Starting /dee2/code/volunteer_pipeline.sh SRR5578507 current disk space = 1521986568192 free memory = 1592477476 SRR5578507 SRAfilesize a4c689e9443c8221d924f75e36aa47cf SRR5578507.sra SRR5578507.sra file validated SRR5578507 is paired end SRR5578507 is conventional basespace SRR5578507 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR5578507_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.04025 34.0 33.0 34.0 32.0 34.0 2 33.15125 34.0 33.0 34.0 32.0 34.0 3 33.21475 34.0 33.0 34.0 32.0 34.0 4 33.23625 34.0 33.0 34.0 33.0 34.0 5 33.33975 34.0 33.0 34.0 33.0 34.0 6 36.83025 38.0 37.0 38.0 35.0 38.0 7 37.267 38.0 38.0 38.0 36.0 38.0 8 37.437 38.0 38.0 38.0 37.0 38.0 9 37.41825 38.0 38.0 38.0 37.0 38.0 10-14 37.403499999999994 38.0 38.0 38.0 37.0 38.0 15-19 37.43475 38.0 38.0 38.0 37.0 38.0 20-24 37.355650000000004 38.0 38.0 38.0 37.0 38.0 25-29 37.30355 38.0 38.0 38.0 37.0 38.0 30-34 37.2174 38.0 38.0 38.0 37.0 38.0 35-39 37.167 38.0 38.0 38.0 36.8 38.0 40-44 36.97859999999999 38.0 38.0 38.0 36.0 38.0 45-49 36.945 38.0 38.0 38.0 36.0 38.0 50-54 36.91305 38.0 38.0 38.0 36.0 38.0 55-59 36.883799999999994 38.0 38.0 38.0 35.6 38.0 60-64 36.84685 38.0 38.0 38.0 35.2 38.0 65-69 36.72195 38.0 38.0 38.0 35.0 38.0 70-74 36.55245000000001 38.0 38.0 38.0 34.6 38.0 75-79 36.28385 38.0 38.0 38.0 34.0 38.0 80-84 36.1239 38.0 38.0 38.0 33.8 38.0 85-89 35.94585 38.0 38.0 38.0 33.4 38.0 90-94 35.9009 38.0 38.0 38.0 33.0 38.0 95-99 35.76645 38.0 37.6 38.0 33.0 38.0 100-104 35.682900000000004 38.0 37.2 38.0 32.6 38.0 105-109 35.46535 38.0 36.8 38.0 31.2 38.0 110-114 35.209649999999996 38.0 36.2 38.0 30.2 38.0 115-119 35.070949999999996 38.0 36.0 38.0 29.4 38.0 120-124 34.68595 38.0 35.0 38.0 27.8 38.0 125-129 34.5327 38.0 35.0 38.0 27.2 38.0 130-134 34.114250000000006 38.0 35.0 38.0 24.4 38.0 135-139 33.83715 38.0 34.6 38.0 23.0 38.0 140-144 33.24835 38.0 34.0 38.0 18.4 38.0 145-149 32.5421 38.0 33.8 38.0 13.8 38.0 150-151 28.314 36.0 17.5 37.5 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 6 2.0 7 2.0 8 4.0 9 2.0 10 3.0 11 3.0 12 1.0 13 3.0 14 8.0 15 6.0 16 5.0 17 10.0 18 24.0 19 13.0 20 10.0 21 7.0 22 4.0 23 13.0 24 9.0 25 15.0 26 12.0 27 24.0 28 25.0 29 29.0 30 58.0 31 60.0 32 71.0 33 116.0 34 189.0 35 263.0 36 784.0 37 2225.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 47.28884254431699 10.922836287799791 9.306569343065693 32.481751824817515 2 27.025 12.875 28.749999999999996 31.35 3 25.982478097622025 16.420525657071337 23.429286608260323 34.16770963704631 4 27.425 24.525 22.175 25.874999999999996 5 26.724999999999998 28.025 24.375 20.875 6 25.2 29.75 24.325 20.724999999999998 7 18.45 24.175 38.824999999999996 18.55 8 20.375 24.675 30.025000000000002 24.925 9 22.8 21.15 31.65 24.4 10-14 24.375 26.52 25.074999999999996 24.03 15-19 23.580000000000002 25.679999999999996 25.445 25.295 20-24 24.42 24.085 25.564999999999998 25.929999999999996 25-29 23.69 24.97 26.16 25.180000000000003 30-34 23.195 25.575 25.324999999999996 25.905 35-39 24.14 24.635 25.66 25.564999999999998 40-44 24.73 24.490000000000002 25.155 25.624999999999996 45-49 24.925 25.8 24.755 24.52 50-54 24.93 24.685000000000002 24.735 25.650000000000002 55-59 25.03 24.959999999999997 25.014999999999997 24.995 60-64 24.03 25.564999999999998 24.64 25.765 65-69 24.115000000000002 25.95 24.595 25.34 70-74 24.545 25.674999999999997 24.060000000000002 25.72 75-79 24.755 24.535 24.41 26.3 80-84 24.45 25.324999999999996 24.67 25.555 85-89 25.509999999999998 24.595 24.610000000000003 25.285000000000004 90-94 25.619999999999997 24.67 24.165 25.545 95-99 25.025 24.46 25.424999999999997 25.09 100-104 25.424999999999997 24.95 24.279999999999998 25.345000000000002 105-109 24.725 25.115 25.019999999999996 25.14 110-114 24.215 24.87 24.145 26.77 115-119 25.145 25.21 23.945 25.7 120-124 25.69 24.6 23.695 26.015 125-129 24.575 25.685000000000002 23.56 26.179999999999996 130-134 25.4 25.790000000000003 23.215 25.595000000000002 135-139 24.235 25.39 24.69 25.685000000000002 140-144 24.77 25.825 23.805 25.6 145-149 24.39 26.26 23.565 25.785000000000004 150-151 25.112499999999997 25.85 22.7625 26.275 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.5 2 2.0 3 2.0 4 2.0 5 2.5 6 2.0 7 1.0 8 0.5 9 0.5 10 0.0 11 0.5 12 0.5 13 0.0 14 0.0 15 0.0 16 0.0 17 0.5 18 0.5 19 0.0 20 1.0 21 1.5 22 0.5 23 0.5 24 0.5 25 0.0 26 1.0 27 2.5 28 2.5 29 12.0 30 24.0 31 28.5 32 39.0 33 52.0 34 55.5 35 67.5 36 89.0 37 104.5 38 109.0 39 108.0 40 117.5 41 126.0 42 114.5 43 108.0 44 111.5 45 114.0 46 123.5 47 135.0 48 137.0 49 139.0 50 144.0 51 140.5 52 139.0 53 127.0 54 106.0 55 97.5 56 94.5 57 88.0 58 92.5 59 97.5 60 87.5 61 82.0 62 79.0 63 70.5 64 64.5 65 63.5 66 63.5 67 66.5 68 67.5 69 59.5 70 48.5 71 32.5 72 29.5 73 30.0 74 21.5 75 18.0 76 16.0 77 11.5 78 8.5 79 6.0 80 2.0 81 1.5 82 1.0 83 1.5 84 1.5 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 4.1000000000000005 2 0.0 3 0.125 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 87.675 #Duplication Level Percentage of deduplicated Percentage of total 1 93.41317365269461 81.89999999999999 2 3.9349871685201028 6.9 3 1.1976047904191618 3.15 4 0.6558311947533505 2.3 5 0.2566295979469632 1.125 6 0.19960079840319359 1.05 7 0.11405759908753922 0.7000000000000001 8 0.05702879954376961 0.4 9 0.0 0.0 >10 0.1710863986313088 2.475 >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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACTCATTCATCTCGTATGC 26 0.65 TruSeq Adapter, Index 3 (97% over 36bp) GCCTTATGTGATAGATGCCTCTTTAAAATATCTAAGTGCTGGGGTTATGA 21 0.525 No Hit GGAAGCTATACTATATAGGTGGCTATCTATCCCTACCAAGGCTTATATTG 17 0.42500000000000004 No Hit GGGAAGCTATACTATATAGGTGGCTATCTATCCCTACCAAGGCTTATATT 12 0.3 No Hit GCCTCACTTAGTTACAGTTTTATGGATAATTGGGATATTCTTTGGTATAG 12 0.3 No Hit CCCATTTTTAGTTATAATGATGCCTTATGTGATAGATGCCTCTTTAAAAT 11 0.27499999999999997 No Hit GGATAATTGGGATATTCTTTGGTATAGTTGGGATTTTAATATCATTAATA 8 0.2 No Hit GCCTCTTTAAAATATCTAAGTGCTGGGGTTATGAGTAGGGATGAGCATAA 8 0.2 No Hit GATGCCTTATGTGATAGATGCCTCTTTAAAATATCTAAGTGCTGGGGTTA 7 0.17500000000000002 No Hit CTTATGTGATAGATGCCTCTTTAAAATATCTAAGTGCTGGGGTTATGAGT 7 0.17500000000000002 No Hit GGGGATAATTGCGCGGTTTTGACTGCGGAAGGAAGCCAAGGCCCACCTAA 7 0.17500000000000002 No Hit CCGGGGAACAGTCGCATGACGAGGCAGTTTCCAGAAACGTGTATCACATC 7 0.17500000000000002 No Hit GCTGGGGTTATGAGTAGGGATGAGCATAAACCAACAACTCTCAAAGAAGA 6 0.15 No Hit GTGATAGATGCCTCTTTAAAATATCTAAGTGCTGGGGTTATGAGTAGGGA 6 0.15 No Hit GTAGTTTATAAGGAATATATCCCATTTTTAGTTATAATGATGCCTTATGT 6 0.15 No Hit ATAACAATAGGAAATATCAGAAATCCAATAAGAATCAGCAATTCAGGAAG 6 0.15 No Hit GGGGTTATGAGTAGGGATGAGCATAAACCAACAACTCTCAAAGAAGATGG 6 0.15 No Hit GCTATCTATCCCTACCAAGGCTTATATTGAAGTATAAACCAATGAGAGAG 6 0.15 No Hit GTCGAGACTGAAAAGCTATAACCCGCAGACCCGAGCGAAAGCGGCGGTCC 6 0.15 No Hit GGACGGGGATAATTGCGCGGTTTTGACTGCGGAAGGAAGCCAAGGCCCAC 5 0.125 No Hit GGCTATCTATCCCTACCAAGGCTTATATTGAAGTATAAACCAATGAGAGA 5 0.125 No Hit GTGGCTATCTATCCCTACCAAGGCTTATATTGAAGTATAAACCAATGAGA 5 0.125 No Hit GCAGTTTCCAGAAACGTGTATCACATCTAGGCATGGAATCTTATGCCAGC 5 0.125 No Hit GCCATTCGGACCTACCGTAAGCCTATATTTCGTTTTTCTGAGACCTATCC 5 0.125 No Hit GCCCTAACTGCGCAGTTAATAATTCTGGCAATTCGTCTCCACACTAGAAG 5 0.125 No Hit CCTCTTTAAAATATCTAAGTGCTGGGGTTATGAGTAGGGATGAGCATAAA 5 0.125 No Hit GTACAGTTTCCCTGCACACGCACGGAGGCGTACGTGCAGGCAGGATAATG 5 0.125 No Hit GTCTCCTTCCCGCGGTCAAGGCGAAACCGCAGCAAACTTCCTCAGACGCT 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 0.025 0.0 0.0 0.0 0.0 2 0.025 0.0 0.0 0.0 0.0 3 0.025 0.0 0.0 0.0 0.0 4 0.025 0.0 0.0 0.0 0.0 5 0.025 0.0 0.0 0.0 0.0 6 0.025 0.0 0.0 0.0 0.0 7 0.025 0.0 0.0 0.0 0.0 8 0.025 0.0 0.0 0.0 0.0 9 0.025 0.0 0.0 0.0 0.0 10-11 0.025 0.0 0.0 0.0 0.0 12-13 0.025 0.0 0.0 0.0 0.0 14-15 0.025 0.0 0.0 0.0 0.0 16-17 0.025 0.0 0.0 0.0 0.0 18-19 0.025 0.0 0.0 0.0 0.0 20-21 0.025 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 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 0.05 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.0625 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 0.075 0.0 0.0 0.0 0.0 70-71 0.1 0.0 0.0 0.0 0.0 72-73 0.15 0.0 0.0 0.0 0.0 74-75 0.16249999999999998 0.0 0.0 0.0 0.0 76-77 0.1875 0.0 0.0 0.0 0.0 78-79 0.23750000000000002 0.0 0.0 0.0 0.0 80-81 0.3375 0.0 0.0 0.0 0.0 82-83 0.4125 0.0 0.0 0.0 0.0 84-85 0.5375 0.0 0.0 0.0 0.0 86-87 0.675 0.0 0.0 0.0 0.0 88-89 0.8125 0.0 0.0 0.0 0.0 90-91 0.975 0.0 0.0 0.0 0.0 92-93 1.2 0.0 0.0 0.0 0.0 94-95 1.45 0.0 0.0 0.0 0.0 96-97 1.6625 0.0 0.0 0.0 0.0 98-99 1.925 0.0 0.0 0.0 0.0 100-101 2.2 0.0 0.0 0.0 0.0 102-103 2.425 0.0 0.0 0.0 0.0 104-105 2.85 0.0 0.0 0.0 0.0 106-107 3.375 0.0 0.0 0.0 0.0 108-109 3.875 0.0 0.0 0.0 0.0 110-111 4.449999999999999 0.0 0.0 0.0 0.0 112-113 4.925 0.0 0.0 0.0 0.0 114-115 5.5125 0.0 0.0 0.0 0.0 116-117 6.0875 0.0 0.0 0.0 0.0 118-119 6.9 0.0 0.0 0.0 0.0 120-121 7.5625 0.0 0.0 0.0 0.0 122-123 8.225 0.0 0.0 0.0 0.0 124-125 8.825 0.0 0.0 0.0 0.0 126-127 9.412500000000001 0.0 0.0 0.0 0.0 128-129 10.3 0.0 0.0 0.0 0.0 130-131 11.274999999999999 0.0 0.0 0.0 0.0 132-133 12.05 0.0 0.0 0.0 0.0 134-135 13.1625 0.0 0.0 0.0 0.0 136-137 14.0875 0.0 0.0 0.0 0.0 138-139 14.9875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR5578507 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR5578507_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.737 33.0 33.0 34.0 32.0 34.0 2 32.8165 33.0 33.0 34.0 32.0 34.0 3 32.74125 33.0 33.0 34.0 32.0 34.0 4 32.74625 33.0 33.0 34.0 32.0 34.0 5 32.76125 33.0 33.0 34.0 32.0 34.0 6 36.792 38.0 38.0 38.0 36.0 38.0 7 36.76375 38.0 38.0 38.0 36.0 38.0 8 36.8535 38.0 38.0 38.0 36.0 38.0 9 36.768 38.0 38.0 38.0 36.0 38.0 10-14 36.797850000000004 38.0 38.0 38.0 36.0 38.0 15-19 36.7095 38.0 38.0 38.0 35.8 38.0 20-24 36.70155 38.0 38.0 38.0 35.6 38.0 25-29 36.67865 38.0 38.0 38.0 35.6 38.0 30-34 36.701 38.0 38.0 38.0 36.0 38.0 35-39 36.6634 38.0 38.0 38.0 35.8 38.0 40-44 36.634499999999996 38.0 38.0 38.0 35.6 38.0 45-49 36.589 38.0 38.0 38.0 35.0 38.0 50-54 36.43865 38.0 38.0 38.0 34.2 38.0 55-59 36.39275 38.0 38.0 38.0 34.2 38.0 60-64 36.36675 38.0 38.0 38.0 34.6 38.0 65-69 36.279900000000005 38.0 38.0 38.0 34.0 38.0 70-74 35.931850000000004 38.0 38.0 38.0 33.6 38.0 75-79 35.897850000000005 38.0 38.0 38.0 33.4 38.0 80-84 35.8682 38.0 38.0 38.0 33.8 38.0 85-89 35.6801 38.0 38.0 38.0 33.0 38.0 90-94 35.6117 38.0 38.0 38.0 32.4 38.0 95-99 35.40625 38.0 37.8 38.0 31.4 38.0 100-104 35.138 38.0 36.6 38.0 29.8 38.0 105-109 34.962149999999994 38.0 36.2 38.0 28.6 38.0 110-114 34.9142 38.0 36.0 38.0 28.8 38.0 115-119 34.627300000000005 38.0 35.6 38.0 27.0 38.0 120-124 34.31675 38.0 35.0 38.0 24.2 38.0 125-129 33.833000000000006 38.0 34.8 38.0 22.8 38.0 130-134 33.316199999999995 38.0 34.0 38.0 18.2 38.0 135-139 32.58820000000001 38.0 32.8 38.0 13.2 38.0 140-144 31.9212 38.0 31.6 38.0 12.6 38.0 145-149 30.44225 37.6 29.8 38.0 4.2 38.0 150-151 24.850749999999998 32.5 15.0 37.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 14.0 3 6.0 4 5.0 5 7.0 6 0.0 7 1.0 8 7.0 9 5.0 10 4.0 11 4.0 12 6.0 13 8.0 14 8.0 15 7.0 16 18.0 17 19.0 18 6.0 19 7.0 20 10.0 21 8.0 22 13.0 23 12.0 24 15.0 25 22.0 26 20.0 27 36.0 28 34.0 29 45.0 30 57.0 31 73.0 32 86.0 33 120.0 34 185.0 35 348.0 36 739.0 37 2045.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 41.725 17.75 12.575 27.950000000000003 2 30.65 22.975 22.5 23.875 3 25.374999999999996 25.0 25.474999999999998 24.15 4 26.075 29.349999999999998 19.925 24.65 5 27.224999999999998 31.7 19.325 21.75 6 24.6 32.225 20.175 23.0 7 23.425 20.65 30.825000000000003 25.1 8 23.549999999999997 23.45 24.125 28.875 9 25.025 23.625 24.8 26.55 10-14 26.46 25.155 22.03 26.355 15-19 26.545 24.490000000000002 23.575 25.39 20-24 26.540000000000003 24.81 22.955000000000002 25.695 25-29 27.27 24.335 22.485 25.91 30-34 27.029999999999998 24.2 23.53 25.240000000000002 35-39 26.71 23.705000000000002 23.745 25.840000000000003 40-44 27.295 23.825 23.630000000000003 25.25 45-49 26.919999999999998 23.31 23.97 25.8 50-54 26.215 23.315 24.759999999999998 25.71 55-59 25.814999999999998 23.830000000000002 25.169999999999998 25.185000000000002 60-64 25.180000000000003 24.555 24.37 25.895000000000003 65-69 25.46 24.785 24.865000000000002 24.89 70-74 25.52 24.85 23.76 25.869999999999997 75-79 25.35 24.86 23.955000000000002 25.835 80-84 25.650000000000002 25.275 23.35 25.724999999999998 85-89 25.019999999999996 25.259999999999998 24.165 25.555 90-94 25.995 25.44 24.0 24.565 95-99 26.015 25.46 23.76 24.765 100-104 25.645 25.495 23.785 25.074999999999996 105-109 26.055 26.41 23.32 24.215 110-114 25.445 26.075 23.47 25.009999999999998 115-119 26.534999999999997 26.395000000000003 22.830000000000002 24.240000000000002 120-124 26.195 26.119999999999997 23.315 24.37 125-129 27.250000000000004 26.26 22.95 23.54 130-134 26.615 25.485000000000003 24.08 23.82 135-139 27.384999999999998 26.424999999999997 23.5 22.689999999999998 140-144 27.589999999999996 26.205000000000002 24.0 22.205 145-149 28.51 26.055 23.66 21.775 150-151 29.1625 25.0125 23.05 22.775000000000002 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.5 4 0.5 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.5 19 0.5 20 0.0 21 0.0 22 1.5 23 3.0 24 2.5 25 2.0 26 2.5 27 2.0 28 1.5 29 5.0 30 10.5 31 22.0 32 28.0 33 23.0 34 24.5 35 41.0 36 64.5 37 85.5 38 105.5 39 123.5 40 153.5 41 124.5 42 80.0 43 93.5 44 98.0 45 101.5 46 108.0 47 114.0 48 127.0 49 132.0 50 124.0 51 114.0 52 125.0 53 143.0 54 150.0 55 134.5 56 119.5 57 119.5 58 117.0 59 111.5 60 96.0 61 93.5 62 92.5 63 87.5 64 76.5 65 69.5 66 73.0 67 72.5 68 71.0 69 60.5 70 45.0 71 40.5 72 42.5 73 37.0 74 29.0 75 19.0 76 17.0 77 14.5 78 8.5 79 7.0 80 3.0 81 1.0 82 1.5 83 1.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.5 89 0.5 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 85.2 #Duplication Level Percentage of deduplicated Percentage of total 1 92.72300469483568 79.0 2 4.078638497652582 6.950000000000001 3 1.4671361502347418 3.75 4 0.6161971830985915 2.1 5 0.3227699530516432 1.375 6 0.2934272300469483 1.5 7 0.08802816901408451 0.525 8 0.08802816901408451 0.6 9 0.0 0.0 >10 0.3227699530516432 4.2 >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 GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG 26 0.65 Illumina Single End PCR Primer 1 (100% over 50bp) GGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTC 24 0.6 No Hit AATTAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGA 18 0.44999999999999996 No Hit CCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCCTCCTATGG 16 0.4 No Hit CATTAATTAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAAT 14 0.35000000000000003 No Hit ATTAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAG 14 0.35000000000000003 No Hit CCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCCTCCTATGGT 13 0.325 No Hit GAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCCTCC 12 0.3 No Hit GCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCC 11 0.27499999999999997 No Hit GGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTT 10 0.25 No Hit GCCACAGGCGTCATACTTCCCAAGAAGCGGCCATAGCCCAGATGCGAGGT 10 0.25 No Hit GCCCAAGCTGCTCACAGTATACGGGCGTCGGCATCCAGACCGTCGGCTGA 8 0.2 No Hit AGCTGCTCACAGTATACGGGCGTCGGCATCCAGACCGTCGGCTGATCGTG 8 0.2 No Hit TAATTAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGG 8 0.2 No Hit GGACATTAATTAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCC 7 0.17500000000000002 No Hit TAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGT 7 0.17500000000000002 No Hit GGGATAGATAGCCACCTATATAGTATAGCTTCCCATCTTCTTTGAGAGTT 7 0.17500000000000002 No Hit CTTCAATATAAGCCTTGGTAGGGATAGATAGCCACCTATATAGTATAGCT 6 0.15 No Hit GTGAGGCTCTCTCATTGGTTTATACTTCAATATAAGCCTTGGTAGGGATA 6 0.15 No Hit TGGGAGTATTTGCACTTGTGGTAACGGTATTTGCATTATTGATGGTTTTT 6 0.15 No Hit GGACGGGAGGTATCCCAATAGGAGGTTTCCTCCTATGGTTTTCAAAACAA 6 0.15 No Hit ATTACTTCCATTTCCGCCCAAGCTGCTCACAGTATACGGGCGTCGGCATC 6 0.15 No Hit CGGGCGTCGGCATCCAGACCGTCGGCTGATCGTGGTTTTACTAGGCTAGA 6 0.15 No Hit ATTAATTAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATA 6 0.15 No Hit TCCATTTCCGCCCAAGCTGCTCACAGTATACGGGCGTCGGCATCCAGACC 6 0.15 No Hit GGGAGGTATCCCAATAGGAGGTTTCCTCCTATGGTTTTCAAAACAATCAC 6 0.15 No Hit GTAGGAATGGGAGTATTTGCACTTGTGGTAACGGTATTTGCATTATTGAT 6 0.15 No Hit AAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCCTCCTA 5 0.125 No Hit GCCACCTATATAGTATAGCTTCCCATCTTCTTTGAGAGTTGTTGGTTTAT 5 0.125 No Hit GCTGCTCACAGTATACGGGCGTCGGCATCCAGACCGTCGGCTGATCGTGG 5 0.125 No Hit GGTAGGAATGGGAGTATTTGCACTTGTGGTAACGGTATTTGCATTATTGA 5 0.125 No Hit TGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCCTC 5 0.125 No Hit AAAGAATATCCCAATTATCCATAAAACTGTAACTAAGTGAGGCTCTCTCA 5 0.125 No Hit CCCAAGCTGCTCACAGTATACGGGCGTCGGCATCCAGACCGTCGGCTGAT 5 0.125 No Hit CAATAGGAGGTTTCCTCCTATGGTTTTCAAAACAATCACCATCATGCTAT 5 0.125 No Hit AGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTT 5 0.125 No Hit GCCGCTGGTATTTGCTGTAAAGAGGGGCGTTGAGTCCGTCCGACTTCACT 5 0.125 No Hit GCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCCTCCTATG 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 0.025 0.0 0.0 0.0 0.0 2 0.025 0.0 0.0 0.0 0.0 3 0.025 0.0 0.0 0.0 0.0 4 0.025 0.0 0.0 0.0 0.0 5 0.025 0.0 0.0 0.0 0.0 6 0.025 0.0 0.0 0.0 0.0 7 0.025 0.0 0.0 0.0 0.0 8 0.025 0.0 0.0 0.0 0.0 9 0.025 0.0 0.0 0.0 0.0 10-11 0.025 0.0 0.0 0.0 0.0 12-13 0.025 0.0 0.0 0.0 0.0 14-15 0.025 0.0 0.0 0.0 0.0 16-17 0.025 0.0 0.0 0.0 0.0 18-19 0.025 0.0 0.0 0.0 0.0 20-21 0.025 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 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 0.05 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.0625 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 0.075 0.0 0.0 0.0 0.0 70-71 0.1 0.0 0.0 0.0 0.0 72-73 0.15 0.0 0.0 0.0 0.0 74-75 0.16249999999999998 0.0 0.0 0.0 0.0 76-77 0.1875 0.0 0.0 0.0 0.0 78-79 0.225 0.0 0.0 0.0 0.0 80-81 0.30000000000000004 0.0 0.0 0.0 0.0 82-83 0.3875 0.0 0.0 0.0 0.0 84-85 0.5 0.0 0.0 0.0 0.0 86-87 0.625 0.0 0.0 0.0 0.0 88-89 0.7625 0.0 0.0 0.0 0.0 90-91 0.925 0.0 0.0 0.0 0.0 92-93 1.125 0.0 0.0 0.0 0.0 94-95 1.375 0.0 0.0 0.0 0.0 96-97 1.6 0.0 0.0 0.0 0.0 98-99 1.875 0.0 0.0 0.0 0.0 100-101 2.15 0.0 0.0 0.0 0.0 102-103 2.3499999999999996 0.0 0.0 0.0 0.0 104-105 2.825 0.0 0.0 0.0 0.0 106-107 3.325 0.0 0.0 0.0 0.0 108-109 3.7750000000000004 0.0 0.0 0.0 0.0 110-111 4.3375 0.0 0.0 0.0 0.0 112-113 4.825 0.0 0.0 0.0 0.0 114-115 5.4375 0.0 0.0 0.0 0.0 116-117 6.025 0.0 0.0 0.0 0.0 118-119 6.8125 0.0 0.0 0.0 0.0 120-121 7.475 0.0 0.0 0.0 0.0 122-123 8.1625 0.0 0.0 0.0 0.0 124-125 8.85 0.0 0.0 0.0 0.0 126-127 9.475 0.0 0.0 0.0 0.0 128-129 10.350000000000001 0.0 0.0 0.0 0.0 130-131 11.25 0.0 0.0 0.0 0.0 132-133 11.9875 0.0 0.0 0.0 0.0 134-135 13.149999999999999 0.0 0.0 0.0 0.0 136-137 14.100000000000001 0.0 0.0 0.0 0.0 138-139 15.0125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGCTGAA 20 3.5877043E-4 108.75 1 GCCCTAA 25 8.7132835E-4 87.0 9 ACTAAGT 25 8.7132835E-4 87.0 145 CTGAAAG 25 8.7132835E-4 87.0 3 GCTGAAA 25 8.7132835E-4 87.0 2 AAGCCCT 25 8.7132835E-4 87.0 7 GAAAGCC 25 8.7132835E-4 87.0 5 TGAAAGC 25 8.7132835E-4 87.0 4 AGCCCTA 25 8.7132835E-4 87.0 8 AAAGCCC 30 0.0017973486 72.5 6 AATGATA 40 0.0076550315 18.125 85-89 >>END_MODULE Read 1028458 spots for SRR5578507.sra Written 1028458 spots for SRR5578507.sra Read 1028458 spots for SRR5578507.sra Written 1028458 spots for SRR5578507.sra Read 1028458 spots for SRR5578507.sra Written 1028458 spots for SRR5578507.sra Read 1028458 spots for SRR5578507.sra Written 1028458 spots for SRR5578507.sra Read 1028458 spots for SRR5578507.sra Written 1028458 spots for SRR5578507.sra Read 1028458 spots for SRR5578507.sra Written 1028458 spots for SRR5578507.sra Read 1028474 spots for SRR5578507.sra Written 1028474 spots for SRR5578507.sra Read 1028458 spots for SRR5578507.sra Written 1028458 spots for SRR5578507.sra Read 1028458 spots for SRR5578507.sra Written 1028458 spots for SRR5578507.sra Read 1028458 spots for SRR5578507.sra Written 1028458 spots for SRR5578507.sra Read 1028458 spots for SRR5578507.sra Written 1028458 spots for SRR5578507.sra Read 1028458 spots for SRR5578507.sra Written 1028458 spots for SRR5578507.sra Read 1028458 spots for SRR5578507.sra Written 1028458 spots for SRR5578507.sra Read 1028458 spots for SRR5578507.sra Written 1028458 spots for SRR5578507.sra Read 1028458 spots for SRR5578507.sra Written 1028458 spots for SRR5578507.sra Read 1028458 spots for SRR5578507.sra Written 1028458 spots for SRR5578507.sra Read 1028458 spots for SRR5578507.sra Written 1028458 spots for SRR5578507.sra Read 1028458 spots for SRR5578507.sra Written 1028458 spots for SRR5578507.sra Read 1028458 spots for SRR5578507.sra Written 1028458 spots for SRR5578507.sra Read 1028458 spots for SRR5578507.sra Written 1028458 spots for SRR5578507.sra SRR ids: ['SRR5578507.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd__jji3yb7 SRR5578507.sra spots: 20569176 blocks: [[1, 1028458], [1028459, 2056916], [2056917, 3085374], [3085375, 4113832], [4113833, 5142290], [5142291, 6170748], [6170749, 7199206], [7199207, 8227664], [8227665, 9256122], [9256123, 10284580], [10284581, 11313038], [11313039, 12341496], [12341497, 13369954], [13369955, 14398412], [14398413, 15426870], [15426871, 16455328], [16455329, 17483786], [17483787, 18512244], [18512245, 19540702], [19540703, 20569176]] SRR5578507 file size 6948518 SRR5578507 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 SRR5578507 SRR5578507_1.fastq SRR5578507_2.fastq Input file: SRR5578507_1.fastq Paired file: SRR5578507_2.fastq trimmed: SRR5578507-trimmed-pair1.fastq, SRR5578507-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 Mon Dec 9 21:23:57 2024 >> started Mon Dec 9 21:24:21 2024 >> done (24.134s) 20569176 read pairs processed; of these: 58635 ( 0.29%) short read pairs filtered out after trimming by size control 172766 ( 0.84%) empty read pairs filtered out after trimming by size control 20337775 (98.88%) read pairs available; of these: 11928692 (58.65%) trimmed read pairs available after processing 8409083 (41.35%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 10 0.00% 19 20 0.00% 20 15 0.00% 21 37 0.00% 22 29 0.00% 23 40 0.00% 24 37 0.00% 25 33 0.00% 26 38 0.00% 27 40 0.00% 28 35 0.00% 29 34 0.00% 30 53 0.00% 31 48 0.00% 32 51 0.00% 33 41 0.00% 34 54 0.00% 35 56 0.00% 36 61 0.00% 37 69 0.00% 38 69 0.00% 39 80 0.00% 40 86 0.00% 41 101 0.00% 42 113 0.00% 43 128 0.00% 44 173 0.00% 45 175 0.00% 46 197 0.00% 47 221 0.00% 48 236 0.00% 49 321 0.00% 50 305 0.00% 51 342 0.00% 52 351 0.00% 53 372 0.00% 54 400 0.00% 55 481 0.00% 56 538 0.00% 57 583 0.00% 58 664 0.00% 59 747 0.00% 60 902 0.00% 61 967 0.00% 62 1158 0.01% 63 1248 0.01% 64 1412 0.01% 65 1699 0.01% 66 2156 0.01% 67 2698 0.01% 68 3614 0.02% 69 6840 0.03% 70 5512 0.03% 71 3834 0.02% 72 4005 0.02% 73 4325 0.02% 74 4970 0.02% 75 5601 0.03% 76 6070 0.03% 77 6651 0.03% 78 7486 0.04% 79 8377 0.04% 80 9186 0.05% 81 10512 0.05% 82 12358 0.06% 83 14000 0.07% 84 17658 0.09% 85 20694 0.10% 86 22419 0.11% 87 24302 0.12% 88 25471 0.13% 89 26906 0.13% 90 28154 0.14% 91 28991 0.14% 92 30956 0.15% 93 32816 0.16% 94 34028 0.17% 95 36827 0.18% 96 37871 0.19% 97 40239 0.20% 98 42155 0.21% 99 44684 0.22% 100 46753 0.23% 101 49010 0.24% 102 51122 0.25% 103 54654 0.27% 104 57989 0.29% 105 60984 0.30% 106 63482 0.31% 107 65229 0.32% 108 68040 0.33% 109 68785 0.34% 110 69654 0.34% 111 73236 0.36% 112 77546 0.38% 113 83171 0.41% 114 88230 0.43% 115 90051 0.44% 116 90954 0.45% 117 91687 0.45% 118 91930 0.45% 119 93432 0.46% 120 96772 0.48% 121 97370 0.48% 122 100758 0.50% 123 104649 0.51% 124 107773 0.53% 125 111032 0.55% 126 113578 0.56% 127 113062 0.56% 128 111395 0.55% 129 117821 0.58% 130 116893 0.57% 131 119054 0.59% 132 122878 0.60% 133 127073 0.62% 134 129957 0.64% 135 131404 0.65% 136 133064 0.65% 137 136734 0.67% 138 142638 0.70% 139 148628 0.73% 140 153733 0.76% 141 157653 0.78% 142 175313 0.86% 143 184671 0.91% 144 201636 0.99% 145 228788 1.12% 146 271913 1.34% 147 343828 1.69% 148 492931 2.42% 149 948789 4.67% 150 4323729 21.26% 151 8409083 41.35% 20337775 reads passed initial QC criterion=sequence-density sequence-density=0.88 sequence-density-rank=1 fanout-score=5.39 fanout-score-rank=11 prefix-density=1.51 prefix-fanout=3.1 sequence=CGGCCGTTCTTGATCTCCTTCACCTTGAGCTCAGC criterion=fanout-score sequence-density=0.01 sequence-density-rank=36 fanout-score=44.50 fanout-score-rank=1 prefix-density=0.34 prefix-fanout=1.3 sequence=TTTTTTTTCTCGTTCTTTGGTCGCAATCCTGCGTAATCAACGCCGCAACTTTACGTCGGATTAGCTCTTCTTTGATTAGCATGAAACTCCAAGGTCCGGGGGGGTCACTTATCCTGGGCTTCATCCAATGGTGGGTGCTAACTCTTTAATAGCCTTCAGTGACTGTGAGATGCCGTCTACGAGTGGCACGAATCGCACGGATGTTTGGTTAAAGAACAGTCGCAGTTTTCCTCAAATCCCGCCACGAAACTAAGCGATTGAACTCTTGCCTGGTTACTGTATGCCCCTGTGTTATTGCAGCGTCTCGATTAGGGGGAAACCTTGTCACCGTCAGCTTATTCCCGAGGCATATGGCCCTACTTAACTGATCTGAAGTATTACGGTAACCGCGACGATAATAACCCGGACCAAATATAGCCTGATATGAGCGTGCCCGTCCATAGTCCCAGAGACGGGCGGAGGCTCTTAACCGTACGAGACAATCTCC criterion=sequence-density sequence-density=0.71 sequence-density-rank=1 fanout-score=2.66 fanout-score-rank=21 prefix-density=0.83 prefix-fanout=2.3 sequence=GAACCTGCCGGC criterion=fanout-score sequence-density=0.01 sequence-density-rank=30 fanout-score=20.57 fanout-score-rank=1 prefix-density=0.13 prefix-fanout=1.2 sequence=CCTGGAGATTGTCTCGTACGGTTAAGAGCCTCCGCCCGTCTCTGGGACTATGGACGGGCACGCTCATATCAGGCTATATTTGGTCCGGGTTATTATCGTCGCGGTTACCGTAATACTTCAGATCAGTTAAGTAGGGCCATATGCCTCGGGAATAAGCTGACGGTGACAAGGTTTCCCCCTAATCGAGACGCTGCAATAACACAGGGGCATACAGTAACCAGGCAAGAGTTCAATCGCTTAGTTTCGTGGCGGGATTTGAGGAAAACTGCGACTGTTCTTTAACCAAACATCCGTGCGATTCGTGCCACTCGTAGACGGCATCTCACAGTCACTGAAGGCTATTAAAGAGTTAGCACCCACCATTGGATGAAGCCCAGGATAAGTGACCCCCCCGGACCTTGGAGTTTCATGCTAATCAAAGAAGAGCTAATCCGACGTAAAGTTGCGGCGTTGATTACGCAGGATTGCGACCA SRR5578507 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 09 21:25:50 Started mapping on | Dec 09 21:25:50 Finished on | Dec 09 21:53:22 Mapping speed, Million of reads per hour | 44.32 Number of input reads | 20337775 Average input read length | 285 UNIQUE READS: Uniquely mapped reads number | 12110918 Uniquely mapped reads % | 59.55% Average mapped length | 284.78 Number of splices: Total | 9731529 Number of splices: Annotated (sjdb) | 9132713 Number of splices: GT/AG | 9611042 Number of splices: GC/AG | 107655 Number of splices: AT/AC | 4082 Number of splices: Non-canonical | 8750 Mismatch rate per base, % | 0.12% Deletion rate per base | 0.00% Deletion average length | 1.36 Insertion rate per base | 0.00% Insertion average length | 1.22 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 97999 % of reads mapped to multiple loci | 0.48% Number of reads mapped to too many loci | 15766 % of reads mapped to too many loci | 0.08% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 39.60% % of reads unmapped: other | 0.29% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 8149791 8149791 8149791 N_multimapping 97999 97999 97999 N_noFeature 254191 11726722 360942 N_ambiguous 346902 1492 69633 UnstrandedReadsAssigned:11509825 PositiveStrandReadsAssigned:382704 NegativeStrandReadsAssigned:11680343 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=138 echo kmer=133 SRR5578507 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: SRR5578507-trimmed-pair1.fastq SRR5578507-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 20,337,775 reads, 11,720,090 reads pseudoaligned [quant] estimated average fragment length: 207.922 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,069 rounds 52973 SRR5578507.ke.tsv 35125 SRR5578507.se.tsv 88098 total ==> SRR5578507.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 729.21 40.2557 5.09668 PNS24247 1044 837.078 7.17333 0.791165 PNS24249 1928 1721.08 73.8906 3.96371 PNS24246 1044 837.078 7.17333 0.791165 PNS24248 1044 837.078 7.17333 0.791165 PNS24244 1471 1264.08 39.3337 2.87279 PNS24243 293 116.366 0 0 KQK14069 1603 1396.08 2363.55 156.303 KQK14071 474 273.948 44.1064 14.8644 ==> SRR5578507.se.tsv <== BRADI_1g14170v3 2461 BRADI_1g53295v3 7 BRADI_1g59795v3 401 BRADI_1g07683v3 0 BRADI_1g00485v3 15 BRADI_1g20270v3 1546 BRADI_1g74790v3 215 BRADI_1g09890v3 26 BRADI_1g77505v3 342 BRADI_1g48960v3 0 SRR5578507 completed mapping pipeline successfully