Starting /dee2/code/volunteer_pipeline.sh SRR12671023 current disk space = 3050386837504 free memory = 1449954480 SRR12671023 SRAfilesize d64340296c2e4eaef62bd649cc3aa448 SRR12671023.sra SRR12671023.sra file validated SRR12671023 is paired end SRR12671023 is conventional basespace SRR12671023 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12671023_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 36.42225 37.0 37.0 37.0 37.0 37.0 2 36.3965 37.0 37.0 37.0 37.0 37.0 3 36.494 37.0 37.0 37.0 37.0 37.0 4 36.5695 37.0 37.0 37.0 37.0 37.0 5 36.604 37.0 37.0 37.0 37.0 37.0 6 36.6135 37.0 37.0 37.0 37.0 37.0 7 36.5325 37.0 37.0 37.0 37.0 37.0 8 36.6235 37.0 37.0 37.0 37.0 37.0 9 36.548 37.0 37.0 37.0 37.0 37.0 10-14 36.617999999999995 37.0 37.0 37.0 37.0 37.0 15-19 36.5822 37.0 37.0 37.0 37.0 37.0 20-24 36.547399999999996 37.0 37.0 37.0 37.0 37.0 25-29 36.496 37.0 37.0 37.0 37.0 37.0 30-34 36.500099999999996 37.0 37.0 37.0 37.0 37.0 35-39 36.4627 37.0 37.0 37.0 37.0 37.0 40-44 36.441599999999994 37.0 37.0 37.0 37.0 37.0 45-49 36.4024 37.0 37.0 37.0 37.0 37.0 50-54 36.361 37.0 37.0 37.0 37.0 37.0 55-59 36.358799999999995 37.0 37.0 37.0 37.0 37.0 60-64 36.3809 37.0 37.0 37.0 37.0 37.0 65-69 36.3493 37.0 37.0 37.0 37.0 37.0 70-74 36.33989999999999 37.0 37.0 37.0 37.0 37.0 75-79 36.2955 37.0 37.0 37.0 37.0 37.0 80-84 36.2564 37.0 37.0 37.0 37.0 37.0 85-89 36.250099999999996 37.0 37.0 37.0 37.0 37.0 90-94 36.2548 37.0 37.0 37.0 37.0 37.0 95-99 36.197700000000005 37.0 37.0 37.0 37.0 37.0 100-104 36.153200000000005 37.0 37.0 37.0 37.0 37.0 105-109 36.1283 37.0 37.0 37.0 37.0 37.0 110-114 36.1102 37.0 37.0 37.0 37.0 37.0 115-119 36.065000000000005 37.0 37.0 37.0 37.0 37.0 120-124 35.9942 37.0 37.0 37.0 37.0 37.0 125-129 35.9798 37.0 37.0 37.0 37.0 37.0 130-134 35.794200000000004 37.0 37.0 37.0 37.0 37.0 135-139 35.8635 37.0 37.0 37.0 37.0 37.0 140-144 35.7719 37.0 37.0 37.0 37.0 37.0 145-149 35.637 37.0 37.0 37.0 37.0 37.0 150-151 35.54275 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 19 2.0 20 0.0 21 2.0 22 1.0 23 4.0 24 2.0 25 8.0 26 4.0 27 10.0 28 7.0 29 25.0 30 27.0 31 48.0 32 60.0 33 63.0 34 122.0 35 257.0 36 2710.0 37 648.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 39.85996499124781 11.127781945486372 4.426106526631658 44.58614653663416 2 16.075 11.1 42.675000000000004 30.15 3 15.475 13.275 30.3 40.949999999999996 4 22.45 23.075000000000003 24.474999999999998 30.0 5 23.75 29.725 26.075 20.45 6 18.7 33.825 25.15 22.325 7 15.825 27.224999999999998 40.699999999999996 16.25 8 15.35 25.2 35.975 23.474999999999998 9 15.575 23.175 36.225 25.025 10-14 18.955 30.09 28.285 22.67 15-19 19.985 28.08 27.575 24.36 20-24 20.29 28.185 28.060000000000002 23.465 25-29 19.405 28.349999999999998 28.194999999999997 24.05 30-34 19.08 28.775000000000002 28.12 24.025 35-39 19.675 28.199999999999996 28.16 23.965 40-44 20.119999999999997 28.475 27.265 24.14 45-49 20.29 28.475 27.37 23.865 50-54 19.895 28.345 27.915 23.845 55-59 20.23 28.555000000000003 27.66 23.555 60-64 20.25 28.349999999999998 27.765 23.635 65-69 20.05 28.634999999999998 28.110000000000003 23.205000000000002 70-74 20.380000000000003 28.285 27.715 23.62 75-79 20.09 28.37 27.985 23.555 80-84 20.16 28.349999999999998 28.175 23.315 85-89 19.985 28.465 27.72 23.830000000000002 90-94 20.345 28.360000000000003 28.000000000000004 23.294999999999998 95-99 20.02 28.225 27.775 23.98 100-104 20.25 28.199999999999996 28.299999999999997 23.25 105-109 20.315 27.905 28.08 23.7 110-114 20.68 27.689999999999998 28.044999999999998 23.585 115-119 20.115 28.67 27.950000000000003 23.265 120-124 20.255000000000003 28.255000000000003 28.03 23.46 125-129 20.75 28.28 27.339999999999996 23.630000000000003 130-134 20.735 28.38 27.750000000000004 23.135 135-139 20.695 28.02 27.634999999999998 23.65 140-144 20.625 27.625 27.915 23.835 145-149 20.697069706970698 28.6028602860286 27.742774277427745 22.95729572957296 150-151 20.75 28.349999999999998 27.6 23.3 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.5 2 0.5 3 0.0 4 0.0 5 0.0 6 0.5 7 0.5 8 0.0 9 0.5 10 0.5 11 0.0 12 0.5 13 0.5 14 0.0 15 0.0 16 0.0 17 0.0 18 0.5 19 0.5 20 1.5 21 1.5 22 0.5 23 1.0 24 2.5 25 4.0 26 4.0 27 5.5 28 8.0 29 14.5 30 22.0 31 30.5 32 40.0 33 49.0 34 52.0 35 71.0 36 85.5 37 113.5 38 139.0 39 155.5 40 187.0 41 216.0 42 250.5 43 232.0 44 241.0 45 270.5 46 263.0 47 255.5 48 220.5 49 190.0 50 177.0 51 149.0 52 123.0 53 101.0 54 83.0 55 64.0 56 48.5 57 37.5 58 24.5 59 20.5 60 14.5 61 8.0 62 4.5 63 3.5 64 2.5 65 2.0 66 2.0 67 1.5 68 0.5 69 0.5 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 0.0 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 0.025 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 0.01 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 89.075 #Duplication Level Percentage of deduplicated Percentage of total 1 89.19449901768172 79.45 2 9.710917765927588 17.299999999999997 3 0.8981195621667135 2.4 4 0.11226494527083919 0.4 5 0.056132472635419595 0.25 6 0.0 0.0 7 0.0 0.0 8 0.028066236317709797 0.2 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 CATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTC 8 0.2 No Hit CTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCG 5 0.125 No Hit CGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAG 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #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 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.025 0.0 0.0 0.0 0.0 68-69 0.037500000000000006 0.0 0.0 0.0 0.0 70-71 0.05 0.0 0.0 0.0 0.0 72-73 0.05 0.0 0.0 0.0 0.0 74-75 0.05 0.0 0.0 0.0 0.0 76-77 0.0625 0.0 0.0 0.0 0.0 78-79 0.075 0.0 0.0 0.0 0.0 80-81 0.15000000000000002 0.0 0.0 0.0 0.0 82-83 0.2625 0.0 0.0 0.0 0.0 84-85 0.2875 0.0 0.0 0.0 0.0 86-87 0.3625 0.0 0.0 0.0 0.0 88-89 0.375 0.0 0.0 0.0 0.0 90-91 0.4 0.0 0.0 0.0 0.0 92-93 0.4875 0.0 0.0 0.0 0.0 94-95 0.575 0.0 0.0 0.0 0.0 96-97 0.6 0.0 0.0 0.0 0.0 98-99 0.6875 0.0 0.0 0.0 0.0 100-101 0.725 0.0 0.0 0.0 0.0 102-103 0.75 0.0 0.0 0.0 0.0 104-105 0.85 0.0 0.0 0.0 0.0 106-107 0.925 0.0 0.0 0.0 0.0 108-109 1.0875 0.0 0.0 0.0 0.0 110-111 1.1875 0.0 0.0 0.0 0.0 112-113 1.3125 0.0 0.0 0.0 0.0 114-115 1.475 0.0 0.0 0.0 0.0 116-117 1.6375000000000002 0.0 0.0 0.0 0.0 118-119 2.0 0.0 0.0 0.0 0.0 120-121 2.2125 0.0 0.0 0.0 0.0 122-123 2.5 0.0 0.0 0.0 0.0 124-125 2.7750000000000004 0.0 0.0 0.0 0.0 126-127 3.0 0.0 0.0 0.0 0.0 128-129 3.275 0.0 0.0 0.0 0.0 130-131 3.6125 0.0 0.0 0.0 0.0 132-133 4.0125 0.0 0.0 0.0 0.0 134-135 4.3125 0.0 0.0 0.0 0.0 136-137 4.5625 0.0 0.0 0.0 0.0 138-139 4.7875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR12671023 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12671023_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 43 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.1015 37.0 37.0 37.0 37.0 37.0 2 36.1355 37.0 37.0 37.0 37.0 37.0 3 36.16 37.0 37.0 37.0 37.0 37.0 4 36.222 37.0 37.0 37.0 37.0 37.0 5 36.242 37.0 37.0 37.0 37.0 37.0 6 36.2765 37.0 37.0 37.0 37.0 37.0 7 36.2945 37.0 37.0 37.0 37.0 37.0 8 36.2365 37.0 37.0 37.0 37.0 37.0 9 36.4725 37.0 37.0 37.0 37.0 37.0 10-14 36.360699999999994 37.0 37.0 37.0 37.0 37.0 15-19 36.3274 37.0 37.0 37.0 37.0 37.0 20-24 36.3218 37.0 37.0 37.0 37.0 37.0 25-29 36.2558 37.0 37.0 37.0 37.0 37.0 30-34 36.2724 37.0 37.0 37.0 37.0 37.0 35-39 36.1558 37.0 37.0 37.0 37.0 37.0 40-44 36.1359 37.0 37.0 37.0 37.0 37.0 45-49 36.2256 37.0 37.0 37.0 37.0 37.0 50-54 36.1299 37.0 37.0 37.0 37.0 37.0 55-59 36.1265 37.0 37.0 37.0 37.0 37.0 60-64 36.14149999999999 37.0 37.0 37.0 37.0 37.0 65-69 36.107600000000005 37.0 37.0 37.0 37.0 37.0 70-74 36.101099999999995 37.0 37.0 37.0 37.0 37.0 75-79 36.0304 37.0 37.0 37.0 37.0 37.0 80-84 36.0127 37.0 37.0 37.0 37.0 37.0 85-89 36.0016 37.0 37.0 37.0 37.0 37.0 90-94 35.943200000000004 37.0 37.0 37.0 37.0 37.0 95-99 35.9698 37.0 37.0 37.0 37.0 37.0 100-104 35.9309 37.0 37.0 37.0 37.0 37.0 105-109 35.8688 37.0 37.0 37.0 37.0 37.0 110-114 35.8608 37.0 37.0 37.0 37.0 37.0 115-119 35.80785 37.0 37.0 37.0 37.0 37.0 120-124 35.6862 37.0 37.0 37.0 37.0 37.0 125-129 35.63100000000001 37.0 37.0 37.0 37.0 37.0 130-134 35.592400000000005 37.0 37.0 37.0 37.0 37.0 135-139 35.6477 37.0 37.0 37.0 37.0 37.0 140-144 35.57885 37.0 37.0 37.0 37.0 37.0 145-149 35.326699999999995 37.0 37.0 37.0 34.6 37.0 150-151 35.06225 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 11 1.0 12 0.0 13 0.0 14 2.0 15 1.0 16 1.0 17 4.0 18 0.0 19 1.0 20 3.0 21 1.0 22 2.0 23 4.0 24 7.0 25 5.0 26 9.0 27 11.0 28 14.0 29 25.0 30 33.0 31 45.0 32 62.0 33 87.0 34 175.0 35 443.0 36 2615.0 37 449.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 37.225 25.724999999999998 7.2749999999999995 29.775000000000002 2 23.974999999999998 26.35 35.699999999999996 13.975000000000001 3 18.325 27.975 35.949999999999996 17.75 4 23.45 33.975 23.925 18.65 5 24.349999999999998 37.9 21.525 16.225 6 18.15 41.475 22.45 17.925 7 19.075 23.025000000000002 38.2 19.7 8 16.275000000000002 25.674999999999997 32.1 25.95 9 21.75 23.05 31.25 23.95 10-14 22.53 30.11 26.674999999999997 20.685000000000002 15-19 22.31 28.28 28.355000000000004 21.055 20-24 22.23 28.405 28.33 21.035 25-29 22.175 28.549999999999997 28.155 21.12 30-34 22.985 27.96 28.265 20.79 35-39 22.720000000000002 28.15 27.800000000000004 21.33 40-44 21.845 28.625 28.63 20.9 45-49 22.720000000000002 28.415000000000003 27.865000000000002 21.0 50-54 21.985 28.634999999999998 28.065 21.315 55-59 22.43 28.075 28.544999999999998 20.95 60-64 21.7 28.53 28.68 21.09 65-69 22.3 28.21 28.51 20.979999999999997 70-74 22.8 27.839999999999996 27.92 21.44 75-79 22.96 27.97 27.74 21.33 80-84 23.155 28.265 27.715 20.865000000000002 85-89 22.555 28.810000000000002 27.58 21.055 90-94 22.475 28.139999999999997 28.57 20.815 95-99 22.655 28.02 28.165000000000003 21.16 100-104 23.385 28.384999999999998 28.060000000000002 20.169999999999998 105-109 22.835 28.945 27.3 20.919999999999998 110-114 23.46 28.465 27.875 20.200000000000003 115-119 23.52617630881544 29.06145307265363 27.43637181859093 19.975998799939997 120-124 23.94 27.744999999999997 27.689999999999998 20.625 125-129 24.104999999999997 28.185 27.715 19.994999999999997 130-134 23.575 28.799999999999997 26.974999999999998 20.65 135-139 24.03 27.345000000000002 28.28 20.345 140-144 24.116205810290513 27.91139556977849 27.771388569428474 20.201010050502525 145-149 24.77 28.28 27.095000000000002 19.855 150-151 24.925 26.8375 28.625 19.6125 >>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 1.0 7 1.0 8 0.5 9 1.0 10 2.0 11 2.0 12 0.5 13 0.5 14 1.0 15 0.5 16 0.0 17 0.5 18 0.5 19 0.0 20 0.0 21 1.5 22 2.0 23 2.0 24 5.0 25 7.5 26 6.5 27 8.0 28 12.0 29 16.5 30 23.0 31 28.0 32 40.5 33 59.0 34 65.0 35 78.5 36 97.0 37 113.0 38 156.5 39 196.5 40 218.0 41 229.5 42 240.5 43 254.0 44 263.0 45 246.5 46 238.5 47 227.5 48 217.0 49 196.5 50 154.0 51 128.5 52 102.5 53 77.5 54 60.0 55 53.0 56 42.5 57 31.0 58 21.5 59 20.0 60 14.0 61 9.5 62 8.5 63 5.0 64 3.5 65 2.0 66 0.0 67 1.0 68 1.0 69 0.5 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 0.0 80 0.0 81 0.0 82 0.0 83 0.5 84 1.0 85 1.0 86 0.5 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 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 0.005 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.005 145-149 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 88.85 #Duplication Level Percentage of deduplicated Percentage of total 1 89.19527293190771 79.25 2 9.735509285312324 17.299999999999997 3 0.8441193021947102 2.25 4 0.11254924029262803 0.4 5 0.056274620146314014 0.25 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.056274620146314014 0.5499999999999999 >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 11 0.27499999999999997 No Hit AGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATC 11 0.27499999999999997 No Hit CAGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTA 5 0.125 No Hit ATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAATCAAT 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #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 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.025 0.0 0.0 0.0 0.0 68-69 0.037500000000000006 0.0 0.0 0.0 0.0 70-71 0.05 0.0 0.0 0.0 0.0 72-73 0.05 0.0 0.0 0.0 0.0 74-75 0.05 0.0 0.0 0.0 0.0 76-77 0.0625 0.0 0.0 0.0 0.0 78-79 0.075 0.0 0.0 0.0 0.0 80-81 0.15000000000000002 0.0 0.0 0.0 0.0 82-83 0.2625 0.0 0.0 0.0 0.0 84-85 0.2875 0.0 0.0 0.0 0.0 86-87 0.35 0.0 0.0 0.0 0.0 88-89 0.35 0.0 0.0 0.0 0.0 90-91 0.375 0.0 0.0 0.0 0.0 92-93 0.4625 0.0 0.0 0.0 0.0 94-95 0.55 0.0 0.0 0.0 0.0 96-97 0.575 0.0 0.0 0.0 0.0 98-99 0.6625 0.0 0.0 0.0 0.0 100-101 0.7 0.0 0.0 0.0 0.0 102-103 0.725 0.0 0.0 0.0 0.0 104-105 0.825 0.0 0.0 0.0 0.0 106-107 0.9 0.0 0.0 0.0 0.0 108-109 1.0625 0.0 0.0 0.0 0.0 110-111 1.1625 0.0 0.0 0.0 0.0 112-113 1.2875 0.0 0.0 0.0 0.0 114-115 1.4500000000000002 0.0 0.0 0.0 0.0 116-117 1.6124999999999998 0.0 0.0 0.0 0.0 118-119 1.9749999999999999 0.0 0.0 0.0 0.0 120-121 2.175 0.0 0.0 0.0 0.0 122-123 2.4625 0.0 0.0 0.0 0.0 124-125 2.75 0.0 0.0 0.0 0.0 126-127 2.9749999999999996 0.0 0.0 0.0 0.0 128-129 3.25 0.0 0.0 0.0 0.0 130-131 3.625 0.0 0.0 0.0 0.0 132-133 4.0375 0.0 0.0 0.0 0.0 134-135 4.3375 0.0 0.0 0.0 0.0 136-137 4.5875 0.0 0.0 0.0 0.0 138-139 4.7875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AAAAAAA 35 0.0035366106 20.714287 110-114 >>END_MODULE Read 565155 spots for SRR12671023.sra Written 565155 spots for SRR12671023.sra Read 565155 spots for SRR12671023.sra Written 565155 spots for SRR12671023.sra Read 565155 spots for SRR12671023.sra Written 565155 spots for SRR12671023.sra Read 565155 spots for SRR12671023.sra Written 565155 spots for SRR12671023.sra Read 565155 spots for SRR12671023.sra Written 565155 spots for SRR12671023.sra Read 565155 spots for SRR12671023.sra Written 565155 spots for SRR12671023.sra Read 565155 spots for SRR12671023.sra Written 565155 spots for SRR12671023.sra Read 565155 spots for SRR12671023.sra Written 565155 spots for SRR12671023.sra Read 565155 spots for SRR12671023.sra Written 565155 spots for SRR12671023.sra Read 565155 spots for SRR12671023.sra Written 565155 spots for SRR12671023.sra Read 565155 spots for SRR12671023.sra Written 565155 spots for SRR12671023.sra Read 565155 spots for SRR12671023.sra Written 565155 spots for SRR12671023.sra Read 565155 spots for SRR12671023.sra Written 565155 spots for SRR12671023.sra Read 565155 spots for SRR12671023.sra Written 565155 spots for SRR12671023.sra Read 565155 spots for SRR12671023.sra Written 565155 spots for SRR12671023.sra Read 565155 spots for SRR12671023.sra Written 565155 spots for SRR12671023.sra Read 565155 spots for SRR12671023.sra Written 565155 spots for SRR12671023.sra Read 565155 spots for SRR12671023.sra Written 565155 spots for SRR12671023.sra Read 565155 spots for SRR12671023.sra Written 565155 spots for SRR12671023.sra Read 565160 spots for SRR12671023.sra Written 565160 spots for SRR12671023.sra SRR ids: ['SRR12671023.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_n7aqm0gq SRR12671023.sra spots: 11303105 blocks: [[1, 565155], [565156, 1130310], [1130311, 1695465], [1695466, 2260620], [2260621, 2825775], [2825776, 3390930], [3390931, 3956085], [3956086, 4521240], [4521241, 5086395], [5086396, 5651550], [5651551, 6216705], [6216706, 6781860], [6781861, 7347015], [7347016, 7912170], [7912171, 8477325], [8477326, 9042480], [9042481, 9607635], [9607636, 10172790], [10172791, 10737945], [10737946, 11303105]] SRR12671023 file size 3819589 SRR12671023 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 SRR12671023 SRR12671023_1.fastq SRR12671023_2.fastq Input file: SRR12671023_1.fastq Paired file: SRR12671023_2.fastq trimmed: SRR12671023-trimmed-pair1.fastq, SRR12671023-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 13:40:35 2025 >> started Tue Feb 11 13:40:48 2025 >> done (12.922s) 11303105 read pairs processed; of these: 63 ( 0.00%) short read pairs filtered out after trimming by size control 478 ( 0.00%) empty read pairs filtered out after trimming by size control 11302564 (100.00%) read pairs available; of these: 799792 ( 7.08%) trimmed read pairs available after processing 10502772 (92.92%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 4 0.00% 19 3 0.00% 20 4 0.00% 21 6 0.00% 22 2 0.00% 23 8 0.00% 24 6 0.00% 25 7 0.00% 26 6 0.00% 27 4 0.00% 28 10 0.00% 29 11 0.00% 30 13 0.00% 31 15 0.00% 32 8 0.00% 33 27 0.00% 34 17 0.00% 35 14 0.00% 36 13 0.00% 37 10 0.00% 38 16 0.00% 39 14 0.00% 40 27 0.00% 41 22 0.00% 42 17 0.00% 43 25 0.00% 44 15 0.00% 45 29 0.00% 46 24 0.00% 47 26 0.00% 48 27 0.00% 49 33 0.00% 50 42 0.00% 51 44 0.00% 52 43 0.00% 53 56 0.00% 54 59 0.00% 55 68 0.00% 56 67 0.00% 57 76 0.00% 58 84 0.00% 59 99 0.00% 60 127 0.00% 61 154 0.00% 62 168 0.00% 63 160 0.00% 64 229 0.00% 65 194 0.00% 66 235 0.00% 67 246 0.00% 68 282 0.00% 69 354 0.00% 70 432 0.00% 71 479 0.00% 72 546 0.00% 73 587 0.01% 74 662 0.01% 75 769 0.01% 76 796 0.01% 77 871 0.01% 78 1054 0.01% 79 1002 0.01% 80 1266 0.01% 81 1464 0.01% 82 1495 0.01% 83 1681 0.01% 84 1959 0.02% 85 2104 0.02% 86 2172 0.02% 87 2441 0.02% 88 2553 0.02% 89 2626 0.02% 90 3025 0.03% 91 3113 0.03% 92 3248 0.03% 93 3400 0.03% 94 3845 0.03% 95 4049 0.04% 96 4391 0.04% 97 4659 0.04% 98 4919 0.04% 99 5029 0.04% 100 5351 0.05% 101 5454 0.05% 102 5944 0.05% 103 6075 0.05% 104 6450 0.06% 105 6665 0.06% 106 6955 0.06% 107 7303 0.06% 108 7656 0.07% 109 7863 0.07% 110 8022 0.07% 111 8393 0.07% 112 8735 0.08% 113 8934 0.08% 114 9273 0.08% 115 10116 0.09% 116 10534 0.09% 117 10593 0.09% 118 11243 0.10% 119 11511 0.10% 120 12354 0.11% 121 12240 0.11% 122 12580 0.11% 123 12934 0.11% 124 13584 0.12% 125 13656 0.12% 126 14160 0.13% 127 14495 0.13% 128 15020 0.13% 129 15436 0.14% 130 15822 0.14% 131 16102 0.14% 132 16517 0.15% 133 17021 0.15% 134 17440 0.15% 135 17752 0.16% 136 18073 0.16% 137 18798 0.17% 138 19218 0.17% 139 20569 0.18% 140 20507 0.18% 141 21014 0.19% 142 21376 0.19% 143 21632 0.19% 144 22764 0.20% 145 22522 0.20% 146 23244 0.21% 147 23519 0.21% 148 25192 0.22% 149 24807 0.22% 150 26487 0.23% 151 10502772 92.92% 11302564 reads passed initial QC criterion=sequence-density sequence-density=0.37 sequence-density-rank=1 fanout-score=2.01 fanout-score-rank=26 prefix-density=0.37 prefix-fanout=2.0 sequence=CGGTAGACCCAACCTTTCTCCAACTCGAATTCCAAGCAAGGAACCCACTT criterion=fanout-score sequence-density=0.01 sequence-density-rank=32 fanout-score=533.91 fanout-score-rank=1 prefix-density=0.23 prefix-fanout=17.8 sequence=TGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGGTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGGAGTATGAATGTGTTCTCTG criterion=sequence-density sequence-density=0.46 sequence-density-rank=1 fanout-score=2.33 fanout-score-rank=29 prefix-density=0.48 prefix-fanout=2.2 sequence=TGTAAGAGATGGCTTCCTC criterion=fanout-score sequence-density=0.01 sequence-density-rank=37 fanout-score=22.49 fanout-score-rank=1 prefix-density=0.04 prefix-fanout=3.3 sequence=GGGAAACTTACCAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTATGGGTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGTTAACGAACGAGACCTCAGCCTGCTAACTAGCTATGCGGAGGTGACCCTCCGCGGCCAGCTTCTTAGAGGGACTATGGCCTTCCAGGCCAAGGAAGTTTGAGGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCACGCGCGCTACACTGAT SRR12671023 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 13:41:45 Started mapping on | Feb 11 13:41:46 Finished on | Feb 11 13:43:19 Mapping speed, Million of reads per hour | 437.52 Number of input reads | 11302564 Average input read length | 298 UNIQUE READS: Uniquely mapped reads number | 10513251 Uniquely mapped reads % | 93.02% Average mapped length | 297.22 Number of splices: Total | 10505164 Number of splices: Annotated (sjdb) | 10277032 Number of splices: GT/AG | 10302332 Number of splices: GC/AG | 164585 Number of splices: AT/AC | 6611 Number of splices: Non-canonical | 31636 Mismatch rate per base, % | 0.40% Deletion rate per base | 0.03% Deletion average length | 2.99 Insertion rate per base | 0.03% Insertion average length | 2.29 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 277876 % of reads mapped to multiple loci | 2.46% Number of reads mapped to too many loci | 87595 % of reads mapped to too many loci | 0.78% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.57% % of reads unmapped: other | 0.18% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 511437 511437 511437 N_multimapping 277876 277876 277876 N_noFeature 475217 10321477 526019 N_ambiguous 215049 772 73665 UnstrandedReadsAssigned:9822985 PositiveStrandReadsAssigned:191002 NegativeStrandReadsAssigned:9913567 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12671023 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: SRR12671023-trimmed-pair1.fastq SRR12671023-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 11,302,564 reads, 9,905,244 reads pseudoaligned [quant] estimated average fragment length: 275.288 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,010 rounds 52401 SRR12671023.ke.tsv 34699 SRR12671023.se.tsv 87100 total ==> SRR12671023.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1743.71 583 26.3675 Potri.005G024800.1.v4.1 1035 760.712 237 24.5699 Potri.004G059700.1.v4.1 961 686.943 1 0.114803 Potri.007G009000.2.v4.1 1416 1141.71 0 0 Potri.003G141000.2.v4.1 2943 2668.71 588 17.376 Potri.016G087400.1.v4.1 270 77.5285 550 559.469 Potri.015G069301.1.v4.1 564 306.275 0 0 Potri.010G195200.1.v4.1 1773 1498.71 131 6.89331 Potri.012G127500.1.v4.1 977 702.864 137 15.3718 ==> SRR12671023.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 53 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 162 Potri.001G212900.v4.1 2 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 2 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 2 SRR12671023 completed mapping pipeline successfully