Starting /dee2/code/volunteer_pipeline.sh SRR12951302 current disk space = 1543252381696 free memory = 1476469868 SRR12951302 SRAfilesize 5378c7ff2e976cb94b86c9ba9bd24994 SRR12951302.sra SRR12951302.sra file validated SRR12951302 is paired end SRR12951302 is conventional basespace SRR12951302 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12951302_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 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.5785 37.0 37.0 37.0 37.0 37.0 2 36.33825 37.0 37.0 37.0 37.0 37.0 3 36.581 37.0 37.0 37.0 37.0 37.0 4 36.58 37.0 37.0 37.0 37.0 37.0 5 36.616 37.0 37.0 37.0 37.0 37.0 6 36.6235 37.0 37.0 37.0 37.0 37.0 7 36.567 37.0 37.0 37.0 37.0 37.0 8 36.6755 37.0 37.0 37.0 37.0 37.0 9 36.63 37.0 37.0 37.0 37.0 37.0 10-14 36.599000000000004 37.0 37.0 37.0 37.0 37.0 15-19 36.588300000000004 37.0 37.0 37.0 37.0 37.0 20-24 36.548700000000004 37.0 37.0 37.0 37.0 37.0 25-29 36.5227 37.0 37.0 37.0 37.0 37.0 30-34 36.4935 37.0 37.0 37.0 37.0 37.0 35-39 36.4553 37.0 37.0 37.0 37.0 37.0 40-44 36.44279999999999 37.0 37.0 37.0 37.0 37.0 45-49 36.2796 37.0 37.0 37.0 37.0 37.0 50-54 36.362 37.0 37.0 37.0 37.0 37.0 55-59 36.1996 37.0 37.0 37.0 37.0 37.0 60-64 36.2057 37.0 37.0 37.0 37.0 37.0 65-69 36.1331 37.0 37.0 37.0 37.0 37.0 70-74 36.173 37.0 37.0 37.0 37.0 37.0 75-79 36.3352 37.0 37.0 37.0 37.0 37.0 80-84 36.2727 37.0 37.0 37.0 37.0 37.0 85-89 36.1863 37.0 37.0 37.0 37.0 37.0 90-94 36.219899999999996 37.0 37.0 37.0 37.0 37.0 95-99 36.188599999999994 37.0 37.0 37.0 37.0 37.0 100-104 36.218599999999995 37.0 37.0 37.0 37.0 37.0 105-109 36.205600000000004 37.0 37.0 37.0 37.0 37.0 110-114 36.1731 37.0 37.0 37.0 37.0 37.0 115-119 36.1447 37.0 37.0 37.0 37.0 37.0 120-124 36.0466 37.0 37.0 37.0 37.0 37.0 125-129 36.0048 37.0 37.0 37.0 37.0 37.0 130-134 35.91949999999999 37.0 37.0 37.0 37.0 37.0 135-139 35.9134 37.0 37.0 37.0 37.0 37.0 140-144 35.7346 37.0 37.0 37.0 37.0 37.0 145-149 35.6789 37.0 37.0 37.0 37.0 37.0 150-151 35.56625 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 22 2.0 23 2.0 24 2.0 25 4.0 26 6.0 27 8.0 28 10.0 29 23.0 30 35.0 31 33.0 32 42.0 33 80.0 34 150.0 35 285.0 36 2798.0 37 520.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 47.199999999999996 11.450000000000001 5.425 35.925000000000004 2 21.93224592220828 12.321204516938518 32.82308657465496 32.923462986198246 3 20.4 15.475 27.525 36.6 4 25.674999999999997 21.425 22.3 30.599999999999998 5 27.250000000000004 26.400000000000002 23.150000000000002 23.200000000000003 6 25.5 30.55 21.575 22.375 7 19.275000000000002 24.75 36.775000000000006 19.2 8 19.525000000000002 25.1 29.425 25.95 9 21.75 19.900000000000002 32.324999999999996 26.025 10-14 23.635 25.595000000000002 24.355 26.415 15-19 24.404999999999998 24.91 24.55 26.135 20-24 23.95 25.555 24.645 25.85 25-29 24.12 24.8 24.535 26.545 30-34 23.915 24.805 24.865000000000002 26.415 35-39 23.885 24.16 24.73 27.224999999999998 40-44 24.0 25.345000000000002 24.529999999999998 26.125 45-49 24.775 24.8 24.845 25.580000000000002 50-54 23.82 25.085 24.555 26.540000000000003 55-59 24.224999999999998 24.895 24.755 26.125 60-64 24.515 24.135 24.935 26.415 65-69 24.515 24.9 23.880000000000003 26.705000000000002 70-74 24.895 24.645 24.11 26.35 75-79 25.44 23.645 24.279999999999998 26.634999999999998 80-84 25.215 24.195 23.75 26.840000000000003 85-89 25.905 24.235 24.145 25.715 90-94 25.86 23.98 23.73 26.43 95-99 25.635 24.695 24.095 25.575 100-104 26.450000000000003 24.169999999999998 23.715 25.665 105-109 26.045 23.755000000000003 23.61 26.590000000000003 110-114 25.180000000000003 24.47 23.625 26.724999999999998 115-119 25.635 24.099999999999998 23.29 26.974999999999998 120-124 26.290000000000003 24.07 23.06 26.58 125-129 25.14 24.5 23.54 26.82 130-134 25.624999999999996 23.865 23.375 27.134999999999998 135-139 25.740000000000002 25.074999999999996 22.325 26.86 140-144 25.77 24.555 22.470000000000002 27.205000000000002 145-149 25.88 23.87 23.355 26.895000000000003 150-151 25.25 23.9 23.1125 27.737499999999997 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 1.0 1 0.5 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 0.5 15 0.5 16 0.0 17 0.0 18 0.5 19 0.5 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 1.0 26 2.5 27 3.5 28 2.5 29 3.0 30 5.5 31 7.5 32 13.5 33 14.0 34 16.0 35 23.0 36 37.5 37 58.0 38 72.0 39 87.5 40 105.5 41 126.5 42 158.0 43 171.0 44 168.0 45 182.0 46 189.5 47 189.0 48 181.0 49 161.5 50 149.5 51 123.5 52 112.5 53 116.5 54 105.0 55 101.0 56 102.0 57 106.0 58 93.5 59 69.0 60 60.0 61 68.0 62 66.0 63 63.0 64 74.0 65 95.5 66 90.5 67 70.0 68 65.5 69 54.0 70 46.0 71 48.5 72 40.5 73 21.0 74 18.0 75 19.5 76 14.0 77 9.0 78 4.0 79 3.0 80 4.0 81 1.5 82 0.5 83 1.5 84 1.0 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 0.375 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 78.675 #Duplication Level Percentage of deduplicated Percentage of total 1 80.29869717190977 63.175000000000004 2 14.775977121067681 23.25 3 3.686050206545917 8.7 4 1.0486177311725453 3.3000000000000003 5 0.09532888465204957 0.375 6 0.03177629488401652 0.15 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.06355258976803305 1.05 >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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGACCATTATCTCGTAT 32 0.8 TruSeq Adapter, Index 4 (97% over 39bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGACCATTATCGCGTAT 10 0.25 TruSeq Adapter, Index 4 (97% over 39bp) ATTGAAATACCATACTGGTTGCTGATTATTTTTCACTGCAACCTGCAGTA 6 0.15 No Hit GTCAGTGATGTTCTGGCAGTAGTACAGGCCCAGGGATCGCAGGTGAGGGC 5 0.125 No Hit GACCTTCTGCCCCATGCCGCAGTGGCCCGGGTAGCCGCAGAGGTAGTAGT 5 0.125 No Hit CTCCTCCTTTGCTGTGACCAACAATAGCTTTTACATCATACTTCTCCTGA 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 0.025 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 0.05 0.0 0.0 0.0 0.0 44-45 0.075 0.0 0.0 0.0 0.0 46-47 0.075 0.0 0.0 0.0 0.0 48-49 0.075 0.0 0.0 0.0 0.0 50-51 0.075 0.0 0.0 0.0 0.0 52-53 0.075 0.0 0.0 0.0 0.0 54-55 0.1 0.0 0.0 0.0 0.0 56-57 0.125 0.0 0.0 0.0 0.0 58-59 0.175 0.0 0.0 0.0 0.0 60-61 0.1875 0.0 0.0 0.0 0.0 62-63 0.2 0.0 0.0 0.0 0.0 64-65 0.25 0.0 0.0 0.0 0.0 66-67 0.25 0.0 0.0 0.0 0.0 68-69 0.25 0.0 0.0 0.0 0.0 70-71 0.275 0.0 0.0 0.0 0.0 72-73 0.3375 0.0 0.0 0.0 0.0 74-75 0.3625 0.0 0.0 0.0 0.0 76-77 0.5 0.0 0.0 0.0 0.0 78-79 0.575 0.0 0.0 0.0 0.0 80-81 0.7625 0.0 0.0 0.0 0.0 82-83 0.8125 0.0 0.0 0.0 0.0 84-85 0.925 0.0 0.0 0.0 0.0 86-87 1.0625 0.0 0.0 0.0 0.0 88-89 1.3375 0.0 0.0 0.0 0.0 90-91 1.7625 0.0 0.0 0.0 0.0 92-93 2.1624999999999996 0.0 0.0 0.0 0.0 94-95 2.5 0.0 0.0 0.0 0.0 96-97 3.1500000000000004 0.0 0.0 0.0 0.0 98-99 3.5999999999999996 0.0 0.0 0.0 0.0 100-101 3.9125 0.0 0.0 0.0 0.0 102-103 4.475 0.0 0.0 0.0 0.0 104-105 5.35 0.0 0.0 0.0 0.0 106-107 6.075 0.0 0.0 0.0 0.0 108-109 6.4 0.0 0.0 0.0 0.0 110-111 6.775 0.0 0.0 0.0 0.0 112-113 7.4125 0.0 0.0 0.0 0.0 114-115 7.9625 0.0 0.0 0.0 0.0 116-117 8.6625 0.0 0.0 0.0 0.0 118-119 9.3 0.0 0.0 0.0 0.0 120-121 10.162500000000001 0.0 0.0 0.0 0.0 122-123 11.037500000000001 0.0 0.0 0.0 0.0 124-125 11.525 0.0 0.0 0.0 0.0 126-127 12.2125 0.0 0.0 0.0 0.0 128-129 13.2 0.0 0.0 0.0 0.0 130-131 14.2125 0.0 0.0 0.0 0.0 132-133 14.95 0.0 0.0 0.0 0.0 134-135 15.6875 0.0 0.0 0.0 0.0 136-137 16.5625 0.0 0.0 0.0 0.0 138-139 17.6375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TGCAAAA 10 0.006830828 145.0 5 TATGCAA 10 0.006830828 145.0 3 GCAAAAT 10 0.006830828 145.0 6 AAAATCA 10 0.006830828 145.0 8 CTATGCA 10 0.006830828 145.0 2 >>END_MODULE SRR12951302 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12951302_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 52 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.3475 37.0 37.0 37.0 37.0 37.0 2 36.172 37.0 37.0 37.0 37.0 37.0 3 36.149 37.0 37.0 37.0 37.0 37.0 4 36.1535 37.0 37.0 37.0 37.0 37.0 5 36.2225 37.0 37.0 37.0 37.0 37.0 6 36.06 37.0 37.0 37.0 37.0 37.0 7 36.18 37.0 37.0 37.0 37.0 37.0 8 36.2 37.0 37.0 37.0 37.0 37.0 9 36.112 37.0 37.0 37.0 37.0 37.0 10-14 36.2186 37.0 37.0 37.0 37.0 37.0 15-19 36.18000000000001 37.0 37.0 37.0 37.0 37.0 20-24 36.0697 37.0 37.0 37.0 37.0 37.0 25-29 35.973 37.0 37.0 37.0 37.0 37.0 30-34 35.927800000000005 37.0 37.0 37.0 37.0 37.0 35-39 35.829600000000006 37.0 37.0 37.0 37.0 37.0 40-44 35.864700000000006 37.0 37.0 37.0 37.0 37.0 45-49 35.8011 37.0 37.0 37.0 37.0 37.0 50-54 35.7827 37.0 37.0 37.0 37.0 37.0 55-59 35.807599999999994 37.0 37.0 37.0 37.0 37.0 60-64 35.7965 37.0 37.0 37.0 37.0 37.0 65-69 35.7678 37.0 37.0 37.0 37.0 37.0 70-74 35.6711 37.0 37.0 37.0 37.0 37.0 75-79 35.673700000000004 37.0 37.0 37.0 37.0 37.0 80-84 35.721199999999996 37.0 37.0 37.0 37.0 37.0 85-89 35.716499999999996 37.0 37.0 37.0 37.0 37.0 90-94 35.7596 37.0 37.0 37.0 37.0 37.0 95-99 35.732000000000006 37.0 37.0 37.0 37.0 37.0 100-104 35.7564 37.0 37.0 37.0 37.0 37.0 105-109 35.6317 37.0 37.0 37.0 37.0 37.0 110-114 35.6024 37.0 37.0 37.0 37.0 37.0 115-119 35.6091 37.0 37.0 37.0 37.0 37.0 120-124 35.5419 37.0 37.0 37.0 37.0 37.0 125-129 35.445 37.0 37.0 37.0 37.0 37.0 130-134 35.253 37.0 37.0 37.0 34.6 37.0 135-139 35.053700000000006 37.0 37.0 37.0 29.8 37.0 140-144 34.88680000000001 37.0 37.0 37.0 25.0 37.0 145-149 34.64620000000001 37.0 37.0 37.0 25.0 37.0 150-151 34.349000000000004 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 2.0 14 4.0 15 7.0 16 6.0 17 3.0 18 1.0 19 5.0 20 2.0 21 12.0 22 15.0 23 15.0 24 10.0 25 14.0 26 13.0 27 18.0 28 21.0 29 13.0 30 23.0 31 42.0 32 48.0 33 111.0 34 210.0 35 435.0 36 2654.0 37 315.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 42.65 21.75 8.15 27.450000000000003 2 30.65 23.625 23.9 21.825 3 24.675 25.7 27.450000000000003 22.175 4 28.599999999999998 30.25 19.6 21.55 5 28.299999999999997 31.424999999999997 18.4 21.875 6 24.875 34.699999999999996 19.025 21.4 7 24.625 18.95 32.05 24.375 8 24.05 22.825 22.55 30.575000000000003 9 24.65 21.825 25.25 28.275 10-14 28.115000000000002 24.86 21.855 25.169999999999998 15-19 27.785 23.445 23.235 25.535000000000004 20-24 27.82 24.060000000000002 22.73 25.39 25-29 27.735 24.15 22.64 25.474999999999998 30-34 26.865 24.490000000000002 23.105 25.540000000000003 35-39 26.334999999999997 24.365000000000002 23.405 25.895000000000003 40-44 26.87 24.36 23.325000000000003 25.445 45-49 26.529999999999998 25.195 23.105 25.169999999999998 50-54 27.33 24.33 23.5 24.84 55-59 28.015 24.425 23.02 24.54 60-64 27.450000000000003 24.295 23.41 24.845 65-69 27.57 23.575 23.53 25.324999999999996 70-74 28.03 24.404999999999998 23.13 24.435000000000002 75-79 27.029999999999998 24.995 23.34 24.635 80-84 27.425 24.94 23.200000000000003 24.435000000000002 85-89 28.43 24.355 22.685 24.529999999999998 90-94 27.975 23.77 23.505000000000003 24.75 95-99 28.035 24.68 22.645 24.64 100-104 28.610000000000003 24.375 22.439999999999998 24.575 105-109 28.38 24.55 23.485 23.585 110-114 28.405 25.4 22.720000000000002 23.474999999999998 115-119 28.999999999999996 24.855 22.84 23.305 120-124 29.175 25.27 23.03 22.525000000000002 125-129 28.71 25.195 22.185 23.91 130-134 30.354999999999997 25.36 22.07 22.215 135-139 30.175 25.085 22.505 22.235 140-144 30.5 24.6 22.715 22.185 145-149 32.345 24.015 22.025 21.615000000000002 150-151 32.125 24.212500000000002 21.6625 22.0 >>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 0.5 6 0.5 7 0.5 8 1.5 9 1.0 10 0.5 11 0.5 12 0.0 13 2.0 14 3.5 15 2.0 16 0.5 17 0.5 18 0.5 19 0.0 20 0.5 21 0.5 22 0.5 23 1.5 24 2.0 25 2.5 26 4.0 27 5.0 28 3.5 29 1.5 30 6.5 31 9.5 32 7.5 33 9.5 34 19.0 35 30.0 36 33.0 37 42.5 38 54.0 39 65.0 40 81.0 41 106.5 42 146.5 43 158.5 44 143.5 45 153.0 46 162.5 47 161.5 48 158.5 49 154.0 50 159.5 51 154.5 52 139.0 53 133.0 54 120.5 55 106.5 56 97.0 57 88.0 58 87.5 59 88.5 60 89.5 61 87.0 62 74.5 63 64.0 64 71.0 65 80.5 66 71.0 67 60.0 68 73.5 69 75.0 70 62.0 71 50.0 72 38.5 73 32.0 74 24.5 75 18.5 76 15.0 77 13.0 78 11.5 79 8.5 80 7.0 81 6.0 82 3.0 83 1.5 84 2.5 85 2.5 86 1.0 87 0.5 88 0.5 89 1.5 90 1.5 91 2.0 92 3.0 93 3.0 94 2.5 95 3.0 96 4.0 97 4.0 98 6.0 99 5.0 100 5.0 >>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 79.425 #Duplication Level Percentage of deduplicated Percentage of total 1 80.67359143846396 64.075 2 14.353163361661943 22.8 3 3.8715769593956564 9.225 4 0.9442870632672332 3.0 5 0.09442870632672333 0.375 6 0.03147623544224111 0.15 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.03147623544224111 0.375 >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 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 15 0.375 No Hit ATTTATGATCCAGTTTAACAAGAATACATTTGGTCTTGCAGCTGGTGGAC 6 0.15 No Hit GTAACATACAAGGATGCTAGCACTTGTTTCCTCTGCTAGGTGGTACACAG 5 0.125 No Hit GGGATAAGCATCTTTCGCTTTGATTTCAGTGGAAATGGAGAAAGTGGAGG 5 0.125 No Hit GGCCACCTGGTCCACGGGCAAGGACTCCGTCGTCCTCAACACCACCGGCA 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 0.025 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 0.05 0.0 0.0 0.0 0.0 44-45 0.075 0.0 0.0 0.0 0.0 46-47 0.075 0.0 0.0 0.0 0.0 48-49 0.075 0.0 0.0 0.0 0.0 50-51 0.075 0.0 0.0 0.0 0.0 52-53 0.075 0.0 0.0 0.0 0.0 54-55 0.1 0.0 0.0 0.0 0.0 56-57 0.125 0.0 0.0 0.0 0.0 58-59 0.175 0.0 0.0 0.0 0.0 60-61 0.1875 0.0 0.0 0.0 0.0 62-63 0.2 0.0 0.0 0.0 0.0 64-65 0.25 0.0 0.0 0.0 0.0 66-67 0.25 0.0 0.0 0.0 0.0 68-69 0.25 0.0 0.0 0.0 0.0 70-71 0.275 0.0 0.0 0.0 0.0 72-73 0.3375 0.0 0.0 0.0 0.0 74-75 0.3625 0.0 0.0 0.0 0.0 76-77 0.5 0.0 0.0 0.0 0.0 78-79 0.575 0.0 0.0 0.0 0.0 80-81 0.7375 0.0 0.0 0.0 0.0 82-83 0.7875000000000001 0.0 0.0 0.0 0.0 84-85 0.9 0.0 0.0 0.0 0.0 86-87 1.0375 0.0 0.0 0.0 0.0 88-89 1.3125 0.0 0.0 0.0 0.0 90-91 1.7375 0.0 0.0 0.0 0.0 92-93 2.15 0.0 0.0 0.0 0.0 94-95 2.5 0.0 0.0 0.0 0.0 96-97 3.1500000000000004 0.0 0.0 0.0 0.0 98-99 3.6125 0.0 0.0 0.0 0.0 100-101 3.9375 0.0 0.0 0.0 0.0 102-103 4.4875 0.0 0.0 0.0 0.0 104-105 5.375 0.0 0.0 0.0 0.0 106-107 6.1 0.0 0.0 0.0 0.0 108-109 6.425 0.0 0.0 0.0 0.0 110-111 6.8 0.0 0.0 0.0 0.0 112-113 7.4375 0.0 0.0 0.0 0.0 114-115 7.987500000000001 0.0 0.0 0.0 0.0 116-117 8.662500000000001 0.0 0.0 0.0 0.0 118-119 9.275 0.0 0.0 0.0 0.0 120-121 10.125 0.0 0.0 0.0 0.0 122-123 10.9875 0.0 0.0 0.0 0.0 124-125 11.475 0.0 0.0 0.0 0.0 126-127 12.1125 0.0 0.0 0.0 0.0 128-129 13.0875 0.0 0.0 0.0 0.0 130-131 14.075 0.0 0.0 0.0 0.0 132-133 14.775 0.0 0.0 0.0 0.0 134-135 15.4625 0.0 0.0 0.0 0.0 136-137 16.3125 0.0 0.0 0.0 0.0 138-139 17.3625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTCTGGC 10 0.006830828 145.0 7 GACAAGT 10 0.006830828 145.0 9 TATTTTG 10 0.006830828 145.0 3 ACGCGTC 10 0.006830828 145.0 8 CATTGTG 20 0.00593511 29.0 140-144 >>END_MODULE Read 1466232 spots for SRR12951302.sra Written 1466232 spots for SRR12951302.sra Read 1466232 spots for SRR12951302.sra Written 1466232 spots for SRR12951302.sra Read 1466232 spots for SRR12951302.sra Written 1466232 spots for SRR12951302.sra Read 1466232 spots for SRR12951302.sra Written 1466232 spots for SRR12951302.sra Read 1466232 spots for SRR12951302.sra Written 1466232 spots for SRR12951302.sra Read 1466232 spots for SRR12951302.sra Written 1466232 spots for SRR12951302.sra Read 1466232 spots for SRR12951302.sra Written 1466232 spots for SRR12951302.sra Read 1466232 spots for SRR12951302.sra Written 1466232 spots for SRR12951302.sra Read 1466232 spots for SRR12951302.sra Written 1466232 spots for SRR12951302.sra Read 1466232 spots for SRR12951302.sra Written 1466232 spots for SRR12951302.sra Read 1466232 spots for SRR12951302.sra Written 1466232 spots for SRR12951302.sra Read 1466232 spots for SRR12951302.sra Written 1466232 spots for SRR12951302.sra Read 1466232 spots for SRR12951302.sra Written 1466232 spots for SRR12951302.sra Read 1466249 spots for SRR12951302.sra Written 1466249 spots for SRR12951302.sra Read 1466232 spots for SRR12951302.sra Written 1466232 spots for SRR12951302.sra Read 1466232 spots for SRR12951302.sra Written 1466232 spots for SRR12951302.sra Read 1466232 spots for SRR12951302.sra Written 1466232 spots for SRR12951302.sra Read 1466232 spots for SRR12951302.sra Written 1466232 spots for SRR12951302.sra Read 1466232 spots for SRR12951302.sra Written 1466232 spots for SRR12951302.sra Read 1466232 spots for SRR12951302.sra Written 1466232 spots for SRR12951302.sra SRR ids: ['SRR12951302.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_t1w3gx2b SRR12951302.sra spots: 29324657 blocks: [[1, 1466232], [1466233, 2932464], [2932465, 4398696], [4398697, 5864928], [5864929, 7331160], [7331161, 8797392], [8797393, 10263624], [10263625, 11729856], [11729857, 13196088], [13196089, 14662320], [14662321, 16128552], [16128553, 17594784], [17594785, 19061016], [19061017, 20527248], [20527249, 21993480], [21993481, 23459712], [23459713, 24925944], [24925945, 26392176], [26392177, 27858408], [27858409, 29324657]] SRR12951302 file size 9944101 SRR12951302 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 SRR12951302 SRR12951302_1.fastq SRR12951302_2.fastq Input file: SRR12951302_1.fastq Paired file: SRR12951302_2.fastq trimmed: SRR12951302-trimmed-pair1.fastq, SRR12951302-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 Sat Dec 7 11:10:46 2024 >> started Sat Dec 7 11:14:33 2024 >> done (227.670s) 29324657 read pairs processed; of these: 278 ( 0.00%) short read pairs filtered out after trimming by size control 309974 ( 1.06%) empty read pairs filtered out after trimming by size control 29014405 (98.94%) read pairs available; of these: 5792107 (19.96%) trimmed read pairs available after processing 23222298 (80.04%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 18 0.00% 19 20 0.00% 20 30 0.00% 21 54 0.00% 22 54 0.00% 23 67 0.00% 24 119 0.00% 25 101 0.00% 26 125 0.00% 27 128 0.00% 28 130 0.00% 29 163 0.00% 30 176 0.00% 31 167 0.00% 32 162 0.00% 33 134 0.00% 34 175 0.00% 35 186 0.00% 36 193 0.00% 37 195 0.00% 38 212 0.00% 39 217 0.00% 40 216 0.00% 41 265 0.00% 42 254 0.00% 43 271 0.00% 44 261 0.00% 45 333 0.00% 46 384 0.00% 47 377 0.00% 48 436 0.00% 49 474 0.00% 50 542 0.00% 51 613 0.00% 52 666 0.00% 53 727 0.00% 54 758 0.00% 55 898 0.00% 56 948 0.00% 57 1046 0.00% 58 1178 0.00% 59 1434 0.00% 60 1535 0.01% 61 1878 0.01% 62 2143 0.01% 63 2391 0.01% 64 2476 0.01% 65 2751 0.01% 66 2937 0.01% 67 3411 0.01% 68 3876 0.01% 69 4374 0.02% 70 4903 0.02% 71 5585 0.02% 72 6637 0.02% 73 7405 0.03% 74 8058 0.03% 75 8996 0.03% 76 9987 0.03% 77 10597 0.04% 78 11594 0.04% 79 12979 0.04% 80 14297 0.05% 81 16325 0.06% 82 18398 0.06% 83 20366 0.07% 84 22161 0.08% 85 23761 0.08% 86 25862 0.09% 87 26965 0.09% 88 28921 0.10% 89 30319 0.10% 90 32877 0.11% 91 35260 0.12% 92 37779 0.13% 93 40545 0.14% 94 43737 0.15% 95 45134 0.16% 96 47969 0.17% 97 49657 0.17% 98 51049 0.18% 99 53005 0.18% 100 54964 0.19% 101 57158 0.20% 102 59503 0.21% 103 62633 0.22% 104 64204 0.22% 105 67221 0.23% 106 69022 0.24% 107 71153 0.25% 108 71718 0.25% 109 74605 0.26% 110 75045 0.26% 111 77366 0.27% 112 79825 0.28% 113 82574 0.28% 114 84548 0.29% 115 87103 0.30% 116 89283 0.31% 117 90744 0.31% 118 91425 0.32% 119 92048 0.32% 120 93338 0.32% 121 95578 0.33% 122 96985 0.33% 123 98955 0.34% 124 101800 0.35% 125 103419 0.36% 126 103979 0.36% 127 105950 0.37% 128 105705 0.36% 129 107579 0.37% 130 108011 0.37% 131 107893 0.37% 132 111162 0.38% 133 112316 0.39% 134 113163 0.39% 135 115761 0.40% 136 116553 0.40% 137 117257 0.40% 138 117954 0.41% 139 118253 0.41% 140 117869 0.41% 141 119340 0.41% 142 120487 0.42% 143 120570 0.42% 144 122057 0.42% 145 123109 0.42% 146 123200 0.42% 147 123747 0.43% 148 124880 0.43% 149 124394 0.43% 150 124894 0.43% 151 23222298 80.04% 29014405 reads passed initial QC criterion=sequence-density sequence-density=0.22 sequence-density-rank=1 fanout-score=3.59 fanout-score-rank=25 prefix-density=0.26 prefix-fanout=3.1 sequence=GTGATGGTCTTGCC criterion=fanout-score sequence-density=0.06 sequence-density-rank=28 fanout-score=214.55 fanout-score-rank=1 prefix-density=0.80 prefix-fanout=17.2 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.66 sequence-density-rank=1 fanout-score=2.06 fanout-score-rank=30 prefix-density=0.66 prefix-fanout=2.0 sequence=CGGTTCCGGTTC criterion=fanout-score sequence-density=0.12 sequence-density-rank=19 fanout-score=181.71 fanout-score-rank=1 prefix-density=0.99 prefix-fanout=22.8 sequence=CGCCGCCGCCGC SRR12951302 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 11:19:43 Started mapping on | Dec 07 11:19:45 Finished on | Dec 07 11:44:44 Mapping speed, Million of reads per hour | 69.68 Number of input reads | 29014405 Average input read length | 290 UNIQUE READS: Uniquely mapped reads number | 26970514 Uniquely mapped reads % | 92.96% Average mapped length | 289.53 Number of splices: Total | 23582420 Number of splices: Annotated (sjdb) | 21958979 Number of splices: GT/AG | 23254530 Number of splices: GC/AG | 271457 Number of splices: AT/AC | 14281 Number of splices: Non-canonical | 42152 Mismatch rate per base, % | 0.23% Deletion rate per base | 0.01% Deletion average length | 2.26 Insertion rate per base | 0.01% Insertion average length | 2.39 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 292969 % of reads mapped to multiple loci | 1.01% Number of reads mapped to too many loci | 109521 % of reads mapped to too many loci | 0.38% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.84% % of reads unmapped: other | 1.82% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1750922 1750922 1750922 N_multimapping 292969 292969 292969 N_noFeature 911279 26234824 1138413 N_ambiguous 592695 3216 84704 UnstrandedReadsAssigned:25466540 PositiveStrandReadsAssigned:732474 NegativeStrandReadsAssigned:25747397 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=149 echo kmer=145 SRR12951302 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: SRR12951302-trimmed-pair1.fastq SRR12951302-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 29,014,405 reads, 26,228,814 reads pseudoaligned [quant] estimated average fragment length: 233.098 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,085 rounds 52973 SRR12951302.ke.tsv 35125 SRR12951302.se.tsv 88098 total ==> SRR12951302.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 704.347 0 0 PNS24247 1044 811.902 101.382 6.68007 PNS24249 1928 1695.9 447.392 14.1128 PNS24246 1044 811.902 101.382 6.68007 PNS24248 1044 811.902 101.382 6.68007 PNS24244 1471 1238.9 280.463 12.1106 PNS24243 293 112.408 1 0.475914 KQK14069 1603 1370.9 24499.6 956.047 KQK14071 474 259.723 746.182 153.695 ==> SRR12951302.se.tsv <== BRADI_1g14170v3 27201 BRADI_1g53295v3 171 BRADI_1g59795v3 508 BRADI_1g07683v3 0 BRADI_1g00485v3 27 BRADI_1g20270v3 1192 BRADI_1g74790v3 3022 BRADI_1g09890v3 0 BRADI_1g77505v3 249 BRADI_1g48960v3 0 SRR12951302 completed mapping pipeline successfully