Starting /dee2/code/volunteer_pipeline.sh SRR12670163 current disk space = 3055888334848 free memory = 1449122168 SRR12670163 SRAfilesize 76252f9bdee93677cd58eed0b201a474 SRR12670163.sra SRR12670163.sra file validated SRR12670163 is paired end SRR12670163 is conventional basespace SRR12670163 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670163_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 36.631 37.0 37.0 37.0 37.0 37.0 2 36.46275 37.0 37.0 37.0 37.0 37.0 3 36.589 37.0 37.0 37.0 37.0 37.0 4 36.6705 37.0 37.0 37.0 37.0 37.0 5 36.6495 37.0 37.0 37.0 37.0 37.0 6 36.6995 37.0 37.0 37.0 37.0 37.0 7 36.6365 37.0 37.0 37.0 37.0 37.0 8 36.6195 37.0 37.0 37.0 37.0 37.0 9 36.627 37.0 37.0 37.0 37.0 37.0 10-14 36.65 37.0 37.0 37.0 37.0 37.0 15-19 36.610099999999996 37.0 37.0 37.0 37.0 37.0 20-24 36.586 37.0 37.0 37.0 37.0 37.0 25-29 36.5507 37.0 37.0 37.0 37.0 37.0 30-34 36.5096 37.0 37.0 37.0 37.0 37.0 35-39 36.4864 37.0 37.0 37.0 37.0 37.0 40-44 36.4647 37.0 37.0 37.0 37.0 37.0 45-49 36.4567 37.0 37.0 37.0 37.0 37.0 50-54 36.455099999999995 37.0 37.0 37.0 37.0 37.0 55-59 36.432100000000005 37.0 37.0 37.0 37.0 37.0 60-64 36.389300000000006 37.0 37.0 37.0 37.0 37.0 65-69 36.361000000000004 37.0 37.0 37.0 37.0 37.0 70-74 36.35359999999999 37.0 37.0 37.0 37.0 37.0 75-79 36.3644 37.0 37.0 37.0 37.0 37.0 80-84 36.3321 37.0 37.0 37.0 37.0 37.0 85-89 36.28580000000001 37.0 37.0 37.0 37.0 37.0 90-94 36.2824 37.0 37.0 37.0 37.0 37.0 95-99 36.2428 37.0 37.0 37.0 37.0 37.0 100-104 36.2663 37.0 37.0 37.0 37.0 37.0 105-109 36.2201 37.0 37.0 37.0 37.0 37.0 110-114 36.148199999999996 37.0 37.0 37.0 37.0 37.0 115-119 36.1557 37.0 37.0 37.0 37.0 37.0 120-124 35.976 37.0 37.0 37.0 37.0 37.0 125-129 35.8069 37.0 37.0 37.0 37.0 37.0 130-134 35.7284 37.0 37.0 37.0 37.0 37.0 135-139 35.4203 37.0 37.0 37.0 37.0 37.0 140-144 35.0879 37.0 37.0 37.0 32.2 37.0 145-149 34.8276 37.0 37.0 37.0 25.0 37.0 150-151 34.46525 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 24 1.0 25 3.0 26 3.0 27 8.0 28 6.0 29 26.0 30 23.0 31 28.0 32 90.0 33 85.0 34 159.0 35 358.0 36 2778.0 37 432.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 46.2 11.65 4.475 37.675 2 18.89862327909887 13.341677096370464 38.04755944931164 29.712140175219027 3 17.025000000000002 17.825 27.675 37.475 4 21.45 26.450000000000003 24.7 27.400000000000002 5 22.275 32.275 24.474999999999998 20.974999999999998 6 21.05 33.975 24.375 20.599999999999998 7 15.65 26.025 41.825 16.5 8 16.7 23.674999999999997 34.775 24.85 9 18.175 22.025 35.8 24.0 10-14 20.349999999999998 28.725 28.025 22.900000000000002 15-19 20.41 28.15 28.225 23.215 20-24 19.470000000000002 28.310000000000002 28.299999999999997 23.919999999999998 25-29 19.91 28.53 27.485 24.075 30-34 20.285 28.189999999999998 28.185 23.34 35-39 19.93 28.249999999999996 28.310000000000002 23.51 40-44 20.035 27.87 28.845 23.25 45-49 20.369999999999997 28.310000000000002 28.025 23.294999999999998 50-54 19.825 28.305000000000003 28.065 23.805 55-59 20.45 27.93 27.73 23.89 60-64 20.1 28.405 28.299999999999997 23.195 65-69 19.98 28.255000000000003 27.800000000000004 23.965 70-74 20.695 27.765 27.88 23.66 75-79 20.46 28.165000000000003 27.605 23.77 80-84 20.669999999999998 28.64 27.0 23.69 85-89 20.645 28.665000000000003 27.16 23.53 90-94 20.96 28.625 27.634999999999998 22.78 95-99 20.880000000000003 28.115000000000002 27.05 23.955000000000002 100-104 20.244999999999997 28.875 27.134999999999998 23.745 105-109 21.265 28.585 26.619999999999997 23.53 110-114 21.6 28.499999999999996 26.375 23.525 115-119 21.605 27.815 26.424999999999997 24.154999999999998 120-124 21.11 28.515 26.195 24.18 125-129 21.375 28.235 26.650000000000002 23.74 130-134 21.94 28.410000000000004 25.81 23.84 135-139 21.93 28.205000000000002 25.85 24.015 140-144 23.150000000000002 27.134999999999998 25.355 24.36 145-149 22.259999999999998 28.32 25.180000000000003 24.240000000000002 150-151 23.7 26.400000000000002 25.55 24.349999999999998 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.5 2 0.5 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 1.0 18 0.5 19 0.0 20 0.0 21 0.5 22 0.5 23 2.0 24 3.0 25 2.0 26 4.0 27 9.0 28 14.5 29 18.0 30 16.5 31 18.0 32 31.0 33 43.5 34 52.0 35 62.5 36 83.5 37 114.0 38 148.0 39 170.0 40 190.0 41 201.5 42 228.0 43 262.5 44 248.5 45 247.5 46 256.5 47 239.0 48 241.5 49 218.5 50 172.5 51 140.0 52 108.5 53 94.0 54 88.0 55 79.5 56 60.5 57 39.5 58 24.5 59 18.5 60 12.5 61 9.0 62 6.5 63 5.0 64 4.5 65 2.0 66 2.0 67 2.0 68 1.0 69 0.5 70 0.5 71 0.0 72 0.0 73 0.0 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.125 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 81.2 #Duplication Level Percentage of deduplicated Percentage of total 1 81.80418719211822 66.425 2 14.439655172413794 23.45 3 2.8017241379310347 6.825 4 0.7389162561576355 2.4 5 0.18472906403940886 0.75 6 0.03078817733990148 0.15 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 GCAACGATTAAGTCAGTATCCAAATCCTGTATTGATGAGAATATCTTTTC 6 0.15 No Hit GGCAGTATTAAATTAGAGAATTACATTCTATATGTTACTAAAATAACAAA 5 0.125 No Hit CCCAGGTCCATCAAAAGGATAACCATCCCCATGATCACCGCTGTAGAATG 5 0.125 No Hit GTCTAGGTGGAGGAGCTATGCCGCTAGGGTTTCCAGCACCAGGCATTCCA 5 0.125 No Hit AGCCAATCTGCGAGACACAGCACCATTATCCTCCTCCTGTACTGCCTGCT 5 0.125 No Hit CTACAACTTTGCTCTTGTCAAATTTGCAAGTGCCACCGTCAGTTCCAGTG 5 0.125 No Hit GTCACGAGCTATGGCCCATACATTCACCAAAACAGTCGAGCCCTTCGGAA 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 0.0125 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 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 0.037500000000000006 0.0 0.0 0.0 0.0 54-55 0.11249999999999999 0.0 0.0 0.0 0.0 56-57 0.175 0.0 0.0 0.0 0.0 58-59 0.175 0.0 0.0 0.0 0.0 60-61 0.2 0.0 0.0 0.0 0.0 62-63 0.225 0.0 0.0 0.0 0.0 64-65 0.225 0.0 0.0 0.0 0.0 66-67 0.275 0.0 0.0 0.0 0.0 68-69 0.45 0.0 0.0 0.0 0.0 70-71 0.575 0.0 0.0 0.0 0.0 72-73 0.6625000000000001 0.0 0.0 0.0 0.0 74-75 0.75 0.0 0.0 0.0 0.0 76-77 1.1 0.0 0.0 0.0 0.0 78-79 1.2374999999999998 0.0 0.0 0.0 0.0 80-81 1.525 0.0 0.0 0.0 0.0 82-83 1.7999999999999998 0.0 0.0 0.0 0.0 84-85 2.0125 0.0 0.0 0.0 0.0 86-87 2.275 0.0 0.0 0.0 0.0 88-89 2.7750000000000004 0.0 0.0 0.0 0.0 90-91 3.1125 0.0 0.0 0.0 0.0 92-93 3.7625 0.0 0.0 0.0 0.0 94-95 4.225 0.0 0.0 0.0 0.0 96-97 4.9 0.0 0.0 0.0 0.0 98-99 5.45 0.0 0.0 0.0 0.0 100-101 5.9375 0.0 0.0 0.0 0.0 102-103 7.025 0.0 0.0 0.0 0.0 104-105 8.162500000000001 0.0 0.0 0.0 0.0 106-107 8.9875 0.0 0.0 0.0 0.0 108-109 9.825 0.0 0.0 0.0 0.0 110-111 10.6375 0.0 0.0 0.0 0.0 112-113 11.6125 0.0 0.0 0.0 0.0 114-115 12.575 0.0 0.0 0.0 0.0 116-117 13.525 0.0 0.0 0.0 0.0 118-119 14.4875 0.0 0.0 0.0 0.0 120-121 15.375 0.0 0.0 0.0 0.0 122-123 16.175 0.0 0.0 0.0 0.0 124-125 17.174999999999997 0.0 0.0 0.0 0.0 126-127 18.1 0.0 0.0 0.0 0.0 128-129 18.8875 0.0 0.0 0.0 0.0 130-131 19.8875 0.0 0.0 0.0 0.0 132-133 20.887500000000003 0.0 0.0 0.0 0.0 134-135 21.975 0.0 0.0 0.0 0.0 136-137 23.225 0.0 0.0 0.0 0.0 138-139 24.450000000000003 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GTTGCTT 10 0.006830828 145.0 1 >>END_MODULE SRR12670163 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670163_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 36.3895 37.0 37.0 37.0 37.0 37.0 2 36.1255 37.0 37.0 37.0 37.0 37.0 3 36.154 37.0 37.0 37.0 37.0 37.0 4 36.3235 37.0 37.0 37.0 37.0 37.0 5 36.222 37.0 37.0 37.0 37.0 37.0 6 36.275 37.0 37.0 37.0 37.0 37.0 7 36.2025 37.0 37.0 37.0 37.0 37.0 8 36.298 37.0 37.0 37.0 37.0 37.0 9 36.323 37.0 37.0 37.0 37.0 37.0 10-14 36.313399999999994 37.0 37.0 37.0 37.0 37.0 15-19 36.3502 37.0 37.0 37.0 37.0 37.0 20-24 36.2608 37.0 37.0 37.0 37.0 37.0 25-29 36.247299999999996 37.0 37.0 37.0 37.0 37.0 30-34 36.2786 37.0 37.0 37.0 37.0 37.0 35-39 36.1919 37.0 37.0 37.0 37.0 37.0 40-44 36.2141 37.0 37.0 37.0 37.0 37.0 45-49 36.1969 37.0 37.0 37.0 37.0 37.0 50-54 36.1329 37.0 37.0 37.0 37.0 37.0 55-59 36.0973 37.0 37.0 37.0 37.0 37.0 60-64 36.098 37.0 37.0 37.0 37.0 37.0 65-69 36.0954 37.0 37.0 37.0 37.0 37.0 70-74 36.0417 37.0 37.0 37.0 37.0 37.0 75-79 36.017700000000005 37.0 37.0 37.0 37.0 37.0 80-84 35.967800000000004 37.0 37.0 37.0 37.0 37.0 85-89 35.9993 37.0 37.0 37.0 37.0 37.0 90-94 35.9698 37.0 37.0 37.0 37.0 37.0 95-99 35.8283 37.0 37.0 37.0 37.0 37.0 100-104 35.8285 37.0 37.0 37.0 37.0 37.0 105-109 35.7761 37.0 37.0 37.0 37.0 37.0 110-114 35.7432 37.0 37.0 37.0 37.0 37.0 115-119 35.748000000000005 37.0 37.0 37.0 37.0 37.0 120-124 35.4781 37.0 37.0 37.0 37.0 37.0 125-129 35.501099999999994 37.0 37.0 37.0 37.0 37.0 130-134 35.2641 37.0 37.0 37.0 34.6 37.0 135-139 35.0985 37.0 37.0 37.0 29.8 37.0 140-144 34.759800000000006 37.0 37.0 37.0 25.0 37.0 145-149 34.521100000000004 37.0 37.0 37.0 25.0 37.0 150-151 34.265249999999995 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 3.0 14 2.0 15 3.0 16 1.0 17 1.0 18 1.0 19 0.0 20 3.0 21 1.0 22 3.0 23 4.0 24 5.0 25 9.0 26 11.0 27 7.0 28 13.0 29 18.0 30 25.0 31 52.0 32 79.0 33 95.0 34 230.0 35 529.0 36 2645.0 37 259.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 43.45 24.5 7.1 24.95 2 26.6 25.55 31.8 16.05 3 19.775000000000002 27.400000000000002 34.050000000000004 18.775 4 24.45 33.074999999999996 24.95 17.525 5 23.875 37.974999999999994 21.3 16.85 6 21.725 40.575 21.025 16.675 7 20.974999999999998 22.525000000000002 38.1 18.4 8 21.775 25.8 27.55 24.875 9 22.075 24.825 29.775000000000002 23.325000000000003 10-14 23.96 29.044999999999998 26.685 20.31 15-19 23.415 27.395000000000003 28.15 21.04 20-24 22.7 28.945 27.994999999999997 20.36 25-29 23.235 28.34 28.04 20.385 30-34 22.939999999999998 28.99 27.49 20.580000000000002 35-39 22.615 28.294999999999998 28.015 21.075 40-44 23.669999999999998 28.38 27.744999999999997 20.205000000000002 45-49 23.645 28.105000000000004 28.065 20.185 50-54 22.75 29.294999999999998 27.615000000000002 20.34 55-59 23.549999999999997 28.115000000000002 27.665 20.669999999999998 60-64 23.189999999999998 28.315 27.77 20.724999999999998 65-69 23.985 28.439999999999998 26.685 20.89 70-74 22.634999999999998 28.455000000000002 27.49 21.42 75-79 22.535 28.58 27.935 20.95 80-84 23.455000000000002 28.51 27.26 20.775 85-89 23.474999999999998 27.860000000000003 27.72 20.945 90-94 24.325 28.854999999999997 26.88 19.939999999999998 95-99 23.875 28.055000000000003 26.985 21.085 100-104 24.455 28.88 26.61 20.055 105-109 25.035 28.18 27.42 19.365 110-114 26.090000000000003 28.1 26.334999999999997 19.475 115-119 26.375 28.92 25.46 19.245 120-124 27.389999999999997 28.675 25.1 18.834999999999997 125-129 27.555000000000003 28.439999999999998 25.264999999999997 18.740000000000002 130-134 28.53 27.875 25.545 18.05 135-139 27.875 27.46 25.595000000000002 19.07 140-144 29.265 27.075 25.285000000000004 18.375 145-149 30.320000000000004 26.72 25.3 17.66 150-151 31.225 27.075 24.587500000000002 17.1125 >>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 0.5 7 0.5 8 0.5 9 0.5 10 0.5 11 0.5 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.5 19 1.0 20 0.5 21 1.0 22 2.0 23 2.0 24 2.0 25 3.0 26 5.5 27 10.0 28 11.0 29 9.0 30 12.5 31 24.0 32 31.0 33 40.0 34 60.0 35 74.0 36 90.5 37 115.5 38 125.5 39 145.5 40 192.5 41 240.0 42 274.5 43 275.0 44 280.5 45 284.0 46 256.5 47 243.5 48 209.5 49 174.0 50 158.5 51 130.0 52 99.5 53 82.5 54 74.5 55 58.5 56 51.5 57 39.5 58 25.5 59 24.0 60 18.5 61 7.0 62 5.0 63 8.0 64 4.5 65 2.0 66 1.5 67 0.5 68 1.5 69 1.5 70 0.0 71 0.0 72 0.5 73 0.5 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 1.0 82 1.0 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 0.5 93 0.5 94 0.0 95 0.0 96 0.5 97 0.5 98 0.0 99 0.0 100 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 81.0 #Duplication Level Percentage of deduplicated Percentage of total 1 82.00617283950618 66.425 2 14.19753086419753 23.0 3 2.7160493827160495 6.6000000000000005 4 0.8333333333333334 2.7 5 0.12345679012345678 0.5 6 0.06172839506172839 0.3 7 0.0 0.0 8 0.0 0.0 9 0.030864197530864196 0.22499999999999998 >10 0.030864197530864196 0.25 >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 10 0.25 No Hit AGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAA 9 0.22499999999999998 No Hit AGGGAGCACTGCATAGCTTATAAGCTTGTAAGAGATGGCTTCCTCCTCTA 6 0.15 No Hit GCCGCATTGGGTTTCTTGATTTCGGAATTGTTGGTCGCATATCCCCAAAA 6 0.15 No Hit ACTTATAGTGCTAGGTGGGGTCAACTTCTTTGGGGTCTTGTTCACTCTAT 5 0.125 No Hit AGGAGAGCTTGCGAGCTTGAGTGAGCAGCAGCTTGTGGACTGCGACCATG 5 0.125 No Hit CATGGCACAGTTCCTGCACCCTTGATGGCACTAAGTTGATTGTCTCTGGT 5 0.125 No Hit GCTTCTTGCACCACCATGCACTAACCACTCCTGCTAGATCAACCCCATCA 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 0.0125 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 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 0.037500000000000006 0.0 0.0 0.0 0.0 54-55 0.11249999999999999 0.0 0.0 0.0 0.0 56-57 0.175 0.0 0.0 0.0 0.0 58-59 0.175 0.0 0.0 0.0 0.0 60-61 0.2 0.0 0.0 0.0 0.0 62-63 0.225 0.0 0.0 0.0 0.0 64-65 0.225 0.0 0.0 0.0 0.0 66-67 0.275 0.0 0.0 0.0 0.0 68-69 0.45 0.0 0.0 0.0 0.0 70-71 0.575 0.0 0.0 0.0 0.0 72-73 0.6625000000000001 0.0 0.0 0.0 0.0 74-75 0.75 0.0 0.0 0.0 0.0 76-77 1.1 0.0 0.0 0.0 0.0 78-79 1.2125 0.0 0.0 0.0 0.0 80-81 1.5 0.0 0.0 0.0 0.0 82-83 1.775 0.0 0.0 0.0 0.0 84-85 1.9875 0.0 0.0 0.0 0.0 86-87 2.25 0.0 0.0 0.0 0.0 88-89 2.75 0.0 0.0 0.0 0.0 90-91 3.075 0.0 0.0 0.0 0.0 92-93 3.7125000000000004 0.0 0.0 0.0 0.0 94-95 4.2 0.0 0.0 0.0 0.0 96-97 4.9 0.0 0.0 0.0 0.0 98-99 5.475 0.0 0.0 0.0 0.0 100-101 5.9375 0.0 0.0 0.0 0.0 102-103 7.0375 0.0 0.0 0.0 0.0 104-105 8.1375 0.0 0.0 0.0 0.0 106-107 8.9375 0.0 0.0 0.0 0.0 108-109 9.75 0.0 0.0 0.0 0.0 110-111 10.55 0.0 0.0 0.0 0.0 112-113 11.4875 0.0 0.0 0.0 0.0 114-115 12.45 0.0 0.0 0.0 0.0 116-117 13.4 0.0 0.0 0.0 0.0 118-119 14.350000000000001 0.0 0.0 0.0 0.0 120-121 15.25 0.0 0.0 0.0 0.0 122-123 16.05 0.0 0.0 0.0 0.0 124-125 17.049999999999997 0.0 0.0 0.0 0.0 126-127 18.0 0.0 0.0 0.0 0.0 128-129 18.7875 0.0 0.0 0.0 0.0 130-131 19.799999999999997 0.0 0.0 0.0 0.0 132-133 20.8125 0.0 0.0 0.0 0.0 134-135 21.9 0.0 0.0 0.0 0.0 136-137 23.15 0.0 0.0 0.0 0.0 138-139 24.3875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGGGGG 75 1.5980913E-7 19.333334 140-144 >>END_MODULE Read 516468 spots for SRR12670163.sra Written 516468 spots for SRR12670163.sra Read 516468 spots for SRR12670163.sra Written 516468 spots for SRR12670163.sra Read 516468 spots for SRR12670163.sra Written 516468 spots for SRR12670163.sra Read 516468 spots for SRR12670163.sra Written 516468 spots for SRR12670163.sra Read 516468 spots for SRR12670163.sra Written 516468 spots for SRR12670163.sra Read 516468 spots for SRR12670163.sra Written 516468 spots for SRR12670163.sra Read 516468 spots for SRR12670163.sra Written 516468 spots for SRR12670163.sra Read 516468 spots for SRR12670163.sra Written 516468 spots for SRR12670163.sra Read 516468 spots for SRR12670163.sra Written 516468 spots for SRR12670163.sra Read 516468 spots for SRR12670163.sra Written 516468 spots for SRR12670163.sra Read 516468 spots for SRR12670163.sra Written 516468 spots for SRR12670163.sra Read 516468 spots for SRR12670163.sra Written 516468 spots for SRR12670163.sra Read 516468 spots for SRR12670163.sra Written 516468 spots for SRR12670163.sra Read 516468 spots for SRR12670163.sra Written 516468 spots for SRR12670163.sra Read 516468 spots for SRR12670163.sra Written 516468 spots for SRR12670163.sra Read 516468 spots for SRR12670163.sra Written 516468 spots for SRR12670163.sra Read 516483 spots for SRR12670163.sra Written 516483 spots for SRR12670163.sra Read 516468 spots for SRR12670163.sra Written 516468 spots for SRR12670163.sra Read 516468 spots for SRR12670163.sra Written 516468 spots for SRR12670163.sra Read 516468 spots for SRR12670163.sra Written 516468 spots for SRR12670163.sra SRR ids: ['SRR12670163.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_4_urxu_5 SRR12670163.sra spots: 10329375 blocks: [[1, 516468], [516469, 1032936], [1032937, 1549404], [1549405, 2065872], [2065873, 2582340], [2582341, 3098808], [3098809, 3615276], [3615277, 4131744], [4131745, 4648212], [4648213, 5164680], [5164681, 5681148], [5681149, 6197616], [6197617, 6714084], [6714085, 7230552], [7230553, 7747020], [7747021, 8263488], [8263489, 8779956], [8779957, 9296424], [9296425, 9812892], [9812893, 10329375]] SRR12670163 file size 3488673 SRR12670163 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 SRR12670163 SRR12670163_1.fastq SRR12670163_2.fastq Input file: SRR12670163_1.fastq Paired file: SRR12670163_2.fastq trimmed: SRR12670163-trimmed-pair1.fastq, SRR12670163-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 08:01:55 2025 >> started Tue Feb 11 08:02:06 2025 >> done (11.011s) 10329375 read pairs processed; of these: 95 ( 0.00%) short read pairs filtered out after trimming by size control 2112 ( 0.02%) empty read pairs filtered out after trimming by size control 10327168 (99.98%) read pairs available; of these: 2929125 (28.36%) trimmed read pairs available after processing 7398043 (71.64%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 8 0.00% 19 15 0.00% 20 22 0.00% 21 14 0.00% 22 29 0.00% 23 37 0.00% 24 46 0.00% 25 48 0.00% 26 68 0.00% 27 38 0.00% 28 81 0.00% 29 80 0.00% 30 68 0.00% 31 91 0.00% 32 73 0.00% 33 94 0.00% 34 94 0.00% 35 103 0.00% 36 132 0.00% 37 167 0.00% 38 141 0.00% 39 140 0.00% 40 147 0.00% 41 171 0.00% 42 165 0.00% 43 189 0.00% 44 183 0.00% 45 174 0.00% 46 212 0.00% 47 269 0.00% 48 310 0.00% 49 369 0.00% 50 418 0.00% 51 466 0.00% 52 490 0.00% 53 571 0.01% 54 568 0.01% 55 616 0.01% 56 716 0.01% 57 839 0.01% 58 990 0.01% 59 1027 0.01% 60 1252 0.01% 61 1364 0.01% 62 1563 0.02% 63 1771 0.02% 64 1954 0.02% 65 2097 0.02% 66 2246 0.02% 67 2529 0.02% 68 2884 0.03% 69 3332 0.03% 70 3806 0.04% 71 4158 0.04% 72 4889 0.05% 73 5378 0.05% 74 5824 0.06% 75 6415 0.06% 76 6825 0.07% 77 7458 0.07% 78 8436 0.08% 79 9078 0.09% 80 10016 0.10% 81 11478 0.11% 82 12530 0.12% 83 13554 0.13% 84 15128 0.15% 85 16144 0.16% 86 16925 0.16% 87 17695 0.17% 88 18821 0.18% 89 19542 0.19% 90 21172 0.21% 91 22577 0.22% 92 24524 0.24% 93 25970 0.25% 94 27357 0.26% 95 28918 0.28% 96 30171 0.29% 97 30738 0.30% 98 31383 0.30% 99 31814 0.31% 100 33438 0.32% 101 34487 0.33% 102 36221 0.35% 103 37308 0.36% 104 39086 0.38% 105 39454 0.38% 106 39651 0.38% 107 40263 0.39% 108 40524 0.39% 109 41270 0.40% 110 42376 0.41% 111 42531 0.41% 112 43646 0.42% 113 44693 0.43% 114 45620 0.44% 115 46304 0.45% 116 46911 0.45% 117 47788 0.46% 118 47022 0.46% 119 47091 0.46% 120 47861 0.46% 121 48354 0.47% 122 48420 0.47% 123 49578 0.48% 124 50475 0.49% 125 50417 0.49% 126 51024 0.49% 127 50679 0.49% 128 50272 0.49% 129 50170 0.49% 130 50404 0.49% 131 50161 0.49% 132 50107 0.49% 133 51213 0.50% 134 51603 0.50% 135 52036 0.50% 136 52242 0.51% 137 51848 0.50% 138 50984 0.49% 139 51592 0.50% 140 50813 0.49% 141 50911 0.49% 142 51083 0.49% 143 51193 0.50% 144 51876 0.50% 145 51946 0.50% 146 51309 0.50% 147 51734 0.50% 148 51504 0.50% 149 50234 0.49% 150 51203 0.50% 151 7398043 71.64% 10327168 reads passed initial QC criterion=sequence-density sequence-density=0.33 sequence-density-rank=1 fanout-score=2.22 fanout-score-rank=34 prefix-density=0.35 prefix-fanout=2.1 sequence=TTCCACATAGTCCAGTAGCGTCCATCATAGTACCCTGGTGAGCTGTGGTGCTCACGGTAGACCCAACCTTTCTCCAACTCGAATTCCAAGCAAGGAACCCACTTCGAGCGAAGAAGGTAATCAATTTCCTTGGCCAATTCCTCCTCTGTGAGATCTGGAAGGTAAGAAAGAGTCTCGAACTTCTTCAATCCAGTTGGTGGCCACACCTGCATGCATTGAACTCGTCCACCATTGCTTGCAATGGAAGTAATGTCATTAGCCTTTCTGGTACTGACTGGGAAAGCTGCGGCAGACTTGAGACCATTGAATGGTGCCACCATGTTGGCTTGTGCCGGGGTGCGGTTGACGGTGGCAACGGCTGCCGATGAGATCATAGAGGAGGAAGCCAT criterion=fanout-score sequence-density=0.08 sequence-density-rank=28 fanout-score=54.06 fanout-score-rank=1 prefix-density=0.38 prefix-fanout=11.3 sequence=CCATCTTCTTCATCTATAGATTTCAATCACAACAG criterion=sequence-density sequence-density=0.50 sequence-density-rank=1 fanout-score=2.15 fanout-score-rank=33 prefix-density=0.51 prefix-fanout=2.1 sequence=TGTAAGAGATGGCTTCCTC criterion=fanout-score sequence-density=0.01 sequence-density-rank=36 fanout-score=28.50 fanout-score-rank=1 prefix-density=0.04 prefix-fanout=4.3 sequence=GGGAAACTTACCAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTATGGGTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGTTAACGAACGAGACCTCAGCCTGCTAACTAGCTATGCGGAGGTGACCCTCCGCGGCCAGCTTCTTAGAGGGACTATGGCCTTCCAGGCCAAGGAAGTTTGAGGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCACGCGCGCTACACTGAT SRR12670163 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 08:02:48 Started mapping on | Feb 11 08:02:49 Finished on | Feb 11 08:03:53 Mapping speed, Million of reads per hour | 580.90 Number of input reads | 10327168 Average input read length | 284 UNIQUE READS: Uniquely mapped reads number | 9513595 Uniquely mapped reads % | 92.12% Average mapped length | 282.35 Number of splices: Total | 8913256 Number of splices: Annotated (sjdb) | 8694668 Number of splices: GT/AG | 8727295 Number of splices: GC/AG | 141841 Number of splices: AT/AC | 5920 Number of splices: Non-canonical | 38200 Mismatch rate per base, % | 0.36% Deletion rate per base | 0.03% Deletion average length | 2.78 Insertion rate per base | 0.02% Insertion average length | 2.35 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 267657 % of reads mapped to multiple loci | 2.59% Number of reads mapped to too many loci | 113255 % of reads mapped to too many loci | 1.10% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.98% % of reads unmapped: other | 0.21% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 545916 545916 545916 N_multimapping 267657 267657 267657 N_noFeature 439378 9367242 504317 N_ambiguous 144815 535 63121 UnstrandedReadsAssigned:8929402 PositiveStrandReadsAssigned:145818 NegativeStrandReadsAssigned:8946157 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=133 echo kmer=129 SRR12670163 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: SRR12670163-trimmed-pair1.fastq SRR12670163-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 10,327,168 reads, 9,034,357 reads pseudoaligned [quant] estimated average fragment length: 201.061 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,068 rounds 52401 SRR12670163.ke.tsv 34699 SRR12670163.se.tsv 87100 total ==> SRR12670163.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1817.94 734 45.5851 Potri.005G024800.1.v4.1 1035 834.939 179 24.205 Potri.004G059700.1.v4.1 961 760.977 0 0 Potri.007G009000.2.v4.1 1416 1215.94 0 0 Potri.003G141000.2.v4.1 2943 2742.94 650 26.7549 Potri.016G087400.1.v4.1 270 109.483 479 493.963 Potri.015G069301.1.v4.1 564 369.662 0 0 Potri.010G195200.1.v4.1 1773 1572.94 52 3.73248 Potri.012G127500.1.v4.1 977 776.954 32 4.65009 ==> SRR12670163.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 40 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 161 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 28 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 0 SRR12670163 completed mapping pipeline successfully