Starting /dee2/code/volunteer_pipeline.sh SRR12670110 current disk space = 3057468502016 free memory = 1579693984 SRR12670110 SRAfilesize d2f517cdbff0dcb6c3a59589681ac018 SRR12670110.sra SRR12670110.sra file validated SRR12670110 is paired end SRR12670110 is conventional basespace SRR12670110 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670110_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 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.6705 37.0 37.0 37.0 37.0 37.0 2 36.48225 37.0 37.0 37.0 37.0 37.0 3 36.5985 37.0 37.0 37.0 37.0 37.0 4 36.7055 37.0 37.0 37.0 37.0 37.0 5 36.6835 37.0 37.0 37.0 37.0 37.0 6 36.705 37.0 37.0 37.0 37.0 37.0 7 36.5295 37.0 37.0 37.0 37.0 37.0 8 36.655 37.0 37.0 37.0 37.0 37.0 9 36.6105 37.0 37.0 37.0 37.0 37.0 10-14 36.6549 37.0 37.0 37.0 37.0 37.0 15-19 36.6186 37.0 37.0 37.0 37.0 37.0 20-24 36.581900000000005 37.0 37.0 37.0 37.0 37.0 25-29 36.572900000000004 37.0 37.0 37.0 37.0 37.0 30-34 36.5854 37.0 37.0 37.0 37.0 37.0 35-39 36.5278 37.0 37.0 37.0 37.0 37.0 40-44 36.4921 37.0 37.0 37.0 37.0 37.0 45-49 36.4849 37.0 37.0 37.0 37.0 37.0 50-54 36.481700000000004 37.0 37.0 37.0 37.0 37.0 55-59 36.503299999999996 37.0 37.0 37.0 37.0 37.0 60-64 36.447399999999995 37.0 37.0 37.0 37.0 37.0 65-69 36.3825 37.0 37.0 37.0 37.0 37.0 70-74 36.3915 37.0 37.0 37.0 37.0 37.0 75-79 36.3464 37.0 37.0 37.0 37.0 37.0 80-84 36.3645 37.0 37.0 37.0 37.0 37.0 85-89 36.3344 37.0 37.0 37.0 37.0 37.0 90-94 36.3326 37.0 37.0 37.0 37.0 37.0 95-99 36.2355 37.0 37.0 37.0 37.0 37.0 100-104 36.2753 37.0 37.0 37.0 37.0 37.0 105-109 36.2385 37.0 37.0 37.0 37.0 37.0 110-114 36.1968 37.0 37.0 37.0 37.0 37.0 115-119 36.2292 37.0 37.0 37.0 37.0 37.0 120-124 36.0642 37.0 37.0 37.0 37.0 37.0 125-129 36.0459 37.0 37.0 37.0 37.0 37.0 130-134 36.018 37.0 37.0 37.0 37.0 37.0 135-139 35.8792 37.0 37.0 37.0 37.0 37.0 140-144 35.7921 37.0 37.0 37.0 37.0 37.0 145-149 35.6516 37.0 37.0 37.0 37.0 37.0 150-151 35.33325 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 23 1.0 24 0.0 25 3.0 26 1.0 27 7.0 28 6.0 29 11.0 30 14.0 31 30.0 32 39.0 33 64.0 34 133.0 35 333.0 36 3017.0 37 341.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 37.025000000000006 11.3 6.075 45.6 2 17.764971185166626 11.676271611125031 38.51165121523428 32.047105988474065 3 16.400000000000002 14.825 28.349999999999998 40.425 4 23.075000000000003 23.575 21.575 31.775 5 23.625 29.375 24.075 22.925 6 20.200000000000003 33.025 24.925 21.85 7 15.725 26.224999999999998 41.775 16.275000000000002 8 17.7 25.900000000000002 33.2 23.200000000000003 9 18.825 22.75 34.725 23.7 10-14 19.905 29.53 27.644999999999996 22.919999999999998 15-19 19.86 27.405 28.235 24.5 20-24 19.915 27.400000000000002 28.185 24.5 25-29 20.775 28.055000000000003 28.225 22.945 30-34 20.674999999999997 28.389999999999997 27.49 23.445 35-39 20.255000000000003 28.9 27.675 23.169999999999998 40-44 21.065 28.08 27.52 23.335 45-49 19.835 27.79 27.975 24.4 50-54 20.52 28.42 27.845 23.215 55-59 19.99 27.97 28.53 23.51 60-64 20.87 27.744999999999997 27.339999999999996 24.044999999999998 65-69 20.29 28.12 28.13 23.46 70-74 20.785 27.76 27.939999999999998 23.515 75-79 19.825 27.975 28.08 24.12 80-84 19.759999999999998 28.705000000000002 27.63 23.905 85-89 19.794999999999998 27.465 28.384999999999998 24.355 90-94 20.755000000000003 27.915 27.315 24.015 95-99 21.01 28.775000000000002 26.55 23.665 100-104 21.08 29.01 26.44 23.47 105-109 21.584999999999997 27.334999999999997 27.62 23.46 110-114 20.815 28.89 26.47 23.825 115-119 21.355 28.205000000000002 26.905 23.535 120-124 21.125 27.985 26.529999999999998 24.36 125-129 21.315 28.389999999999997 26.26 24.035 130-134 21.55 28.65 26.334999999999997 23.465 135-139 21.884999999999998 27.705000000000002 26.02 24.39 140-144 21.12 27.935 26.77 24.175 145-149 21.02 27.165 27.165 24.65 150-151 20.7875 27.287499999999998 27.625 24.3 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.5 17 0.5 18 0.0 19 0.5 20 0.5 21 0.5 22 1.0 23 1.5 24 1.5 25 1.0 26 2.0 27 4.5 28 6.5 29 8.0 30 12.0 31 19.0 32 25.5 33 39.0 34 46.5 35 66.0 36 88.0 37 93.5 38 110.5 39 160.0 40 192.5 41 207.5 42 244.5 43 261.0 44 265.0 45 277.5 46 262.5 47 242.5 48 237.5 49 209.0 50 177.5 51 148.0 52 132.5 53 122.5 54 90.5 55 60.0 56 52.5 57 40.0 58 25.0 59 22.5 60 16.5 61 9.5 62 5.0 63 3.5 64 2.5 65 1.5 66 0.5 67 0.5 68 0.5 69 0.0 70 0.5 71 0.5 72 0.0 73 0.0 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 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 0.22499999999999998 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 81.0 #Duplication Level Percentage of deduplicated Percentage of total 1 82.1604938271605 66.55 2 13.61111111111111 22.05 3 3.117283950617284 7.575 4 0.8950617283950617 2.9000000000000004 5 0.15432098765432098 0.625 6 0.06172839506172839 0.3 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source GCCAATTCATCTAGTGCAAGCTTGTCTCTTCTGGAAGATACTGAAGGTCC 6 0.15 No Hit GCTCTGTGAGGCTTAAAATTTTCTGGAAAGGTGGTAATTGCTTTGCCTAC 6 0.15 No Hit GGTTGGAGGCCACACCTGCATGCATTGAACTCTTCCGCCATTGCTTGCAA 5 0.125 No Hit CCGGAAAAGATTGCACAGGCTCCATCCATGATATTGAGTAGAAGCACTTG 5 0.125 No Hit ACACAACCGGCTTCAACCAAAGACACATTCTCAGTTGTGTAGGCACGGTC 5 0.125 No Hit GGCAGATACATAGAAAACCCCCTCTAAACTAATCACTCTGGTACCTTAAA 5 0.125 No Hit GCACCCATGGTGGCAATTTCCGTGCAGGAATTTCTCTTGGTATCTGGTTT 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 0.025 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 0.15 0.0 0.0 0.0 0.0 64-65 0.1875 0.0 0.0 0.0 0.0 66-67 0.2 0.0 0.0 0.0 0.0 68-69 0.2 0.0 0.0 0.0 0.0 70-71 0.2625 0.0 0.0 0.0 0.0 72-73 0.3125 0.0 0.0 0.0 0.0 74-75 0.375 0.0 0.0 0.0 0.0 76-77 0.44999999999999996 0.0 0.0 0.0 0.0 78-79 0.575 0.0 0.0 0.0 0.0 80-81 0.6375 0.0 0.0 0.0 0.0 82-83 0.7875 0.0 0.0 0.0 0.0 84-85 0.9624999999999999 0.0 0.0 0.0 0.0 86-87 1.1625 0.0 0.0 0.0 0.0 88-89 1.4500000000000002 0.0 0.0 0.0 0.0 90-91 1.825 0.0 0.0 0.0 0.0 92-93 2.2125 0.0 0.0 0.0 0.0 94-95 2.4749999999999996 0.0 0.0 0.0 0.0 96-97 2.925 0.0 0.0 0.0 0.0 98-99 3.425 0.0 0.0 0.0 0.0 100-101 4.2 0.0 0.0 0.0 0.0 102-103 4.85 0.0 0.0 0.0 0.0 104-105 5.3875 0.0 0.0 0.0 0.0 106-107 5.7875 0.0 0.0 0.0 0.0 108-109 6.199999999999999 0.0 0.0 0.0 0.0 110-111 6.675 0.0 0.0 0.0 0.0 112-113 7.2875 0.0 0.0 0.0 0.0 114-115 8.0125 0.0 0.0 0.0 0.0 116-117 8.775 0.0 0.0 0.0 0.0 118-119 9.6125 0.0 0.0 0.0 0.0 120-121 10.65 0.0 0.0 0.0 0.0 122-123 11.5375 0.0 0.0 0.0 0.0 124-125 12.8125 0.0 0.0 0.0 0.0 126-127 13.6625 0.0 0.0 0.0 0.0 128-129 14.6375 0.0 0.0 0.0 0.0 130-131 15.575 0.0 0.0 0.0 0.0 132-133 16.612499999999997 0.0 0.0 0.0 0.0 134-135 17.475 0.0 0.0 0.0 0.0 136-137 18.2375 0.0 0.0 0.0 0.0 138-139 19.15 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GTACTCT 40 0.0076550315 18.125 140-144 >>END_MODULE SRR12670110 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670110_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 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.371 37.0 37.0 37.0 37.0 37.0 2 36.3585 37.0 37.0 37.0 37.0 37.0 3 36.4245 37.0 37.0 37.0 37.0 37.0 4 36.3775 37.0 37.0 37.0 37.0 37.0 5 36.3665 37.0 37.0 37.0 37.0 37.0 6 36.4905 37.0 37.0 37.0 37.0 37.0 7 36.3845 37.0 37.0 37.0 37.0 37.0 8 36.493 37.0 37.0 37.0 37.0 37.0 9 36.455 37.0 37.0 37.0 37.0 37.0 10-14 36.4582 37.0 37.0 37.0 37.0 37.0 15-19 36.468399999999995 37.0 37.0 37.0 37.0 37.0 20-24 36.372 37.0 37.0 37.0 37.0 37.0 25-29 36.3991 37.0 37.0 37.0 37.0 37.0 30-34 36.4145 37.0 37.0 37.0 37.0 37.0 35-39 36.3358 37.0 37.0 37.0 37.0 37.0 40-44 36.3341 37.0 37.0 37.0 37.0 37.0 45-49 36.329100000000004 37.0 37.0 37.0 37.0 37.0 50-54 36.2826 37.0 37.0 37.0 37.0 37.0 55-59 36.2672 37.0 37.0 37.0 37.0 37.0 60-64 36.2757 37.0 37.0 37.0 37.0 37.0 65-69 36.258799999999994 37.0 37.0 37.0 37.0 37.0 70-74 36.213 37.0 37.0 37.0 37.0 37.0 75-79 36.2211 37.0 37.0 37.0 37.0 37.0 80-84 36.1343 37.0 37.0 37.0 37.0 37.0 85-89 36.114799999999995 37.0 37.0 37.0 37.0 37.0 90-94 36.148900000000005 37.0 37.0 37.0 37.0 37.0 95-99 36.0517 37.0 37.0 37.0 37.0 37.0 100-104 36.0363 37.0 37.0 37.0 37.0 37.0 105-109 35.927800000000005 37.0 37.0 37.0 37.0 37.0 110-114 35.9274 37.0 37.0 37.0 37.0 37.0 115-119 36.0202 37.0 37.0 37.0 37.0 37.0 120-124 35.8183 37.0 37.0 37.0 37.0 37.0 125-129 35.7201 37.0 37.0 37.0 37.0 37.0 130-134 35.5737 37.0 37.0 37.0 37.0 37.0 135-139 35.4079 37.0 37.0 37.0 37.0 37.0 140-144 35.3067 37.0 37.0 37.0 37.0 37.0 145-149 34.9889 37.0 37.0 37.0 25.0 37.0 150-151 34.784 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 2.0 13 0.0 14 3.0 15 1.0 16 0.0 17 0.0 18 0.0 19 3.0 20 1.0 21 0.0 22 2.0 23 1.0 24 5.0 25 3.0 26 3.0 27 10.0 28 12.0 29 15.0 30 19.0 31 23.0 32 48.0 33 91.0 34 194.0 35 519.0 36 2712.0 37 333.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 35.199999999999996 22.925 9.825000000000001 32.05 2 27.425 26.900000000000002 30.825000000000003 14.85 3 19.3 29.675 30.9 20.125 4 21.8 33.300000000000004 23.875 21.025 5 23.35 38.5 22.225 15.925 6 19.675 39.975 22.650000000000002 17.7 7 18.3 23.05 39.525 19.125 8 18.825 26.525 30.55 24.099999999999998 9 22.35 23.275000000000002 30.725 23.65 10-14 22.845 28.955 26.985 21.215 15-19 23.25 28.08 27.200000000000003 21.47 20-24 22.95 28.77 27.439999999999998 20.84 25-29 22.115000000000002 28.63 27.88 21.375 30-34 22.919999999999998 28.050000000000004 27.76 21.27 35-39 22.545 27.950000000000003 28.625 20.880000000000003 40-44 22.71 28.215 27.275 21.8 45-49 22.314999999999998 27.88 28.9 20.905 50-54 22.58 28.000000000000004 27.794999999999998 21.625 55-59 22.53 28.299999999999997 27.98 21.19 60-64 23.315 27.084999999999997 28.389999999999997 21.21 65-69 23.095 28.17 28.285 20.45 70-74 23.115 27.845 27.345000000000002 21.695 75-79 23.095 27.57 27.85 21.485000000000003 80-84 23.745 27.900000000000002 27.894999999999996 20.46 85-89 24.0 27.87 27.32 20.810000000000002 90-94 24.14 27.715 27.195000000000004 20.95 95-99 24.285 27.85 26.950000000000003 20.915 100-104 24.29 27.939999999999998 26.61 21.16 105-109 24.785 27.584999999999997 27.500000000000004 20.13 110-114 24.205 28.48 27.1 20.215 115-119 25.430000000000003 28.21 26.5 19.86 120-124 25.900000000000002 28.535 26.669999999999998 18.895 125-129 25.795 27.715 26.39 20.1 130-134 26.515 27.725 26.040000000000003 19.72 135-139 27.46 27.250000000000004 26.14 19.15 140-144 28.9 27.125 25.095 18.88 145-149 29.28 26.840000000000003 25.7 18.18 150-151 30.325000000000003 26.724999999999998 25.112499999999997 17.837500000000002 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.5 9 0.5 10 0.0 11 0.0 12 0.0 13 0.5 14 0.5 15 0.0 16 0.0 17 0.5 18 0.5 19 0.0 20 0.5 21 0.5 22 1.5 23 2.0 24 1.5 25 5.0 26 5.0 27 2.0 28 2.0 29 5.5 30 15.0 31 23.0 32 35.5 33 40.5 34 48.0 35 68.0 36 79.0 37 104.5 38 136.0 39 174.0 40 210.5 41 227.0 42 255.0 43 267.0 44 262.5 45 268.0 46 259.5 47 251.5 48 227.0 49 191.0 50 167.0 51 136.5 52 123.5 53 102.0 54 79.5 55 58.5 56 39.0 57 36.0 58 23.5 59 18.0 60 14.5 61 9.0 62 7.5 63 5.0 64 1.5 65 1.0 66 1.0 67 0.0 68 0.5 69 1.0 70 0.5 71 0.5 72 0.5 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 0.5 99 0.5 100 1.0 >>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 80.7 #Duplication Level Percentage of deduplicated Percentage of total 1 82.06319702602231 66.225 2 13.754646840148698 22.2 3 3.004956629491945 7.2749999999999995 4 0.8054522924411399 2.6 5 0.21685254027261464 0.8750000000000001 6 0.09293680297397769 0.44999999999999996 7 0.030978934324659233 0.17500000000000002 8 0.030978934324659233 0.2 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 AGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATC 8 0.2 No Hit AGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAA 7 0.17500000000000002 No Hit TCTCATTGGACCGGGTTTAAGTCACCTGAACAGCTTTCACGTGTCAGAAA 6 0.15 No Hit AGCAAATAATATACTGCTCAATGAACATGGGATAGCAAAGTTGAGTGACT 6 0.15 No Hit AACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAA 6 0.15 No Hit CAGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTA 5 0.125 No Hit CTGGGGAAGCCAAAGCACTGGTGCAATTCCAATCTCCTTATATTTTGTCC 5 0.125 No Hit CATCACTTCACTTTATTTCCTCTCTCTCTCAACAACCCCATTTCCTTTTT 5 0.125 No Hit GACGACTTCTCTAGGGCAATGCACGAGTTCCTTCCAGTTTCTATGCGTGA 5 0.125 No Hit ATCCCAATATGTTGATATTAAGCCACTGGATGAGCTAATTAATGAGCAAA 5 0.125 No Hit AACCACATATAGAGGGTGTAATAGCTAAGTAGCCTGTAAGAGATGGCTTC 5 0.125 No Hit AGCAGGTTTTGGTTCTGATATTGGAACTGAAAAGTTCATGAACATAAAGT 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 0.025 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 0.15 0.0 0.0 0.0 0.0 64-65 0.1875 0.0 0.0 0.0 0.0 66-67 0.2 0.0 0.0 0.0 0.0 68-69 0.225 0.0 0.0 0.0 0.0 70-71 0.2875 0.0 0.0 0.0 0.0 72-73 0.3375 0.0 0.0 0.0 0.0 74-75 0.4 0.0 0.0 0.0 0.0 76-77 0.475 0.0 0.0 0.0 0.0 78-79 0.6 0.0 0.0 0.0 0.0 80-81 0.6625000000000001 0.0 0.0 0.0 0.0 82-83 0.7875 0.0 0.0 0.0 0.0 84-85 0.9624999999999999 0.0 0.0 0.0 0.0 86-87 1.1625 0.0 0.0 0.0 0.0 88-89 1.4500000000000002 0.0 0.0 0.0 0.0 90-91 1.825 0.0 0.0 0.0 0.0 92-93 2.2875 0.0 0.0 0.0 0.0 94-95 2.55 0.0 0.0 0.0 0.0 96-97 3.0 0.0 0.0 0.0 0.0 98-99 3.5 0.0 0.0 0.0 0.0 100-101 4.275 0.0 0.0 0.0 0.0 102-103 4.9375 0.0 0.0 0.0 0.0 104-105 5.4875 0.0 0.0 0.0 0.0 106-107 5.8875 0.0 0.0 0.0 0.0 108-109 6.300000000000001 0.0 0.0 0.0 0.0 110-111 6.775 0.0 0.0 0.0 0.0 112-113 7.387499999999999 0.0 0.0 0.0 0.0 114-115 8.1125 0.0 0.0 0.0 0.0 116-117 8.875 0.0 0.0 0.0 0.0 118-119 9.7 0.0 0.0 0.0 0.0 120-121 10.7375 0.0 0.0 0.0 0.0 122-123 11.6375 0.0 0.0 0.0 0.0 124-125 12.925 0.0 0.0 0.0 0.0 126-127 13.7625 0.0 0.0 0.0 0.0 128-129 14.75 0.0 0.0 0.025 0.0 130-131 15.7 0.0 0.0 0.05 0.0 132-133 16.7625 0.0 0.0 0.05 0.0 134-135 17.65 0.0 0.0 0.05 0.0 136-137 18.4 0.0 0.0 0.05 0.0 138-139 19.35 0.0 0.0 0.05 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGGGGG 115 8.824045E-7 13.869566 140-144 >>END_MODULE Read 568474 spots for SRR12670110.sra Written 568474 spots for SRR12670110.sra Read 568474 spots for SRR12670110.sra Written 568474 spots for SRR12670110.sra Read 568474 spots for SRR12670110.sra Written 568474 spots for SRR12670110.sra Read 568474 spots for SRR12670110.sra Written 568474 spots for SRR12670110.sra Read 568474 spots for SRR12670110.sra Written 568474 spots for SRR12670110.sra Read 568474 spots for SRR12670110.sra Written 568474 spots for SRR12670110.sra Read 568474 spots for SRR12670110.sra Written 568474 spots for SRR12670110.sra Read 568474 spots for SRR12670110.sra Written 568474 spots for SRR12670110.sra Read 568474 spots for SRR12670110.sra Written 568474 spots for SRR12670110.sra Read 568474 spots for SRR12670110.sra Written 568474 spots for SRR12670110.sra Read 568474 spots for SRR12670110.sra Written 568474 spots for SRR12670110.sra Read 568474 spots for SRR12670110.sra Written 568474 spots for SRR12670110.sra Read 568474 spots for SRR12670110.sra Written 568474 spots for SRR12670110.sra Read 568474 spots for SRR12670110.sra Written 568474 spots for SRR12670110.sra Read 568474 spots for SRR12670110.sra Written 568474 spots for SRR12670110.sra Read 568474 spots for SRR12670110.sra Written 568474 spots for SRR12670110.sra Read 568474 spots for SRR12670110.sra Written 568474 spots for SRR12670110.sra Read 568474 spots for SRR12670110.sra Written 568474 spots for SRR12670110.sra Read 568474 spots for SRR12670110.sra Written 568474 spots for SRR12670110.sra Read 568484 spots for SRR12670110.sra Written 568484 spots for SRR12670110.sra SRR ids: ['SRR12670110.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_chm_23f1 SRR12670110.sra spots: 11369490 blocks: [[1, 568474], [568475, 1136948], [1136949, 1705422], [1705423, 2273896], [2273897, 2842370], [2842371, 3410844], [3410845, 3979318], [3979319, 4547792], [4547793, 5116266], [5116267, 5684740], [5684741, 6253214], [6253215, 6821688], [6821689, 7390162], [7390163, 7958636], [7958637, 8527110], [8527111, 9095584], [9095585, 9664058], [9664059, 10232532], [10232533, 10801006], [10801007, 11369490]] SRR12670110 file size 3842149 SRR12670110 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 SRR12670110 SRR12670110_1.fastq SRR12670110_2.fastq Input file: SRR12670110_1.fastq Paired file: SRR12670110_2.fastq trimmed: SRR12670110-trimmed-pair1.fastq, SRR12670110-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 Feb 11 00:03:21 2025 >> started Tue Feb 11 00:03:36 2025 >> done (15.800s) 11369490 read pairs processed; of these: 31 ( 0.00%) short read pairs filtered out after trimming by size control 1936 ( 0.02%) empty read pairs filtered out after trimming by size control 11367523 (99.98%) read pairs available; of these: 2654662 (23.35%) trimmed read pairs available after processing 8712861 (76.65%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 19 3 0.00% 20 2 0.00% 21 4 0.00% 22 1 0.00% 23 8 0.00% 24 10 0.00% 25 11 0.00% 26 10 0.00% 27 22 0.00% 28 23 0.00% 29 19 0.00% 30 14 0.00% 31 29 0.00% 32 29 0.00% 33 26 0.00% 34 45 0.00% 35 48 0.00% 36 72 0.00% 37 53 0.00% 38 68 0.00% 39 84 0.00% 40 78 0.00% 41 92 0.00% 42 85 0.00% 43 117 0.00% 44 106 0.00% 45 89 0.00% 46 107 0.00% 47 141 0.00% 48 140 0.00% 49 212 0.00% 50 221 0.00% 51 276 0.00% 52 279 0.00% 53 316 0.00% 54 310 0.00% 55 341 0.00% 56 383 0.00% 57 488 0.00% 58 517 0.00% 59 675 0.01% 60 749 0.01% 61 850 0.01% 62 1006 0.01% 63 1115 0.01% 64 1125 0.01% 65 1185 0.01% 66 1400 0.01% 67 1584 0.01% 68 1655 0.01% 69 1941 0.02% 70 2174 0.02% 71 2555 0.02% 72 2903 0.03% 73 3318 0.03% 74 3615 0.03% 75 4108 0.04% 76 4491 0.04% 77 4810 0.04% 78 5336 0.05% 79 5737 0.05% 80 6549 0.06% 81 7273 0.06% 82 7990 0.07% 83 8855 0.08% 84 10174 0.09% 85 10927 0.10% 86 11850 0.10% 87 12296 0.11% 88 13111 0.12% 89 14017 0.12% 90 15442 0.14% 91 16383 0.14% 92 17519 0.15% 93 18915 0.17% 94 20566 0.18% 95 21638 0.19% 96 22934 0.20% 97 23953 0.21% 98 24450 0.22% 99 25369 0.22% 100 26856 0.24% 101 27242 0.24% 102 28775 0.25% 103 30426 0.27% 104 31086 0.27% 105 32636 0.29% 106 33444 0.29% 107 35088 0.31% 108 35165 0.31% 109 36281 0.32% 110 36330 0.32% 111 36845 0.32% 112 38621 0.34% 113 38604 0.34% 114 40223 0.35% 115 41090 0.36% 116 42160 0.37% 117 43192 0.38% 118 43848 0.39% 119 43801 0.39% 120 44443 0.39% 121 45712 0.40% 122 45756 0.40% 123 46331 0.41% 124 47022 0.41% 125 47551 0.42% 126 48195 0.42% 127 48520 0.43% 128 48820 0.43% 129 49059 0.43% 130 50198 0.44% 131 49519 0.44% 132 49901 0.44% 133 50399 0.44% 134 50179 0.44% 135 50589 0.45% 136 51046 0.45% 137 51251 0.45% 138 51289 0.45% 139 53024 0.47% 140 52627 0.46% 141 53296 0.47% 142 53634 0.47% 143 52756 0.46% 144 53636 0.47% 145 53166 0.47% 146 52709 0.46% 147 53224 0.47% 148 53626 0.47% 149 53300 0.47% 150 54749 0.48% 151 8712861 76.65% 11367523 reads passed initial QC criterion=sequence-density sequence-density=0.47 sequence-density-rank=1 fanout-score=2.02 fanout-score-rank=26 prefix-density=0.47 prefix-fanout=2.0 sequence=TGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGGAGTATGAATGTGTTCTCTGTGT criterion=fanout-score sequence-density=0.02 sequence-density-rank=33 fanout-score=229.43 fanout-score-rank=1 prefix-density=0.25 prefix-fanout=17.4 sequence=TGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAG criterion=sequence-density sequence-density=0.99 sequence-density-rank=1 fanout-score=2.03 fanout-score-rank=29 prefix-density=0.98 prefix-fanout=2.0 sequence=CTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCA criterion=fanout-score sequence-density=0.01 sequence-density-rank=31 fanout-score=19.00 fanout-score-rank=1 prefix-density=0.04 prefix-fanout=4.8 sequence=AAAGGATGGTAGAGTAGCATCCTTAGCGTTGCTGGTTTACTTTCCTAACAATCCTCAAAACCATTCTTCTTAGACTCTCTATACATTCCAAATAACCTAATTTGTACTGTATAGATATATAGTCTACGTCAAGCTTAAATAAATCCTCATTAACATGGCCCCAGGAGTGCCTATAGATGGGAATATTTTGGGTACCGGGAAGGTTTCCACAGTTAACACTGGCTATTCTAAGAGGGCCTACGTGACATTTTTAGCCGGCAACGGGGATTATGTTAAAGGGGTAGTTGGGTTGGCTAAGGGTTTGCGCAAGGTGAAGAGTGCATACCCTCTTGTCGTAGCAATCTTGCCGGATGTGCCCGAGGAACACCGTGACATTTTGAGGTCTCAAGGTTGCATTGTTCGTGAGATCGAGCCTATTTATCCACCTGAGAACCAGATTCAGTTTGCCATGGCCTACTACGTGATCAACTACTCCAAGCTCCGAATTTGGAATTTTGAGGAGTACAGCAAG SRR12670110 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 00:04:18 Started mapping on | Feb 11 00:04:18 Finished on | Feb 11 00:05:28 Mapping speed, Million of reads per hour | 584.62 Number of input reads | 11367523 Average input read length | 288 UNIQUE READS: Uniquely mapped reads number | 10731745 Uniquely mapped reads % | 94.41% Average mapped length | 287.39 Number of splices: Total | 10461974 Number of splices: Annotated (sjdb) | 10223055 Number of splices: GT/AG | 10242700 Number of splices: GC/AG | 174209 Number of splices: AT/AC | 6199 Number of splices: Non-canonical | 38866 Mismatch rate per base, % | 0.35% Deletion rate per base | 0.03% Deletion average length | 2.92 Insertion rate per base | 0.02% Insertion average length | 2.38 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 265279 % of reads mapped to multiple loci | 2.33% Number of reads mapped to too many loci | 110816 % of reads mapped to too many loci | 0.97% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.12% % of reads unmapped: other | 0.17% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 370499 370499 370499 N_multimapping 265279 265279 265279 N_noFeature 450778 10571034 518936 N_ambiguous 158485 660 65499 UnstrandedReadsAssigned:10122482 PositiveStrandReadsAssigned:160051 NegativeStrandReadsAssigned:10147310 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=143 echo kmer=139 SRR12670110 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: SRR12670110-trimmed-pair1.fastq SRR12670110-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 11,367,523 reads, 10,185,995 reads pseudoaligned [quant] estimated average fragment length: 213.76 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,036 rounds 52401 SRR12670110.ke.tsv 34699 SRR12670110.se.tsv 87100 total ==> SRR12670110.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1805.24 332 17.7158 Potri.005G024800.1.v4.1 1035 822.24 240 28.117 Potri.004G059700.1.v4.1 961 748.323 0 0 Potri.007G009000.2.v4.1 1416 1203.24 0 0 Potri.003G141000.2.v4.1 2943 2730.24 683 24.0977 Potri.016G087400.1.v4.1 270 102.792 408 382.346 Potri.015G069301.1.v4.1 564 358.923 0 0 Potri.010G195200.1.v4.1 1773 1560.24 76 4.69222 Potri.012G127500.1.v4.1 977 764.272 35 4.4114 ==> SRR12670110.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 16 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 158 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 7 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 0 SRR12670110 completed mapping pipeline successfully