Starting /dee2/code/volunteer_pipeline.sh SRR7171083 current disk space = 3087998447616 free memory = 1582738984 SRR7171083 SRAfilesize 96645315f97798807bc5790935f6adc3 SRR7171083.sra SRR7171083.sra file validated SRR7171083 is paired end SRR7171083 is conventional basespace SRR7171083 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7171083_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 43 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 20.9695 18.0 18.0 25.0 18.0 32.0 2 28.79875 29.0 27.0 31.0 27.0 33.0 3 30.052 31.0 29.0 33.0 27.0 33.0 4 31.08925 33.0 31.0 33.0 29.0 33.0 5 32.39725 33.0 33.0 33.0 31.0 33.0 6 35.8095 38.0 37.0 38.0 31.0 38.0 7 36.90725 38.0 38.0 38.0 35.0 38.0 8 37.384 38.0 38.0 38.0 37.0 38.0 9 37.53825 38.0 38.0 38.0 37.0 38.0 10-14 37.5004 38.0 38.0 38.0 37.6 38.0 15-19 37.463800000000006 38.0 38.0 38.0 37.2 38.0 20-24 37.49075 38.0 38.0 38.0 37.6 38.0 25-29 37.4765 38.0 38.0 38.0 37.6 38.0 30-34 37.36765 38.0 38.0 38.0 37.0 38.0 35-39 37.34265 38.0 38.0 38.0 37.0 38.0 40-44 37.26035 38.0 38.0 38.0 37.0 38.0 45-49 37.26745 38.0 38.0 38.0 37.0 38.0 50-54 37.106700000000004 38.0 38.0 38.0 36.6 38.0 55-59 37.007200000000005 38.0 38.0 38.0 36.0 38.0 60-64 37.038 38.0 38.0 38.0 36.0 38.0 65-69 35.8304 38.0 36.8 38.0 30.8 38.0 70-74 36.10934999999999 38.0 37.2 38.0 30.4 38.0 75-79 36.5278 38.0 38.0 38.0 34.8 38.0 80-84 36.4083 38.0 38.0 38.0 34.6 38.0 85-89 36.26675 38.0 38.0 38.0 34.2 38.0 90-94 36.118100000000005 38.0 38.0 38.0 34.0 38.0 95-99 35.9814 38.0 38.0 38.0 33.6 38.0 100-104 35.90955 38.0 37.6 38.0 33.4 38.0 105-109 35.72945 38.0 37.2 38.0 33.0 38.0 110-114 35.571850000000005 38.0 37.0 38.0 31.4 38.0 115-119 35.28115 38.0 37.0 38.0 30.6 38.0 120-124 35.1005 38.0 36.2 38.0 29.4 38.0 125-129 34.65825 38.0 35.6 38.0 27.2 38.0 130-134 34.026599999999995 38.0 33.8 38.0 24.0 38.0 135-139 33.9497 38.0 33.8 38.0 23.4 38.0 140-144 33.1144 38.0 33.0 38.0 17.6 38.0 145-149 32.160399999999996 38.0 33.0 38.0 10.2 38.0 150-151 26.636125 33.0 17.5 37.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 1.0 3 0.0 4 0.0 5 0.0 6 0.0 7 1.0 8 3.0 9 0.0 10 5.0 11 1.0 12 0.0 13 2.0 14 2.0 15 3.0 16 4.0 17 3.0 18 15.0 19 29.0 20 6.0 21 9.0 22 8.0 23 10.0 24 10.0 25 19.0 26 15.0 27 27.0 28 27.0 29 45.0 30 39.0 31 68.0 32 83.0 33 101.0 34 178.0 35 362.0 36 991.0 37 1933.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 33.24795081967213 12.807377049180326 19.4672131147541 34.47745901639344 2 19.529882470617654 18.204551137784446 35.80895223805952 26.456614153538382 3 16.25 23.375 30.3 30.075000000000003 4 19.875 28.9 26.075 25.15 5 21.375 34.425 25.174999999999997 19.025 6 17.1 37.15 27.85 17.9 7 13.425 24.325 45.35 16.900000000000002 8 15.5 25.424999999999997 34.225 24.85 9 16.85 25.15 33.85 24.15 10-14 18.459999999999997 31.795 26.66 23.085 15-19 19.18 30.659999999999997 26.695 23.465 20-24 18.67 30.630000000000003 27.47 23.23 25-29 19.07 29.945 27.894999999999996 23.09 30-34 18.7 30.395 27.13 23.775 35-39 19.025 29.805 27.169999999999998 24.0 40-44 19.13 30.605 27.33 22.935 45-49 19.49 29.7 27.29 23.52 50-54 19.314999999999998 29.970000000000002 27.41 23.305 55-59 18.970000000000002 29.435 27.675 23.919999999999998 60-64 19.205 29.085 27.884999999999998 23.825 65-69 19.564999999999998 30.285 26.86 23.29 70-74 19.585 30.135 26.529999999999998 23.75 75-79 18.96 30.869999999999997 26.41 23.76 80-84 19.42 29.985 26.400000000000002 24.195 85-89 19.48 30.65 25.945 23.925 90-94 20.28 28.815 26.224999999999998 24.68 95-99 20.10701070107011 29.487948794879486 26.407640764076408 23.997399739974 100-104 19.765 29.805 25.855 24.575 105-109 20.285 29.005 26.419999999999998 24.29 110-114 20.76 28.895 26.19 24.154999999999998 115-119 20.45 29.585 25.55 24.415 120-124 20.560000000000002 29.904999999999998 24.654999999999998 24.88 125-129 20.990000000000002 28.665000000000003 25.919999999999998 24.425 130-134 20.76 29.14 24.855 25.245 135-139 21.065 28.355000000000004 25.264999999999997 25.314999999999998 140-144 20.419999999999998 28.645 25.405 25.53 145-149 20.474999999999998 28.825 24.42 26.279999999999998 150-151 20.92296148074037 28.676838419209606 25.312656328164078 25.087543771885944 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 3.0 1 3.0 2 2.5 3 1.5 4 1.0 5 0.5 6 0.0 7 0.5 8 1.0 9 0.5 10 0.5 11 0.5 12 0.0 13 0.5 14 1.5 15 1.0 16 0.0 17 0.5 18 1.0 19 0.5 20 1.5 21 3.0 22 3.5 23 3.5 24 5.5 25 12.0 26 14.0 27 17.0 28 23.5 29 29.5 30 41.5 31 66.0 32 80.5 33 92.0 34 117.5 35 132.0 36 146.5 37 160.0 38 158.5 39 163.5 40 185.0 41 185.5 42 193.0 43 199.0 44 186.0 45 184.0 46 169.5 47 153.0 48 143.0 49 131.5 50 126.0 51 129.5 52 126.0 53 114.5 54 107.5 55 92.0 56 71.5 57 58.5 58 41.0 59 33.5 60 24.5 61 16.0 62 15.0 63 7.5 64 4.0 65 3.0 66 3.0 67 2.0 68 2.0 69 1.5 70 0.5 71 1.0 72 0.5 73 0.5 74 0.5 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 2.4 2 0.025 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 0.01 100-104 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 0.05 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 95.65 #Duplication Level Percentage of deduplicated Percentage of total 1 97.54312598013591 93.30000000000001 2 1.67276529012023 3.2 3 0.4443282801881861 1.275 4 0.10454783063251437 0.4 5 0.07841087297438579 0.375 6 0.10454783063251437 0.6 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.052273915316257184 0.8500000000000001 >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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACTCCGCGAAATCTCGTAT 23 0.575 TruSeq Adapter, Index 6 (97% over 36bp) TATCGGAAGAGCACACGTCTGAACTCCAGTCACTCCGCGAAATCTCGTAT 11 0.27499999999999997 TruSeq Adapter, Index 3 (97% over 34bp) GTCGGTTCGGTCCTCCAGTTAGTGTTACCCAACCTTCAACCTGCCCATGG 6 0.15 No Hit GTCAGCATTCGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTC 6 0.15 No Hit CCTCCATCAGGCAGTTTCCCAGACATTACTCACCCGTCCGCCACTCGTCA 6 0.15 No Hit CCCCACTGCTGCCTCCCGTAGGAGTCTGGACCGTGTCTCAGTTCCAGTGT 6 0.15 No Hit TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 5 0.125 No Hit GATTAACGCTTGCACCCTCCGTATTACCGCGGCTGCTGGCACGGAGTTAG 5 0.125 No Hit CCCATATTCAGACAGGATACCACGTGTCCCGCCCTACTCATCGAGCTCAC 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 0.05 0.0 0.0 0.0 0.0 2 0.05 0.0 0.0 0.0 0.0 3 0.05 0.0 0.0 0.0 0.0 4 0.05 0.0 0.0 0.0 0.0 5 0.05 0.0 0.0 0.0 0.0 6 0.05 0.0 0.0 0.0 0.0 7 0.05 0.0 0.0 0.0 0.0 8 0.05 0.0 0.0 0.0 0.0 9 0.05 0.0 0.0 0.0 0.0 10-11 0.05 0.0 0.0 0.0 0.0 12-13 0.05 0.0 0.0 0.0 0.0 14-15 0.05 0.0 0.0 0.0 0.0 16-17 0.05 0.0 0.0 0.0 0.0 18-19 0.05 0.0 0.0 0.0 0.0 20-21 0.05 0.0 0.0 0.0 0.0 22-23 0.05 0.0 0.0 0.0 0.0 24-25 0.05 0.0 0.0 0.0 0.0 26-27 0.05 0.0 0.0 0.0 0.0 28-29 0.05 0.0 0.0 0.0 0.0 30-31 0.05 0.0 0.0 0.0 0.0 32-33 0.075 0.0 0.0 0.0 0.0 34-35 0.075 0.0 0.0 0.0 0.0 36-37 0.075 0.0 0.0 0.0 0.0 38-39 0.075 0.0 0.0 0.0 0.0 40-41 0.075 0.0 0.0 0.0 0.0 42-43 0.075 0.0 0.0 0.0 0.0 44-45 0.075 0.0 0.0 0.0 0.0 46-47 0.0875 0.0 0.0 0.0 0.0 48-49 0.125 0.0 0.0 0.0 0.0 50-51 0.125 0.0 0.0 0.0 0.0 52-53 0.125 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 0.125 0.0 0.0 0.0 0.0 62-63 0.125 0.0 0.0 0.0 0.0 64-65 0.1375 0.0 0.0 0.0 0.0 66-67 0.15 0.0 0.0 0.0 0.0 68-69 0.2 0.0 0.0 0.0 0.0 70-71 0.21250000000000002 0.0 0.0 0.0 0.0 72-73 0.275 0.0 0.0 0.0 0.0 74-75 0.325 0.0 0.0 0.0 0.0 76-77 0.3375 0.0 0.0 0.0 0.0 78-79 0.4125 0.0 0.0 0.0 0.0 80-81 0.5 0.0 0.0 0.0 0.0 82-83 0.5874999999999999 0.0 0.0 0.0 0.0 84-85 0.6375 0.0 0.0 0.0 0.0 86-87 0.825 0.0 0.0 0.0 0.0 88-89 1.025 0.0 0.0 0.0 0.0 90-91 1.2374999999999998 0.0 0.0 0.0 0.0 92-93 1.35 0.0 0.0 0.0 0.0 94-95 1.8 0.0 0.0 0.0 0.0 96-97 2.0875 0.0 0.0 0.0 0.0 98-99 2.4375 0.0 0.0 0.0 0.0 100-101 3.0125 0.0 0.0 0.0 0.0 102-103 3.425 0.0 0.0 0.0 0.0 104-105 3.825 0.0 0.0 0.0 0.0 106-107 4.375 0.0 0.0 0.0 0.0 108-109 5.0125 0.0 0.0 0.0 0.0 110-111 5.7125 0.0 0.0 0.0 0.0 112-113 6.3375 0.0 0.0 0.0 0.0 114-115 7.262499999999999 0.0 0.0 0.0 0.0 116-117 8.075 0.0 0.0 0.0 0.0 118-119 8.7625 0.0 0.0 0.0 0.0 120-121 9.3875 0.0 0.0 0.0 0.0 122-123 10.125 0.0 0.0 0.0 0.0 124-125 10.8625 0.0 0.0 0.0 0.0 126-127 11.8125 0.0 0.0 0.0 0.0 128-129 12.587499999999999 0.0 0.0 0.0 0.0 130-131 13.425 0.0 0.0 0.0 0.0 132-133 14.475 0.0 0.0 0.0 0.0 134-135 15.5625 0.0 0.0 0.0 0.0 136-137 16.3625 0.0 0.0 0.0 0.0 138-139 17.35 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR7171083 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7171083_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 31.82425 33.0 33.0 34.0 27.0 34.0 2 32.6425 33.0 33.0 34.0 32.0 34.0 3 32.8735 33.0 33.0 34.0 32.0 34.0 4 32.9475 34.0 33.0 34.0 32.0 34.0 5 33.01725 34.0 33.0 34.0 33.0 34.0 6 37.23525 38.0 38.0 38.0 37.0 38.0 7 37.279 38.0 38.0 38.0 37.0 38.0 8 37.26575 38.0 38.0 38.0 37.0 38.0 9 37.2805 38.0 38.0 38.0 37.0 38.0 10-14 37.03275 38.0 38.0 38.0 36.6 38.0 15-19 37.1092 38.0 38.0 38.0 36.8 38.0 20-24 35.612300000000005 38.0 36.0 38.0 27.0 38.0 25-29 37.00345 38.0 38.0 38.0 36.6 38.0 30-34 37.164699999999996 38.0 38.0 38.0 37.0 38.0 35-39 37.12904999999999 38.0 38.0 38.0 37.0 38.0 40-44 37.0728 38.0 38.0 38.0 37.0 38.0 45-49 36.9205 38.0 38.0 38.0 37.0 38.0 50-54 36.427 38.0 37.8 38.0 34.0 38.0 55-59 36.846650000000004 38.0 38.0 38.0 36.2 38.0 60-64 36.86675 38.0 38.0 38.0 36.0 38.0 65-69 36.76885 38.0 38.0 38.0 36.0 38.0 70-74 36.75775 38.0 38.0 38.0 36.0 38.0 75-79 36.70455 38.0 38.0 38.0 36.0 38.0 80-84 35.5794 38.0 37.0 38.0 29.6 38.0 85-89 36.2509 38.0 38.0 38.0 34.8 38.0 90-94 36.3249 38.0 38.0 38.0 35.0 38.0 95-99 36.178700000000006 38.0 38.0 38.0 34.2 38.0 100-104 35.98485 38.0 38.0 38.0 33.8 38.0 105-109 35.233799999999995 38.0 37.0 38.0 27.8 38.0 110-114 35.42985 38.0 37.0 38.0 31.0 38.0 115-119 35.34435 38.0 37.0 38.0 31.0 38.0 120-124 35.060700000000004 38.0 36.6 38.0 30.2 38.0 125-129 34.872550000000004 38.0 36.2 38.0 29.0 38.0 130-134 34.0778 38.0 34.8 38.0 24.0 38.0 135-139 33.50275 38.0 33.6 38.0 20.6 38.0 140-144 32.6568 38.0 33.0 38.0 15.0 38.0 145-149 31.82455 38.0 33.0 38.0 8.4 38.0 150-151 25.775 33.0 17.5 37.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 7.0 3 8.0 4 6.0 5 7.0 6 2.0 7 1.0 8 3.0 9 2.0 10 0.0 11 1.0 12 1.0 13 3.0 14 3.0 15 3.0 16 1.0 17 8.0 18 12.0 19 15.0 20 14.0 21 6.0 22 7.0 23 6.0 24 12.0 25 20.0 26 17.0 27 19.0 28 31.0 29 29.0 30 54.0 31 71.0 32 74.0 33 103.0 34 163.0 35 319.0 36 792.0 37 2180.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 40.550000000000004 19.900000000000002 13.975000000000001 25.575 2 27.925 24.525 30.599999999999998 16.950000000000003 3 21.975 27.025 32.25 18.75 4 24.8 34.225 22.400000000000002 18.575 5 27.625 35.525 20.4 16.45 6 21.575 38.5 22.925 17.0 7 21.2 19.225 39.900000000000006 19.675 8 22.175 24.375 27.825 25.624999999999996 9 24.474999999999998 25.2 27.725 22.6 10-14 25.44 27.49 25.665 21.404999999999998 15-19 24.9 27.325 27.015 20.76 20-24 26.040000000000003 27.02 26.51 20.43 25-29 24.7 28.09 27.095000000000002 20.115 30-34 25.145 27.834999999999997 27.27 19.75 35-39 24.93 27.189999999999998 27.63 20.25 40-44 24.97 27.650000000000002 28.005000000000003 19.375 45-49 24.884999999999998 27.015 27.845 20.255000000000003 50-54 25.025 26.919999999999998 27.865000000000002 20.19 55-59 24.404999999999998 26.955000000000002 28.360000000000003 20.28 60-64 24.775 26.57 28.645 20.01 65-69 24.545 26.865 29.145 19.445 70-74 24.75 27.395000000000003 28.194999999999997 19.66 75-79 24.52 27.634999999999998 28.375 19.470000000000002 80-84 24.05 28.694999999999997 27.73 19.525000000000002 85-89 24.884999999999998 28.015 28.310000000000002 18.790000000000003 90-94 24.7 27.195000000000004 28.895 19.21 95-99 24.505 27.42 29.049999999999997 19.025 100-104 25.240000000000002 27.57 28.235 18.955 105-109 24.43 27.750000000000004 28.29 19.53 110-114 25.255 27.54 28.115000000000002 19.09 115-119 25.935000000000002 28.005000000000003 27.800000000000004 18.26 120-124 25.759999999999998 28.115000000000002 28.065 18.060000000000002 125-129 25.779999999999998 27.735 28.345 18.14 130-134 26.729999999999997 27.089999999999996 27.905 18.275 135-139 26.455000000000002 27.83 27.295 18.42 140-144 27.02 27.99 27.325 17.665 145-149 26.939999999999998 27.855 27.305 17.9 150-151 27.91046642490934 26.84756783793923 27.32274602976116 17.919219707390273 >>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 0.5 7 1.0 8 0.5 9 0.0 10 1.0 11 1.0 12 0.0 13 0.0 14 0.0 15 0.5 16 0.5 17 0.5 18 2.0 19 2.0 20 0.5 21 0.5 22 1.5 23 2.0 24 1.5 25 2.0 26 5.0 27 6.0 28 7.0 29 16.0 30 20.0 31 30.0 32 39.0 33 50.5 34 70.0 35 81.5 36 89.0 37 114.0 38 135.5 39 151.5 40 185.0 41 191.0 42 195.5 43 222.0 44 229.0 45 218.5 46 221.0 47 221.5 48 190.0 49 173.5 50 171.0 51 145.5 52 123.0 53 118.5 54 120.0 55 102.5 56 77.0 57 61.5 58 47.0 59 36.5 60 30.5 61 26.5 62 26.5 63 17.0 64 6.5 65 2.0 66 2.0 67 2.5 68 1.0 69 0.5 70 0.0 71 0.0 72 0.5 73 0.5 74 0.0 75 0.5 76 1.0 77 0.5 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 0.0 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 0.0375 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 96.45 #Duplication Level Percentage of deduplicated Percentage of total 1 98.0300673924313 94.55 2 1.2960082944530846 2.5 3 0.336962156557802 0.975 4 0.2592016588906169 1.0 5 0.02592016588906169 0.125 6 0.02592016588906169 0.15 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.02592016588906169 0.7000000000000001 >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 GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGGCTATAGTGTAGATCT 28 0.7000000000000001 Illumina Single End PCR Primer 1 (97% over 34bp) CTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAA 6 0.15 No Hit GGGAGACACACGGCGGGTGCTAACGTCCGTCGTGAAGAGGGAAACAACCC 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 0.05 0.0 0.0 0.0 0.0 2 0.05 0.0 0.0 0.0 0.0 3 0.05 0.0 0.0 0.0 0.0 4 0.05 0.0 0.0 0.0 0.0 5 0.05 0.0 0.0 0.0 0.0 6 0.05 0.0 0.0 0.0 0.0 7 0.05 0.0 0.0 0.0 0.0 8 0.05 0.0 0.0 0.0 0.0 9 0.05 0.0 0.0 0.0 0.0 10-11 0.05 0.0 0.0 0.0 0.0 12-13 0.05 0.0 0.0 0.0 0.0 14-15 0.05 0.0 0.0 0.0 0.0 16-17 0.05 0.0 0.0 0.0 0.0 18-19 0.05 0.0 0.0 0.0 0.0 20-21 0.05 0.0 0.0 0.0 0.0 22-23 0.05 0.0 0.0 0.0 0.0 24-25 0.05 0.0 0.0 0.0 0.0 26-27 0.05 0.0 0.0 0.0 0.0 28-29 0.05 0.0 0.0 0.0 0.0 30-31 0.05 0.0 0.0 0.0 0.0 32-33 0.05 0.0 0.0 0.0 0.0 34-35 0.05 0.0 0.0 0.0 0.0 36-37 0.05 0.0 0.0 0.0 0.0 38-39 0.05 0.0 0.0 0.0 0.0 40-41 0.05 0.0 0.0 0.0 0.0 42-43 0.05 0.0 0.0 0.0 0.0 44-45 0.05 0.0 0.0 0.0 0.0 46-47 0.0625 0.0 0.0 0.0 0.0 48-49 0.1 0.0 0.0 0.0 0.0 50-51 0.1 0.0 0.0 0.0 0.0 52-53 0.1 0.0 0.0 0.0 0.0 54-55 0.1 0.0 0.0 0.0 0.0 56-57 0.1 0.0 0.0 0.0 0.0 58-59 0.1 0.0 0.0 0.0 0.0 60-61 0.1 0.0 0.0 0.0 0.0 62-63 0.1 0.0 0.0 0.0 0.0 64-65 0.1125 0.0 0.0 0.0 0.0 66-67 0.125 0.0 0.0 0.0 0.0 68-69 0.175 0.0 0.0 0.0 0.0 70-71 0.1875 0.0 0.0 0.0 0.0 72-73 0.2375 0.0 0.0 0.0 0.0 74-75 0.275 0.0 0.0 0.0 0.0 76-77 0.30000000000000004 0.0 0.0 0.0 0.0 78-79 0.35 0.0 0.0 0.0 0.0 80-81 0.42500000000000004 0.0 0.0 0.0 0.0 82-83 0.5125 0.0 0.0 0.0 0.0 84-85 0.5625 0.0 0.0 0.0 0.0 86-87 0.7375 0.0 0.0 0.0 0.0 88-89 0.925 0.0 0.0 0.0 0.0 90-91 1.1375000000000002 0.0 0.0 0.0 0.0 92-93 1.2875 0.0 0.0 0.0 0.0 94-95 1.7375 0.0 0.0 0.0 0.0 96-97 1.9625 0.0 0.0 0.0 0.0 98-99 2.275 0.0 0.0 0.0 0.0 100-101 2.8375000000000004 0.0 0.0 0.0 0.0 102-103 3.2375 0.0 0.0 0.0 0.0 104-105 3.6375 0.0 0.0 0.0 0.0 106-107 4.199999999999999 0.0 0.0 0.0 0.0 108-109 4.825 0.0 0.0 0.0 0.0 110-111 5.475 0.0 0.0 0.0 0.0 112-113 6.050000000000001 0.0 0.0 0.0 0.0 114-115 6.975 0.0 0.0 0.0 0.0 116-117 7.7625 0.0 0.0 0.0 0.0 118-119 8.462499999999999 0.0 0.0 0.0 0.0 120-121 9.1 0.0 0.0 0.0 0.0 122-123 9.8375 0.0 0.0 0.0 0.0 124-125 10.6125 0.0 0.0 0.0 0.0 126-127 11.5625 0.0 0.0 0.0 0.0 128-129 12.35 0.0 0.0 0.0 0.0 130-131 13.15 0.0 0.0 0.0 0.0 132-133 14.212499999999999 0.0 0.0 0.0 0.0 134-135 15.2625 0.0 0.0 0.0 0.0 136-137 16.0875 0.0 0.0 0.0 0.0 138-139 17.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TAACCGG 10 0.006830828 145.0 9 AATGGCT 10 0.006830828 145.0 5 ATTTGAA 10 0.006830828 145.0 6 >>END_MODULE Read 745800 spots for SRR7171083.sra Written 745800 spots for SRR7171083.sra Read 745800 spots for SRR7171083.sra Written 745800 spots for SRR7171083.sra Read 745800 spots for SRR7171083.sra Written 745800 spots for SRR7171083.sra Read 745800 spots for SRR7171083.sra Written 745800 spots for SRR7171083.sra Read 745800 spots for SRR7171083.sra Written 745800 spots for SRR7171083.sra Read 745800 spots for SRR7171083.sra Written 745800 spots for SRR7171083.sra Read 745800 spots for SRR7171083.sra Written 745800 spots for SRR7171083.sra Read 745800 spots for SRR7171083.sra Written 745800 spots for SRR7171083.sra Read 745800 spots for SRR7171083.sra Written 745800 spots for SRR7171083.sra Read 745800 spots for SRR7171083.sra Written 745800 spots for SRR7171083.sra Read 745800 spots for SRR7171083.sra Written 745800 spots for SRR7171083.sra Read 745800 spots for SRR7171083.sra Written 745800 spots for SRR7171083.sra Read 745800 spots for SRR7171083.sra Written 745800 spots for SRR7171083.sra Read 745800 spots for SRR7171083.sra Written 745800 spots for SRR7171083.sra Read 745800 spots for SRR7171083.sra Written 745800 spots for SRR7171083.sra Read 745800 spots for SRR7171083.sra Written 745800 spots for SRR7171083.sra Read 745806 spots for SRR7171083.sra Written 745806 spots for SRR7171083.sra Read 745800 spots for SRR7171083.sra Written 745800 spots for SRR7171083.sra Read 745800 spots for SRR7171083.sra Written 745800 spots for SRR7171083.sra Read 745800 spots for SRR7171083.sra Written 745800 spots for SRR7171083.sra SRR ids: ['SRR7171083.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_0eyatymv SRR7171083.sra spots: 14916006 blocks: [[1, 745800], [745801, 1491600], [1491601, 2237400], [2237401, 2983200], [2983201, 3729000], [3729001, 4474800], [4474801, 5220600], [5220601, 5966400], [5966401, 6712200], [6712201, 7458000], [7458001, 8203800], [8203801, 8949600], [8949601, 9695400], [9695401, 10441200], [10441201, 11187000], [11187001, 11932800], [11932801, 12678600], [12678601, 13424400], [13424401, 14170200], [14170201, 14916006]] SRR7171083 file size 5032844 SRR7171083 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 SRR7171083 SRR7171083_1.fastq SRR7171083_2.fastq Input file: SRR7171083_1.fastq Paired file: SRR7171083_2.fastq trimmed: SRR7171083-trimmed-pair1.fastq, SRR7171083-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 Fri Feb 14 02:16:18 2025 >> started Fri Feb 14 02:16:35 2025 >> done (16.507s) 14916006 read pairs processed; of these: 16742 ( 0.11%) short read pairs filtered out after trimming by size control 158384 ( 1.06%) empty read pairs filtered out after trimming by size control 14740880 (98.83%) read pairs available; of these: 9997535 (67.82%) trimmed read pairs available after processing 4743345 (32.18%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 7 0.00% 19 9 0.00% 20 9 0.00% 21 18 0.00% 22 15 0.00% 23 23 0.00% 24 24 0.00% 25 31 0.00% 26 36 0.00% 27 26 0.00% 28 33 0.00% 29 42 0.00% 30 38 0.00% 31 65 0.00% 32 45 0.00% 33 54 0.00% 34 47 0.00% 35 63 0.00% 36 61 0.00% 37 62 0.00% 38 64 0.00% 39 92 0.00% 40 79 0.00% 41 113 0.00% 42 117 0.00% 43 124 0.00% 44 116 0.00% 45 176 0.00% 46 236 0.00% 47 213 0.00% 48 250 0.00% 49 293 0.00% 50 336 0.00% 51 374 0.00% 52 436 0.00% 53 430 0.00% 54 449 0.00% 55 488 0.00% 56 604 0.00% 57 616 0.00% 58 707 0.00% 59 816 0.01% 60 931 0.01% 61 1091 0.01% 62 1197 0.01% 63 1364 0.01% 64 1540 0.01% 65 1586 0.01% 66 1686 0.01% 67 1902 0.01% 68 2095 0.01% 69 2364 0.02% 70 2885 0.02% 71 3191 0.02% 72 3670 0.02% 73 4251 0.03% 74 4645 0.03% 75 5573 0.04% 76 9256 0.06% 77 8151 0.06% 78 6848 0.05% 79 7665 0.05% 80 8203 0.06% 81 9152 0.06% 82 10450 0.07% 83 12165 0.08% 84 14842 0.10% 85 15723 0.11% 86 17294 0.12% 87 18826 0.13% 88 20951 0.14% 89 22217 0.15% 90 23145 0.16% 91 24637 0.17% 92 25613 0.17% 93 29344 0.20% 94 30140 0.20% 95 32864 0.22% 96 33688 0.23% 97 34142 0.23% 98 35440 0.24% 99 37204 0.25% 100 39690 0.27% 101 39468 0.27% 102 42448 0.29% 103 44384 0.30% 104 46690 0.32% 105 50844 0.34% 106 50623 0.34% 107 50768 0.34% 108 52657 0.36% 109 57015 0.39% 110 57992 0.39% 111 56616 0.38% 112 58511 0.40% 113 64749 0.44% 114 62943 0.43% 115 67276 0.46% 116 69249 0.47% 117 67402 0.46% 118 69762 0.47% 119 70745 0.48% 120 72210 0.49% 121 71620 0.49% 122 75101 0.51% 123 78183 0.53% 124 79006 0.54% 125 80210 0.54% 126 81846 0.56% 127 83355 0.57% 128 85759 0.58% 129 87759 0.60% 130 90077 0.61% 131 90537 0.61% 132 93814 0.64% 133 97121 0.66% 134 103315 0.70% 135 107269 0.73% 136 108959 0.74% 137 114847 0.78% 138 119519 0.81% 139 126091 0.86% 140 129524 0.88% 141 139596 0.95% 142 145161 0.98% 143 157200 1.07% 144 175562 1.19% 145 203152 1.38% 146 238799 1.62% 147 310343 2.11% 148 462446 3.14% 149 905112 6.14% 150 3628442 24.61% 151 4743345 32.18% 14740880 reads passed initial QC criterion=sequence-density sequence-density=0.31 sequence-density-rank=1 fanout-score=2.79 fanout-score-rank=35 prefix-density=0.79 prefix-fanout=1.1 sequence=CACTCGTCAGCGAAACAGCAAGCTGTTTCCTGTTACC criterion=fanout-score sequence-density=0.01 sequence-density-rank=43 fanout-score=65.11 fanout-score-rank=1 prefix-density=0.19 prefix-fanout=1.9 sequence=AGGTGATCCAACCGCAGGTTCCCCTACGGTTACCTTGTTACGACTTCACCCCAGTCATGAATCACAAAGTGGTAAGCGCCCTCCCGAAGGTTAAGCTACCTACTTCTTTTGCAACCCACTCCCATGGTGTGACGGGCGGTGTGTACAAGGCCCGGGAACGTATTCACCGTGGCATTCTGATCCACGATTACTAGCGATTCCGACTTCATGGAGTCGAGTTGCAGACTCCAATCCGGACTACGACGCACTTTATGAGGTCCGCTTGCTCTCGCGAGGTCGCTTCTCTTTGTATGCGCCATTGTAGCACGTGTGTAGCCCTGGTCGTAAGGGCCATGATGACTTGACGTCATCCCCACCTTCCTCCAGTTTATCACTGGCAGTCTCCTTTGAGTTCCCGGCCGGACCGCTGGCAACAAAGGATAAGGGTTGCGCTCGTTGCGGGACTTAACCCAACATTTCACAACACGAGCTGACGACAGCCATGCAGCACCTGTCTCACGGTTCCCGAAGG criterion=sequence-density sequence-density=1.21 sequence-density-rank=1 fanout-score=1.98 fanout-score-rank=35 prefix-density=1.23 prefix-fanout=2.0 sequence=GCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATG criterion=fanout-score sequence-density=0.05 sequence-density-rank=35 fanout-score=16.47 fanout-score-rank=1 prefix-density=0.32 prefix-fanout=2.6 sequence=GAAGCAAGCAAGGTTGTGTGCTTAAAAAGTATGGACGGCTCAT SRR7171083 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 14 02:17:22 Started mapping on | Feb 14 02:17:23 Finished on | Feb 14 02:20:49 Mapping speed, Million of reads per hour | 257.61 Number of input reads | 14740880 Average input read length | 284 UNIQUE READS: Uniquely mapped reads number | 12020226 Uniquely mapped reads % | 81.54% Average mapped length | 283.97 Number of splices: Total | 6748295 Number of splices: Annotated (sjdb) | 6539637 Number of splices: GT/AG | 6586420 Number of splices: GC/AG | 107204 Number of splices: AT/AC | 6837 Number of splices: Non-canonical | 47834 Mismatch rate per base, % | 0.50% Deletion rate per base | 0.04% Deletion average length | 2.43 Insertion rate per base | 0.04% Insertion average length | 2.13 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 399709 % of reads mapped to multiple loci | 2.71% Number of reads mapped to too many loci | 56766 % of reads mapped to too many loci | 0.39% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 15.04% % of reads unmapped: other | 0.32% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 2346076 2346076 2346076 N_multimapping 399709 399709 399709 N_noFeature 409383 11738273 502200 N_ambiguous 289799 1241 100586 UnstrandedReadsAssigned:11321044 PositiveStrandReadsAssigned:280712 NegativeStrandReadsAssigned:11417440 Dataset is classified negative stranded MeadianReadLen=150 20thPercentileLength=136 echo kmer=131 SRR7171083 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: SRR7171083-trimmed-pair1.fastq SRR7171083-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 14,740,880 reads, 11,536,877 reads pseudoaligned [quant] estimated average fragment length: 194.042 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,243 rounds 52401 SRR7171083.ke.tsv 34699 SRR7171083.se.tsv 87100 total ==> SRR7171083.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1824.96 631 28.1359 Potri.005G024800.1.v4.1 1035 841.958 287 27.738 Potri.004G059700.1.v4.1 961 767.958 5 0.529806 Potri.007G009000.2.v4.1 1416 1222.96 0 0 Potri.003G141000.2.v4.1 2943 2749.96 769.459 22.769 Potri.016G087400.1.v4.1 270 98.6444 463 381.938 Potri.015G069301.1.v4.1 564 371.711 0 0 Potri.010G195200.1.v4.1 1773 1579.96 416 21.4256 Potri.012G127500.1.v4.1 977 783.958 50 5.18993 ==> SRR7171083.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 126 Potri.001G233950.v4.1 1 Potri.001G122700.v4.1 467 Potri.001G212900.v4.1 8 Potri.001G182400.v4.1 2 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 2 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 3 SRR7171083 completed mapping pipeline successfully