Starting /dee2/code/volunteer_pipeline.sh SRR12690129 current disk space = 3058202886144 free memory = 1234701672 SRR12690129 SRAfilesize c8348f3e713cbfd23a54bc6b6e3c02f0 SRR12690129.sra SRR12690129.sra file validated SRR12690129 is paired end SRR12690129 is conventional basespace SRR12690129 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12690129_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 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.641 37.0 37.0 37.0 37.0 37.0 2 36.23775 37.0 37.0 37.0 37.0 37.0 3 36.543 37.0 37.0 37.0 37.0 37.0 4 36.64 37.0 37.0 37.0 37.0 37.0 5 36.6595 37.0 37.0 37.0 37.0 37.0 6 36.655 37.0 37.0 37.0 37.0 37.0 7 36.555 37.0 37.0 37.0 37.0 37.0 8 36.551 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 36.6245 37.0 37.0 37.0 37.0 37.0 15-19 36.5888 37.0 37.0 37.0 37.0 37.0 20-24 36.5477 37.0 37.0 37.0 37.0 37.0 25-29 36.521100000000004 37.0 37.0 37.0 37.0 37.0 30-34 36.5252 37.0 37.0 37.0 37.0 37.0 35-39 36.5235 37.0 37.0 37.0 37.0 37.0 40-44 36.4809 37.0 37.0 37.0 37.0 37.0 45-49 36.4337 37.0 37.0 37.0 37.0 37.0 50-54 36.4112 37.0 37.0 37.0 37.0 37.0 55-59 36.3881 37.0 37.0 37.0 37.0 37.0 60-64 36.3579 37.0 37.0 37.0 37.0 37.0 65-69 36.342200000000005 37.0 37.0 37.0 37.0 37.0 70-74 36.3411 37.0 37.0 37.0 37.0 37.0 75-79 36.2541 37.0 37.0 37.0 37.0 37.0 80-84 36.2654 37.0 37.0 37.0 37.0 37.0 85-89 36.247699999999995 37.0 37.0 37.0 37.0 37.0 90-94 36.249900000000004 37.0 37.0 37.0 37.0 37.0 95-99 36.1831 37.0 37.0 37.0 37.0 37.0 100-104 36.1129 37.0 37.0 37.0 37.0 37.0 105-109 36.159200000000006 37.0 37.0 37.0 37.0 37.0 110-114 36.1439 37.0 37.0 37.0 37.0 37.0 115-119 36.076 37.0 37.0 37.0 37.0 37.0 120-124 35.9832 37.0 37.0 37.0 37.0 37.0 125-129 35.9457 37.0 37.0 37.0 37.0 37.0 130-134 35.951299999999996 37.0 37.0 37.0 37.0 37.0 135-139 35.991099999999996 37.0 37.0 37.0 37.0 37.0 140-144 35.770999999999994 37.0 37.0 37.0 37.0 37.0 145-149 35.73009999999999 37.0 37.0 37.0 37.0 37.0 150-151 35.6025 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 18 1.0 19 0.0 20 0.0 21 1.0 22 0.0 23 2.0 24 2.0 25 2.0 26 2.0 27 4.0 28 14.0 29 15.0 30 18.0 31 35.0 32 45.0 33 75.0 34 130.0 35 292.0 36 3039.0 37 323.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 42.3 12.275 6.5 38.925 2 18.641509433962263 13.132075471698112 37.86163522012579 30.364779874213838 3 15.35 16.475 30.55 37.625 4 21.15 24.575 25.900000000000002 28.375 5 23.799999999999997 31.0 24.25 20.95 6 20.424999999999997 34.75 23.9 20.925 7 15.7 25.45 41.5 17.349999999999998 8 18.475 26.6 30.825000000000003 24.099999999999998 9 17.474999999999998 23.575 35.5 23.45 10-14 19.384999999999998 29.575000000000003 27.825 23.215 15-19 19.919999999999998 28.4 27.715 23.965 20-24 20.044999999999998 28.365000000000002 28.194999999999997 23.395 25-29 20.415 28.155 27.61 23.82 30-34 19.67 27.994999999999997 27.794999999999998 24.54 35-39 20.51 28.115000000000002 26.88 24.495 40-44 20.150000000000002 29.195 27.589999999999996 23.064999999999998 45-49 20.005 28.904999999999998 26.810000000000002 24.279999999999998 50-54 19.82 28.610000000000003 27.82 23.75 55-59 19.415 28.49 28.125 23.97 60-64 20.02 28.499999999999996 27.71 23.77 65-69 20.560000000000002 28.610000000000003 27.315 23.515 70-74 20.16 27.639999999999997 28.134999999999998 24.065 75-79 20.515 27.99 27.985 23.51 80-84 20.294999999999998 28.34 27.35 24.015 85-89 20.035 28.27 27.74 23.955000000000002 90-94 20.105 28.255000000000003 27.639999999999997 24.0 95-99 20.085 28.17 28.075 23.669999999999998 100-104 20.57 28.299999999999997 27.134999999999998 23.995 105-109 20.305 28.03 28.375 23.29 110-114 20.535 28.535 27.150000000000002 23.78 115-119 20.49 28.67 27.310000000000002 23.53 120-124 20.905 28.360000000000003 26.61 24.125 125-129 20.46 28.65 26.724999999999998 24.165 130-134 20.91 28.389999999999997 26.729999999999997 23.97 135-139 20.72 28.095 26.77 24.415 140-144 20.875 28.315 26.93 23.880000000000003 145-149 20.755000000000003 27.735 27.785 23.724999999999998 150-151 20.925 27.675 26.737499999999997 24.6625 >>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 0.5 10 0.5 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 1.0 19 1.0 20 1.0 21 2.0 22 3.0 23 2.0 24 1.0 25 2.0 26 4.5 27 10.0 28 11.0 29 14.0 30 22.5 31 26.5 32 34.5 33 39.0 34 44.5 35 71.5 36 81.0 37 102.0 38 136.0 39 145.5 40 184.0 41 217.5 42 223.5 43 255.0 44 279.5 45 267.0 46 253.5 47 240.5 48 230.5 49 207.5 50 176.0 51 152.5 52 117.0 53 96.5 54 79.5 55 65.0 56 61.0 57 42.5 58 26.5 59 19.0 60 11.0 61 8.5 62 8.0 63 4.5 64 3.0 65 2.0 66 1.5 67 3.0 68 2.5 69 0.5 70 0.0 71 1.0 72 1.0 73 1.0 74 1.0 75 0.5 76 0.5 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 0.625 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 87.35000000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 88.06525472238123 76.925 2 9.988551803091013 17.45 3 1.5455065827132226 4.05 4 0.25758443045220375 0.8999999999999999 5 0.11448196908986834 0.5 6 0.0 0.0 7 0.028620492272467084 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 CTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAAC 7 0.17500000000000002 No Hit CCATCGTTCTCGGTTGCTGGAACCTCCATGACTCCAGTGTAGACATGGCT 5 0.125 No Hit CACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCC 5 0.125 No Hit ATTCGGTGTAACGTACTACTCTGTTTTTTCTATTAACCAAAAGTAAGTTG 5 0.125 No Hit CCTTCAAACTTGCACCTTTTTCCACCACCATGGCGGACACAAAATTGTGT 5 0.125 No Hit >>END_MODULE >>Adapter Content warn #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 0.0 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.037500000000000006 0.0 0.0 0.0 0.0 68-69 0.05 0.0 0.0 0.0 0.0 70-71 0.075 0.0 0.0 0.0 0.0 72-73 0.075 0.0 0.0 0.0 0.0 74-75 0.1125 0.0 0.0 0.0 0.0 76-77 0.1375 0.0 0.0 0.0 0.0 78-79 0.16249999999999998 0.0 0.0 0.0 0.0 80-81 0.175 0.0 0.0 0.0 0.0 82-83 0.2 0.0 0.0 0.0 0.0 84-85 0.3125 0.0 0.0 0.0 0.0 86-87 0.35 0.0 0.0 0.0 0.0 88-89 0.4 0.0 0.0 0.0 0.0 90-91 0.44999999999999996 0.0 0.0 0.0 0.0 92-93 0.5375 0.0 0.0 0.0 0.0 94-95 0.6875 0.0 0.0 0.0 0.0 96-97 0.925 0.0 0.0 0.0 0.0 98-99 1.0750000000000002 0.0 0.0 0.0 0.0 100-101 1.2125 0.0 0.0 0.0 0.0 102-103 1.4375 0.0 0.0 0.0 0.0 104-105 1.7125 0.0 0.0 0.0 0.0 106-107 1.9125 0.0 0.0 0.0 0.0 108-109 2.1875 0.0 0.0 0.0 0.0 110-111 2.4000000000000004 0.0 0.0 0.0 0.0 112-113 2.6625 0.0 0.0 0.0 0.0 114-115 3.075 0.0 0.0 0.0 0.0 116-117 3.4 0.0 0.0 0.0 0.0 118-119 3.7249999999999996 0.0 0.0 0.0 0.0 120-121 4.05 0.0 0.0 0.0 0.0 122-123 4.5 0.0 0.0 0.0 0.0 124-125 5.15 0.0 0.0 0.0 0.0 126-127 5.612500000000001 0.0 0.0 0.0 0.0 128-129 6.075 0.0 0.0 0.0 0.0 130-131 6.5625 0.0 0.0 0.0 0.0 132-133 6.825 0.0 0.0 0.0 0.0 134-135 7.3625 0.0 0.0 0.0 0.0 136-137 8.025 0.0 0.0 0.0 0.0 138-139 8.625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR12690129 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12690129_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 36.3395 37.0 37.0 37.0 37.0 37.0 2 35.9755 37.0 37.0 37.0 37.0 37.0 3 36.184 37.0 37.0 37.0 37.0 37.0 4 36.2695 37.0 37.0 37.0 37.0 37.0 5 36.393 37.0 37.0 37.0 37.0 37.0 6 36.283 37.0 37.0 37.0 37.0 37.0 7 36.266 37.0 37.0 37.0 37.0 37.0 8 36.3245 37.0 37.0 37.0 37.0 37.0 9 36.36 37.0 37.0 37.0 37.0 37.0 10-14 36.3116 37.0 37.0 37.0 37.0 37.0 15-19 36.3356 37.0 37.0 37.0 37.0 37.0 20-24 36.2934 37.0 37.0 37.0 37.0 37.0 25-29 36.28959999999999 37.0 37.0 37.0 37.0 37.0 30-34 36.28150000000001 37.0 37.0 37.0 37.0 37.0 35-39 36.2547 37.0 37.0 37.0 37.0 37.0 40-44 36.2006 37.0 37.0 37.0 37.0 37.0 45-49 36.1553 37.0 37.0 37.0 37.0 37.0 50-54 36.1285 37.0 37.0 37.0 37.0 37.0 55-59 36.11560000000001 37.0 37.0 37.0 37.0 37.0 60-64 36.1197 37.0 37.0 37.0 37.0 37.0 65-69 36.0822 37.0 37.0 37.0 37.0 37.0 70-74 36.0265 37.0 37.0 37.0 37.0 37.0 75-79 36.076800000000006 37.0 37.0 37.0 37.0 37.0 80-84 36.0246 37.0 37.0 37.0 37.0 37.0 85-89 36.0027 37.0 37.0 37.0 37.0 37.0 90-94 35.8703 37.0 37.0 37.0 37.0 37.0 95-99 35.898 37.0 37.0 37.0 37.0 37.0 100-104 35.9554 37.0 37.0 37.0 37.0 37.0 105-109 35.9548 37.0 37.0 37.0 37.0 37.0 110-114 35.861399999999996 37.0 37.0 37.0 37.0 37.0 115-119 35.7657 37.0 37.0 37.0 37.0 37.0 120-124 35.744800000000005 37.0 37.0 37.0 37.0 37.0 125-129 35.637 37.0 37.0 37.0 37.0 37.0 130-134 35.5499 37.0 37.0 37.0 37.0 37.0 135-139 35.5154 37.0 37.0 37.0 37.0 37.0 140-144 35.4029 37.0 37.0 37.0 37.0 37.0 145-149 35.2981 37.0 37.0 37.0 32.2 37.0 150-151 34.8215 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 1.0 14 3.0 15 1.0 16 0.0 17 0.0 18 0.0 19 1.0 20 1.0 21 2.0 22 1.0 23 5.0 24 4.0 25 5.0 26 9.0 27 11.0 28 22.0 29 20.0 30 28.0 31 28.0 32 44.0 33 90.0 34 189.0 35 557.0 36 2712.0 37 266.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 39.15 24.825 10.5 25.525 2 27.400000000000002 28.1 28.775000000000002 15.725 3 19.525000000000002 28.249999999999996 33.175 19.05 4 22.575 36.15 23.400000000000002 17.875 5 25.15 38.05 19.7 17.1 6 20.1 41.325 21.775 16.8 7 19.325 24.125 38.45 18.099999999999998 8 21.25 25.924999999999997 28.175 24.65 9 21.575 25.324999999999996 30.099999999999998 23.0 10-14 22.58 30.14 26.424999999999997 20.855 15-19 23.669999999999998 28.785 27.46 20.085 20-24 23.04 28.685 27.665 20.61 25-29 22.58 28.494999999999997 27.865000000000002 21.060000000000002 30-34 22.335 28.050000000000004 28.205000000000002 21.41 35-39 23.080000000000002 27.985 27.765 21.17 40-44 22.735 28.055000000000003 28.62 20.59 45-49 22.39 28.33 28.689999999999998 20.59 50-54 22.495 28.555000000000003 27.944999999999997 21.005 55-59 23.015 27.935 28.185 20.865000000000002 60-64 22.605 28.29 28.345 20.76 65-69 23.080000000000002 27.615000000000002 28.165000000000003 21.14 70-74 22.7 27.169999999999998 28.42 21.709999999999997 75-79 22.795 27.279999999999998 28.244999999999997 21.68 80-84 23.175 27.465 27.83 21.529999999999998 85-89 23.375 27.284999999999997 28.595 20.745 90-94 23.335 28.225 27.845 20.595 95-99 23.580000000000002 28.185 27.54 20.695 100-104 23.97 28.199999999999996 27.224999999999998 20.605 105-109 24.84 28.134999999999998 27.195000000000004 19.830000000000002 110-114 24.355 27.87 27.284999999999997 20.49 115-119 25.41 28.33 26.729999999999997 19.53 120-124 24.945 28.4 27.115000000000002 19.54 125-129 25.180000000000003 27.92 27.365000000000002 19.535 130-134 25.074999999999996 27.67 27.21 20.044999999999998 135-139 25.074999999999996 28.03 26.575 20.32 140-144 25.145 27.595 27.275 19.985 145-149 25.759999999999998 27.560000000000002 26.685 19.994999999999997 150-151 26.55 27.6625 26.337500000000002 19.45 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.5 3 1.0 4 1.0 5 1.0 6 0.5 7 0.0 8 1.0 9 1.0 10 0.0 11 1.0 12 1.0 13 0.5 14 1.0 15 0.5 16 1.0 17 1.0 18 0.0 19 0.5 20 1.0 21 0.5 22 1.5 23 2.5 24 2.0 25 4.5 26 6.5 27 8.0 28 13.5 29 15.0 30 21.5 31 24.5 32 23.5 33 34.5 34 53.5 35 75.0 36 97.0 37 125.5 38 148.5 39 163.0 40 187.0 41 218.5 42 261.0 43 291.5 44 274.5 45 261.5 46 265.5 47 245.0 48 218.5 49 181.5 50 141.5 51 126.5 52 111.0 53 80.0 54 63.0 55 50.0 56 36.0 57 39.0 58 32.0 59 17.0 60 12.0 61 11.5 62 9.0 63 8.5 64 5.0 65 0.5 66 1.5 67 2.5 68 1.0 69 0.5 70 1.5 71 2.0 72 1.0 73 0.5 74 1.5 75 1.0 76 0.0 77 0.5 78 0.5 79 0.0 80 0.0 81 0.0 82 0.0 83 0.5 84 0.5 85 0.0 86 0.0 87 0.0 88 0.5 89 0.5 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.5 100 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 86.35000000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 88.27446438911407 76.225 2 9.264620729588882 16.0 3 1.7371163867979156 4.5 4 0.3474232773595831 1.2 5 0.1447596988998263 0.625 6 0.08685581933989578 0.44999999999999996 7 0.05790387955993051 0.35000000000000003 8 0.028951939779965255 0.2 9 0.05790387955993051 0.44999999999999996 >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 AGATATTCGAAATGGCTTTCTGTACACAAGCTGTTATCCTGATTCTATCC 9 0.22499999999999998 No Hit CCTAAGCAAAGAACAACTTCGTATTTAGTTCATCCATTTGCTTCATCAAT 9 0.22499999999999998 No Hit GTTCTACAATGAACACATTCATGGCTACGACTATCTTGCTGCTTTTTGGT 8 0.2 No Hit CAAAAACACAAAAACCTATAGAACTTGCCTTCACTCGAAGTCCAGAATGA 7 0.17500000000000002 No Hit AGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAA 7 0.17500000000000002 No Hit TCTACAATGAACACATTCATGGCTACGACTATCTTGCTGCTTTTTGGTTT 6 0.15 No Hit AGCAATAGCAATTAGCAAAGCCCACCTTGGTTTTAATTACTAGAATTTAC 6 0.15 No Hit AGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATC 6 0.15 No Hit CAGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTA 5 0.125 No Hit GCAATTAGCAAAGCCCACCTTGGTTTTAATTACTAGAATTTACACAGTTT 5 0.125 No Hit TGCCAATTCTTAGGATGCACCAAAGGAGCACAAGGGAGCACTATGTTCTG 5 0.125 No Hit CAACAATTGAGTACTCAAGATTTGGTTTGCACCCTCAGTACATTTCTTGA 5 0.125 No Hit CAAAAACAAAAAACCTATAGAACTTGCCTTCACTCGAAGTCCAGAATGAG 5 0.125 No Hit >>END_MODULE >>Adapter Content warn #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 0.0 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.037500000000000006 0.0 0.0 0.0 0.0 68-69 0.05 0.0 0.0 0.0 0.0 70-71 0.075 0.0 0.0 0.0 0.0 72-73 0.075 0.0 0.0 0.0 0.0 74-75 0.1125 0.0 0.0 0.0 0.0 76-77 0.1375 0.0 0.0 0.0 0.0 78-79 0.16249999999999998 0.0 0.0 0.0 0.0 80-81 0.175 0.0 0.0 0.0 0.0 82-83 0.2 0.0 0.0 0.0 0.0 84-85 0.3125 0.0 0.0 0.0 0.0 86-87 0.35 0.0 0.0 0.0 0.0 88-89 0.4 0.0 0.0 0.0 0.0 90-91 0.44999999999999996 0.0 0.0 0.0 0.0 92-93 0.5375 0.0 0.0 0.0 0.0 94-95 0.6875 0.0 0.0 0.0 0.0 96-97 0.925 0.0 0.0 0.0 0.0 98-99 1.0750000000000002 0.0 0.0 0.0 0.0 100-101 1.1875 0.0 0.0 0.0 0.0 102-103 1.4125 0.0 0.0 0.0 0.0 104-105 1.6875 0.0 0.0 0.0 0.0 106-107 1.8875 0.0 0.0 0.0 0.0 108-109 2.15 0.0 0.0 0.0 0.0 110-111 2.375 0.0 0.0 0.0 0.0 112-113 2.6125 0.0 0.0 0.0 0.0 114-115 3.025 0.0 0.0 0.0 0.0 116-117 3.35 0.0 0.0 0.0 0.0 118-119 3.675 0.0 0.0 0.0 0.0 120-121 4.0375 0.0 0.0 0.0 0.0 122-123 4.5 0.0 0.0 0.0 0.0 124-125 5.15 0.0 0.0 0.0 0.0 126-127 5.612500000000001 0.0 0.0 0.0 0.0 128-129 6.075 0.0 0.0 0.0 0.0 130-131 6.5875 0.0 0.0 0.0 0.0 132-133 6.875 0.0 0.0 0.0 0.0 134-135 7.4125 0.0 0.0 0.0 0.0 136-137 8.0625 0.0 0.0 0.0 0.0 138-139 8.65 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GCACATG 10 0.006830828 145.0 2 >>END_MODULE Read 923677 spots for SRR12690129.sra Written 923677 spots for SRR12690129.sra Read 923677 spots for SRR12690129.sra Written 923677 spots for SRR12690129.sra Read 923677 spots for SRR12690129.sra Written 923677 spots for SRR12690129.sra Read 923677 spots for SRR12690129.sra Written 923677 spots for SRR12690129.sra Read 923677 spots for SRR12690129.sra Written 923677 spots for SRR12690129.sra Read 923677 spots for SRR12690129.sra Written 923677 spots for SRR12690129.sra Read 923692 spots for SRR12690129.sra Written 923692 spots for SRR12690129.sra Read 923677 spots for SRR12690129.sra Written 923677 spots for SRR12690129.sra Read 923677 spots for SRR12690129.sra Written 923677 spots for SRR12690129.sra Read 923677 spots for SRR12690129.sra Written 923677 spots for SRR12690129.sra Read 923677 spots for SRR12690129.sra Written 923677 spots for SRR12690129.sra Read 923677 spots for SRR12690129.sra Written 923677 spots for SRR12690129.sra Read 923677 spots for SRR12690129.sra Written 923677 spots for SRR12690129.sra Read 923677 spots for SRR12690129.sra Written 923677 spots for SRR12690129.sra Read 923677 spots for SRR12690129.sra Written 923677 spots for SRR12690129.sra Read 923677 spots for SRR12690129.sra Written 923677 spots for SRR12690129.sra Read 923677 spots for SRR12690129.sra Written 923677 spots for SRR12690129.sra Read 923677 spots for SRR12690129.sra Written 923677 spots for SRR12690129.sra Read 923677 spots for SRR12690129.sra Written 923677 spots for SRR12690129.sra Read 923677 spots for SRR12690129.sra Written 923677 spots for SRR12690129.sra SRR ids: ['SRR12690129.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_dkl8bg9_ SRR12690129.sra spots: 18473555 blocks: [[1, 923677], [923678, 1847354], [1847355, 2771031], [2771032, 3694708], [3694709, 4618385], [4618386, 5542062], [5542063, 6465739], [6465740, 7389416], [7389417, 8313093], [8313094, 9236770], [9236771, 10160447], [10160448, 11084124], [11084125, 12007801], [12007802, 12931478], [12931479, 13855155], [13855156, 14778832], [14778833, 15702509], [15702510, 16626186], [16626187, 17549863], [17549864, 18473555]] SRR12690129 file size 6256421 SRR12690129 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 SRR12690129 SRR12690129_1.fastq SRR12690129_2.fastq Input file: SRR12690129_1.fastq Paired file: SRR12690129_2.fastq trimmed: SRR12690129-trimmed-pair1.fastq, SRR12690129-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- number of concurrent threads (-t): 20 Mon Feb 10 17:03:04 2025 >> started Mon Feb 10 17:03:33 2025 >> done (28.388s) 18473555 read pairs processed; of these: 47 ( 0.00%) short read pairs filtered out after trimming by size control 2273 ( 0.01%) empty read pairs filtered out after trimming by size control 18471235 (99.99%) read pairs available; of these: 2321699 (12.57%) trimmed read pairs available after processing 16149536 (87.43%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 4 0.00% 19 4 0.00% 20 9 0.00% 21 6 0.00% 22 10 0.00% 23 16 0.00% 24 10 0.00% 25 21 0.00% 26 16 0.00% 27 11 0.00% 28 24 0.00% 29 25 0.00% 30 22 0.00% 31 15 0.00% 32 29 0.00% 33 21 0.00% 34 23 0.00% 35 23 0.00% 36 29 0.00% 37 30 0.00% 38 31 0.00% 39 29 0.00% 40 38 0.00% 41 34 0.00% 42 36 0.00% 43 47 0.00% 44 55 0.00% 45 35 0.00% 46 63 0.00% 47 65 0.00% 48 84 0.00% 49 76 0.00% 50 104 0.00% 51 128 0.00% 52 129 0.00% 53 150 0.00% 54 142 0.00% 55 173 0.00% 56 186 0.00% 57 206 0.00% 58 235 0.00% 59 292 0.00% 60 340 0.00% 61 392 0.00% 62 438 0.00% 63 471 0.00% 64 584 0.00% 65 574 0.00% 66 692 0.00% 67 751 0.00% 68 871 0.00% 69 964 0.01% 70 1140 0.01% 71 1239 0.01% 72 1499 0.01% 73 1752 0.01% 74 1877 0.01% 75 2020 0.01% 76 2231 0.01% 77 2537 0.01% 78 2899 0.02% 79 3221 0.02% 80 3562 0.02% 81 4018 0.02% 82 4515 0.02% 83 4883 0.03% 84 5744 0.03% 85 6162 0.03% 86 6446 0.03% 87 6748 0.04% 88 7402 0.04% 89 7976 0.04% 90 8762 0.05% 91 9665 0.05% 92 10060 0.05% 93 11217 0.06% 94 12269 0.07% 95 12791 0.07% 96 13716 0.07% 97 14326 0.08% 98 15047 0.08% 99 16015 0.09% 100 17049 0.09% 101 17533 0.09% 102 18834 0.10% 103 20287 0.11% 104 21094 0.11% 105 22000 0.12% 106 22598 0.12% 107 24037 0.13% 108 23959 0.13% 109 24938 0.14% 110 25739 0.14% 111 27008 0.15% 112 28691 0.16% 113 28631 0.16% 114 30784 0.17% 115 32052 0.17% 116 32909 0.18% 117 33687 0.18% 118 34720 0.19% 119 35747 0.19% 120 37771 0.20% 121 38064 0.21% 122 40043 0.22% 123 40507 0.22% 124 41376 0.22% 125 41420 0.22% 126 43138 0.23% 127 43332 0.23% 128 44117 0.24% 129 44351 0.24% 130 46127 0.25% 131 46250 0.25% 132 47021 0.25% 133 47548 0.26% 134 49066 0.27% 135 49782 0.27% 136 52210 0.28% 137 52564 0.28% 138 53342 0.29% 139 54601 0.30% 140 54311 0.29% 141 56635 0.31% 142 57381 0.31% 143 58149 0.31% 144 61410 0.33% 145 62346 0.34% 146 62879 0.34% 147 64756 0.35% 148 66095 0.36% 149 65176 0.35% 150 67132 0.36% 151 16149536 87.43% 18471235 reads passed initial QC criterion=sequence-density sequence-density=0.59 sequence-density-rank=1 fanout-score=2.16 fanout-score-rank=34 prefix-density=0.62 prefix-fanout=2.1 sequence=TACGTGCTTAAT criterion=fanout-score sequence-density=0.01 sequence-density-rank=33 fanout-score=152.08 fanout-score-rank=1 prefix-density=0.26 prefix-fanout=7.5 sequence=TGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGGTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGGAGTATGAATGTGTTCTCTGTG criterion=sequence-density sequence-density=1.35 sequence-density-rank=1 fanout-score=2.59 fanout-score-rank=24 prefix-density=1.48 prefix-fanout=2.4 sequence=CCTCAGCAACCAGGTAAAGAATATGTCATGTGCCCACTTCCGCTAGCCATAAACCCTGACTACAAGCCTTCCGAAAAACTCAACGGAAAGGTAGCTCTGGTGACTGGAGGGGATTCCGGGATAGGAAGATCTGTATGCTACCATTTTGCATTAGAGGGTGCAACTGTGGCCTTTACATATGTACAAGGCATTGAGGACAGAGACAAGGATGACACCCTAAAGATGCTACTGAAGGCTAAGTCAAGCGATGCAGAGGATCCAATTGCCATAGCTACTGATGTTTCATCAGAAGAAGATTGCAAGAGGGTTGTCGAACAAGTTGCGAGTAAATATGGGCGGATTGATATTTTGGTCAACAATGCTGGCGTACAGCATTATACCAACTTGGTAGAAGAGATTACCGAGGAATGGCTTGTGAGGTTGTTCAGAACCAACATATTTGGTTATTTCTTCATGACCAAGCATTCATTAAAGCACATGAAGGAAGGAAGTTGTATAATCAACACAGCAT criterion=fanout-score sequence-density=0.01 sequence-density-rank=35 fanout-score=89.46 fanout-score-rank=1 prefix-density=0.37 prefix-fanout=2.2 sequence=TATATATACACCAGTGCTCTAACAAGCTTGTCATCCAACAAAATCCCAAACACAAAACCAGAAAATGAAGATTTGGGTCTTCTCAGTTTTCTCTCTATTACTGTCCCTTTTCCTAGGAGTCTCAGCTGAGCAATGTGGAAGGCAGGCTGGGGGTGCCCTTTGTCCGGGAGGTCAATGTTGTAGCCAATTTGGTTGGTGTGGCAACACTGATGCT SRR12690129 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 10 17:04:16 Started mapping on | Feb 10 17:04:16 Finished on | Feb 10 17:06:06 Mapping speed, Million of reads per hour | 604.51 Number of input reads | 18471235 Average input read length | 295 UNIQUE READS: Uniquely mapped reads number | 16750909 Uniquely mapped reads % | 90.69% Average mapped length | 294.58 Number of splices: Total | 14384431 Number of splices: Annotated (sjdb) | 13851650 Number of splices: GT/AG | 14140366 Number of splices: GC/AG | 150551 Number of splices: AT/AC | 7380 Number of splices: Non-canonical | 86134 Mismatch rate per base, % | 0.39% Deletion rate per base | 0.04% Deletion average length | 2.86 Insertion rate per base | 0.02% Insertion average length | 2.46 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 708709 % of reads mapped to multiple loci | 3.84% Number of reads mapped to too many loci | 358142 % of reads mapped to too many loci | 1.94% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.14% % of reads unmapped: other | 0.40% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1011617 1011617 1011617 N_multimapping 708709 708709 708709 N_noFeature 646449 16323645 854600 N_ambiguous 304766 1947 84706 UnstrandedReadsAssigned:15799694 PositiveStrandReadsAssigned:425317 NegativeStrandReadsAssigned:15811603 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12690129 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: SRR12690129-trimmed-pair1.fastq SRR12690129-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 18,471,235 reads, 16,183,847 reads pseudoaligned [quant] estimated average fragment length: 245.128 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 967 rounds 52401 SRR12690129.ke.tsv 34699 SRR12690129.se.tsv 87100 total ==> SRR12690129.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1773.87 1601.8 37.0494 Potri.005G024800.1.v4.1 1035 790.872 3217 166.893 Potri.004G059700.1.v4.1 961 717.024 0 0 Potri.007G009000.2.v4.1 1416 1171.87 0 0 Potri.003G141000.2.v4.1 2943 2698.87 680 10.3376 Potri.016G087400.1.v4.1 270 86.338 1066 506.582 Potri.015G069301.1.v4.1 564 330.936 0 0 Potri.010G195200.1.v4.1 1773 1528.87 1555 41.7304 Potri.012G127500.1.v4.1 977 732.967 37 2.07115 ==> SRR12690129.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 1 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 132 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 3 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 6 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 0 SRR12690129 completed mapping pipeline successfully