Starting /dee2/code/volunteer_pipeline.sh SRR12670144 current disk space = 3056964435968 free memory = 1462122012 SRR12670144 SRAfilesize caed29f7e60eae30e21d784b45a17475 SRR12670144.sra SRR12670144.sra file validated SRR12670144 is paired end SRR12670144 is conventional basespace SRR12670144 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670144_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 36.525 37.0 37.0 37.0 37.0 37.0 2 36.51675 37.0 37.0 37.0 37.0 37.0 3 36.7085 37.0 37.0 37.0 37.0 37.0 4 36.691 37.0 37.0 37.0 37.0 37.0 5 36.651 37.0 37.0 37.0 37.0 37.0 6 36.6275 37.0 37.0 37.0 37.0 37.0 7 36.57 37.0 37.0 37.0 37.0 37.0 8 36.684 37.0 37.0 37.0 37.0 37.0 9 36.615 37.0 37.0 37.0 37.0 37.0 10-14 36.6219 37.0 37.0 37.0 37.0 37.0 15-19 36.616800000000005 37.0 37.0 37.0 37.0 37.0 20-24 36.5986 37.0 37.0 37.0 37.0 37.0 25-29 36.5554 37.0 37.0 37.0 37.0 37.0 30-34 36.559000000000005 37.0 37.0 37.0 37.0 37.0 35-39 36.5389 37.0 37.0 37.0 37.0 37.0 40-44 36.5547 37.0 37.0 37.0 37.0 37.0 45-49 36.4925 37.0 37.0 37.0 37.0 37.0 50-54 36.425200000000004 37.0 37.0 37.0 37.0 37.0 55-59 36.4293 37.0 37.0 37.0 37.0 37.0 60-64 36.397999999999996 37.0 37.0 37.0 37.0 37.0 65-69 36.35359999999999 37.0 37.0 37.0 37.0 37.0 70-74 36.3481 37.0 37.0 37.0 37.0 37.0 75-79 36.3193 37.0 37.0 37.0 37.0 37.0 80-84 36.2956 37.0 37.0 37.0 37.0 37.0 85-89 36.3054 37.0 37.0 37.0 37.0 37.0 90-94 36.2513 37.0 37.0 37.0 37.0 37.0 95-99 36.2365 37.0 37.0 37.0 37.0 37.0 100-104 36.218399999999995 37.0 37.0 37.0 37.0 37.0 105-109 36.2085 37.0 37.0 37.0 37.0 37.0 110-114 36.1661 37.0 37.0 37.0 37.0 37.0 115-119 36.1585 37.0 37.0 37.0 37.0 37.0 120-124 36.0359 37.0 37.0 37.0 37.0 37.0 125-129 35.9208 37.0 37.0 37.0 37.0 37.0 130-134 35.9216 37.0 37.0 37.0 37.0 37.0 135-139 35.7662 37.0 37.0 37.0 37.0 37.0 140-144 35.5824 37.0 37.0 37.0 37.0 37.0 145-149 35.4205 37.0 37.0 37.0 37.0 37.0 150-151 35.194500000000005 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 22 1.0 23 0.0 24 0.0 25 2.0 26 3.0 27 10.0 28 12.0 29 8.0 30 18.0 31 35.0 32 37.0 33 79.0 34 155.0 35 358.0 36 2908.0 37 374.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 37.2 10.85 5.7250000000000005 46.225 2 17.77221526908636 12.440550688360451 37.72215269086358 32.065081351689614 3 17.1 15.7 28.225 38.975 4 23.25 24.349999999999998 21.65 30.75 5 22.675 30.049999999999997 24.6 22.675 6 18.775 34.300000000000004 24.5 22.425 7 15.024999999999999 25.75 41.275 17.95 8 16.25 25.624999999999996 33.7 24.425 9 17.974999999999998 22.95 34.1 24.975 10-14 20.05 29.175 27.389999999999997 23.385 15-19 20.04 27.97 27.839999999999996 24.15 20-24 19.885 27.58 28.444999999999997 24.09 25-29 20.215 27.860000000000003 28.449999999999996 23.474999999999998 30-34 20.380000000000003 27.46 28.655 23.505000000000003 35-39 20.915 27.49 27.62 23.974999999999998 40-44 20.365 27.79 28.16 23.685000000000002 45-49 21.005 27.935 27.52 23.54 50-54 20.875 28.37 27.43 23.325000000000003 55-59 20.225 27.865000000000002 28.060000000000002 23.849999999999998 60-64 20.52 28.03 27.915 23.535 65-69 20.880000000000003 28.34 27.785 22.994999999999997 70-74 21.125 28.515 27.05 23.31 75-79 21.05 28.215 26.875 23.86 80-84 20.635 27.975 27.71 23.68 85-89 21.235 28.485 27.034999999999997 23.244999999999997 90-94 21.029999999999998 28.744999999999997 26.640000000000004 23.585 95-99 21.08 27.994999999999997 27.29 23.635 100-104 21.485000000000003 28.965000000000003 26.045 23.505000000000003 105-109 21.175 28.73 26.419999999999998 23.674999999999997 110-114 21.505 27.46 26.645000000000003 24.39 115-119 21.82 28.77 25.835 23.575 120-124 22.31 28.835 25.05 23.805 125-129 22.45 28.43 25.165 23.955000000000002 130-134 21.605 28.26 25.77 24.365000000000002 135-139 22.24 27.735 25.3 24.725 140-144 21.51 26.875 26.525 25.09 145-149 22.585 26.784999999999997 25.91 24.72 150-151 23.0375 26.4125 26.487500000000004 24.0625 >>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 0.5 20 1.0 21 0.5 22 0.0 23 1.5 24 2.0 25 0.5 26 1.5 27 4.0 28 6.5 29 9.0 30 13.0 31 20.0 32 31.5 33 36.0 34 52.5 35 62.5 36 66.5 37 97.5 38 128.5 39 137.0 40 159.0 41 216.5 42 237.5 43 249.5 44 265.0 45 277.0 46 279.5 47 245.0 48 237.0 49 220.0 50 192.0 51 175.0 52 135.5 53 103.5 54 87.5 55 61.5 56 41.5 57 29.5 58 26.5 59 25.5 60 14.5 61 12.5 62 15.0 63 9.0 64 2.0 65 2.0 66 1.5 67 3.0 68 1.5 69 0.5 70 0.5 71 1.0 72 1.0 73 0.0 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.125 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 82.425 #Duplication Level Percentage of deduplicated Percentage of total 1 82.98453139217472 68.4 2 14.012738853503185 23.1 3 2.1231422505307855 5.25 4 0.6066120715802245 2.0 5 0.18198362147406735 0.75 6 0.030330603579011222 0.15 7 0.060661207158022444 0.35000000000000003 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 AACCTCGTCAATACTTGAAACATCACACCCTCCAGATCTAATGACAGAAT 7 0.17500000000000002 No Hit CCTCTCGAAGCACCTCATCCATGCTGGCTGCTCTTTTCCAAGTAACTGGC 7 0.17500000000000002 No Hit GGCTAGCATGGTGGAGTTCATGGAGATGTTTACTTCTTCATTTCCATGGT 6 0.15 No Hit GTTGTCATTGTTCCCTTGACAATGCCGAATTCCTCATCCATGACCTTCAC 5 0.125 No Hit CTCGCCTCAGTATCAGTGAGTTCCACTAAACTGAACAGAAAACTTCCTGT 5 0.125 No Hit GCCAGCAATTCTGTAACCCTCAACGGCACCCATCAAGACCACCTGTGTAG 5 0.125 No Hit CATACAAGCCGATCTTCAAATTGTTTTGGGGAGGATTTCTTTGGTGGAGG 5 0.125 No Hit GCCATGGTGAAATCGGTAGACACGCTGCTCTTAGGAAGCAGTGCTAGAGC 5 0.125 No Hit CCTTTATCGACGCAGAAATAAGTTCCGGATTTACGAGCATACTGCTCCGA 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 0.0125 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 0.05 0.0 0.0 0.0 0.0 50-51 0.075 0.0 0.0 0.0 0.0 52-53 0.0875 0.0 0.0 0.0 0.0 54-55 0.15 0.0 0.0 0.0 0.0 56-57 0.2 0.0 0.0 0.0 0.0 58-59 0.2 0.0 0.0 0.0 0.0 60-61 0.21250000000000002 0.0 0.0 0.0 0.0 62-63 0.2625 0.0 0.0 0.0 0.0 64-65 0.4125 0.0 0.0 0.0 0.0 66-67 0.5375000000000001 0.0 0.0 0.0 0.0 68-69 0.6875 0.0 0.0 0.0 0.0 70-71 0.775 0.0 0.0 0.0 0.0 72-73 0.8625 0.0 0.0 0.0 0.0 74-75 1.1 0.0 0.0 0.0 0.0 76-77 1.2875 0.0 0.0 0.0 0.0 78-79 1.7 0.0 0.0 0.0 0.0 80-81 1.9875 0.0 0.0 0.0 0.0 82-83 2.4 0.0 0.0 0.0 0.0 84-85 2.9000000000000004 0.0 0.0 0.0 0.0 86-87 3.5374999999999996 0.0 0.0 0.0 0.0 88-89 4.25 0.0 0.0 0.0 0.0 90-91 4.95 0.0 0.0 0.0 0.0 92-93 5.762499999999999 0.0 0.0 0.0 0.0 94-95 6.575 0.0 0.0 0.0 0.0 96-97 7.3625 0.0 0.0 0.0 0.0 98-99 8.225000000000001 0.0 0.0 0.0 0.0 100-101 9.125 0.0 0.0 0.0 0.0 102-103 10.0875 0.0 0.0 0.0 0.0 104-105 10.9 0.0 0.0 0.0 0.0 106-107 11.8625 0.0 0.0 0.0 0.0 108-109 13.125 0.0 0.0 0.0 0.0 110-111 14.4375 0.0 0.0 0.0 0.0 112-113 15.712499999999999 0.0 0.0 0.0 0.0 114-115 16.9 0.0 0.0 0.0 0.0 116-117 18.1875 0.0 0.0 0.0 0.0 118-119 19.3375 0.0 0.0 0.0 0.0 120-121 20.2875 0.0 0.0 0.0 0.0 122-123 21.85 0.0 0.0 0.0 0.0 124-125 23.05 0.0 0.0 0.0 0.0 126-127 23.987499999999997 0.0 0.0 0.0 0.0 128-129 24.9625 0.0 0.0 0.0 0.0 130-131 25.887500000000003 0.0 0.0 0.0 0.0 132-133 26.975 0.0 0.0 0.0 0.0 134-135 27.7375 0.0 0.0 0.0 0.0 136-137 28.575000000000003 0.0 0.0 0.0 0.0 138-139 29.8 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTTCATG 10 0.006830828 145.0 6 GTGAACA 10 0.006830828 145.0 1 >>END_MODULE SRR12670144 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670144_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.3395 37.0 37.0 37.0 37.0 37.0 2 36.158 37.0 37.0 37.0 37.0 37.0 3 36.1725 37.0 37.0 37.0 37.0 37.0 4 36.29 37.0 37.0 37.0 37.0 37.0 5 36.443 37.0 37.0 37.0 37.0 37.0 6 36.272 37.0 37.0 37.0 37.0 37.0 7 36.3675 37.0 37.0 37.0 37.0 37.0 8 36.3875 37.0 37.0 37.0 37.0 37.0 9 36.4635 37.0 37.0 37.0 37.0 37.0 10-14 36.368900000000004 37.0 37.0 37.0 37.0 37.0 15-19 36.4037 37.0 37.0 37.0 37.0 37.0 20-24 36.3566 37.0 37.0 37.0 37.0 37.0 25-29 36.303399999999996 37.0 37.0 37.0 37.0 37.0 30-34 36.265 37.0 37.0 37.0 37.0 37.0 35-39 36.3114 37.0 37.0 37.0 37.0 37.0 40-44 36.274899999999995 37.0 37.0 37.0 37.0 37.0 45-49 36.2704 37.0 37.0 37.0 37.0 37.0 50-54 36.2473 37.0 37.0 37.0 37.0 37.0 55-59 36.214 37.0 37.0 37.0 37.0 37.0 60-64 36.1622 37.0 37.0 37.0 37.0 37.0 65-69 36.2439 37.0 37.0 37.0 37.0 37.0 70-74 36.1388 37.0 37.0 37.0 37.0 37.0 75-79 36.087 37.0 37.0 37.0 37.0 37.0 80-84 36.083600000000004 37.0 37.0 37.0 37.0 37.0 85-89 36.0351 37.0 37.0 37.0 37.0 37.0 90-94 36.0428 37.0 37.0 37.0 37.0 37.0 95-99 35.9084 37.0 37.0 37.0 37.0 37.0 100-104 35.9122 37.0 37.0 37.0 37.0 37.0 105-109 35.8399 37.0 37.0 37.0 37.0 37.0 110-114 35.7171 37.0 37.0 37.0 37.0 37.0 115-119 35.658699999999996 37.0 37.0 37.0 37.0 37.0 120-124 35.5403 37.0 37.0 37.0 37.0 37.0 125-129 35.3155 37.0 37.0 37.0 32.2 37.0 130-134 35.0641 37.0 37.0 37.0 32.2 37.0 135-139 34.8027 37.0 37.0 37.0 25.0 37.0 140-144 34.5126 37.0 37.0 37.0 25.0 37.0 145-149 34.2861 37.0 37.0 37.0 25.0 37.0 150-151 33.977999999999994 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 2.0 14 0.0 15 0.0 16 1.0 17 1.0 18 0.0 19 0.0 20 1.0 21 2.0 22 4.0 23 3.0 24 7.0 25 6.0 26 8.0 27 6.0 28 10.0 29 19.0 30 9.0 31 62.0 32 85.0 33 127.0 34 256.0 35 602.0 36 2536.0 37 253.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 38.275 20.4 11.95 29.375 2 27.500000000000004 26.450000000000003 31.674999999999997 14.374999999999998 3 20.3 28.375 32.525 18.8 4 24.675 32.675 24.325 18.325 5 25.624999999999996 36.925000000000004 23.150000000000002 14.299999999999999 6 20.025000000000002 39.550000000000004 22.375 18.05 7 20.349999999999998 20.775 40.075 18.8 8 20.724999999999998 25.124999999999996 29.925 24.224999999999998 9 22.85 25.624999999999996 29.325000000000003 22.2 10-14 22.865 29.575000000000003 26.82 20.74 15-19 23.380000000000003 28.000000000000004 28.04 20.580000000000002 20-24 23.075000000000003 28.12 27.675 21.13 25-29 22.835 28.060000000000002 28.749999999999996 20.355 30-34 22.62 28.365000000000002 28.355000000000004 20.66 35-39 23.1 28.075 28.005000000000003 20.82 40-44 23.75 27.900000000000002 27.595 20.755000000000003 45-49 23.365 27.38 28.09 21.165 50-54 23.13 27.200000000000003 28.38 21.29 55-59 23.21 27.700000000000003 28.105000000000004 20.985 60-64 23.145 27.839999999999996 27.639999999999997 21.375 65-69 23.46 27.715 28.244999999999997 20.580000000000002 70-74 23.525 27.455000000000002 27.68 21.34 75-79 23.22 27.915 27.235 21.63 80-84 23.34 27.765 27.575 21.32 85-89 24.03 28.244999999999997 26.729999999999997 20.995 90-94 24.485 28.244999999999997 26.740000000000002 20.53 95-99 24.855 28.194999999999997 26.755000000000003 20.195 100-104 25.0 29.025000000000002 26.14 19.835 105-109 26.52 28.415000000000003 25.755 19.31 110-114 27.089999999999996 27.894999999999996 25.535000000000004 19.48 115-119 27.36 28.625 25.650000000000002 18.365000000000002 120-124 28.65 27.744999999999997 25.324999999999996 18.279999999999998 125-129 28.57 26.840000000000003 25.95 18.64 130-134 30.28 27.005000000000003 24.91 17.805 135-139 31.635 26.565 24.86 16.939999999999998 140-144 32.285000000000004 26.075 25.115 16.525000000000002 145-149 33.93 25.515 24.345 16.21 150-151 34.7125 25.15 23.3375 16.8 >>END_MODULE >>Per sequence GC content warn #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 0.5 12 0.5 13 1.0 14 1.0 15 0.5 16 0.5 17 0.5 18 1.0 19 1.0 20 0.5 21 0.0 22 0.0 23 1.5 24 5.0 25 4.0 26 4.0 27 8.0 28 8.5 29 10.0 30 12.5 31 17.0 32 28.0 33 40.5 34 55.0 35 71.5 36 77.0 37 99.0 38 128.0 39 146.5 40 180.5 41 238.5 42 277.0 43 272.0 44 280.5 45 277.0 46 251.0 47 233.0 48 203.5 49 191.0 50 176.0 51 156.5 52 120.0 53 82.5 54 83.5 55 60.5 56 46.5 57 45.0 58 29.0 59 24.0 60 16.5 61 9.0 62 5.5 63 2.5 64 2.0 65 0.5 66 0.5 67 1.0 68 1.5 69 0.5 70 0.5 71 1.0 72 1.5 73 1.0 74 0.0 75 0.0 76 0.5 77 0.5 78 0.0 79 0.0 80 0.0 81 0.5 82 0.5 83 0.0 84 0.0 85 0.0 86 0.0 87 0.5 88 0.5 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 1.5 >>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 82.425 #Duplication Level Percentage of deduplicated Percentage of total 1 83.43949044585987 68.77499999999999 2 13.345465574764937 22.0 3 2.335456475583864 5.775 4 0.5156202608431908 1.7000000000000002 5 0.21231422505307856 0.8750000000000001 6 0.060661207158022444 0.3 7 0.060661207158022444 0.35000000000000003 8 0.0 0.0 9 0.030330603579011222 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 AGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAA 9 0.22499999999999998 No Hit TGTTATGATGGGAGCTAGCAATTCTGGTGGATACGAACCTCTCGAGATAC 7 0.17500000000000002 No Hit GGCATTTAGTAACATGGCTGTTGGTTACAATAATGTTGATGTAAATGCTG 7 0.17500000000000002 No Hit GAAAACTCTTCAGATGCATCAGTTGCCCTGATTGTGGGTATAACTGGCTT 6 0.15 No Hit GGGAGCACTGCATAGCTTATAAGCTTGTAAGAGATGGCTTCCTCCTCTAT 6 0.15 No Hit CCAAGCTTGATCCACGCACAAAGCATCTTGGCCATCTGGGCTACACAGGT 5 0.125 No Hit AGGGAGCACTGCATAGCTTATAAGCTTGTAAGAGATGGCTTCCTCCTCTA 5 0.125 No Hit TGTTGAGGAGTTACAGGTGGAAAAACTCCCTGGTTTACAAGGGTAGAGAC 5 0.125 No Hit GGGAAAGATGTGCTGCCTCTTCATCAATGATCTTGATGCCGGAGCTGGGA 5 0.125 No Hit AGTAATTAAAAAAAAAAAAAGAAGGGAAATAGGAGGCGTAAGAAAGTAAT 5 0.125 No Hit TAATAATTAGATAATTTTAAAATAGATAATTTAAAAATGTTATGCCGCCA 5 0.125 No Hit CCGAACATGGCTGCAACGACTGCTGTTGCCGCGTCCTATTTTTCGGGGAC 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 0.0125 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 0.05 0.0 0.0 0.0 0.0 50-51 0.075 0.0 0.0 0.0 0.0 52-53 0.0875 0.0 0.0 0.0 0.0 54-55 0.15 0.0 0.0 0.0 0.0 56-57 0.2 0.0 0.0 0.0 0.0 58-59 0.2 0.0 0.0 0.0 0.0 60-61 0.21250000000000002 0.0 0.0 0.0 0.0 62-63 0.2625 0.0 0.0 0.0 0.0 64-65 0.4125 0.0 0.0 0.0 0.0 66-67 0.5375000000000001 0.0 0.0 0.0 0.0 68-69 0.6875 0.0 0.0 0.0 0.0 70-71 0.775 0.0 0.0 0.0 0.0 72-73 0.8625 0.0 0.0 0.0 0.0 74-75 1.1 0.0 0.0 0.0 0.0 76-77 1.2875 0.0 0.0 0.0 0.0 78-79 1.6875 0.0 0.0 0.0 0.0 80-81 1.9625 0.0 0.0 0.0 0.0 82-83 2.375 0.0 0.0 0.0 0.0 84-85 2.9000000000000004 0.0 0.0 0.0 0.0 86-87 3.525 0.0 0.0 0.0 0.0 88-89 4.225 0.0 0.0 0.0 0.0 90-91 4.925 0.0 0.0 0.0 0.0 92-93 5.6875 0.0 0.0 0.0 0.0 94-95 6.5125 0.0 0.0 0.0 0.0 96-97 7.3125 0.0 0.0 0.0 0.0 98-99 8.2 0.0 0.0 0.0 0.0 100-101 9.1 0.0 0.0 0.0 0.0 102-103 10.0625 0.0 0.0 0.0 0.0 104-105 10.8625 0.0 0.0 0.0 0.0 106-107 11.8 0.0 0.0 0.0 0.0 108-109 13.0375 0.0 0.0 0.0 0.0 110-111 14.3375 0.0 0.0 0.0 0.0 112-113 15.6375 0.0 0.0 0.0 0.0 114-115 16.8 0.0 0.0 0.0 0.0 116-117 18.137500000000003 0.0 0.0 0.0 0.0 118-119 19.3125 0.0 0.0 0.0 0.0 120-121 20.275 0.0 0.0 0.0 0.0 122-123 21.875 0.0 0.0 0.0 0.0 124-125 23.112499999999997 0.0 0.0 0.0 0.0 126-127 24.0625 0.0 0.0 0.0 0.0 128-129 25.012500000000003 0.0 0.0 0.0 0.0 130-131 25.9375 0.0 0.0 0.0 0.0 132-133 27.0375 0.0 0.0 0.0 0.0 134-135 27.825000000000003 0.0 0.0 0.0 0.0 136-137 28.674999999999997 0.0 0.0 0.0 0.0 138-139 29.8875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTCAAAG 10 0.006830828 145.0 2 TCAAAGT 10 0.006830828 145.0 3 GGGGTGG 10 0.006830828 145.0 145 >>END_MODULE Read 513102 spots for SRR12670144.sra Written 513102 spots for SRR12670144.sra Read 513102 spots for SRR12670144.sra Written 513102 spots for SRR12670144.sra Read 513102 spots for SRR12670144.sra Written 513102 spots for SRR12670144.sra Read 513102 spots for SRR12670144.sra Written 513102 spots for SRR12670144.sra Read 513102 spots for SRR12670144.sra Written 513102 spots for SRR12670144.sra Read 513102 spots for SRR12670144.sra Written 513102 spots for SRR12670144.sra Read 513102 spots for SRR12670144.sra Written 513102 spots for SRR12670144.sra Read 513102 spots for SRR12670144.sra Written 513102 spots for SRR12670144.sra Read 513116 spots for SRR12670144.sra Written 513116 spots for SRR12670144.sra Read 513102 spots for SRR12670144.sra Written 513102 spots for SRR12670144.sra Read 513102 spots for SRR12670144.sra Written 513102 spots for SRR12670144.sra Read 513102 spots for SRR12670144.sra Written 513102 spots for SRR12670144.sra Read 513102 spots for SRR12670144.sra Written 513102 spots for SRR12670144.sra Read 513102 spots for SRR12670144.sra Written 513102 spots for SRR12670144.sra Read 513102 spots for SRR12670144.sra Written 513102 spots for SRR12670144.sra Read 513102 spots for SRR12670144.sra Written 513102 spots for SRR12670144.sra Read 513102 spots for SRR12670144.sra Written 513102 spots for SRR12670144.sra Read 513102 spots for SRR12670144.sra Written 513102 spots for SRR12670144.sra Read 513102 spots for SRR12670144.sra Written 513102 spots for SRR12670144.sra Read 513102 spots for SRR12670144.sra Written 513102 spots for SRR12670144.sra SRR ids: ['SRR12670144.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_9ss3afhh SRR12670144.sra spots: 10262054 blocks: [[1, 513102], [513103, 1026204], [1026205, 1539306], [1539307, 2052408], [2052409, 2565510], [2565511, 3078612], [3078613, 3591714], [3591715, 4104816], [4104817, 4617918], [4617919, 5131020], [5131021, 5644122], [5644123, 6157224], [6157225, 6670326], [6670327, 7183428], [7183429, 7696530], [7696531, 8209632], [8209633, 8722734], [8722735, 9235836], [9235837, 9748938], [9748939, 10262054]] SRR12670144 file size 3465794 SRR12670144 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 SRR12670144 SRR12670144_1.fastq SRR12670144_2.fastq Input file: SRR12670144_1.fastq Paired file: SRR12670144_2.fastq trimmed: SRR12670144-trimmed-pair1.fastq, SRR12670144-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 02:22:53 2025 >> started Tue Feb 11 02:28:54 2025 >> done (361.587s) 10262054 read pairs processed; of these: 39 ( 0.00%) short read pairs filtered out after trimming by size control 2690 ( 0.03%) empty read pairs filtered out after trimming by size control 10259325 (99.97%) read pairs available; of these: 3412324 (33.26%) trimmed read pairs available after processing 6847001 (66.74%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 4 0.00% 19 6 0.00% 20 3 0.00% 21 0 0.00% 22 3 0.00% 23 6 0.00% 24 16 0.00% 25 13 0.00% 26 12 0.00% 27 31 0.00% 28 13 0.00% 29 33 0.00% 30 38 0.00% 31 59 0.00% 32 60 0.00% 33 65 0.00% 34 84 0.00% 35 103 0.00% 36 105 0.00% 37 170 0.00% 38 168 0.00% 39 192 0.00% 40 215 0.00% 41 251 0.00% 42 266 0.00% 43 260 0.00% 44 331 0.00% 45 351 0.00% 46 392 0.00% 47 498 0.00% 48 593 0.01% 49 710 0.01% 50 824 0.01% 51 952 0.01% 52 980 0.01% 53 1116 0.01% 54 1225 0.01% 55 1260 0.01% 56 1419 0.01% 57 1538 0.01% 58 1837 0.02% 59 2236 0.02% 60 2717 0.03% 61 3135 0.03% 62 3417 0.03% 63 3800 0.04% 64 4235 0.04% 65 4430 0.04% 66 4930 0.05% 67 5409 0.05% 68 6207 0.06% 69 6904 0.07% 70 7853 0.08% 71 8860 0.09% 72 9975 0.10% 73 11020 0.11% 74 11919 0.12% 75 12909 0.13% 76 13860 0.14% 77 14945 0.15% 78 16213 0.16% 79 17328 0.17% 80 18515 0.18% 81 20823 0.20% 82 22312 0.22% 83 24355 0.24% 84 26507 0.26% 85 27817 0.27% 86 29196 0.28% 87 30285 0.30% 88 31450 0.31% 89 32938 0.32% 90 34084 0.33% 91 35536 0.35% 92 36744 0.36% 93 39033 0.38% 94 41029 0.40% 95 42913 0.42% 96 43654 0.43% 97 44723 0.44% 98 44925 0.44% 99 45403 0.44% 100 45628 0.44% 101 46002 0.45% 102 47524 0.46% 103 48714 0.47% 104 49017 0.48% 105 50021 0.49% 106 50699 0.49% 107 50868 0.50% 108 51120 0.50% 109 51056 0.50% 110 50337 0.49% 111 50868 0.50% 112 51034 0.50% 113 51065 0.50% 114 51884 0.51% 115 52712 0.51% 116 52514 0.51% 117 52786 0.51% 118 52470 0.51% 119 51915 0.51% 120 52285 0.51% 121 51606 0.50% 122 51775 0.50% 123 51574 0.50% 124 51649 0.50% 125 51512 0.50% 126 52201 0.51% 127 52212 0.51% 128 51428 0.50% 129 51037 0.50% 130 51243 0.50% 131 50455 0.49% 132 50065 0.49% 133 49940 0.49% 134 49080 0.48% 135 49686 0.48% 136 49210 0.48% 137 49216 0.48% 138 49610 0.48% 139 50050 0.49% 140 48883 0.48% 141 49012 0.48% 142 48719 0.47% 143 47834 0.47% 144 48309 0.47% 145 47720 0.47% 146 47497 0.46% 147 47581 0.46% 148 47715 0.47% 149 47270 0.46% 150 46970 0.46% 151 6847001 66.74% 10259325 reads passed initial QC criterion=sequence-density sequence-density=0.35 sequence-density-rank=1 fanout-score=2.24 fanout-score-rank=26 prefix-density=0.37 prefix-fanout=2.1 sequence=TTCCACATAGTCCAGTAGCGTCCATCATAGTACCCTGGTGAGCTGTGGTGCTCACGGTAGACCCAACCTTTCTCCAACTCGAATTCCAAGCAAGGAACCCACTTCGAGCGAAGAAGGTAATCAATTTCCTTGGCCAATTCCTCCTCTGTGAGATCTGGAAGGTAAGAAAGAGTCTCGAACTTCTTCAATCCAGTTGGTGGCCACACCTGCATGCATTGAACTCGTCCACCATTGCTTGCAATGGAAGTAATGTCATTAGCCTTTCTGGTACTGACTGGGAAAGCTGCGGCAGACTTGAGACCATTGAATGGTGCCACCAT criterion=fanout-score sequence-density=0.02 sequence-density-rank=32 fanout-score=134.98 fanout-score-rank=1 prefix-density=0.25 prefix-fanout=12.9 sequence=TGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAG criterion=sequence-density sequence-density=0.59 sequence-density-rank=1 fanout-score=2.02 fanout-score-rank=28 prefix-density=0.59 prefix-fanout=2.0 sequence=CTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCA criterion=fanout-score sequence-density=0.12 sequence-density-rank=21 fanout-score=44.46 fanout-score-rank=1 prefix-density=0.39 prefix-fanout=13.5 sequence=AAAGAAAAGAAAA SRR12670144 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 03:26:38 Started mapping on | Feb 11 03:26:56 Finished on | Feb 11 04:49:48 Mapping speed, Million of reads per hour | 7.43 Number of input reads | 10259325 Average input read length | 278 UNIQUE READS: Uniquely mapped reads number | 9683591 Uniquely mapped reads % | 94.39% Average mapped length | 276.90 Number of splices: Total | 9039180 Number of splices: Annotated (sjdb) | 8846162 Number of splices: GT/AG | 8847463 Number of splices: GC/AG | 156090 Number of splices: AT/AC | 5503 Number of splices: Non-canonical | 30124 Mismatch rate per base, % | 0.35% Deletion rate per base | 0.03% Deletion average length | 2.88 Insertion rate per base | 0.02% Insertion average length | 2.34 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 232880 % of reads mapped to multiple loci | 2.27% Number of reads mapped to too many loci | 97187 % of reads mapped to too many loci | 0.95% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.21% % of reads unmapped: other | 0.18% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 342854 342854 342854 N_multimapping 232880 232880 232880 N_noFeature 427248 9539847 500718 N_ambiguous 123757 582 53095 UnstrandedReadsAssigned:9132586 PositiveStrandReadsAssigned:143162 NegativeStrandReadsAssigned:9129778 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=123 echo kmer=119 SRR12670144 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: SRR12670144-trimmed-pair1.fastq SRR12670144-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 10,259,325 reads, 9,202,867 reads pseudoaligned [quant] estimated average fragment length: 194.902 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,070 rounds 52401 SRR12670144.ke.tsv 34699 SRR12670144.se.tsv 87100 total ==> SRR12670144.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1824.1 304 19.878 Potri.005G024800.1.v4.1 1035 841.098 133 18.8605 Potri.004G059700.1.v4.1 961 767.155 1 0.155476 Potri.007G009000.2.v4.1 1416 1222.1 0 0 Potri.003G141000.2.v4.1 2943 2749.1 433.423 18.8048 Potri.016G087400.1.v4.1 270 116.984 362 369.087 Potri.015G069301.1.v4.1 564 376.595 0 0 Potri.010G195200.1.v4.1 1773 1579.1 20 1.51067 Potri.012G127500.1.v4.1 977 783.127 20 3.04611 ==> SRR12670144.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 33 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 139 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 8 SRR12670144 completed mapping pipeline successfully