Starting /dee2/code/volunteer_pipeline.sh SRR18694364 current disk space = 1525839126528 free memory = 1570797568 SRR18694364 SRAfilesize 7004ac5f6b95dd10b2dcb90a199ad03c SRR18694364.sra SRR18694364.sra file validated SRR18694364 is paired end SRR18694364 is conventional basespace SRR18694364 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR18694364_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 36.212 37.0 37.0 37.0 37.0 37.0 2 36.04025 37.0 37.0 37.0 37.0 37.0 3 36.465 37.0 37.0 37.0 37.0 37.0 4 36.531 37.0 37.0 37.0 37.0 37.0 5 36.503 37.0 37.0 37.0 37.0 37.0 6 36.5575 37.0 37.0 37.0 37.0 37.0 7 36.525 37.0 37.0 37.0 37.0 37.0 8 36.592 37.0 37.0 37.0 37.0 37.0 9 36.653 37.0 37.0 37.0 37.0 37.0 10-14 36.613 37.0 37.0 37.0 37.0 37.0 15-19 36.6436 37.0 37.0 37.0 37.0 37.0 20-24 36.6317 37.0 37.0 37.0 37.0 37.0 25-29 36.548700000000004 37.0 37.0 37.0 37.0 37.0 30-34 36.5675 37.0 37.0 37.0 37.0 37.0 35-39 36.6733 37.0 37.0 37.0 37.0 37.0 40-44 36.598 37.0 37.0 37.0 37.0 37.0 45-49 36.4165 37.0 37.0 37.0 37.0 37.0 50-54 36.5252 37.0 37.0 37.0 37.0 37.0 55-59 36.52419999999999 37.0 37.0 37.0 37.0 37.0 60-64 36.4939 37.0 37.0 37.0 37.0 37.0 65-69 36.3429 37.0 37.0 37.0 37.0 37.0 70-74 36.3788 37.0 37.0 37.0 37.0 37.0 75-79 36.4782 37.0 37.0 37.0 37.0 37.0 80-84 36.397000000000006 37.0 37.0 37.0 37.0 37.0 85-89 36.210300000000004 37.0 37.0 37.0 37.0 37.0 90-94 35.392100000000006 37.0 37.0 37.0 29.8 37.0 95-99 36.124399999999994 37.0 37.0 37.0 37.0 37.0 100-104 36.1485 37.0 37.0 37.0 37.0 37.0 105-109 36.1456 37.0 37.0 37.0 37.0 37.0 110-114 36.1815 37.0 37.0 37.0 37.0 37.0 115-119 36.5106 37.0 37.0 37.0 37.0 37.0 120-124 36.5733 37.0 37.0 37.0 37.0 37.0 125-129 36.5268 37.0 37.0 37.0 37.0 37.0 130-134 36.5171 37.0 37.0 37.0 37.0 37.0 135-139 36.4404 37.0 37.0 37.0 37.0 37.0 140-144 36.297599999999996 37.0 37.0 37.0 37.0 37.0 145-149 36.267 37.0 37.0 37.0 37.0 37.0 150-151 33.83525 37.0 31.0 37.0 24.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 24 2.0 25 0.0 26 2.0 27 1.0 28 4.0 29 8.0 30 9.0 31 13.0 32 26.0 33 53.0 34 118.0 35 334.0 36 3239.0 37 191.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 46.1 8.475000000000001 5.8999999999999995 39.525 2 22.796886768767262 10.092894802912378 35.07406477529501 32.03615365302536 3 20.849999999999998 13.950000000000001 25.275 39.925 4 28.15 21.175 21.3 29.375 5 27.900000000000002 27.450000000000003 22.625 22.025 6 23.45 31.1 22.625 22.825 7 18.2 23.799999999999997 39.475 18.525 8 19.775000000000002 22.85 31.175000000000004 26.200000000000003 9 20.0 20.125 34.675 25.2 10-14 23.365 27.115000000000002 25.564999999999998 23.955000000000002 15-19 23.685000000000002 24.59 26.325 25.4 20-24 23.985 25.805 25.85 24.36 25-29 23.375 24.94 25.290000000000003 26.395000000000003 30-34 24.03 24.455 25.495 26.02 35-39 23.419999999999998 24.725 25.905 25.95 40-44 23.945 24.7 25.715 25.64 45-49 23.585 25.009999999999998 25.155 26.25 50-54 23.61 25.14 24.93 26.32 55-59 23.48 24.735 25.865 25.919999999999998 60-64 22.985 25.019999999999996 25.31 26.685 65-69 23.025000000000002 25.195 26.240000000000002 25.540000000000003 70-74 23.74 25.0 25.169999999999998 26.090000000000003 75-79 23.395 25.224999999999998 24.785 26.595000000000002 80-84 23.165 25.06 25.835 25.94 85-89 23.78 24.995 25.145 26.08 90-94 23.369999999999997 24.665 25.585 26.38 95-99 23.695 24.14 25.619999999999997 26.545 100-104 23.955000000000002 25.395 25.290000000000003 25.36 105-109 23.895 25.025 24.905 26.174999999999997 110-114 23.565 26.06 24.8 25.575 115-119 23.765 24.735 25.080000000000002 26.419999999999998 120-124 23.94 25.3 24.81 25.95 125-129 24.415 25.369999999999997 24.375 25.840000000000003 130-134 24.72 25.1 24.385 25.795 135-139 24.085 24.68 24.740000000000002 26.495 140-144 23.599999999999998 25.380000000000003 24.37 26.650000000000002 145-149 23.73 25.305 24.59 26.375 150-151 23.724999999999998 25.8 25.0625 25.412499999999998 >>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 0.5 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 0.5 25 0.5 26 0.5 27 3.5 28 3.5 29 5.5 30 6.5 31 5.5 32 11.5 33 15.0 34 21.5 35 35.0 36 45.5 37 56.0 38 78.5 39 87.5 40 97.0 41 125.0 42 134.0 43 155.0 44 174.5 45 170.0 46 197.0 47 202.5 48 178.0 49 170.0 50 186.0 51 204.0 52 184.0 53 161.5 54 144.5 55 134.5 56 125.5 57 103.5 58 80.5 59 72.5 60 74.5 61 70.0 62 62.0 63 55.5 64 55.5 65 54.5 66 49.0 67 40.5 68 32.5 69 30.5 70 29.0 71 21.5 72 16.0 73 12.0 74 5.5 75 4.0 76 3.5 77 2.0 78 2.0 79 1.0 80 0.5 81 1.0 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 0.42500000000000004 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 84.775 #Duplication Level Percentage of deduplicated Percentage of total 1 86.43468003538779 73.275 2 10.763786493659687 18.25 3 2.0347979946918313 5.175 4 0.5308168681804777 1.7999999999999998 5 0.08846947803007962 0.375 6 0.08846947803007962 0.44999999999999996 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.058979652020053085 0.675 >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 GGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGC 14 0.35000000000000003 No Hit GGCGCCCGAGCGGCCTTCAAATTCGCCCAGATCTGTTGGCCGCTGAATTA 13 0.325 No Hit GTCAGCCTTTTATCTAATAAATGCGCCCCTCCCAGAAGTCGGGGTTTGTT 6 0.15 No Hit GTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACT 6 0.15 No Hit CTTGCGACCATACTCCCCCCGGAACCCAAAGACTTTGATTTCTCATAAGG 6 0.15 No Hit CTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGG 5 0.125 No Hit GGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTC 5 0.125 No Hit CTCCTCAGAAGTGGCTTCTTAATGTCACTCTCAACTTTCTCGAGAGCTTC 5 0.125 No Hit >>END_MODULE >>Adapter Content warn #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 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.075 0.0 0.0 0.0 0.0 66-67 0.075 0.0 0.0 0.0 0.0 68-69 0.1 0.0 0.0 0.0 0.0 70-71 0.1 0.0 0.0 0.0 0.0 72-73 0.1 0.0 0.0 0.0 0.0 74-75 0.125 0.0 0.0 0.0 0.0 76-77 0.1375 0.0 0.0 0.0 0.0 78-79 0.16249999999999998 0.0 0.0 0.0 0.0 80-81 0.21250000000000002 0.0 0.0 0.0 0.0 82-83 0.25 0.0 0.0 0.0 0.0 84-85 0.275 0.0 0.0 0.0 0.0 86-87 0.3125 0.0 0.0 0.0 0.0 88-89 0.36250000000000004 0.0 0.0 0.0 0.0 90-91 0.4375 0.0 0.0 0.0 0.0 92-93 0.48750000000000004 0.0 0.0 0.0 0.0 94-95 0.55 0.0 0.0 0.0 0.0 96-97 0.625 0.0 0.0 0.0 0.0 98-99 0.675 0.0 0.0 0.0 0.0 100-101 0.8125 0.0 0.0 0.0 0.0 102-103 1.0125 0.0 0.0 0.0 0.0 104-105 1.125 0.0 0.0 0.0 0.0 106-107 1.3624999999999998 0.0 0.0 0.0 0.0 108-109 1.5875 0.0 0.0 0.0 0.0 110-111 1.7999999999999998 0.0 0.0 0.0 0.0 112-113 2.0 0.0 0.0 0.0 0.0 114-115 2.15 0.0 0.0 0.0 0.0 116-117 2.3625 0.0 0.0 0.0 0.0 118-119 2.4875 0.0 0.0 0.0 0.0 120-121 2.7 0.0 0.0 0.0 0.0 122-123 2.9375 0.0 0.0 0.0 0.0 124-125 3.4625 0.0 0.0 0.0 0.0 126-127 3.8 0.0 0.0 0.0 0.0 128-129 4.3875 0.0 0.0 0.0 0.0 130-131 4.8875 0.0 0.0 0.0 0.0 132-133 5.300000000000001 0.0 0.0 0.0 0.0 134-135 6.0 0.0 0.0 0.0 0.0 136-137 6.5375 0.0 0.0 0.0 0.0 138-139 6.9125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR18694364 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR18694364_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 34.3865 37.0 37.0 37.0 25.0 37.0 2 35.2205 37.0 37.0 37.0 25.0 37.0 3 35.0645 37.0 37.0 37.0 25.0 37.0 4 35.3085 37.0 37.0 37.0 25.0 37.0 5 35.128 37.0 37.0 37.0 25.0 37.0 6 35.2745 37.0 37.0 37.0 25.0 37.0 7 35.131 37.0 37.0 37.0 25.0 37.0 8 35.3055 37.0 37.0 37.0 25.0 37.0 9 35.469 37.0 37.0 37.0 37.0 37.0 10-14 35.5125 37.0 37.0 37.0 37.0 37.0 15-19 35.4862 37.0 37.0 37.0 34.6 37.0 20-24 35.4016 37.0 37.0 37.0 34.6 37.0 25-29 35.4989 37.0 37.0 37.0 32.2 37.0 30-34 35.7445 37.0 37.0 37.0 37.0 37.0 35-39 35.6186 37.0 37.0 37.0 37.0 37.0 40-44 35.321799999999996 37.0 37.0 37.0 29.8 37.0 45-49 35.4594 37.0 37.0 37.0 37.0 37.0 50-54 34.9301 37.0 37.0 37.0 29.8 37.0 55-59 34.2187 37.0 37.0 37.0 25.0 37.0 60-64 34.9921 37.0 37.0 37.0 27.4 37.0 65-69 34.2509 37.0 34.6 37.0 27.4 37.0 70-74 32.9403 37.0 29.8 37.0 22.2 37.0 75-79 33.5493 37.0 34.6 37.0 22.2 37.0 80-84 34.5465 37.0 37.0 37.0 25.0 37.0 85-89 32.73350000000001 37.0 32.2 37.0 19.4 37.0 90-94 34.090700000000005 37.0 37.0 37.0 25.0 37.0 95-99 33.944100000000006 37.0 37.0 37.0 25.0 37.0 100-104 33.45440000000001 37.0 37.0 37.0 25.0 37.0 105-109 34.238099999999996 37.0 37.0 37.0 25.0 37.0 110-114 34.5479 37.0 37.0 37.0 25.0 37.0 115-119 34.4401 37.0 37.0 37.0 25.0 37.0 120-124 34.0565 37.0 37.0 37.0 25.0 37.0 125-129 34.0185 37.0 37.0 37.0 25.0 37.0 130-134 33.6729 37.0 34.6 37.0 25.0 37.0 135-139 32.094 37.0 27.4 37.0 13.8 37.0 140-144 31.601199999999995 37.0 25.0 37.0 11.0 37.0 145-149 31.1435 37.0 25.0 37.0 11.0 37.0 150-151 30.787 37.0 25.0 37.0 11.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 16 1.0 17 6.0 18 2.0 19 2.0 20 4.0 21 4.0 22 3.0 23 4.0 24 7.0 25 7.0 26 13.0 27 21.0 28 23.0 29 40.0 30 66.0 31 152.0 32 292.0 33 540.0 34 1188.0 35 1440.0 36 185.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 42.775 18.8 9.975000000000001 28.449999999999996 2 30.525000000000002 20.775 27.975 20.724999999999998 3 21.3 23.5 30.325000000000003 24.875 4 27.400000000000002 30.099999999999998 20.849999999999998 21.65 5 27.900000000000002 32.9 19.325 19.875 6 23.400000000000002 35.225 19.475 21.9 7 22.975 19.325 34.775 22.925 8 22.275 22.925 26.125 28.675 9 24.85 22.3 26.575 26.275 10-14 25.105 26.83 23.66 24.404999999999998 15-19 25.715 24.98 24.615000000000002 24.69 20-24 25.77 26.115 23.674999999999997 24.44 25-29 26.3 25.330000000000002 24.41 23.96 30-34 25.324999999999996 25.1 25.31 24.265 35-39 25.46 26.015 24.490000000000002 24.035 40-44 25.765 24.759999999999998 25.169999999999998 24.305 45-49 25.755 25.619999999999997 24.935 23.69 50-54 24.474999999999998 25.56 25.805 24.16 55-59 25.395 25.080000000000002 25.355 24.169999999999998 60-64 26.474999999999998 25.655 24.529999999999998 23.34 65-69 26.340000000000003 25.11 24.69 23.86 70-74 26.72 25.2 24.279999999999998 23.799999999999997 75-79 27.575 23.515 25.05 23.86 80-84 26.22 25.919999999999998 24.125 23.735 85-89 23.835 27.41 24.474999999999998 24.279999999999998 90-94 26.6 25.25 24.95 23.200000000000003 95-99 26.25 25.180000000000003 24.435000000000002 24.135 100-104 26.135 25.385 24.86 23.62 105-109 26.56 25.655 24.89 22.895 110-114 26.355 25.924999999999997 24.505 23.215 115-119 26.85 25.790000000000003 24.545 22.814999999999998 120-124 26.634999999999998 25.540000000000003 24.685000000000002 23.14 125-129 26.38 25.669999999999998 24.425 23.525 130-134 27.52 26.305 23.745 22.43 135-139 26.58 24.94 25.15 23.330000000000002 140-144 26.68 25.81 24.215 23.294999999999998 145-149 27.215 25.779999999999998 24.104999999999997 22.900000000000002 150-151 25.025 26.5875 26.6 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 0.5 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 0.5 17 1.0 18 1.0 19 0.5 20 0.5 21 1.0 22 2.0 23 1.5 24 0.5 25 0.5 26 1.0 27 2.0 28 1.5 29 5.5 30 9.5 31 10.5 32 10.0 33 10.0 34 17.0 35 31.5 36 49.5 37 59.0 38 68.5 39 89.5 40 118.0 41 133.0 42 152.5 43 174.5 44 180.5 45 185.0 46 194.0 47 185.0 48 176.5 49 174.5 50 165.0 51 143.0 52 121.5 53 141.5 54 151.5 55 127.0 56 110.5 57 101.0 58 86.0 59 85.5 60 90.0 61 82.5 62 69.0 63 64.0 64 60.0 65 56.5 66 58.0 67 46.5 68 41.0 69 41.0 70 32.5 71 23.5 72 13.0 73 11.0 74 11.0 75 6.0 76 4.5 77 4.5 78 2.0 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 0.5 88 0.5 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 86.5 #Duplication Level Percentage of deduplicated Percentage of total 1 88.46820809248554 76.525 2 8.988439306358382 15.55 3 1.8497109826589597 4.8 4 0.4335260115606936 1.5 5 0.08670520231213873 0.375 6 0.05780346820809249 0.3 7 0.028901734104046246 0.17500000000000002 8 0.028901734104046246 0.2 9 0.0 0.0 >10 0.05780346820809249 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 CCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGCAA 12 0.3 No Hit GGTTTTACTCCACATTCACTACATGTTATTAACCTTTATTTCTTGTTCTT 11 0.27499999999999997 No Hit GGAGTCTGACATGCGTGCGAGTCGACGGGTTCTGAAACCTGGGATGCGCA 8 0.2 No Hit CTCCGCAGCTAGCTTCTTAGAGGGACTATCGCCGTTTAGGCGACGGAAGT 7 0.17500000000000002 No Hit GTTTGAGGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCAC 6 0.15 No Hit ACCAGGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAT 6 0.15 No Hit AGAAAAGGCAGATCTTCTTTCTGATTCTCAGAGAATTAAATATACTATTG 5 0.125 No Hit GATTAAGCCATGCATGTGCAAGTATGAACTAATTTGAACTGTGAAACTGC 5 0.125 No Hit GGCGGGACTACCCGCTGAGTTTAAGCATATAAATAAGCGGAGGAGAAGAA 5 0.125 No Hit >>END_MODULE >>Adapter Content warn #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 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.075 0.0 0.0 0.0 0.0 66-67 0.075 0.0 0.0 0.0 0.0 68-69 0.1 0.0 0.0 0.0 0.0 70-71 0.1 0.0 0.0 0.0 0.0 72-73 0.1 0.0 0.0 0.0 0.0 74-75 0.125 0.0 0.0 0.0 0.0 76-77 0.125 0.0 0.0 0.0 0.0 78-79 0.1375 0.0 0.0 0.0 0.0 80-81 0.15 0.0 0.0 0.0 0.0 82-83 0.175 0.0 0.0 0.0 0.0 84-85 0.2 0.0 0.0 0.0 0.0 86-87 0.2375 0.0 0.0 0.0 0.0 88-89 0.2875 0.0 0.0 0.0 0.0 90-91 0.3625 0.0 0.0 0.0 0.0 92-93 0.4125 0.0 0.0 0.0 0.0 94-95 0.475 0.0 0.0 0.0 0.0 96-97 0.55 0.0 0.0 0.0 0.0 98-99 0.6000000000000001 0.0 0.0 0.0 0.0 100-101 0.7124999999999999 0.0 0.0 0.0 0.0 102-103 0.9125000000000001 0.0 0.0 0.0 0.0 104-105 1.025 0.0 0.0 0.0 0.0 106-107 1.2374999999999998 0.0 0.0 0.0 0.0 108-109 1.4625 0.0 0.0 0.0 0.0 110-111 1.6625 0.0 0.0 0.0 0.0 112-113 1.85 0.0 0.0 0.0 0.0 114-115 2.0 0.0 0.0 0.0 0.0 116-117 2.2125 0.0 0.0 0.0 0.0 118-119 2.3375 0.0 0.0 0.0 0.0 120-121 2.55 0.0 0.0 0.0 0.0 122-123 2.7625 0.0 0.0 0.0 0.0 124-125 3.2875 0.0 0.0 0.0 0.0 126-127 3.5999999999999996 0.0 0.0 0.0 0.0 128-129 4.2125 0.0 0.0 0.0 0.0 130-131 4.725 0.0 0.0 0.0 0.0 132-133 5.1375 0.0 0.0 0.0 0.0 134-135 5.825 0.0 0.0 0.0 0.0 136-137 6.362500000000001 0.0 0.0 0.0 0.0 138-139 6.75 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTCCTGC 10 0.006830828 145.0 6 >>END_MODULE Read 779603 spots for SRR18694364.sra Written 779603 spots for SRR18694364.sra Read 779603 spots for SRR18694364.sra Written 779603 spots for SRR18694364.sra Read 779603 spots for SRR18694364.sra Written 779603 spots for SRR18694364.sra Read 779603 spots for SRR18694364.sra Written 779603 spots for SRR18694364.sra Read 779603 spots for SRR18694364.sra Written 779603 spots for SRR18694364.sra Read 779603 spots for SRR18694364.sra Written 779603 spots for SRR18694364.sra Read 779603 spots for SRR18694364.sra Written 779603 spots for SRR18694364.sra Read 779603 spots for SRR18694364.sra Written 779603 spots for SRR18694364.sra Read 779603 spots for SRR18694364.sra Written 779603 spots for SRR18694364.sra Read 779603 spots for SRR18694364.sra Written 779603 spots for SRR18694364.sra Read 779603 spots for SRR18694364.sra Written 779603 spots for SRR18694364.sra Read 779603 spots for SRR18694364.sra Written 779603 spots for SRR18694364.sra Read 779603 spots for SRR18694364.sra Written 779603 spots for SRR18694364.sra Read 779603 spots for SRR18694364.sra Written 779603 spots for SRR18694364.sra Read 779603 spots for SRR18694364.sra Written 779603 spots for SRR18694364.sra Read 779603 spots for SRR18694364.sra Written 779603 spots for SRR18694364.sra Read 779603 spots for SRR18694364.sra Written 779603 spots for SRR18694364.sra Read 779615 spots for SRR18694364.sra Written 779615 spots for SRR18694364.sra Read 779603 spots for SRR18694364.sra Written 779603 spots for SRR18694364.sra Read 779603 spots for SRR18694364.sra Written 779603 spots for SRR18694364.sra SRR ids: ['SRR18694364.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_ptt8d5ea SRR18694364.sra spots: 15592072 blocks: [[1, 779603], [779604, 1559206], [1559207, 2338809], [2338810, 3118412], [3118413, 3898015], [3898016, 4677618], [4677619, 5457221], [5457222, 6236824], [6236825, 7016427], [7016428, 7796030], [7796031, 8575633], [8575634, 9355236], [9355237, 10134839], [10134840, 10914442], [10914443, 11694045], [11694046, 12473648], [12473649, 13253251], [13253252, 14032854], [14032855, 14812457], [14812458, 15592072]] SRR18694364 file size 5277167 SRR18694364 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 SRR18694364 SRR18694364_1.fastq SRR18694364_2.fastq Input file: SRR18694364_1.fastq Paired file: SRR18694364_2.fastq trimmed: SRR18694364-trimmed-pair1.fastq, SRR18694364-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 06:03:38 2024 >> started Tue Dec 10 06:03:56 2024 >> done (17.904s) 15592072 read pairs processed; of these: 133 ( 0.00%) short read pairs filtered out after trimming by size control 2120 ( 0.01%) empty read pairs filtered out after trimming by size control 15589819 (99.99%) read pairs available; of these: 1777595 (11.40%) trimmed read pairs available after processing 13812224 (88.60%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 8 0.00% 19 15 0.00% 20 13 0.00% 21 15 0.00% 22 23 0.00% 23 12 0.00% 24 25 0.00% 25 17 0.00% 26 26 0.00% 27 22 0.00% 28 28 0.00% 29 34 0.00% 30 36 0.00% 31 44 0.00% 32 40 0.00% 33 31 0.00% 34 40 0.00% 35 40 0.00% 36 39 0.00% 37 33 0.00% 38 48 0.00% 39 43 0.00% 40 39 0.00% 41 48 0.00% 42 75 0.00% 43 45 0.00% 44 69 0.00% 45 57 0.00% 46 63 0.00% 47 71 0.00% 48 73 0.00% 49 88 0.00% 50 116 0.00% 51 95 0.00% 52 113 0.00% 53 106 0.00% 54 114 0.00% 55 124 0.00% 56 160 0.00% 57 129 0.00% 58 179 0.00% 59 207 0.00% 60 228 0.00% 61 249 0.00% 62 305 0.00% 63 342 0.00% 64 349 0.00% 65 317 0.00% 66 433 0.00% 67 460 0.00% 68 536 0.00% 69 558 0.00% 70 680 0.00% 71 813 0.01% 72 863 0.01% 73 1075 0.01% 74 1149 0.01% 75 1169 0.01% 76 1368 0.01% 77 1458 0.01% 78 1541 0.01% 79 1887 0.01% 80 2065 0.01% 81 2142 0.01% 82 2605 0.02% 83 2840 0.02% 84 3157 0.02% 85 3506 0.02% 86 4138 0.03% 87 4346 0.03% 88 4614 0.03% 89 4902 0.03% 90 5451 0.03% 91 5718 0.04% 92 6520 0.04% 93 7069 0.05% 94 7436 0.05% 95 8189 0.05% 96 8645 0.06% 97 9142 0.06% 98 9705 0.06% 99 10329 0.07% 100 11026 0.07% 101 11629 0.07% 102 11908 0.08% 103 12703 0.08% 104 13397 0.09% 105 14260 0.09% 106 15016 0.10% 107 15469 0.10% 108 15969 0.10% 109 16793 0.11% 110 17559 0.11% 111 18479 0.12% 112 19360 0.12% 113 20025 0.13% 114 21142 0.14% 115 22108 0.14% 116 22721 0.15% 117 23624 0.15% 118 23889 0.15% 119 25357 0.16% 120 27293 0.18% 121 26894 0.17% 122 28350 0.18% 123 30293 0.19% 124 31081 0.20% 125 31862 0.20% 126 32756 0.21% 127 33219 0.21% 128 34278 0.22% 129 36053 0.23% 130 36588 0.23% 131 37782 0.24% 132 38941 0.25% 133 40185 0.26% 134 39877 0.26% 135 41322 0.27% 136 42948 0.28% 137 43412 0.28% 138 44075 0.28% 139 45562 0.29% 140 46732 0.30% 141 47438 0.30% 142 49072 0.31% 143 50303 0.32% 144 51808 0.33% 145 51566 0.33% 146 52617 0.34% 147 54365 0.35% 148 55274 0.35% 149 56057 0.36% 150 56256 0.36% 151 13812224 88.60% 15589819 reads passed initial QC criterion=sequence-density sequence-density=0.20 sequence-density-rank=1 fanout-score=4.16 fanout-score-rank=26 prefix-density=0.24 prefix-fanout=3.5 sequence=GTGATGGTCTTGCC criterion=fanout-score sequence-density=0.04 sequence-density-rank=35 fanout-score=24.30 fanout-score-rank=1 prefix-density=0.17 prefix-fanout=4.9 sequence=AGCATCACCGTTCTTCAAGAACTTGGGCTCCTTCTCCAGCTCCTT criterion=sequence-density sequence-density=0.27 sequence-density-rank=1 fanout-score=2.67 fanout-score-rank=29 prefix-density=0.31 prefix-fanout=2.4 sequence=CTGAACGCCTCTAAGTCAGAATCCA criterion=fanout-score sequence-density=0.01 sequence-density-rank=36 fanout-score=90.76 fanout-score-rank=1 prefix-density=0.08 prefix-fanout=7.9 sequence=GTGCTCATCATCTTGTTTAATACCAAAGCTCTTCATATTCTCCTCCTTGATTTCATCAGCTTGAGGTTAGAGAGATTTGGAAGATGTCTTGCAGCTGTGGATCAAGCTGCAACTGTGGCTCAAACTGCACTTGCGGGAAGATGTACCCAGACCTGGCAGAGCAGGCCAGCACCACCAGCAGCACCCAGGCCCAGGTGGTGGTTCTCGGCATGGCGCCGGAGAAGAAACAGGAGCAGTTCGAGATGGCCGGCGTGTCCGGCGAAGGGTGCAGCTGCGG SRR18694364 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 10 06:10:50 Started mapping on | Dec 10 06:10:51 Finished on | Dec 10 06:18:53 Mapping speed, Million of reads per hour | 116.44 Number of input reads | 15589819 Average input read length | 296 UNIQUE READS: Uniquely mapped reads number | 11052126 Uniquely mapped reads % | 70.89% Average mapped length | 295.37 Number of splices: Total | 11572781 Number of splices: Annotated (sjdb) | 10901797 Number of splices: GT/AG | 11416793 Number of splices: GC/AG | 129445 Number of splices: AT/AC | 7375 Number of splices: Non-canonical | 19168 Mismatch rate per base, % | 0.43% Deletion rate per base | 0.01% Deletion average length | 2.40 Insertion rate per base | 0.01% Insertion average length | 2.55 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 138547 % of reads mapped to multiple loci | 0.89% Number of reads mapped to too many loci | 178494 % of reads mapped to too many loci | 1.14% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 14.02% % of reads unmapped: other | 13.05% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 4399146 4399146 4399146 N_multimapping 138547 138547 138547 N_noFeature 383079 10780682 465064 N_ambiguous 223793 1265 34766 UnstrandedReadsAssigned:10445254 PositiveStrandReadsAssigned:270179 NegativeStrandReadsAssigned:10552296 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR18694364 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: SRR18694364-trimmed-pair1.fastq SRR18694364-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 15,589,819 reads, 10,777,276 reads pseudoaligned [quant] estimated average fragment length: 248.897 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,151 rounds 52973 SRR18694364.ke.tsv 35125 SRR18694364.se.tsv 88098 total ==> SRR18694364.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 688.575 0 0 PNS24247 1044 796.103 52.0249 9.31458 PNS24249 1928 1680.1 42.2857 3.58739 PNS24246 1044 796.103 52.0249 9.31458 PNS24248 1044 796.103 52.0249 9.31458 PNS24244 1471 1223.1 102.64 11.9611 PNS24243 293 95.7302 0 0 KQK14069 1603 1355.1 2733.51 287.521 KQK14071 474 242.815 37.5836 22.062 ==> SRR18694364.se.tsv <== BRADI_1g14170v3 3011 BRADI_1g53295v3 48 BRADI_1g59795v3 218 BRADI_1g07683v3 0 BRADI_1g00485v3 10 BRADI_1g20270v3 305 BRADI_1g74790v3 222 BRADI_1g09890v3 0 BRADI_1g77505v3 65 BRADI_1g48960v3 0 SRR18694364 completed mapping pipeline successfully