Starting /dee2/code/volunteer_pipeline.sh SRR12670137 current disk space = 3056961417216 free memory = 1580040208 SRR12670137 SRAfilesize 1430343e2a0ea091e5dccaaa7a6528a8 SRR12670137.sra SRR12670137.sra file validated SRR12670137 is paired end SRR12670137 is conventional basespace SRR12670137 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670137_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.558 37.0 37.0 37.0 37.0 37.0 2 36.49975 37.0 37.0 37.0 37.0 37.0 3 36.552 37.0 37.0 37.0 37.0 37.0 4 36.7125 37.0 37.0 37.0 37.0 37.0 5 36.65 37.0 37.0 37.0 37.0 37.0 6 36.756 37.0 37.0 37.0 37.0 37.0 7 36.6345 37.0 37.0 37.0 37.0 37.0 8 36.639 37.0 37.0 37.0 37.0 37.0 9 36.6085 37.0 37.0 37.0 37.0 37.0 10-14 36.6305 37.0 37.0 37.0 37.0 37.0 15-19 36.6349 37.0 37.0 37.0 37.0 37.0 20-24 36.602599999999995 37.0 37.0 37.0 37.0 37.0 25-29 36.5293 37.0 37.0 37.0 37.0 37.0 30-34 36.5048 37.0 37.0 37.0 37.0 37.0 35-39 36.4762 37.0 37.0 37.0 37.0 37.0 40-44 36.4854 37.0 37.0 37.0 37.0 37.0 45-49 36.474199999999996 37.0 37.0 37.0 37.0 37.0 50-54 36.3928 37.0 37.0 37.0 37.0 37.0 55-59 36.425200000000004 37.0 37.0 37.0 37.0 37.0 60-64 36.3627 37.0 37.0 37.0 37.0 37.0 65-69 36.340500000000006 37.0 37.0 37.0 37.0 37.0 70-74 36.3584 37.0 37.0 37.0 37.0 37.0 75-79 36.313199999999995 37.0 37.0 37.0 37.0 37.0 80-84 36.33319999999999 37.0 37.0 37.0 37.0 37.0 85-89 36.2692 37.0 37.0 37.0 37.0 37.0 90-94 36.234 37.0 37.0 37.0 37.0 37.0 95-99 36.2288 37.0 37.0 37.0 37.0 37.0 100-104 36.24720000000001 37.0 37.0 37.0 37.0 37.0 105-109 36.2345 37.0 37.0 37.0 37.0 37.0 110-114 36.1371 37.0 37.0 37.0 37.0 37.0 115-119 36.159299999999995 37.0 37.0 37.0 37.0 37.0 120-124 36.0368 37.0 37.0 37.0 37.0 37.0 125-129 35.9747 37.0 37.0 37.0 37.0 37.0 130-134 35.9271 37.0 37.0 37.0 37.0 37.0 135-139 35.797700000000006 37.0 37.0 37.0 37.0 37.0 140-144 35.5125 37.0 37.0 37.0 37.0 37.0 145-149 35.39 37.0 37.0 37.0 37.0 37.0 150-151 35.1445 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 1.0 22 0.0 23 1.0 24 1.0 25 4.0 26 6.0 27 8.0 28 9.0 29 20.0 30 24.0 31 27.0 32 50.0 33 74.0 34 137.0 35 327.0 36 2889.0 37 422.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 34.875 10.424999999999999 5.675 49.025 2 17.60581016779364 13.82419233658903 37.69095917856248 30.879038317054846 3 15.975 15.475 27.325 41.225 4 21.2 23.849999999999998 23.925 31.025000000000002 5 21.125 30.8 26.1 21.975 6 20.8 34.150000000000006 24.3 20.75 7 15.35 26.150000000000002 40.575 17.925 8 17.95 25.174999999999997 32.475 24.4 9 16.5 23.825 35.9 23.775 10-14 19.62 30.095 27.52 22.765 15-19 20.155 27.495000000000005 28.27 24.08 20-24 20.405 28.105000000000004 27.42 24.07 25-29 19.655 27.875 28.17 24.3 30-34 19.425 28.54 27.46 24.575 35-39 19.975 28.58 27.515 23.93 40-44 20.815 27.905 27.839999999999996 23.44 45-49 20.68 28.59 27.075 23.655 50-54 20.685000000000002 28.01 27.375 23.93 55-59 20.830000000000002 27.005000000000003 27.860000000000003 24.305 60-64 20.18 28.125 27.345000000000002 24.349999999999998 65-69 20.665 28.225 27.575 23.535 70-74 20.044999999999998 28.335 27.315 24.305 75-79 20.005 28.325 27.87 23.799999999999997 80-84 20.875 28.74 26.855 23.53 85-89 20.3 28.365000000000002 27.055 24.279999999999998 90-94 21.16 28.27 26.724999999999998 23.845 95-99 20.380000000000003 28.08 28.07 23.47 100-104 20.77 28.410000000000004 26.945000000000004 23.875 105-109 20.7 28.715000000000003 26.195 24.39 110-114 20.330000000000002 28.139999999999997 27.034999999999997 24.495 115-119 20.845 28.83 26.07 24.255 120-124 21.02 28.660000000000004 25.795 24.525 125-129 20.315 29.244999999999997 25.455 24.985 130-134 20.48 28.499999999999996 25.174999999999997 25.845000000000002 135-139 20.235 28.715000000000003 25.169999999999998 25.88 140-144 21.505 27.985 25.869999999999997 24.64 145-149 20.7 27.27 25.629999999999995 26.400000000000002 150-151 20.599999999999998 28.3875 24.9 26.1125 >>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 0.0 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 0.5 18 1.0 19 0.5 20 0.0 21 0.0 22 0.5 23 3.5 24 3.5 25 1.5 26 3.0 27 3.5 28 6.5 29 12.5 30 18.5 31 17.5 32 22.0 33 34.5 34 47.0 35 64.0 36 83.0 37 105.5 38 136.5 39 167.0 40 195.0 41 202.0 42 218.5 43 252.5 44 247.0 45 245.0 46 266.5 47 260.5 48 215.0 49 199.5 50 187.5 51 145.5 52 120.5 53 104.0 54 84.5 55 78.5 56 76.5 57 52.5 58 34.5 59 23.0 60 22.0 61 21.0 62 7.5 63 3.0 64 1.5 65 2.0 66 2.0 67 0.5 68 0.0 69 0.0 70 0.0 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 0.17500000000000002 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 79.85 #Duplication Level Percentage of deduplicated Percentage of total 1 81.46524733876018 65.05 2 13.869755792110205 22.15 3 3.1308703819661865 7.5 4 1.158422041327489 3.6999999999999997 5 0.28177833437695676 1.125 6 0.06261740763932373 0.3 7 0.031308703819661866 0.17500000000000002 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 ACCACATGCTCCACCGCTTGTGCGGGCCCCCGTCAATTCCTTTGAGTTTC 7 0.17500000000000002 No Hit CTCACTTGAAAATTACGGAAACACATTGCACAACATGTATCTGCCTAAAT 6 0.15 No Hit CTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAAC 6 0.15 No Hit CCTGGAAGGATCATTCAAGCCCAGCTGATTGGCTATGAATAGCCTAAGTC 5 0.125 No Hit TCTTATGGTCTCCATCAGTTTCAATATTTTCAGAATATGTGGGTAGCAGG 5 0.125 No Hit CACCTTTTGGTCGTCCCAAATGACTAGAAAGAATAACTTTGGCCCCTTTT 5 0.125 No Hit CTGCATTGTAACCAAGAAATCCTTCAACTTTGTCCCTTTGGTTTCAGCCT 5 0.125 No Hit GAAAAAGAAGGAAGTAAAGACAGCAGGTTCGCACTTCCCCTACTTTGCTT 5 0.125 No Hit GGAGCATTTGTAGAGAGGGATTTGATAAGATGATGAGCCTGAAATCGCCC 5 0.125 No Hit CTCCTCCCACTGCTACTCTCTTCTTTGTTCTTCATCTCCACGTTGACTCC 5 0.125 No Hit AGCCGCAAAAGTTTTCCATTTTCTGTAGCATCCCCAGGATAAAGAACAGC 5 0.125 No Hit CACGCCTTTGATATGAACTCGAAATGGGCCTCTGGTATGTCTTGTGACAC 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 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.07500000000000001 0.0 0.0 0.0 0.0 62-63 0.125 0.0 0.0 0.0 0.0 64-65 0.21250000000000002 0.0 0.0 0.0 0.0 66-67 0.225 0.0 0.0 0.0 0.0 68-69 0.2625 0.0 0.0 0.0 0.0 70-71 0.35 0.0 0.0 0.0 0.0 72-73 0.42500000000000004 0.0 0.0 0.0 0.0 74-75 0.675 0.0 0.0 0.0 0.0 76-77 0.8875 0.0 0.0 0.0 0.0 78-79 1.1 0.0 0.0 0.0 0.0 80-81 1.4125 0.0 0.0 0.0 0.0 82-83 1.5 0.0 0.0 0.0 0.0 84-85 1.9 0.0 0.0 0.0 0.0 86-87 2.4125 0.0 0.0 0.0 0.0 88-89 2.6875 0.0 0.0 0.0 0.0 90-91 3.2625 0.0 0.0 0.0 0.0 92-93 3.6125 0.0 0.0 0.0 0.0 94-95 4.237500000000001 0.0 0.0 0.0 0.0 96-97 4.800000000000001 0.0 0.0 0.0 0.0 98-99 5.5375 0.0 0.0 0.0 0.0 100-101 6.425000000000001 0.0 0.0 0.0 0.0 102-103 7.35 0.0 0.0 0.0 0.0 104-105 8.024999999999999 0.0 0.0 0.0 0.0 106-107 9.149999999999999 0.0 0.0 0.0 0.0 108-109 9.8875 0.0 0.0 0.0 0.0 110-111 10.7375 0.0 0.0 0.0 0.0 112-113 11.7375 0.0 0.0 0.0 0.0 114-115 12.5625 0.0 0.0 0.0 0.0 116-117 13.625 0.0 0.0 0.0 0.0 118-119 14.837499999999999 0.0 0.0 0.0 0.0 120-121 16.025 0.0 0.0 0.0 0.0 122-123 16.95 0.0 0.0 0.0 0.0 124-125 18.3125 0.0 0.0 0.0 0.0 126-127 19.2 0.0 0.0 0.0 0.0 128-129 20.225 0.0 0.0 0.0 0.0 130-131 21.3 0.0 0.0 0.0 0.0 132-133 22.2375 0.0 0.0 0.0 0.0 134-135 23.25 0.0 0.0 0.0 0.0 136-137 24.25 0.0 0.0 0.0 0.0 138-139 25.425 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TGTTGGC 10 0.006830828 145.0 7 ACCATGT 10 0.006830828 145.0 3 AACCATG 10 0.006830828 145.0 2 ATGTTGG 10 0.006830828 145.0 6 GTTGGCC 10 0.006830828 145.0 8 CATGTTG 15 1.1411342E-4 145.0 5 CCTATCT 30 0.0017973486 72.5 145 >>END_MODULE SRR12670137 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670137_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 36.395 37.0 37.0 37.0 37.0 37.0 2 36.1785 37.0 37.0 37.0 37.0 37.0 3 36.213 37.0 37.0 37.0 37.0 37.0 4 36.3075 37.0 37.0 37.0 37.0 37.0 5 36.403 37.0 37.0 37.0 37.0 37.0 6 36.393 37.0 37.0 37.0 37.0 37.0 7 36.4155 37.0 37.0 37.0 37.0 37.0 8 36.37 37.0 37.0 37.0 37.0 37.0 9 36.4295 37.0 37.0 37.0 37.0 37.0 10-14 36.4388 37.0 37.0 37.0 37.0 37.0 15-19 36.4024 37.0 37.0 37.0 37.0 37.0 20-24 36.3868 37.0 37.0 37.0 37.0 37.0 25-29 36.33200000000001 37.0 37.0 37.0 37.0 37.0 30-34 36.336200000000005 37.0 37.0 37.0 37.0 37.0 35-39 36.3322 37.0 37.0 37.0 37.0 37.0 40-44 36.2692 37.0 37.0 37.0 37.0 37.0 45-49 36.2884 37.0 37.0 37.0 37.0 37.0 50-54 36.2235 37.0 37.0 37.0 37.0 37.0 55-59 36.1645 37.0 37.0 37.0 37.0 37.0 60-64 36.152499999999996 37.0 37.0 37.0 37.0 37.0 65-69 36.2204 37.0 37.0 37.0 37.0 37.0 70-74 36.10269999999999 37.0 37.0 37.0 37.0 37.0 75-79 36.1574 37.0 37.0 37.0 37.0 37.0 80-84 36.0994 37.0 37.0 37.0 37.0 37.0 85-89 36.087599999999995 37.0 37.0 37.0 37.0 37.0 90-94 36.104400000000005 37.0 37.0 37.0 37.0 37.0 95-99 36.0098 37.0 37.0 37.0 37.0 37.0 100-104 35.9655 37.0 37.0 37.0 37.0 37.0 105-109 35.9536 37.0 37.0 37.0 37.0 37.0 110-114 35.896100000000004 37.0 37.0 37.0 37.0 37.0 115-119 35.9381 37.0 37.0 37.0 37.0 37.0 120-124 35.79599999999999 37.0 37.0 37.0 37.0 37.0 125-129 35.694399999999995 37.0 37.0 37.0 37.0 37.0 130-134 35.4711 37.0 37.0 37.0 37.0 37.0 135-139 35.42530000000001 37.0 37.0 37.0 37.0 37.0 140-144 35.2102 37.0 37.0 37.0 34.6 37.0 145-149 34.8818 37.0 37.0 37.0 25.0 37.0 150-151 34.537 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 1.0 15 0.0 16 1.0 17 0.0 18 0.0 19 0.0 20 0.0 21 2.0 22 3.0 23 3.0 24 5.0 25 6.0 26 5.0 27 6.0 28 14.0 29 19.0 30 20.0 31 30.0 32 58.0 33 108.0 34 200.0 35 521.0 36 2668.0 37 327.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 35.8 21.0 10.75 32.45 2 24.9 26.174999999999997 32.800000000000004 16.125 3 18.775 28.849999999999998 32.375 20.0 4 23.724999999999998 34.150000000000006 24.224999999999998 17.9 5 27.725 34.925 22.3 15.049999999999999 6 20.9 38.1 23.25 17.75 7 20.8 22.825 38.175 18.2 8 21.875 23.9 30.125 24.099999999999998 9 21.575 23.75 31.75 22.925 10-14 22.85 28.895 27.200000000000003 21.055 15-19 23.52 27.755000000000003 27.655 21.07 20-24 23.68 28.294999999999998 27.175 20.849999999999998 25-29 23.315 27.715 28.095 20.875 30-34 22.689999999999998 28.62 27.685 21.005 35-39 22.53 27.98 28.645 20.845 40-44 22.065 28.605000000000004 28.37 20.96 45-49 23.29 27.74 28.155 20.815 50-54 22.46 28.615000000000002 27.805000000000003 21.12 55-59 23.3 28.285 27.54 20.875 60-64 23.064999999999998 27.725 28.749999999999996 20.46 65-69 23.5 27.73 28.07 20.7 70-74 24.235 28.375 26.805 20.585 75-79 24.05 27.950000000000003 27.315 20.685000000000002 80-84 23.685000000000002 28.98 26.745 20.59 85-89 24.205 28.68 27.034999999999997 20.080000000000002 90-94 24.565 27.875 27.134999999999998 20.424999999999997 95-99 24.755 28.205000000000002 26.745 20.294999999999998 100-104 25.755 27.355 26.479999999999997 20.41 105-109 25.635 28.13 26.740000000000002 19.495 110-114 25.31 28.16 26.445 20.085 115-119 26.384999999999998 27.955000000000002 25.979999999999997 19.68 120-124 26.97 27.79 26.035000000000004 19.205 125-129 26.495 28.08 25.855 19.57 130-134 27.62 28.595 24.45 19.335 135-139 27.395000000000003 27.810000000000002 25.485000000000003 19.31 140-144 27.810000000000002 27.884999999999998 25.2 19.105 145-149 28.499999999999996 28.515 24.91 18.075 150-151 29.262500000000003 26.9625 25.3125 18.462500000000002 >>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 0.5 16 0.5 17 0.5 18 0.5 19 0.0 20 1.5 21 1.5 22 1.5 23 3.5 24 2.5 25 1.0 26 3.0 27 5.0 28 8.0 29 11.5 30 16.0 31 22.0 32 21.0 33 32.5 34 54.0 35 65.0 36 90.5 37 120.5 38 144.5 39 184.0 40 215.5 41 238.0 42 246.5 43 245.5 44 251.0 45 247.0 46 241.5 47 233.5 48 214.0 49 194.0 50 176.0 51 146.5 52 125.0 53 110.0 54 91.0 55 63.0 56 39.5 57 35.5 58 27.5 59 18.0 60 15.0 61 12.0 62 7.0 63 3.5 64 1.5 65 3.0 66 3.0 67 0.5 68 0.5 69 1.0 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 0.5 80 0.5 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 0.5 96 1.0 97 0.5 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 79.9 #Duplication Level Percentage of deduplicated Percentage of total 1 81.91489361702128 65.45 2 13.391739674593243 21.4 3 3.254067584480601 7.8 4 0.9073842302878597 2.9000000000000004 5 0.344180225281602 1.375 6 0.0625782227784731 0.3 7 0.09386733416770963 0.525 8 0.0 0.0 9 0.0 0.0 >10 0.03128911138923655 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 GAGGGAATTTCCGGTGGAGCGGTGAAATGCGTAGAGATCGGAAAGAACAC 7 0.17500000000000002 No Hit CACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAATC 7 0.17500000000000002 No Hit AGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAA 7 0.17500000000000002 No Hit ATTATAATATCAGATATTATGAAGATCAGGATATTGGGATGCTTAGGAAT 6 0.15 No Hit GAATGTTACACTGCTTGGAACTATAGAAAACATGCTGTTCAACACAGTCT 6 0.15 No Hit CCTAAAACACCACACCCACGGCCACAGACTGCATCAACTCTCCACTGGAC 5 0.125 No Hit AAGGGTTTGGCCTTTCTGAAGGTCTTGGATAATGGGGAGTTTGAGGGAAT 5 0.125 No Hit GGATGGGCTTGACCTCCTGCATGTAGATAGTGGATTTGTTTTGCAATGAA 5 0.125 No Hit CAGATAATGAAGCAGACAAGATCAGTACCGTCAGTCTTGCCATTGACTTC 5 0.125 No Hit AGAGGGTGTAATAGCTAAGTAGCCTGTAAGAGATGGCTTCCTCTGTGATT 5 0.125 No Hit AGCAAAGAACTTGCAGAGCAGAGATGGCATCCATGACCATGACAGCCTCA 5 0.125 No Hit TGCCAATCGAAAATCGAAGGTGAAGGCACTTGCAGATCATCAAAGAGTGA 5 0.125 No Hit CCTGGTGGCATCAGGATGGGAACACCGGCTCTTACTTCTAGGGGGTTCGT 5 0.125 No Hit GCTGCTGACTTGAAAGGGAAGAAAGTGTTTGTTAGAGCTGATTTGAATGT 5 0.125 No Hit GCAAGAGCTTCTTCTGACGACTTCAATCTATTTCTATTTAATGATGGACA 5 0.125 No Hit GTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAA 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 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.07500000000000001 0.0 0.0 0.0 0.0 62-63 0.125 0.0 0.0 0.0 0.0 64-65 0.21250000000000002 0.0 0.0 0.0 0.0 66-67 0.225 0.0 0.0 0.0 0.0 68-69 0.2625 0.0 0.0 0.0 0.0 70-71 0.35 0.0 0.0 0.0 0.0 72-73 0.42500000000000004 0.0 0.0 0.0 0.0 74-75 0.675 0.0 0.0 0.0 0.0 76-77 0.8875 0.0 0.0 0.0 0.0 78-79 1.1 0.0 0.0 0.0 0.0 80-81 1.4500000000000002 0.0 0.0 0.0 0.0 82-83 1.55 0.0 0.0 0.0 0.0 84-85 1.95 0.0 0.0 0.0 0.0 86-87 2.4625 0.0 0.0 0.0 0.0 88-89 2.75 0.0 0.0 0.0 0.0 90-91 3.3375 0.0 0.0 0.0 0.0 92-93 3.6875 0.0 0.0 0.0 0.0 94-95 4.3125 0.0 0.0 0.0 0.0 96-97 4.9 0.0 0.0 0.0 0.0 98-99 5.6375 0.0 0.0 0.0 0.0 100-101 6.6375 0.0 0.0 0.0 0.0 102-103 7.6125 0.0 0.0 0.0 0.0 104-105 8.3375 0.0 0.0 0.0 0.0 106-107 9.475000000000001 0.0 0.0 0.0 0.0 108-109 10.2375 0.0 0.0 0.0 0.0 110-111 11.075 0.0 0.0 0.0 0.0 112-113 12.0625 0.0 0.0 0.0 0.0 114-115 12.8625 0.0 0.0 0.0 0.0 116-117 13.925 0.0 0.0 0.0 0.0 118-119 15.175 0.0 0.0 0.0 0.0 120-121 16.4 0.0 0.0 0.0 0.0 122-123 17.325 0.0 0.0 0.0 0.0 124-125 18.7 0.0 0.0 0.0 0.0 126-127 19.575 0.0 0.0 0.0 0.0 128-129 20.625 0.0 0.0 0.0 0.0 130-131 21.737499999999997 0.0 0.0 0.0 0.0 132-133 22.6625 0.0 0.0 0.0 0.0 134-135 23.674999999999997 0.0 0.0 0.0 0.0 136-137 24.7 0.0 0.0 0.0 0.0 138-139 25.9 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GTGTAAT 10 0.006830828 145.0 6 TAATAGC 10 0.006830828 145.0 9 GGGTGTA 10 0.006830828 145.0 4 GTAATAG 10 0.006830828 145.0 8 TGTAATA 10 0.006830828 145.0 7 CTGTGTA 40 0.005621335 54.375 145 >>END_MODULE Read 393189 spots for SRR12670137.sra Written 393189 spots for SRR12670137.sra Read 393189 spots for SRR12670137.sra Written 393189 spots for SRR12670137.sra Read 393189 spots for SRR12670137.sra Written 393189 spots for SRR12670137.sra Read 393189 spots for SRR12670137.sra Written 393189 spots for SRR12670137.sra Read 393189 spots for SRR12670137.sra Written 393189 spots for SRR12670137.sra Read 393189 spots for SRR12670137.sra Written 393189 spots for SRR12670137.sra Read 393189 spots for SRR12670137.sra Written 393189 spots for SRR12670137.sra Read 393189 spots for SRR12670137.sra Written 393189 spots for SRR12670137.sra Read 393189 spots for SRR12670137.sra Written 393189 spots for SRR12670137.sra Read 393189 spots for SRR12670137.sra Written 393189 spots for SRR12670137.sra Read 393189 spots for SRR12670137.sra Written 393189 spots for SRR12670137.sra Read 393189 spots for SRR12670137.sra Written 393189 spots for SRR12670137.sra Read 393189 spots for SRR12670137.sra Written 393189 spots for SRR12670137.sra Read 393189 spots for SRR12670137.sra Written 393189 spots for SRR12670137.sra Read 393205 spots for SRR12670137.sra Written 393205 spots for SRR12670137.sra Read 393189 spots for SRR12670137.sra Written 393189 spots for SRR12670137.sra Read 393189 spots for SRR12670137.sra Written 393189 spots for SRR12670137.sra Read 393189 spots for SRR12670137.sra Written 393189 spots for SRR12670137.sra Read 393189 spots for SRR12670137.sra Written 393189 spots for SRR12670137.sra Read 393189 spots for SRR12670137.sra Written 393189 spots for SRR12670137.sra SRR ids: ['SRR12670137.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_32zyambi SRR12670137.sra spots: 7863796 blocks: [[1, 393189], [393190, 786378], [786379, 1179567], [1179568, 1572756], [1572757, 1965945], [1965946, 2359134], [2359135, 2752323], [2752324, 3145512], [3145513, 3538701], [3538702, 3931890], [3931891, 4325079], [4325080, 4718268], [4718269, 5111457], [5111458, 5504646], [5504647, 5897835], [5897836, 6291024], [6291025, 6684213], [6684214, 7077402], [7077403, 7470591], [7470592, 7863796]] SRR12670137 file size 2654933 SRR12670137 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 SRR12670137 SRR12670137_1.fastq SRR12670137_2.fastq Input file: SRR12670137_1.fastq Paired file: SRR12670137_2.fastq trimmed: SRR12670137-trimmed-pair1.fastq, SRR12670137-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 02:23:52 2025 >> started Tue Feb 11 02:33:35 2025 >> done (583.159s) 7863796 read pairs processed; of these: 43 ( 0.00%) short read pairs filtered out after trimming by size control 1330 ( 0.02%) empty read pairs filtered out after trimming by size control 7862423 (99.98%) read pairs available; of these: 2426828 (30.87%) trimmed read pairs available after processing 5435595 (69.13%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 3 0.00% 19 7 0.00% 20 2 0.00% 21 6 0.00% 22 9 0.00% 23 4 0.00% 24 9 0.00% 25 5 0.00% 26 8 0.00% 27 12 0.00% 28 11 0.00% 29 20 0.00% 30 24 0.00% 31 15 0.00% 32 30 0.00% 33 26 0.00% 34 52 0.00% 35 60 0.00% 36 45 0.00% 37 51 0.00% 38 72 0.00% 39 69 0.00% 40 78 0.00% 41 102 0.00% 42 149 0.00% 43 139 0.00% 44 105 0.00% 45 116 0.00% 46 138 0.00% 47 195 0.00% 48 203 0.00% 49 269 0.00% 50 306 0.00% 51 370 0.00% 52 436 0.01% 53 423 0.01% 54 445 0.01% 55 503 0.01% 56 498 0.01% 57 595 0.01% 58 805 0.01% 59 903 0.01% 60 1042 0.01% 61 1244 0.02% 62 1353 0.02% 63 1599 0.02% 64 1674 0.02% 65 1867 0.02% 66 2005 0.03% 67 2233 0.03% 68 2386 0.03% 69 2829 0.04% 70 3375 0.04% 71 3889 0.05% 72 4353 0.06% 73 4884 0.06% 74 5549 0.07% 75 5905 0.08% 76 6402 0.08% 77 6866 0.09% 78 7604 0.10% 79 8148 0.10% 80 8915 0.11% 81 10096 0.13% 82 11337 0.14% 83 12186 0.15% 84 13827 0.18% 85 14702 0.19% 86 15529 0.20% 87 16301 0.21% 88 17333 0.22% 89 18060 0.23% 90 19186 0.24% 91 20636 0.26% 92 21641 0.28% 93 23495 0.30% 94 24875 0.32% 95 25956 0.33% 96 26761 0.34% 97 27522 0.35% 98 27953 0.36% 99 28925 0.37% 100 29656 0.38% 101 30272 0.39% 102 31430 0.40% 103 32694 0.42% 104 33068 0.42% 105 34056 0.43% 106 35578 0.45% 107 35717 0.45% 108 35677 0.45% 109 35652 0.45% 110 36280 0.46% 111 36676 0.47% 112 37359 0.48% 113 37869 0.48% 114 38302 0.49% 115 39272 0.50% 116 40230 0.51% 117 40125 0.51% 118 39522 0.50% 119 39325 0.50% 120 40306 0.51% 121 40498 0.52% 122 40684 0.52% 123 40456 0.51% 124 40284 0.51% 125 40735 0.52% 126 41287 0.53% 127 41177 0.52% 128 40503 0.52% 129 40339 0.51% 130 40320 0.51% 131 40083 0.51% 132 39477 0.50% 133 39974 0.51% 134 40691 0.52% 135 40181 0.51% 136 39926 0.51% 137 39890 0.51% 138 40153 0.51% 139 40617 0.52% 140 39798 0.51% 141 39383 0.50% 142 39231 0.50% 143 39208 0.50% 144 39677 0.50% 145 39297 0.50% 146 39034 0.50% 147 39529 0.50% 148 39285 0.50% 149 39118 0.50% 150 39166 0.50% 151 5435595 69.13% 7862423 reads passed initial QC criterion=sequence-density sequence-density=0.57 sequence-density-rank=1 fanout-score=2.01 fanout-score-rank=33 prefix-density=0.57 prefix-fanout=2.0 sequence=TGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGGAGTATGAATGTGTTCTCTGTGTA criterion=fanout-score sequence-density=0.01 sequence-density-rank=40 fanout-score=31.63 fanout-score-rank=1 prefix-density=0.07 prefix-fanout=6.9 sequence=ACCACACCAGAGGCCACAGACATGGCCAATACATAACAATGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAG criterion=sequence-density sequence-density=1.04 sequence-density-rank=1 fanout-score=2.02 fanout-score-rank=32 prefix-density=1.03 prefix-fanout=2.0 sequence=CTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCATTGTTATGTATTGGCCATGTCTGTGGCCTCTGGTGTGGT criterion=fanout-score sequence-density=0.11 sequence-density-rank=33 fanout-score=33.05 fanout-score-rank=1 prefix-density=0.31 prefix-fanout=11.5 sequence=AAAGAAAAGAAAA SRR12670137 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 02:45:06 Started mapping on | Feb 11 02:45:12 Finished on | Feb 11 03:17:31 Mapping speed, Million of reads per hour | 14.60 Number of input reads | 7862423 Average input read length | 281 UNIQUE READS: Uniquely mapped reads number | 7342239 Uniquely mapped reads % | 93.38% Average mapped length | 280.63 Number of splices: Total | 6761567 Number of splices: Annotated (sjdb) | 6589491 Number of splices: GT/AG | 6624595 Number of splices: GC/AG | 102561 Number of splices: AT/AC | 4154 Number of splices: Non-canonical | 30257 Mismatch rate per base, % | 0.36% Deletion rate per base | 0.03% Deletion average length | 2.88 Insertion rate per base | 0.02% Insertion average length | 2.46 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 199429 % of reads mapped to multiple loci | 2.54% Number of reads mapped to too many loci | 105978 % of reads mapped to too many loci | 1.35% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.50% % of reads unmapped: other | 0.24% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 320755 320755 320755 N_multimapping 199429 199429 199429 N_noFeature 344977 7223915 396615 N_ambiguous 111668 446 44789 UnstrandedReadsAssigned:6885594 PositiveStrandReadsAssigned:117878 NegativeStrandReadsAssigned:6900835 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=129 echo kmer=125 SRR12670137 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: SRR12670137-trimmed-pair1.fastq SRR12670137-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 7,862,423 reads, 6,952,397 reads pseudoaligned [quant] estimated average fragment length: 198.955 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,010 rounds 52401 SRR12670137.ke.tsv 34699 SRR12670137.se.tsv 87100 total ==> SRR12670137.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1820.04 295 21.8562 Potri.005G024800.1.v4.1 1035 837.045 174 28.0307 Potri.004G059700.1.v4.1 961 763.103 0 0 Potri.007G009000.2.v4.1 1416 1218.04 0 0 Potri.003G141000.2.v4.1 2943 2745.04 390 19.158 Potri.016G087400.1.v4.1 270 112.433 377 452.15 Potri.015G069301.1.v4.1 564 372.65 0 0 Potri.010G195200.1.v4.1 1773 1575.04 78 6.67784 Potri.012G127500.1.v4.1 977 779.091 87 15.0579 ==> SRR12670137.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 79 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 110 Potri.001G212900.v4.1 37 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 14 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 1 SRR12670137 completed mapping pipeline successfully