Starting /dee2/code/volunteer_pipeline.sh SRR12670127 current disk space = 3057369452544 free memory = 1174812656 SRR12670127 SRAfilesize 2676580a355f56d49e99040f241e9e48 SRR12670127.sra SRR12670127.sra file validated SRR12670127 is paired end SRR12670127 is conventional basespace SRR12670127 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670127_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 46 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.583 37.0 37.0 37.0 37.0 37.0 2 36.44825 37.0 37.0 37.0 37.0 37.0 3 36.5825 37.0 37.0 37.0 37.0 37.0 4 36.6885 37.0 37.0 37.0 37.0 37.0 5 36.721 37.0 37.0 37.0 37.0 37.0 6 36.7265 37.0 37.0 37.0 37.0 37.0 7 36.598 37.0 37.0 37.0 37.0 37.0 8 36.637 37.0 37.0 37.0 37.0 37.0 9 36.594 37.0 37.0 37.0 37.0 37.0 10-14 36.623000000000005 37.0 37.0 37.0 37.0 37.0 15-19 36.5948 37.0 37.0 37.0 37.0 37.0 20-24 36.507099999999994 37.0 37.0 37.0 37.0 37.0 25-29 36.528299999999994 37.0 37.0 37.0 37.0 37.0 30-34 36.5082 37.0 37.0 37.0 37.0 37.0 35-39 36.449 37.0 37.0 37.0 37.0 37.0 40-44 36.438599999999994 37.0 37.0 37.0 37.0 37.0 45-49 36.339999999999996 37.0 37.0 37.0 37.0 37.0 50-54 36.3212 37.0 37.0 37.0 37.0 37.0 55-59 36.2087 37.0 37.0 37.0 37.0 37.0 60-64 36.2619 37.0 37.0 37.0 37.0 37.0 65-69 36.2118 37.0 37.0 37.0 37.0 37.0 70-74 36.1908 37.0 37.0 37.0 37.0 37.0 75-79 36.312400000000004 37.0 37.0 37.0 37.0 37.0 80-84 36.3108 37.0 37.0 37.0 37.0 37.0 85-89 36.3055 37.0 37.0 37.0 37.0 37.0 90-94 36.261300000000006 37.0 37.0 37.0 37.0 37.0 95-99 36.252599999999994 37.0 37.0 37.0 37.0 37.0 100-104 36.217 37.0 37.0 37.0 37.0 37.0 105-109 36.188199999999995 37.0 37.0 37.0 37.0 37.0 110-114 36.1422 37.0 37.0 37.0 37.0 37.0 115-119 36.1593 37.0 37.0 37.0 37.0 37.0 120-124 36.018299999999996 37.0 37.0 37.0 37.0 37.0 125-129 35.9755 37.0 37.0 37.0 37.0 37.0 130-134 35.8519 37.0 37.0 37.0 37.0 37.0 135-139 35.838 37.0 37.0 37.0 37.0 37.0 140-144 35.5582 37.0 37.0 37.0 37.0 37.0 145-149 35.47859999999999 37.0 37.0 37.0 37.0 37.0 150-151 35.158 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 24 1.0 25 2.0 26 3.0 27 13.0 28 11.0 29 18.0 30 26.0 31 28.0 32 42.0 33 105.0 34 158.0 35 336.0 36 2834.0 37 423.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 37.625 13.125 6.275 42.975 2 20.07015785517414 13.229766975695314 34.4274617890253 32.272613380105234 3 16.950000000000003 14.424999999999999 28.625 40.0 4 21.6 20.575 25.35 32.475 5 23.925 25.75 25.3 25.025 6 23.45 29.95 24.4 22.2 7 16.825000000000003 28.4 38.25 16.525000000000002 8 17.9 27.85 31.35 22.900000000000002 9 19.175 23.599999999999998 34.25 22.975 10-14 20.285 29.32 27.77 22.625 15-19 20.255000000000003 27.77 27.425 24.55 20-24 19.935 27.805000000000003 27.955000000000002 24.305 25-29 20.105 27.365000000000002 28.21 24.32 30-34 20.64 27.744999999999997 27.58 24.035 35-39 20.48 28.315 26.765 24.44 40-44 20.685000000000002 27.884999999999998 27.165 24.265 45-49 20.825 28.02 27.205000000000002 23.95 50-54 21.245 26.855 27.74 24.16 55-59 20.31 27.375 27.810000000000002 24.505 60-64 20.849999999999998 26.96 27.82 24.37 65-69 20.745 27.975 27.389999999999997 23.89 70-74 21.29 26.845000000000002 27.065 24.8 75-79 21.044999999999998 26.46 27.55 24.945 80-84 21.69 28.09 26.605 23.615 85-89 21.91 28.035 25.790000000000003 24.265 90-94 22.435 26.095000000000002 27.35 24.12 95-99 22.615 26.625 26.26 24.5 100-104 22.085 27.67 26.314999999999998 23.93 105-109 21.68 28.335 26.245 23.74 110-114 22.345000000000002 27.105 26.07 24.48 115-119 22.715 27.33 25.585 24.37 120-124 22.455 28.22 24.94 24.385 125-129 22.62 27.845 25.6 23.935000000000002 130-134 22.56 28.42 24.795 24.224999999999998 135-139 22.53 27.325 25.490000000000002 24.654999999999998 140-144 23.055 26.490000000000002 25.775 24.68 145-149 23.615 25.89 25.480000000000004 25.014999999999997 150-151 24.099999999999998 26.337500000000002 25.174999999999997 24.3875 >>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 0.0 18 0.0 19 0.0 20 0.5 21 0.5 22 0.5 23 1.0 24 3.0 25 4.0 26 1.5 27 1.5 28 3.5 29 6.5 30 9.0 31 14.0 32 29.5 33 31.0 34 36.0 35 44.5 36 54.0 37 78.5 38 89.5 39 121.0 40 158.0 41 178.5 42 206.5 43 238.5 44 258.5 45 282.0 46 294.0 47 268.0 48 248.0 49 226.0 50 200.0 51 176.5 52 145.5 53 122.5 54 106.0 55 85.0 56 70.0 57 49.0 58 32.5 59 34.5 60 24.0 61 10.0 62 5.0 63 3.5 64 4.0 65 14.0 66 17.0 67 7.0 68 3.0 69 2.5 70 1.0 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 0.22499999999999998 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 81.65 #Duplication Level Percentage of deduplicated Percentage of total 1 83.4966319657073 68.175 2 12.553582363747703 20.5 3 3.061849357011635 7.5 4 0.5817513778322106 1.9 5 0.1837109614206981 0.75 6 0.0612369871402327 0.3 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0612369871402327 0.8750000000000001 >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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGTGTCGATCTCGTAT 23 0.575 TruSeq Adapter, Index 15 (97% over 37bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGTGTCGATCGCGTAT 12 0.3 TruSeq Adapter, Index 15 (97% over 37bp) GCAACAACGATAACATCATAACCATAACGAGAGAACCGGGAACCAAACAA 6 0.15 No Hit TTTGTTGTCTTTTTTTACCCTCTTACAAATGCAAACAAAAAACAGGCTAC 6 0.15 No Hit AACTCCTTCAAGCTCGCCGATTGAATAAAAAAAGGTTATTATAATTTTGA 5 0.125 No Hit CCACCAGTGGCAAATTTAAGTAGCAAGCAAGCAACAACAGATCCTAGCAA 5 0.125 No Hit CCGCAAACCGTCACGCTTGTGGGTGTCAGTAAAAACCCTATCCCACACTT 5 0.125 No Hit CCTTCTCTTTCCTTCCAGTCCTATCAAGTGAGTGATAATCGTCTAAACAT 5 0.125 No Hit TGTTGGTAGAGCTATTTGTAGGGCAAATTCCCTTGAGATCCTCAGCAAAG 5 0.125 No Hit ACCCCCATCAGCATTCCCAGAGACAAACACACAAGAAACAACTGTATCTG 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 0.025 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.0625 0.0 0.0 0.0 0.0 54-55 0.125 0.0 0.0 0.0 0.0 56-57 0.125 0.0 0.0 0.0 0.0 58-59 0.125 0.0 0.0 0.0 0.0 60-61 0.21250000000000002 0.0 0.0 0.0 0.0 62-63 0.275 0.0 0.0 0.0 0.0 64-65 0.275 0.0 0.0 0.0 0.0 66-67 0.30000000000000004 0.0 0.0 0.0 0.0 68-69 0.3625 0.0 0.0 0.0 0.0 70-71 0.375 0.0 0.0 0.0 0.0 72-73 0.4875 0.0 0.0 0.0 0.0 74-75 0.6125 0.0 0.0 0.0 0.0 76-77 0.7125 0.0 0.0 0.0 0.0 78-79 0.8625 0.0 0.0 0.0 0.0 80-81 1.025 0.0 0.0 0.0 0.0 82-83 1.2875 0.0 0.0 0.0 0.0 84-85 1.6625 0.0 0.0 0.0 0.0 86-87 2.175 0.0 0.0 0.0 0.0 88-89 2.7125000000000004 0.0 0.0 0.0 0.0 90-91 3.125 0.0 0.0 0.0 0.0 92-93 3.575 0.0 0.0 0.0 0.0 94-95 4.0125 0.0 0.0 0.0 0.0 96-97 4.7875 0.0 0.0 0.0 0.0 98-99 5.4375 0.0 0.0 0.0 0.0 100-101 6.012499999999999 0.0 0.0 0.0 0.0 102-103 6.550000000000001 0.0 0.0 0.0 0.0 104-105 7.4625 0.0 0.0 0.0 0.0 106-107 8.675 0.0 0.0 0.0 0.0 108-109 9.7625 0.0 0.0 0.0 0.0 110-111 10.787500000000001 0.0 0.0 0.0 0.0 112-113 11.9 0.0 0.0 0.0 0.0 114-115 12.825 0.0 0.0 0.0 0.0 116-117 13.925 0.0 0.0 0.0 0.0 118-119 15.0625 0.0 0.0 0.0 0.0 120-121 16.375 0.0 0.0 0.0 0.0 122-123 17.424999999999997 0.0 0.0 0.0 0.0 124-125 18.4625 0.0 0.0 0.0 0.0 126-127 19.424999999999997 0.0 0.0 0.0 0.0 128-129 20.3125 0.0 0.0 0.0 0.0 130-131 21.450000000000003 0.0 0.0 0.0 0.0 132-133 22.325000000000003 0.0 0.0 0.0 0.0 134-135 23.3875 0.0 0.0 0.0 0.0 136-137 24.4375 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 CGCATTT 10 0.006830828 145.0 3 >>END_MODULE SRR12670127 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670127_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 46 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.384 37.0 37.0 37.0 37.0 37.0 2 36.355 37.0 37.0 37.0 37.0 37.0 3 36.337 37.0 37.0 37.0 37.0 37.0 4 36.36 37.0 37.0 37.0 37.0 37.0 5 36.4295 37.0 37.0 37.0 37.0 37.0 6 36.374 37.0 37.0 37.0 37.0 37.0 7 36.405 37.0 37.0 37.0 37.0 37.0 8 36.384 37.0 37.0 37.0 37.0 37.0 9 36.2815 37.0 37.0 37.0 37.0 37.0 10-14 36.3471 37.0 37.0 37.0 37.0 37.0 15-19 36.3233 37.0 37.0 37.0 37.0 37.0 20-24 36.245 37.0 37.0 37.0 37.0 37.0 25-29 36.1546 37.0 37.0 37.0 37.0 37.0 30-34 36.1672 37.0 37.0 37.0 37.0 37.0 35-39 36.0762 37.0 37.0 37.0 37.0 37.0 40-44 36.0785 37.0 37.0 37.0 37.0 37.0 45-49 36.082800000000006 37.0 37.0 37.0 37.0 37.0 50-54 36.0838 37.0 37.0 37.0 37.0 37.0 55-59 36.080200000000005 37.0 37.0 37.0 37.0 37.0 60-64 36.0754 37.0 37.0 37.0 37.0 37.0 65-69 36.0204 37.0 37.0 37.0 37.0 37.0 70-74 36.009 37.0 37.0 37.0 37.0 37.0 75-79 35.9478 37.0 37.0 37.0 37.0 37.0 80-84 35.949799999999996 37.0 37.0 37.0 37.0 37.0 85-89 35.93769999999999 37.0 37.0 37.0 37.0 37.0 90-94 36.056 37.0 37.0 37.0 37.0 37.0 95-99 36.011900000000004 37.0 37.0 37.0 37.0 37.0 100-104 35.941199999999995 37.0 37.0 37.0 37.0 37.0 105-109 35.907599999999995 37.0 37.0 37.0 37.0 37.0 110-114 35.9009 37.0 37.0 37.0 37.0 37.0 115-119 35.8834 37.0 37.0 37.0 37.0 37.0 120-124 35.7209 37.0 37.0 37.0 37.0 37.0 125-129 35.5856 37.0 37.0 37.0 37.0 37.0 130-134 35.347500000000004 37.0 37.0 37.0 34.6 37.0 135-139 35.223 37.0 37.0 37.0 34.6 37.0 140-144 35.043699999999994 37.0 37.0 37.0 25.0 37.0 145-149 34.6502 37.0 37.0 37.0 25.0 37.0 150-151 34.41225 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 2.0 13 6.0 14 3.0 15 3.0 16 3.0 17 2.0 18 1.0 19 0.0 20 1.0 21 1.0 22 5.0 23 7.0 24 8.0 25 7.0 26 9.0 27 16.0 28 22.0 29 15.0 30 22.0 31 40.0 32 52.0 33 82.0 34 181.0 35 488.0 36 2679.0 37 345.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 37.1 21.425 10.475 31.0 2 27.025 26.900000000000002 29.175 16.900000000000002 3 23.45 27.250000000000004 29.65 19.650000000000002 4 25.6 34.075 22.975 17.349999999999998 5 26.275 34.275 22.25 17.2 6 23.175 38.025 21.85 16.950000000000003 7 23.125 22.400000000000002 35.699999999999996 18.775 8 23.325000000000003 24.9 28.599999999999998 23.175 9 24.224999999999998 24.275 29.7 21.8 10-14 25.64 28.65 24.75 20.96 15-19 25.435000000000002 28.17 25.6 20.794999999999998 20-24 25.290000000000003 27.725 25.835 21.15 25-29 25.324999999999996 27.92 25.7 21.055 30-34 24.93 27.43 26.484999999999996 21.154999999999998 35-39 24.66 27.96 26.66 20.72 40-44 24.89 28.255000000000003 25.835 21.02 45-49 24.67 27.805000000000003 26.009999999999998 21.515 50-54 25.3 27.67 26.455000000000002 20.575 55-59 25.09 27.08 26.290000000000003 21.54 60-64 24.855 27.74 26.25 21.154999999999998 65-69 25.874999999999996 27.045 26.445 20.635 70-74 26.015 27.555000000000003 25.165 21.265 75-79 24.04 28.07 26.83 21.060000000000002 80-84 25.52 27.689999999999998 25.81 20.979999999999997 85-89 25.605 27.07 26.77 20.555 90-94 25.119999999999997 27.37 26.77 20.74 95-99 26.095000000000002 28.715000000000003 25.145 20.044999999999998 100-104 26.090000000000003 27.58 25.97 20.36 105-109 26.895000000000003 27.42 25.695 19.99 110-114 27.3 27.875 25.405 19.42 115-119 28.185 27.634999999999998 24.975 19.205 120-124 27.845 27.860000000000003 25.145 19.15 125-129 28.49 27.91 25.180000000000003 18.42 130-134 29.145 27.775 25.21 17.87 135-139 29.45 26.724999999999998 25.424999999999997 18.4 140-144 30.819999999999997 27.060000000000002 24.805 17.315 145-149 31.55 26.229999999999997 24.905 17.315 150-151 32.2875 25.124999999999996 25.1 17.4875 >>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 0.0 6 0.0 7 0.5 8 0.5 9 0.5 10 1.0 11 1.5 12 2.0 13 1.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.5 20 0.5 21 1.0 22 1.0 23 0.0 24 0.0 25 0.0 26 1.0 27 2.0 28 3.5 29 3.5 30 3.5 31 6.5 32 8.0 33 13.0 34 20.0 35 30.0 36 58.5 37 72.0 38 83.5 39 123.5 40 149.0 41 178.5 42 230.5 43 262.5 44 272.0 45 273.0 46 280.0 47 290.0 48 282.5 49 257.5 50 211.0 51 158.5 52 140.0 53 131.5 54 100.0 55 79.0 56 62.0 57 45.5 58 37.0 59 29.0 60 18.5 61 9.0 62 7.0 63 3.5 64 3.5 65 3.0 66 0.0 67 0.5 68 0.5 69 0.0 70 1.0 71 1.0 72 1.0 73 1.5 74 0.5 75 0.5 76 1.0 77 1.0 78 1.0 79 0.5 80 0.0 81 0.0 82 0.5 83 0.5 84 0.0 85 0.5 86 1.0 87 0.5 88 1.0 89 1.0 90 0.0 91 1.5 92 1.5 93 2.0 94 2.0 95 1.5 96 5.0 97 5.5 98 4.5 99 3.5 100 3.5 >>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 82.45 #Duplication Level Percentage of deduplicated Percentage of total 1 83.99029714978775 69.25 2 12.249848392965433 20.200000000000003 3 2.7592480291085506 6.825 4 0.6973923590054579 2.3 5 0.21224984839296543 0.8750000000000001 6 0.030321406913280776 0.15 7 0.030321406913280776 0.17500000000000002 8 0.0 0.0 9 0.030321406913280776 0.22499999999999998 >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 CTTCGATTAACAGCTGGTGTCTCACCTCTGTCTCTGCCTCTAAGAGATCA 9 0.22499999999999998 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 7 0.17500000000000002 No Hit CCGTGGTTATGGTGACGGTGGATCTAGGTACTCTTCAAGGGGTGAATCCG 6 0.15 No Hit TCTGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGGGGTAGAGTTTTTGAG 5 0.125 No Hit CTCTTTGTGGCTGTTTCGGTTGGCGCTAACATTTCTGGTGGTCATGTGAA 5 0.125 No Hit TGGAATTCTTGGTGGGCAGGTGGAAGGTGGAGAAATTGACTGGACTTTCT 5 0.125 No Hit GGCATTTCCTGCCCATCCTGAGACTAATAATCCCTTTGGAAGCACAAGTC 5 0.125 No Hit CGAACCGAGATGCTCTAGCACTGCTTCCTAAGAGCAGCGTGTCTACCGAT 5 0.125 No Hit GTGATTGGCCTAGCAGCAGACTCTGGGTGTGGTAAGAGTACCTTCATGAG 5 0.125 No Hit CACCCACTGCAAATGCGAGCACAATTCTCAGATCTCTCGCCGCCAAGAAT 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 0.025 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.0625 0.0 0.0 0.0 0.0 54-55 0.125 0.0 0.0 0.0 0.0 56-57 0.125 0.0 0.0 0.0 0.0 58-59 0.125 0.0 0.0 0.0 0.0 60-61 0.21250000000000002 0.0 0.0 0.0 0.0 62-63 0.275 0.0 0.0 0.0 0.0 64-65 0.275 0.0 0.0 0.0 0.0 66-67 0.30000000000000004 0.0 0.0 0.0 0.0 68-69 0.3625 0.0 0.0 0.0 0.0 70-71 0.375 0.0 0.0 0.0 0.0 72-73 0.4875 0.0 0.0 0.0 0.0 74-75 0.6125 0.0 0.0 0.0 0.0 76-77 0.7125 0.0 0.0 0.0 0.0 78-79 0.8625 0.0 0.0 0.0 0.0 80-81 1.025 0.0 0.0 0.0 0.0 82-83 1.2875 0.0 0.0 0.0 0.0 84-85 1.6875 0.0 0.0 0.0 0.0 86-87 2.1875 0.0 0.0 0.0 0.0 88-89 2.7375 0.0 0.0 0.0 0.0 90-91 3.1500000000000004 0.0 0.0 0.0 0.0 92-93 3.5875 0.0 0.0 0.0 0.0 94-95 4.0125 0.0 0.0 0.0 0.0 96-97 4.7875 0.0 0.0 0.0 0.0 98-99 5.425 0.0 0.0 0.0 0.0 100-101 5.9625 0.0 0.0 0.0 0.0 102-103 6.475 0.0 0.0 0.0 0.0 104-105 7.4125 0.0 0.0 0.0 0.0 106-107 8.625 0.0 0.0 0.0 0.0 108-109 9.7 0.0 0.0 0.0 0.0 110-111 10.7 0.0 0.0 0.0 0.0 112-113 11.8 0.0 0.0 0.0 0.0 114-115 12.725000000000001 0.0 0.0 0.0 0.0 116-117 13.825 0.0 0.0 0.0 0.0 118-119 14.95 0.0 0.0 0.0 0.0 120-121 16.2875 0.0 0.0 0.0 0.0 122-123 17.35 0.0 0.0 0.0 0.0 124-125 18.4125 0.0 0.0 0.0 0.0 126-127 19.4 0.0 0.0 0.0 0.0 128-129 20.2875 0.0 0.0 0.0 0.0 130-131 21.4 0.0 0.0 0.0 0.0 132-133 22.25 0.0 0.0 0.0 0.0 134-135 23.375 0.0 0.0 0.0 0.0 136-137 24.4375 0.0 0.0 0.0 0.0 138-139 25.4375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TGGAATT 10 0.006830828 145.0 2 >>END_MODULE Read 626304 spots for SRR12670127.sra Written 626304 spots for SRR12670127.sra Read 626304 spots for SRR12670127.sra Written 626304 spots for SRR12670127.sra Read 626304 spots for SRR12670127.sra Written 626304 spots for SRR12670127.sra Read 626304 spots for SRR12670127.sra Written 626304 spots for SRR12670127.sra Read 626304 spots for SRR12670127.sra Written 626304 spots for SRR12670127.sra Read 626304 spots for SRR12670127.sra Written 626304 spots for SRR12670127.sra Read 626304 spots for SRR12670127.sra Written 626304 spots for SRR12670127.sra Read 626304 spots for SRR12670127.sra Written 626304 spots for SRR12670127.sra Read 626304 spots for SRR12670127.sra Written 626304 spots for SRR12670127.sra Read 626319 spots for SRR12670127.sra Written 626319 spots for SRR12670127.sra Read 626304 spots for SRR12670127.sra Written 626304 spots for SRR12670127.sra Read 626304 spots for SRR12670127.sra Written 626304 spots for SRR12670127.sra Read 626304 spots for SRR12670127.sra Written 626304 spots for SRR12670127.sra Read 626304 spots for SRR12670127.sra Written 626304 spots for SRR12670127.sra Read 626304 spots for SRR12670127.sra Written 626304 spots for SRR12670127.sra Read 626304 spots for SRR12670127.sra Written 626304 spots for SRR12670127.sra Read 626304 spots for SRR12670127.sra Written 626304 spots for SRR12670127.sra Read 626304 spots for SRR12670127.sra Written 626304 spots for SRR12670127.sra Read 626304 spots for SRR12670127.sra Written 626304 spots for SRR12670127.sra Read 626304 spots for SRR12670127.sra Written 626304 spots for SRR12670127.sra SRR ids: ['SRR12670127.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_5m96xjov SRR12670127.sra spots: 12526095 blocks: [[1, 626304], [626305, 1252608], [1252609, 1878912], [1878913, 2505216], [2505217, 3131520], [3131521, 3757824], [3757825, 4384128], [4384129, 5010432], [5010433, 5636736], [5636737, 6263040], [6263041, 6889344], [6889345, 7515648], [7515649, 8141952], [8141953, 8768256], [8768257, 9394560], [9394561, 10020864], [10020865, 10647168], [10647169, 11273472], [11273473, 11899776], [11899777, 12526095]] SRR12670127 file size 4235214 SRR12670127 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 SRR12670127 SRR12670127_1.fastq SRR12670127_2.fastq Input file: SRR12670127_1.fastq Paired file: SRR12670127_2.fastq trimmed: SRR12670127-trimmed-pair1.fastq, SRR12670127-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- number of concurrent threads (-t): 20 Tue Feb 11 00:20:07 2025 >> started Tue Feb 11 00:20:28 2025 >> done (20.543s) 12526095 read pairs processed; of these: 85 ( 0.00%) short read pairs filtered out after trimming by size control 78153 ( 0.62%) empty read pairs filtered out after trimming by size control 12447857 (99.38%) read pairs available; of these: 3995146 (32.10%) trimmed read pairs available after processing 8452711 (67.90%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 5 0.00% 19 4 0.00% 20 18 0.00% 21 13 0.00% 22 21 0.00% 23 34 0.00% 24 31 0.00% 25 30 0.00% 26 41 0.00% 27 59 0.00% 28 63 0.00% 29 86 0.00% 30 98 0.00% 31 61 0.00% 32 92 0.00% 33 105 0.00% 34 114 0.00% 35 120 0.00% 36 155 0.00% 37 166 0.00% 38 176 0.00% 39 216 0.00% 40 237 0.00% 41 235 0.00% 42 216 0.00% 43 272 0.00% 44 253 0.00% 45 290 0.00% 46 356 0.00% 47 404 0.00% 48 510 0.00% 49 558 0.00% 50 690 0.01% 51 772 0.01% 52 845 0.01% 53 950 0.01% 54 1026 0.01% 55 1022 0.01% 56 1127 0.01% 57 1339 0.01% 58 1468 0.01% 59 1686 0.01% 60 2079 0.02% 61 2410 0.02% 62 2643 0.02% 63 2838 0.02% 64 3115 0.03% 65 3421 0.03% 66 3662 0.03% 67 4039 0.03% 68 4438 0.04% 69 5165 0.04% 70 5775 0.05% 71 6216 0.05% 72 7212 0.06% 73 8095 0.07% 74 8939 0.07% 75 9716 0.08% 76 10780 0.09% 77 11573 0.09% 78 12165 0.10% 79 13996 0.11% 80 14945 0.12% 81 16313 0.13% 82 18406 0.15% 83 20004 0.16% 84 21829 0.18% 85 24128 0.19% 86 25469 0.20% 87 27018 0.22% 88 28221 0.23% 89 29586 0.24% 90 30853 0.25% 91 33129 0.27% 92 35311 0.28% 93 37302 0.30% 94 40027 0.32% 95 42704 0.34% 96 44456 0.36% 97 46629 0.37% 98 46613 0.37% 99 47607 0.38% 100 48801 0.39% 101 49802 0.40% 102 51415 0.41% 103 52771 0.42% 104 54594 0.44% 105 56387 0.45% 106 57814 0.46% 107 58725 0.47% 108 58564 0.47% 109 60520 0.49% 110 59394 0.48% 111 59981 0.48% 112 61364 0.49% 113 61453 0.49% 114 61761 0.50% 115 63781 0.51% 116 65482 0.53% 117 65465 0.53% 118 65389 0.53% 119 65493 0.53% 120 65148 0.52% 121 66069 0.53% 122 65333 0.52% 123 65800 0.53% 124 66238 0.53% 125 66624 0.54% 126 67588 0.54% 127 67735 0.54% 128 68204 0.55% 129 67233 0.54% 130 67334 0.54% 131 66105 0.53% 132 65871 0.53% 133 66005 0.53% 134 66137 0.53% 135 65243 0.52% 136 66147 0.53% 137 65873 0.53% 138 65731 0.53% 139 66940 0.54% 140 65349 0.52% 141 65445 0.53% 142 65615 0.53% 143 64794 0.52% 144 65055 0.52% 145 64866 0.52% 146 64735 0.52% 147 64480 0.52% 148 65173 0.52% 149 64072 0.51% 150 64457 0.52% 151 8452711 67.90% 12447857 reads passed initial QC criterion=sequence-density sequence-density=0.76 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=16 prefix-density=0.76 prefix-fanout=2.0 sequence=CGGTAGACCCAACCTTTCTCCAACTCGAATTCCAAGCAAGGAACCCACTT criterion=fanout-score sequence-density=0.01 sequence-density-rank=22 fanout-score=208.40 fanout-score-rank=1 prefix-density=0.25 prefix-fanout=9.7 sequence=TGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGGTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGGAGTATGAATGTGTTCTCTGTG criterion=sequence-density sequence-density=0.65 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=19 prefix-density=0.65 prefix-fanout=2.0 sequence=CCAGGGTACTATGATGGACGCTACTGGACTATGTGGAA criterion=fanout-score sequence-density=0.01 sequence-density-rank=24 fanout-score=40.60 fanout-score-rank=1 prefix-density=0.05 prefix-fanout=4.9 sequence=AGCAAAACCACATATAGAGGGTGTAATAGCTAAGTAGCCTGTAAGAGATGGCTTCCTCTGTGATTTCATCGGCGGCCGTTGCCACAGTTAACCGCACCCC SRR12670127 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 00:21:05 Started mapping on | Feb 11 00:21:06 Finished on | Feb 11 00:22:23 Mapping speed, Million of reads per hour | 581.98 Number of input reads | 12447857 Average input read length | 281 UNIQUE READS: Uniquely mapped reads number | 11825979 Uniquely mapped reads % | 95.00% Average mapped length | 279.96 Number of splices: Total | 11128122 Number of splices: Annotated (sjdb) | 10926753 Number of splices: GT/AG | 10898125 Number of splices: GC/AG | 192888 Number of splices: AT/AC | 6586 Number of splices: Non-canonical | 30523 Mismatch rate per base, % | 0.33% Deletion rate per base | 0.02% Deletion average length | 2.93 Insertion rate per base | 0.02% Insertion average length | 2.42 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 319904 % of reads mapped to multiple loci | 2.57% Number of reads mapped to too many loci | 35732 % of reads mapped to too many loci | 0.29% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.02% % of reads unmapped: other | 0.12% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 301974 301974 301974 N_multimapping 319904 319904 319904 N_noFeature 230281 11640005 290304 N_ambiguous 210599 553 84395 UnstrandedReadsAssigned:11385099 PositiveStrandReadsAssigned:185421 NegativeStrandReadsAssigned:11451280 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=128 echo kmer=123 SRR12670127 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: SRR12670127-trimmed-pair1.fastq SRR12670127-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 12,447,857 reads, 11,544,773 reads pseudoaligned [quant] estimated average fragment length: 192.685 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,172 rounds 52401 SRR12670127.ke.tsv 34699 SRR12670127.se.tsv 87100 total ==> SRR12670127.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1826.32 304 12.2391 Potri.005G024800.1.v4.1 1035 843.315 128 11.1602 Potri.004G059700.1.v4.1 961 769.327 23 2.1982 Potri.007G009000.2.v4.1 1416 1224.32 0 0 Potri.003G141000.2.v4.1 2943 2751.32 286 7.64321 Potri.016G087400.1.v4.1 270 112.765 590 384.705 Potri.015G069301.1.v4.1 564 375.636 0 0 Potri.010G195200.1.v4.1 1773 1581.32 26 1.20894 Potri.012G127500.1.v4.1 977 785.327 238 22.2831 ==> SRR12670127.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 480 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 200 Potri.001G212900.v4.1 256 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 6 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 8 SRR12670127 completed mapping pipeline successfully