Starting /dee2/code/volunteer_pipeline.sh SRR18694367 current disk space = 1525693140992 free memory = 1551372740 SRR18694367 SRAfilesize e94e61c84e830a34887e96734c545236 SRR18694367.sra SRR18694367.sra file validated SRR18694367 is paired end SRR18694367 is conventional basespace SRR18694367 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR18694367_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 36.1265 37.0 37.0 37.0 37.0 37.0 2 36.119 37.0 37.0 37.0 37.0 37.0 3 36.418 37.0 37.0 37.0 37.0 37.0 4 36.613 37.0 37.0 37.0 37.0 37.0 5 36.5345 37.0 37.0 37.0 37.0 37.0 6 36.642 37.0 37.0 37.0 37.0 37.0 7 36.562 37.0 37.0 37.0 37.0 37.0 8 36.5645 37.0 37.0 37.0 37.0 37.0 9 36.632 37.0 37.0 37.0 37.0 37.0 10-14 36.659800000000004 37.0 37.0 37.0 37.0 37.0 15-19 36.615300000000005 37.0 37.0 37.0 37.0 37.0 20-24 36.6571 37.0 37.0 37.0 37.0 37.0 25-29 36.5769 37.0 37.0 37.0 37.0 37.0 30-34 36.52589999999999 37.0 37.0 37.0 37.0 37.0 35-39 36.6925 37.0 37.0 37.0 37.0 37.0 40-44 36.6024 37.0 37.0 37.0 37.0 37.0 45-49 36.4406 37.0 37.0 37.0 37.0 37.0 50-54 36.521100000000004 37.0 37.0 37.0 37.0 37.0 55-59 36.5416 37.0 37.0 37.0 37.0 37.0 60-64 36.563599999999994 37.0 37.0 37.0 37.0 37.0 65-69 36.3532 37.0 37.0 37.0 37.0 37.0 70-74 36.457499999999996 37.0 37.0 37.0 37.0 37.0 75-79 36.5006 37.0 37.0 37.0 37.0 37.0 80-84 36.4529 37.0 37.0 37.0 37.0 37.0 85-89 36.19969999999999 37.0 37.0 37.0 37.0 37.0 90-94 35.4473 37.0 37.0 37.0 29.8 37.0 95-99 36.1682 37.0 37.0 37.0 37.0 37.0 100-104 36.1856 37.0 37.0 37.0 37.0 37.0 105-109 36.1622 37.0 37.0 37.0 37.0 37.0 110-114 36.2073 37.0 37.0 37.0 37.0 37.0 115-119 36.4979 37.0 37.0 37.0 37.0 37.0 120-124 36.5778 37.0 37.0 37.0 37.0 37.0 125-129 36.5284 37.0 37.0 37.0 37.0 37.0 130-134 36.5253 37.0 37.0 37.0 37.0 37.0 135-139 36.4504 37.0 37.0 37.0 37.0 37.0 140-144 36.2634 37.0 37.0 37.0 37.0 37.0 145-149 36.2364 37.0 37.0 37.0 37.0 37.0 150-151 33.60225 37.0 31.0 37.0 24.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 18 1.0 19 0.0 20 0.0 21 0.0 22 1.0 23 0.0 24 0.0 25 1.0 26 1.0 27 1.0 28 4.0 29 2.0 30 13.0 31 10.0 32 20.0 33 50.0 34 120.0 35 349.0 36 3223.0 37 204.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 43.275000000000006 9.925 5.175 41.625 2 21.77621675865529 9.483191169091821 37.63171098845961 31.10888108379328 3 21.525 12.975 24.349999999999998 41.15 4 27.250000000000004 19.3 20.45 33.0 5 26.25 26.174999999999997 22.825 24.75 6 22.8 30.625000000000004 22.7 23.875 7 17.299999999999997 26.125 37.05 19.525000000000002 8 19.650000000000002 23.125 31.775 25.45 9 19.175 20.875 35.025 24.925 10-14 23.32 26.025 25.69 24.965 15-19 22.455 24.515 26.534999999999997 26.495 20-24 23.055 25.374999999999996 26.245 25.324999999999996 25-29 22.875 24.985 25.905 26.235000000000003 30-34 22.775000000000002 24.86 26.16 26.205000000000002 35-39 23.28 25.15 25.580000000000002 25.990000000000002 40-44 23.115 24.735 25.995 26.155 45-49 23.26 25.5 25.580000000000002 25.66 50-54 23.445 24.84 25.945 25.77 55-59 23.165 25.290000000000003 26.105 25.44 60-64 23.119999999999997 24.81 25.275 26.795 65-69 22.765 25.324999999999996 26.479999999999997 25.430000000000003 70-74 23.669999999999998 25.419999999999998 25.230000000000004 25.679999999999996 75-79 23.52 25.805 25.369999999999997 25.305 80-84 23.830000000000002 24.675 25.8 25.695 85-89 23.46 24.91 25.915 25.715 90-94 23.169999999999998 24.335 26.355 26.14 95-99 22.919999999999998 25.21 25.345000000000002 26.525 100-104 23.445 24.884999999999998 25.509999999999998 26.16 105-109 24.385 24.815 24.9 25.900000000000002 110-114 23.419999999999998 25.945 25.169999999999998 25.465 115-119 23.905 25.485000000000003 24.785 25.825 120-124 23.62 25.064999999999998 25.3 26.015 125-129 23.544999999999998 26.035000000000004 23.825 26.595000000000002 130-134 23.830000000000002 26.115 24.245 25.81 135-139 23.105 25.995 24.654999999999998 26.245 140-144 23.494999999999997 24.86 25.074999999999996 26.57 145-149 24.22 25.6 24.4 25.779999999999998 150-151 23.549999999999997 25.4 24.2 26.85 >>END_MODULE >>Per sequence GC content warn #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 0.0 17 0.0 18 0.0 19 0.0 20 0.5 21 0.5 22 0.0 23 0.0 24 0.5 25 1.5 26 1.5 27 3.5 28 6.5 29 9.0 30 12.5 31 19.0 32 22.0 33 25.5 34 30.5 35 39.5 36 58.0 37 67.0 38 77.0 39 87.0 40 101.5 41 127.5 42 154.5 43 173.0 44 169.0 45 174.5 46 186.0 47 205.0 48 191.5 49 170.0 50 166.5 51 149.5 52 149.5 53 145.0 54 119.5 55 109.0 56 118.5 57 102.5 58 83.5 59 68.5 60 63.5 61 62.0 62 58.5 63 74.0 64 77.0 65 69.0 66 50.5 67 37.0 68 40.0 69 31.5 70 26.5 71 22.5 72 14.5 73 13.0 74 10.5 75 11.5 76 9.0 77 1.5 78 0.5 79 0.5 80 0.0 81 0.5 82 0.5 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 0.35000000000000003 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 81.15 #Duplication Level Percentage of deduplicated Percentage of total 1 83.73382624768946 67.95 2 12.138016019716574 19.7 3 2.803450400492914 6.825 4 0.7701786814540973 2.5 5 0.33887861983980283 1.375 6 0.15403573629081946 0.75 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.06161429451632779 0.8999999999999999 >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 GGGCCCACTTGGAGCTCCCGATTCCATGGCGCGGCTCACCGGAGCAGCCG 25 0.625 No Hit CCTCGCGGTACTTGTTCGCTATCGGTCTCTCGCCTGTATTTAGCCTTGGA 11 0.27499999999999997 No Hit GTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTA 6 0.15 No Hit CCGGCAATTTCAAGCACTCTTTGACTCTCTTTTCAAAGTCCTTTTCATCT 6 0.15 No Hit CTCCAGCTATCCTGAGGGAAACTTCGGAGGGAACCAGCTACTAGATGGTT 6 0.15 No Hit GGGCTACTTCGTAAGTGTTGCAATTTAAGACTTCTCCCGAGCTCGAGTAT 6 0.15 No Hit CCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCT 6 0.15 No Hit CTTCCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGA 5 0.125 No Hit GTGGGCATTTAGCTGCTCGGCTAGACTGCGAACTTCACTCTCAACATCGG 5 0.125 No Hit GCCTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCCG 5 0.125 No Hit GTTGAGACTAGGACGGTATCTGATCGTCTTCGAGCCCCCAACTTTCGTTC 5 0.125 No Hit GAAGAACCGGTTACGGAATCGGATACGCTTTGCATGCGTGAATATGTACC 5 0.125 No Hit GGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGC 5 0.125 No Hit GTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACT 5 0.125 No Hit CGGCAATTTCAAGCACTCTTTGACTCTCTTTTCAAAGTCCTTTTCATCTT 5 0.125 No Hit ATGCCCAAACTTCATACAGATAAGAAGCTCCACTATGCATATGGCTACAG 5 0.125 No Hit GGCATCCTCATCCCAGTCCTCGGGCTTCACAGCATCTGGATCAGGGATTT 5 0.125 No Hit GCTCTTCCGGCCACTGGACCCTACCTCCGGCTGAACCGATTCCAGGGTTG 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 0.0 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 0.0125 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 0.025 0.0 0.0 0.0 0.0 72-73 0.037500000000000006 0.0 0.0 0.0 0.0 74-75 0.0875 0.0 0.0 0.0 0.0 76-77 0.1875 0.0 0.0 0.0 0.0 78-79 0.2 0.0 0.0 0.0 0.0 80-81 0.25 0.0 0.0 0.0 0.0 82-83 0.3375 0.0 0.0 0.0 0.0 84-85 0.4875 0.0 0.0 0.0 0.0 86-87 0.6125 0.0 0.0 0.0 0.0 88-89 0.725 0.0 0.0 0.0 0.0 90-91 0.775 0.0 0.0 0.0 0.0 92-93 0.9125 0.0 0.0 0.0 0.0 94-95 1.1124999999999998 0.0 0.0 0.0 0.0 96-97 1.2625 0.0 0.0 0.0 0.0 98-99 1.4625 0.0 0.0 0.0 0.0 100-101 1.6625 0.0 0.0 0.0 0.0 102-103 1.875 0.0 0.0 0.0 0.0 104-105 2.1875 0.0 0.0 0.0 0.0 106-107 2.4 0.0 0.0 0.0 0.0 108-109 2.8125 0.0 0.0 0.0 0.0 110-111 3.175 0.0 0.0 0.0 0.0 112-113 3.5375 0.0 0.0 0.0 0.0 114-115 3.9000000000000004 0.0 0.0 0.0 0.0 116-117 4.3375 0.0 0.0 0.0 0.0 118-119 4.7875 0.0 0.0 0.0 0.0 120-121 5.112500000000001 0.0 0.0 0.0 0.0 122-123 5.5125 0.0 0.0 0.0 0.0 124-125 6.237500000000001 0.0 0.0 0.0 0.0 126-127 6.75 0.0 0.0 0.0 0.0 128-129 7.4375 0.0 0.0 0.0 0.0 130-131 8.175 0.0 0.0 0.0 0.0 132-133 8.65 0.0 0.0 0.0 0.0 134-135 9.0125 0.0 0.0 0.0 0.0 136-137 9.6125 0.0 0.0 0.0 0.0 138-139 10.6875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GCCTCAT 10 0.006830828 145.0 1 CCTCATC 10 0.006830828 145.0 2 >>END_MODULE SRR18694367 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR18694367_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 34.5495 37.0 37.0 37.0 25.0 37.0 2 35.3365 37.0 37.0 37.0 37.0 37.0 3 35.505 37.0 37.0 37.0 37.0 37.0 4 35.468 37.0 37.0 37.0 37.0 37.0 5 35.505 37.0 37.0 37.0 37.0 37.0 6 35.569 37.0 37.0 37.0 37.0 37.0 7 35.534 37.0 37.0 37.0 37.0 37.0 8 35.7155 37.0 37.0 37.0 37.0 37.0 9 35.7675 37.0 37.0 37.0 37.0 37.0 10-14 35.8115 37.0 37.0 37.0 37.0 37.0 15-19 35.8424 37.0 37.0 37.0 37.0 37.0 20-24 35.6042 37.0 37.0 37.0 34.6 37.0 25-29 35.72769999999999 37.0 37.0 37.0 37.0 37.0 30-34 35.955 37.0 37.0 37.0 37.0 37.0 35-39 35.8035 37.0 37.0 37.0 37.0 37.0 40-44 35.554700000000004 37.0 37.0 37.0 34.6 37.0 45-49 35.7077 37.0 37.0 37.0 37.0 37.0 50-54 35.1226 37.0 37.0 37.0 32.2 37.0 55-59 34.5737 37.0 37.0 37.0 25.0 37.0 60-64 35.1879 37.0 37.0 37.0 27.4 37.0 65-69 34.3734 37.0 34.6 37.0 29.8 37.0 70-74 33.0638 37.0 29.8 37.0 22.2 37.0 75-79 33.6062 37.0 34.6 37.0 22.2 37.0 80-84 34.7076 37.0 37.0 37.0 25.0 37.0 85-89 32.8042 37.0 32.2 37.0 19.4 37.0 90-94 34.282199999999996 37.0 37.0 37.0 25.0 37.0 95-99 34.049 37.0 37.0 37.0 25.0 37.0 100-104 33.5562 37.0 37.0 37.0 25.0 37.0 105-109 34.301199999999994 37.0 37.0 37.0 25.0 37.0 110-114 34.6612 37.0 37.0 37.0 25.0 37.0 115-119 34.5448 37.0 37.0 37.0 25.0 37.0 120-124 34.268 37.0 37.0 37.0 25.0 37.0 125-129 34.0837 37.0 37.0 37.0 25.0 37.0 130-134 33.9415 37.0 34.6 37.0 25.0 37.0 135-139 32.2453 37.0 27.4 37.0 13.8 37.0 140-144 31.670499999999997 37.0 25.0 37.0 11.0 37.0 145-149 31.2113 37.0 25.0 37.0 11.0 37.0 150-151 30.923000000000002 37.0 25.0 37.0 18.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 14 1.0 15 0.0 16 0.0 17 0.0 18 4.0 19 3.0 20 2.0 21 1.0 22 5.0 23 1.0 24 5.0 25 7.0 26 10.0 27 8.0 28 16.0 29 41.0 30 67.0 31 119.0 32 251.0 33 534.0 34 1153.0 35 1530.0 36 242.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 38.45 19.55 7.6 34.4 2 26.775 23.325000000000003 31.2 18.7 3 21.975 23.9 30.875000000000004 23.25 4 26.325 29.475 21.125 23.075000000000003 5 28.525 33.6 20.125 17.75 6 22.825 34.9 20.200000000000003 22.075 7 22.5 20.95 34.825 21.725 8 22.425 22.975 25.45 29.15 9 24.0 21.8 28.050000000000004 26.150000000000002 10-14 26.575 26.0 23.77 23.655 15-19 26.174999999999997 24.985 24.77 24.07 20-24 25.96 25.86 24.335 23.845 25-29 26.005 25.985000000000003 24.474999999999998 23.535 30-34 25.4 25.655 24.39 24.555 35-39 25.5 25.825 24.565 24.11 40-44 25.695 25.695 24.965 23.645 45-49 26.200000000000003 24.884999999999998 24.995 23.919999999999998 50-54 24.54 25.485000000000003 25.669999999999998 24.305 55-59 25.135 25.765 25.264999999999997 23.835 60-64 25.935000000000002 25.509999999999998 24.759999999999998 23.794999999999998 65-69 26.395000000000003 25.869999999999997 24.654999999999998 23.080000000000002 70-74 26.345000000000002 25.369999999999997 24.25 24.035 75-79 27.634999999999998 24.355 24.46 23.549999999999997 80-84 26.674999999999997 25.165 24.775 23.385 85-89 24.2 27.61 24.57 23.62 90-94 26.119999999999997 25.69 24.33 23.86 95-99 25.814999999999998 25.669999999999998 24.445 24.07 100-104 25.905 25.97 25.115 23.01 105-109 26.08 25.580000000000002 25.395 22.945 110-114 26.790000000000003 26.155 24.525 22.53 115-119 27.045 26.369999999999997 24.03 22.555 120-124 27.779999999999998 25.91 24.169999999999998 22.14 125-129 26.775 25.215 24.89 23.119999999999997 130-134 27.49 25.94 23.74 22.830000000000002 135-139 27.68 26.015 23.93 22.375 140-144 28.065 26.369999999999997 23.25 22.314999999999998 145-149 28.244999999999997 25.840000000000003 23.775 22.14 150-151 27.487499999999997 25.5125 25.2125 21.7875 >>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 0.0 9 0.5 10 0.5 11 0.0 12 0.0 13 0.5 14 0.5 15 0.0 16 0.0 17 0.5 18 1.0 19 0.5 20 0.0 21 0.0 22 1.0 23 2.0 24 1.0 25 0.5 26 2.0 27 5.0 28 8.0 29 7.5 30 9.5 31 19.0 32 23.0 33 24.5 34 29.5 35 46.0 36 52.5 37 58.5 38 98.5 39 113.5 40 111.5 41 132.0 42 143.5 43 152.0 44 178.0 45 186.0 46 189.0 47 193.5 48 165.0 49 144.0 50 137.0 51 139.5 52 150.5 53 138.5 54 111.5 55 109.5 56 101.5 57 83.5 58 81.5 59 88.0 60 79.0 61 70.5 62 68.5 63 52.5 64 60.0 65 60.0 66 59.0 67 66.5 68 56.5 69 38.5 70 31.0 71 32.0 72 26.0 73 18.5 74 10.0 75 5.5 76 6.5 77 6.0 78 4.5 79 2.0 80 0.5 81 0.5 82 0.0 83 0.5 84 0.5 85 0.0 86 0.5 87 0.5 88 0.0 89 0.0 90 0.5 91 1.0 92 0.5 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.5 100 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 82.625 #Duplication Level Percentage of deduplicated Percentage of total 1 84.8714069591528 70.125 2 11.376701966717096 18.8 3 2.692889561270802 6.675000000000001 4 0.7564296520423601 2.5 5 0.1815431164901664 0.75 6 0.0 0.0 7 0.0302571860816944 0.17500000000000002 8 0.0605143721633888 0.4 9 0.0 0.0 >10 0.0302571860816944 0.575 >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 GTTCCCTCCGAAGTTTCCCTCAGGATAGCTGGAGCCCATTACGAGTTCTA 23 0.575 No Hit CCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGCAA 8 0.2 No Hit GTCTGACATGCGTGCGAGTCGACGGGTTCTGAAACCTGGGATGCGCAAGG 8 0.2 No Hit GGAGTCTGACATGCGTGCGAGTCGACGGGTTCTGAAACCTGGGATGCGCA 7 0.17500000000000002 No Hit GTTAGCATCCCAATATTAGGCGCTGGTGCAACTGCACCGCCAATAAGTGC 5 0.125 No Hit TGGTGATATTGGACATCGGCACGGTCTTGTGGATAATGTCGCAAGTGGCA 5 0.125 No Hit GATACAGCCGGTCAGGAGGAGTACTCGCGTCTTCGTGCGCTGAGCTACCC 5 0.125 No Hit CTTCATTCTGAAGCACAAGAATCCCAAGACTGGCAAGTATGTTGAACATC 5 0.125 No Hit CTTACCAGGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTT 5 0.125 No Hit CAAGATGATCTTGTAGCTTTCCTTTCAGCACCTGCACAGTTATCGGGAGA 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 0.0 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 0.0125 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 0.025 0.0 0.0 0.0 0.0 72-73 0.025 0.0 0.0 0.0 0.0 74-75 0.05 0.0 0.0 0.0 0.0 76-77 0.1375 0.0 0.0 0.0 0.0 78-79 0.15 0.0 0.0 0.0 0.0 80-81 0.175 0.0 0.0 0.0 0.0 82-83 0.2375 0.0 0.0 0.0 0.0 84-85 0.3875 0.0 0.0 0.0 0.0 86-87 0.5125 0.0 0.0 0.0 0.0 88-89 0.625 0.0 0.0 0.0 0.0 90-91 0.675 0.0 0.0 0.0 0.0 92-93 0.8 0.0 0.0 0.0 0.0 94-95 1.0 0.0 0.0 0.0 0.0 96-97 1.1625 0.0 0.0 0.0 0.0 98-99 1.3624999999999998 0.0 0.0 0.0 0.0 100-101 1.5375 0.0 0.0 0.0 0.0 102-103 1.75 0.0 0.0 0.0 0.0 104-105 2.0625 0.0 0.0 0.0 0.0 106-107 2.275 0.0 0.0 0.0 0.0 108-109 2.6875 0.0 0.0 0.0 0.0 110-111 3.05 0.0 0.0 0.0 0.0 112-113 3.3875 0.0 0.0 0.0 0.0 114-115 3.75 0.0 0.0 0.0 0.0 116-117 4.1875 0.0 0.0 0.0 0.0 118-119 4.637499999999999 0.0 0.0 0.0 0.0 120-121 4.9625 0.0 0.0 0.0 0.0 122-123 5.3625 0.0 0.0 0.0 0.0 124-125 6.0875 0.0 0.0 0.0 0.0 126-127 6.575 0.0 0.0 0.0 0.0 128-129 7.2625 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 8.837499999999999 0.0 0.0 0.0 0.0 136-137 9.412500000000001 0.0 0.0 0.0 0.0 138-139 10.45 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TAGAAGC 10 0.006830828 145.0 8 AGAACTA 10 0.006830828 145.0 3 GAACTAG 10 0.006830828 145.0 4 AACTAGA 10 0.006830828 145.0 5 AAGAACT 10 0.006830828 145.0 2 ACTAGAA 10 0.006830828 145.0 6 CTAGAAG 10 0.006830828 145.0 7 CCTAGTA 10 0.006830828 145.0 7 GTTGTAC 10 0.006830828 145.0 8 >>END_MODULE Read 308715 spots for SRR18694367.sra Written 308715 spots for SRR18694367.sra Read 308715 spots for SRR18694367.sra Written 308715 spots for SRR18694367.sra Read 308715 spots for SRR18694367.sra Written 308715 spots for SRR18694367.sra Read 308715 spots for SRR18694367.sra Written 308715 spots for SRR18694367.sra Read 308715 spots for SRR18694367.sra Written 308715 spots for SRR18694367.sra Read 308715 spots for SRR18694367.sra Written 308715 spots for SRR18694367.sra Read 308715 spots for SRR18694367.sra Written 308715 spots for SRR18694367.sra Read 308715 spots for SRR18694367.sra Written 308715 spots for SRR18694367.sra Read 308715 spots for SRR18694367.sra Written 308715 spots for SRR18694367.sra Read 308715 spots for SRR18694367.sra Written 308715 spots for SRR18694367.sra Read 308715 spots for SRR18694367.sra Written 308715 spots for SRR18694367.sra Read 308728 spots for SRR18694367.sra Written 308728 spots for SRR18694367.sra Read 308715 spots for SRR18694367.sra Written 308715 spots for SRR18694367.sra Read 308715 spots for SRR18694367.sra Written 308715 spots for SRR18694367.sra Read 308715 spots for SRR18694367.sra Written 308715 spots for SRR18694367.sra Read 308715 spots for SRR18694367.sra Written 308715 spots for SRR18694367.sra Read 308715 spots for SRR18694367.sra Written 308715 spots for SRR18694367.sra Read 308715 spots for SRR18694367.sra Written 308715 spots for SRR18694367.sra Read 308715 spots for SRR18694367.sra Written 308715 spots for SRR18694367.sra Read 308715 spots for SRR18694367.sra Written 308715 spots for SRR18694367.sra SRR ids: ['SRR18694367.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_q7_5jy75 SRR18694367.sra spots: 6174313 blocks: [[1, 308715], [308716, 617430], [617431, 926145], [926146, 1234860], [1234861, 1543575], [1543576, 1852290], [1852291, 2161005], [2161006, 2469720], [2469721, 2778435], [2778436, 3087150], [3087151, 3395865], [3395866, 3704580], [3704581, 4013295], [4013296, 4322010], [4322011, 4630725], [4630726, 4939440], [4939441, 5248155], [5248156, 5556870], [5556871, 5865585], [5865586, 6174313]] SRR18694367 file size 2084073 SRR18694367 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 SRR18694367 SRR18694367_1.fastq SRR18694367_2.fastq Input file: SRR18694367_1.fastq Paired file: SRR18694367_2.fastq trimmed: SRR18694367-trimmed-pair1.fastq, SRR18694367-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 06:04:02 2024 >> started Tue Dec 10 06:04:47 2024 >> done (45.330s) 6174313 read pairs processed; of these: 52 ( 0.00%) short read pairs filtered out after trimming by size control 564 ( 0.01%) empty read pairs filtered out after trimming by size control 6173697 (99.99%) read pairs available; of these: 970819 (15.73%) trimmed read pairs available after processing 5202878 (84.27%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 2 0.00% 19 2 0.00% 20 7 0.00% 21 7 0.00% 22 3 0.00% 23 9 0.00% 24 5 0.00% 25 9 0.00% 26 6 0.00% 27 5 0.00% 28 10 0.00% 29 16 0.00% 30 15 0.00% 31 8 0.00% 32 17 0.00% 33 15 0.00% 34 19 0.00% 35 19 0.00% 36 12 0.00% 37 13 0.00% 38 17 0.00% 39 21 0.00% 40 24 0.00% 41 14 0.00% 42 17 0.00% 43 19 0.00% 44 18 0.00% 45 27 0.00% 46 30 0.00% 47 37 0.00% 48 41 0.00% 49 42 0.00% 50 54 0.00% 51 63 0.00% 52 53 0.00% 53 57 0.00% 54 75 0.00% 55 68 0.00% 56 95 0.00% 57 104 0.00% 58 116 0.00% 59 168 0.00% 60 171 0.00% 61 170 0.00% 62 221 0.00% 63 218 0.00% 64 275 0.00% 65 247 0.00% 66 338 0.01% 67 385 0.01% 68 433 0.01% 69 434 0.01% 70 513 0.01% 71 606 0.01% 72 742 0.01% 73 848 0.01% 74 893 0.01% 75 1065 0.02% 76 1128 0.02% 77 1318 0.02% 78 1377 0.02% 79 1531 0.02% 80 1720 0.03% 81 2010 0.03% 82 2264 0.04% 83 2336 0.04% 84 2637 0.04% 85 3035 0.05% 86 3385 0.05% 87 3538 0.06% 88 3759 0.06% 89 3965 0.06% 90 4252 0.07% 91 4561 0.07% 92 4901 0.08% 93 5202 0.08% 94 5578 0.09% 95 5952 0.10% 96 6525 0.11% 97 6840 0.11% 98 6877 0.11% 99 7305 0.12% 100 7578 0.12% 101 7820 0.13% 102 8129 0.13% 103 8511 0.14% 104 9112 0.15% 105 9410 0.15% 106 9617 0.16% 107 10331 0.17% 108 10443 0.17% 109 10836 0.18% 110 11037 0.18% 111 11372 0.18% 112 12108 0.20% 113 12251 0.20% 114 12464 0.20% 115 13409 0.22% 116 13715 0.22% 117 13752 0.22% 118 14097 0.23% 119 14903 0.24% 120 15756 0.26% 121 15671 0.25% 122 16287 0.26% 123 17077 0.28% 124 17109 0.28% 125 17592 0.28% 126 17648 0.29% 127 17901 0.29% 128 18138 0.29% 129 19299 0.31% 130 19441 0.31% 131 19453 0.32% 132 20340 0.33% 133 20519 0.33% 134 19996 0.32% 135 21077 0.34% 136 21560 0.35% 137 22579 0.37% 138 21524 0.35% 139 22592 0.37% 140 23083 0.37% 141 23107 0.37% 142 23595 0.38% 143 23734 0.38% 144 24542 0.40% 145 24156 0.39% 146 24230 0.39% 147 24848 0.40% 148 24857 0.40% 149 25635 0.42% 150 25664 0.42% 151 5202878 84.27% 6173697 reads passed initial QC criterion=sequence-density sequence-density=0.13 sequence-density-rank=1 fanout-score=3.55 fanout-score-rank=20 prefix-density=0.14 prefix-fanout=3.2 sequence=GTGATGGTCTTGCC criterion=fanout-score sequence-density=0.01 sequence-density-rank=43 fanout-score=394.05 fanout-score-rank=1 prefix-density=0.30 prefix-fanout=15.9 sequence=CGCCGCCGCGGTCGCTATCCCGTGCGGCCTCGGTCTTTGGCGGCCTTCCCCCACGACCTGCATCCGGCGTCCGCCCGACGCCAAACTGCTCCCAGGCGACGCCTAACTCGATTAGGCGGACGCCATACAAGTGCAGGTCGTGGCGCCCCCGACGTACAGAAACTATGGTATCACTCTTTTATACACTGAACAAGTCCTGAAAGTTTACTTTCAGTATGACTTGCTAAATTATGTCTATGATGGATCTTAAATTGGATTTTGGTATCCAATCGGAATCTATTTAATCAAAACGTATGAACAGGCCCCAAATATTTATTTAGAGTCAATGTGCTCAAGTTCATGACTAAAATGTTAGATGTAAATAAATGCACTTGAAGAATTCTATCATGAAAATGTGGATTACTGTATAATTGCTTAAACGGCAACTTTTCTCTTTCCTGGCCTCATGTTGTTCAAAACACTATGATTGATATTTGATATTTTATGTTACAAGTTTCGTTTACTTCATGTT criterion=sequence-density sequence-density=0.25 sequence-density-rank=1 fanout-score=2.20 fanout-score-rank=32 prefix-density=0.53 prefix-fanout=1.0 sequence=CAAGTGTAAGGTGTGTATGCTCTCTCTTGTACTAATATTCCTAAAGCAATATAGTACTACTTTGTTCATATAAGTCTCCCGGTTAGGCCTTGTTATTTCTAAGTACTTAGTGCATATAAGTTGTGATTTAACGTGAGCGGATTCGCCCGGAATCACAACGGTCTTGTTTCAACGTGAGTGG criterion=fanout-score sequence-density=0.12 sequence-density-rank=9 fanout-score=93.47 fanout-score-rank=1 prefix-density=0.66 prefix-fanout=17.6 sequence=CGCCGCCGCCGACGTCGCGAGAAGTCCATTGAACCTTATCATTTAGAGGAAGGAG SRR18694367 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 10 06:11:34 Started mapping on | Dec 10 06:11:35 Finished on | Dec 10 06:27:04 Mapping speed, Million of reads per hour | 23.92 Number of input reads | 6173697 Average input read length | 285 UNIQUE READS: Uniquely mapped reads number | 4172003 Uniquely mapped reads % | 67.58% Average mapped length | 287.74 Number of splices: Total | 3558306 Number of splices: Annotated (sjdb) | 3253892 Number of splices: GT/AG | 3509872 Number of splices: GC/AG | 38156 Number of splices: AT/AC | 403 Number of splices: Non-canonical | 9875 Mismatch rate per base, % | 0.48% Deletion rate per base | 0.02% Deletion average length | 2.29 Insertion rate per base | 0.01% Insertion average length | 2.54 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 71150 % of reads mapped to multiple loci | 1.15% Number of reads mapped to too many loci | 111564 % of reads mapped to too many loci | 1.81% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 18.23% % of reads unmapped: other | 11.24% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1930544 1930544 1930544 N_multimapping 71150 71150 71150 N_noFeature 419364 4040398 487839 N_ambiguous 86109 792 22958 UnstrandedReadsAssigned:3666530 PositiveStrandReadsAssigned:130813 NegativeStrandReadsAssigned:3661206 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR18694367 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: SRR18694367-trimmed-pair1.fastq SRR18694367-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 6,173,697 reads, 4,252,232 reads pseudoaligned [quant] estimated average fragment length: 233.824 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,135 rounds 52973 SRR18694367.ke.tsv 35125 SRR18694367.se.tsv 88098 total ==> SRR18694367.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 703.617 51.9832 28.4475 PNS24247 1044 811.176 8.62654 4.09486 PNS24249 1928 1695.18 18.9332 4.30058 PNS24246 1044 811.176 8.62654 4.09486 PNS24248 1044 811.176 8.62654 4.09486 PNS24244 1471 1238.18 38.204 11.8807 PNS24243 293 108.335 0 0 KQK14069 1603 1370.18 37.2929 10.4801 KQK14071 474 257.629 1.74673 2.61065 ==> SRR18694367.se.tsv <== BRADI_1g14170v3 52 BRADI_1g53295v3 250 BRADI_1g59795v3 96 BRADI_1g07683v3 0 BRADI_1g00485v3 5 BRADI_1g20270v3 25 BRADI_1g74790v3 244 BRADI_1g09890v3 0 BRADI_1g77505v3 12 BRADI_1g48960v3 0 SRR18694367 completed mapping pipeline successfully