12 0.0 13 0.0 14 0.0 15 0.5 16 0.5 17 0.0 18 0.5 19 1.5 20 1.0 21 1.0 22 3.0 23 2.0 24 1.0 25 1.5 26 3.0 27 2.5 28 2.0 29 3.5 30 7.0 31 12.0 32 10.0 33 13.0 34 21.0 35 26.0 36 42.5 37 54.5 38 63.0 39 88.0 40 106.5 41 121.5 42 143.0 43 158.5 44 170.0 45 173.5 46 168.0 47 165.0 48 162.5 49 166.5 50 167.0 51 144.5 52 124.5 53 127.5 54 126.5 55 107.5 56 96.0 57 98.5 58 85.5 59 77.0 60 88.5 61 78.5 62 77.5 63 88.0 64 82.5 65 68.0 66 57.5 67 68.5 68 66.0 69 41.5 70 39.5 71 47.5 72 35.5 73 24.0 74 18.0 75 13.5 76 10.0 77 7.5 78 5.0 79 3.5 80 3.0 81 2.0 82 2.5 83 1.5 84 1.0 85 1.0 86 1.0 87 0.5 88 0.5 89 1.5 90 1.5 91 0.5 92 0.5 93 0.5 94 0.5 95 0.5 96 0.5 97 1.0 98 2.5 99 3.5 100 1.5 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.675 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 0.03 25-29 0.05 30-34 0.04 35-39 0.03 40-44 0.04 45-49 0.034999999999999996 50-54 0.03 55-59 0.05 60-64 0.03 65-69 0.015 70-74 0.05 75-79 0.045 80-84 0.025 85-89 0.05 90-94 0.034999999999999996 95-99 0.03 100-104 0.05 105-109 0.05 110-114 0.03 115-119 0.05 120-124 0.05 125-129 0.045 130-134 0.06 135-139 0.055 140-144 0.03 145-149 0.05 150-151 0.0625 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 74.05000000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 75.52329507089804 55.925000000000004 2 17.4544226873734 25.85 3 4.692775151924375 10.424999999999999 4 1.5867656988521268 4.7 5 0.5064145847400405 1.875 6 0.1350438892640108 0.6 7 0.0675219446320054 0.35000000000000003 8 0.0 0.0 9 0.0 0.0 >10 0.0337609723160027 0.27499999999999997 >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 AGCACACACAAGCCTAGAAGCCTTCAGCTTAATCTTCTTCCTAAGCAAGT 11 0.27499999999999997 No Hit GAAGCACACACAAGCCTAGAAGCCTTCAGCTTAATCTTCTTCCTAAGCAA 7 0.17500000000000002 No Hit CCGGCAGCAGCCTAGCAGGAGCTCGCTGCTCGGAGGAGGCGGCCGCGAAT 7 0.17500000000000002 No Hit CACACAGGCAAAACACAGCTGATTCGTGTACTCGATCTCCCCAGCAAGTT 6 0.15 No Hit CAATAGTCGGTCACTTCAGCACTGTTAGCGTAATCCTATAACTATTCTGA 6 0.15 No Hit GGATGCCTCTGCTTCCCCTCCTCCACTCAACTCACATCCCAGCCCCACCT 6 0.15 No Hit GGAATCAGAAGCACCTTGCTCCTTTGCTGCGGTTCCACTCCTCCAAAACT 6 0.15 No Hit CGGACATTGTTTCTCCGCTTGAACTTGCCGCGAGCTGGAGGGTATACAAG 5 0.125 No Hit CTTCAGCACCGAAGGCGAGATCCCGTACAGAGAGGGGCAGTCCATCGGGG 5 0.125 No Hit ATCTGACTAGATGTCATGACAAGCACCAATTAAGCCATCCAGCATTTGAT 5 0.125 No Hit GTTGAACACGATCACCGGTTTCGATTCTTTCTCTTTGCAACCAAATGCTG 5 0.125 No Hit GATCACCTGTGCTTCCTGACGTCGTTGTGCCAACGTGAACTCCGCGCTAA 5 0.125 No Hit GGTCATCATTGAAGAGTTTCTAGAGGGTGAAGAAGCCTCTTTCTTTGCAC 5 0.125 No Hit GTCCGCAGTTCGCACCACCAAATAAGCTCACACATCAATACAAATAAATC 5 0.125 No Hit TACGTATATGGGGAAAAATGAGATACCTGTTATTTTTCCTTTTTCTGCAA 5 0.125 No Hit GGCAAAACACAGCTGATTCGTGTACTCGATCTCCCCAGCAAGTTAAGGCC 5 0.125 No Hit AGAAGCACACACAAGCCTAGAAGCCTTCAGCTTAATCTTCTTCCTAAGCA 5 0.125 No Hit CGGAGCCTCATTCTTCTCCACCCTATCTCCATTCCCTCCTCCTCCGCCGC 5 0.125 No Hit CGTCTACCAAACAATTAAGCGTGCATAGAAACAAGCACGCATCGCTCACC 5 0.125 No Hit CAAGAACACAGTTCCTGGTGATGTTTCAGCTATGGTACCAGGAGGCATCA 5 0.125 No Hit ATCACACACAGGCAAAACACAGCTGATTCGTGTACTCGATCTCCCCAGCA 5 0.125 No Hit AATCTCTTCTAAGAAGACACCTGAGCATTATCCATCTAGCAGAGCAGCAT 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 0.05 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 0.05 0.0 0.0 0.0 0.0 64-65 0.05 0.0 0.0 0.0 0.0 66-67 0.05 0.0 0.0 0.0 0.0 68-69 0.075 0.0 0.0 0.0 0.0 70-71 0.11249999999999999 0.0 0.0 0.0 0.0 72-73 0.16249999999999998 0.0 0.0 0.0 0.0 74-75 0.1875 0.0 0.0 0.0 0.0 76-77 0.325 0.0 0.0 0.0 0.0 78-79 0.4625 0.0 0.0 0.0 0.0 80-81 0.575 0.0 0.0 0.0 0.0 82-83 0.7124999999999999 0.0 0.0 0.0 0.0 84-85 0.8125 0.0 0.0 0.0 0.0 86-87 1.0 0.0 0.0 0.0 0.0 88-89 1.125 0.0 0.0 0.0 0.0 90-91 1.4375 0.0 0.0 0.0 0.0 92-93 1.7875 0.0 0.0 0.0 0.0 94-95 2.15 0.0 0.0 0.0 0.0 96-97 2.5625 0.0 0.0 0.0 0.0 98-99 2.8375 0.0 0.0 0.0 0.0 100-101 3.15 0.0 0.0 0.0 0.0 102-103 3.7625 0.0 0.0 0.0 0.0 104-105 4.25 0.0 0.0 0.0 0.0 106-107 4.875 0.0 0.0 0.0 0.0 108-109 5.5125 0.0 0.0 0.0 0.0 110-111 6.25 0.0 0.0 0.0 0.0 112-113 7.025 0.0 0.0 0.0 0.0 114-115 7.7625 0.0 0.0 0.0 0.0 116-117 8.35 0.0 0.0 0.0 0.0 118-119 8.95 0.0 0.0 0.0 0.0 120-121 9.8375 0.0 0.0 0.0 0.0 122-123 10.412500000000001 0.0 0.0 0.0 0.0 124-125 10.975 0.0 0.0 0.0 0.0 126-127 11.7875 0.0 0.0 0.0 0.0 128-129 12.65 0.0 0.0 0.0 0.0 130-131 13.075 0.0 0.0 0.0 0.0 132-133 13.5625 0.0 0.0 0.0 0.0 134-135 14.3125 0.0 0.0 0.0 0.0 136-137 15.25 0.0 0.0 0.0 0.0 138-139 16.175 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ACAAAAA 10 0.006830828 145.0 5 GCAGCTA 10 0.006830828 145.0 3 >>END_MODULE Read 1351741 spots for SRR13165362.sra Written 1351741 spots for SRR13165362.sra Read 1351741 spots for SRR13165362.sra Written 1351741 spots for SRR13165362.sra Read 1351747 spots for SRR13165362.sra Written 1351747 spots for SRR13165362.sra Read 1351741 spots for SRR13165362.sra Written 1351741 spots for SRR13165362.sra Read 1351741 spots for SRR13165362.sra Written 1351741 spots for SRR13165362.sra Read 1351741 spots for SRR13165362.sra Written 1351741 spots for SRR13165362.sra Read 1351741 spots for SRR13165362.sra Written 1351741 spots for SRR13165362.sra Read 1351741 spots for SRR13165362.sra Written 1351741 spots for SRR13165362.sra Read 1351741 spots for SRR13165362.sra Written 1351741 spots for SRR13165362.sra Read 1351741 spots for SRR13165362.sra Written 1351741 spots for SRR13165362.sra Read 1351741 spots for SRR13165362.sra Written 1351741 spots for SRR13165362.sra Read 1351741 spots for SRR13165362.sra Written 1351741 spots for SRR13165362.sra Read 1351741 spots for SRR13165362.sra Written 1351741 spots for SRR13165362.sra Read 1351741 spots for SRR13165362.sra Written 1351741 spots for SRR13165362.sra Read 1351741 spots for SRR13165362.sra Written 1351741 spots for SRR13165362.sra Read 1351741 spots for SRR13165362.sra Written 1351741 spots for SRR13165362.sra Read 1351741 spots for SRR13165362.sra Written 1351741 spots for SRR13165362.sra Read 1351741 spots for SRR13165362.sra Written 1351741 spots for SRR13165362.sra Read 1351741 spots for SRR13165362.sra Written 1351741 spots for SRR13165362.sra Read 1351741 spots for SRR13165362.sra Written 1351741 spots for SRR13165362.sra SRR ids: ['SRR13165362.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_teqgqmgj SRR13165362.sra spots: 27034826 blocks: [[1, 1351741], [1351742, 2703482], [2703483, 4055223], [4055224, 5406964], [5406965, 6758705], [6758706, 8110446], [8110447, 9462187], [9462188, 10813928], [10813929, 12165669], [12165670, 13517410], [13517411, 14869151], [14869152, 16220892], [16220893, 17572633], [17572634, 18924374], [18924375, 20276115], [20276116, 21627856], [21627857, 22979597], [22979598, 24331338], [24331339, 25683079], [25683080, 27034826]] SRR13165362 file size 9165916 SRR13165362 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 SRR13165362 SRR13165362_1.fastq SRR13165362_2.fastq Input file: SRR13165362_1.fastq Paired file: SRR13165362_2.fastq trimmed: SRR13165362-trimmed-pair1.fastq, SRR13165362-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 Dec 7 16:09:33 2024 >> started Sat Dec 7 16:10:04 2024 >> done (30.820s) 27034826 read pairs processed; of these: 700 ( 0.00%) short read pairs filtered out after trimming by size control 28180 ( 0.10%) empty read pairs filtered out after trimming by size control 27005946 (99.89%) read pairs available; of these: 5527362 (20.47%) trimmed read pairs available after processing 21478584 (79.53%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 39 0.00% 19 33 0.00% 20 42 0.00% 21 54 0.00% 22 53 0.00% 23 61 0.00% 24 107 0.00% 25 103 0.00% 26 109 0.00% 27 109 0.00% 28 157 0.00% 29 94 0.00% 30 146 0.00% 31 156 0.00% 32 186 0.00% 33 193 0.00% 34 200 0.00% 35 199 0.00% 36 197 0.00% 37 214 0.00% 38 212 0.00% 39 249 0.00% 40 226 0.00% 41 304 0.00% 42 294 0.00% 43 319 0.00% 44 323 0.00% 45 336 0.00% 46 352 0.00% 47 426 0.00% 48 530 0.00% 49 572 0.00% 50 680 0.00% 51 782 0.00% 52 817 0.00% 53 861 0.00% 54 936 0.00% 55 1022 0.00% 56 1125 0.00% 57 1259 0.00% 58 1450 0.01% 59 1685 0.01% 60 1993 0.01% 61 2313 0.01% 62 2577 0.01% 63 2782 0.01% 64 3147 0.01% 65 3525 0.01% 66 3728 0.01% 67 4149 0.02% 68 4581 0.02% 69 5076 0.02% 70 5937 0.02% 71 6860 0.03% 72 7781 0.03% 73 9015 0.03% 74 9698 0.04% 75 10567 0.04% 76 11649 0.04% 77 12453 0.05% 78 13942 0.05% 79 15219 0.06% 80 16785 0.06% 81 18498 0.07% 82 20493 0.08% 83 22485 0.08% 84 25768 0.10% 85 27123 0.10% 86 29055 0.11% 87 29939 0.11% 88 32625 0.12% 89 33341 0.12% 90 36155 0.13% 91 38468 0.14% 92 40837 0.15% 93 43658 0.16% 94 47088 0.17% 95 49854 0.18% 96 51817 0.19% 97 53212 0.20% 98 54517 0.20% 99 56472 0.21% 100 59412 0.22% 101 60432 0.22% 102 63075 0.23% 103 65857 0.24% 104 67341 0.25% 105 68967 0.26% 106 70282 0.26% 107 71369 0.26% 108 73230 0.27% 109 75048 0.28% 110 75513 0.28% 111 77199 0.29% 112 79996 0.30% 113 80108 0.30% 114 82825 0.31% 115 85285 0.32% 116 86869 0.32% 117 87595 0.32% 118 87645 0.32% 119 88639 0.33% 120 90774 0.34% 121 90502 0.34% 122 92161 0.34% 123 92732 0.34% 124 95260 0.35% 125 97339 0.36% 126 97098 0.36% 127 98201 0.36% 128 96963 0.36% 129 98522 0.36% 130 98817 0.37% 131 98592 0.37% 132 99920 0.37% 133 101417 0.38% 134 100349 0.37% 135 101345 0.38% 136 101391 0.38% 137 101255 0.37% 138 100682 0.37% 139 102394 0.38% 140 104057 0.39% 141 102584 0.38% 142 105447 0.39% 143 103295 0.38% 144 105894 0.39% 145 107761 0.40% 146 108897 0.40% 147 115309 0.43% 148 108243 0.40% 149 111717 0.41% 150 109363 0.40% 151 21478584 79.53% 27005946 reads passed initial QC criterion=sequence-density sequence-density=1.00 sequence-density-rank=1 fanout-score=2.29 fanout-score-rank=31 prefix-density=1.01 prefix-fanout=2.3 sequence=TGCCGCACTTGCAGGATGACCCGCAGTTGCAGTTTCCTCCGCAGCAAGACATCTTCGGTCGAGTGCTCGAACTTGCTTAGGAAGAAGATTAAGCTGAAGGCTTCTAGGCTTGTGTGTGCTTCTT criterion=fanout-score sequence-density=0.01 sequence-density-rank=38 fanout-score=40.39 fanout-score-rank=1 prefix-density=0.07 prefix-fanout=8.1 sequence=TTGCATCAATGATAATCCCAAAGTAGGAAGTGTGTACGTAGTAGCAAGTGTTATACATACATAAAATTAAGCGATGCGTTTCGATCAAGTACTTGGCATCATCGATCACATACGTACATTTCACAGCAGGTAGCTACGTACATTACAGGCATACGTACATGCAGAGAGATACCCGGCCCTGTGTTGTGTTTGCAATTGCATAGATGAGAATGAGATGACTTGATTCTTAATTAGCCGGCGAGAGCGCTGGTGTTGTAGACGAGGAGGGCGCCGCCGCCGAGGAGGCCGGCCAGGGTGACGGCCCAGATCAGGAGCCCCGTCGTCCCACCGGCGTAGCGGTCGCCAGATTCGGACCATACCTCCGGCGTGTAGATCGGGCTGTAGCCGTCGACGTTGGCGCCGTACTTGTCAACAAACTGGTACACACCCTTTCCCGTGCCCTTCCTGCCGTTGGCGTCGATGTCCACCGTCAAGCCACCTCCGATCCCGAGGGGCTTGTCGACCTTGATCT criterion=sequence-density sequence-density=0.40 sequence-density-rank=1 fanout-score=2.95 fanout-score-rank=23 prefix-density=0.47 prefix-fanout=2.5 sequence=GCACCAGCTGCACCTGC criterion=fanout-score sequence-density=0.10 sequence-density-rank=20 fanout-score=120.28 fanout-score-rank=1 prefix-density=0.72 prefix-fanout=17.4 sequence=GCCGCCGCCGCC SRR13165362 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 16:10:57 Started mapping on | Dec 07 16:10:57 Finished on | Dec 07 16:13:37 Mapping speed, Million of reads per hour | 607.63 Number of input reads | 27005946 Average input read length | 289 UNIQUE READS: Uniquely mapped reads number | 25309967 Uniquely mapped reads % | 93.72% Average mapped length | 288.60 Number of splices: Total | 26124422 Number of splices: Annotated (sjdb) | 24468360 Number of splices: GT/AG | 25760485 Number of splices: GC/AG | 310677 Number of splices: AT/AC | 11761 Number of splices: Non-canonical | 41499 Mismatch rate per base, % | 0.23% Deletion rate per base | 0.01% Deletion average length | 2.66 Insertion rate per base | 0.01% Insertion average length | 2.41 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 449115 % of reads mapped to multiple loci | 1.66% Number of reads mapped to too many loci | 82184 % of reads mapped to too many loci | 0.30% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.03% % of reads unmapped: other | 1.29% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1247175 1247175 1247175 N_multimapping 449115 449115 449115 N_noFeature 1071574 24624072 1279014 N_ambiguous 573055 3949 95472 UnstrandedReadsAssigned:23665338 PositiveStrandReadsAssigned:681946 NegativeStrandReadsAssigned:23935481 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=150 echo kmer=145 SRR13165362 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: SRR13165362-trimmed-pair1.fastq SRR13165362-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 27,005,946 reads, 24,250,372 reads pseudoaligned [quant] estimated average fragment length: 246.971 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,209 rounds 52973 SRR13165362.ke.tsv 35125 SRR13165362.se.tsv 88098 total ==> SRR13165362.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 690.777 0 0 PNS24247 1044 798.029 70.1322 5.26168 PNS24249 1928 1682.03 182.395 6.49239 PNS24246 1044 798.029 70.1322 5.26168 PNS24248 1044 798.029 70.1322 5.26168 PNS24244 1471 1225.03 81.2083 3.96898 PNS24243 293 112.933 0 0 KQK14069 1603 1357.03 871.239 38.4391 KQK14071 474 252.51 14.3715 3.40761 ==> SRR13165362.se.tsv <== BRADI_1g14170v3 979 BRADI_1g53295v3 259 BRADI_1g59795v3 518 BRADI_1g07683v3 0 BRADI_1g00485v3 7 BRADI_1g20270v3 476 BRADI_1g74790v3 604 BRADI_1g09890v3 0 BRADI_1g77505v3 299 BRADI_1g48960v3 0 SRR13165362 completed mapping pipeline successfully