Starting /dee2/code/volunteer_pipeline.sh SRR12670141 current disk space = 3057009577984 free memory = 1079265668 SRR12670141 SRAfilesize 2a0d743699d964faf2d269ef5cc0e3e7 SRR12670141.sra SRR12670141.sra file validated SRR12670141 is paired end SRR12670141 is conventional basespace SRR12670141 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670141_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 36.627 37.0 37.0 37.0 37.0 37.0 2 36.47025 37.0 37.0 37.0 37.0 37.0 3 36.664 37.0 37.0 37.0 37.0 37.0 4 36.6565 37.0 37.0 37.0 37.0 37.0 5 36.585 37.0 37.0 37.0 37.0 37.0 6 36.565 37.0 37.0 37.0 37.0 37.0 7 36.666 37.0 37.0 37.0 37.0 37.0 8 36.6 37.0 37.0 37.0 37.0 37.0 9 36.713 37.0 37.0 37.0 37.0 37.0 10-14 36.633300000000006 37.0 37.0 37.0 37.0 37.0 15-19 36.5938 37.0 37.0 37.0 37.0 37.0 20-24 36.5403 37.0 37.0 37.0 37.0 37.0 25-29 36.5279 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 36.4911 37.0 37.0 37.0 37.0 37.0 40-44 36.4728 37.0 37.0 37.0 37.0 37.0 45-49 36.433299999999996 37.0 37.0 37.0 37.0 37.0 50-54 36.428 37.0 37.0 37.0 37.0 37.0 55-59 36.415 37.0 37.0 37.0 37.0 37.0 60-64 36.3816 37.0 37.0 37.0 37.0 37.0 65-69 36.3409 37.0 37.0 37.0 37.0 37.0 70-74 36.2901 37.0 37.0 37.0 37.0 37.0 75-79 36.3285 37.0 37.0 37.0 37.0 37.0 80-84 36.243 37.0 37.0 37.0 37.0 37.0 85-89 36.2532 37.0 37.0 37.0 37.0 37.0 90-94 36.246399999999994 37.0 37.0 37.0 37.0 37.0 95-99 36.232 37.0 37.0 37.0 37.0 37.0 100-104 36.279399999999995 37.0 37.0 37.0 37.0 37.0 105-109 36.2127 37.0 37.0 37.0 37.0 37.0 110-114 36.1621 37.0 37.0 37.0 37.0 37.0 115-119 36.180099999999996 37.0 37.0 37.0 37.0 37.0 120-124 36.0924 37.0 37.0 37.0 37.0 37.0 125-129 36.065999999999995 37.0 37.0 37.0 37.0 37.0 130-134 36.0574 37.0 37.0 37.0 37.0 37.0 135-139 35.8914 37.0 37.0 37.0 37.0 37.0 140-144 35.794399999999996 37.0 37.0 37.0 37.0 37.0 145-149 35.67960000000001 37.0 37.0 37.0 37.0 37.0 150-151 35.38525 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 16 1.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 2.0 24 0.0 25 1.0 26 7.0 27 8.0 28 9.0 29 18.0 30 22.0 31 33.0 32 44.0 33 58.0 34 115.0 35 321.0 36 2943.0 37 418.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 41.55 10.825 5.7 41.925000000000004 2 19.11433575181386 12.459344508381285 37.45308981736302 30.97322992244183 3 18.625 15.275 28.249999999999996 37.85 4 21.475 23.325000000000003 22.925 32.275 5 23.0 29.925 25.324999999999996 21.75 6 20.549999999999997 32.925 24.325 22.2 7 16.35 27.125 39.875 16.650000000000002 8 16.7 24.15 33.825 25.324999999999996 9 18.15 23.225 35.825 22.8 10-14 20.04 29.375 27.37 23.215 15-19 20.275000000000002 26.965 28.315 24.445 20-24 20.025000000000002 28.775000000000002 27.279999999999998 23.919999999999998 25-29 20.44 27.839999999999996 27.905 23.815 30-34 20.055 28.505000000000003 27.32 24.12 35-39 20.095 28.634999999999998 27.515 23.755000000000003 40-44 20.294999999999998 27.755000000000003 27.99 23.96 45-49 20.685000000000002 28.125 27.38 23.810000000000002 50-54 20.31 27.74 28.395 23.555 55-59 20.544999999999998 27.644999999999996 27.71 24.099999999999998 60-64 20.535 27.74 27.694999999999997 24.03 65-69 20.79 28.4 27.860000000000003 22.95 70-74 20.419999999999998 28.349999999999998 27.089999999999996 24.14 75-79 21.099999999999998 27.589999999999996 28.015 23.294999999999998 80-84 20.674999999999997 27.77 27.93 23.625 85-89 21.515 28.405 26.735 23.345 90-94 20.74 28.055000000000003 27.894999999999996 23.31 95-99 20.86 28.470000000000002 27.485 23.185 100-104 21.845 28.34 26.015 23.799999999999997 105-109 21.17 28.535 26.424999999999997 23.87 110-114 21.59 28.325 26.334999999999997 23.75 115-119 20.605 28.73 26.095000000000002 24.57 120-124 21.345 28.505000000000003 25.795 24.355 125-129 21.165 28.955 25.965 23.915 130-134 21.415 27.77 25.82 24.995 135-139 20.775 28.225 25.979999999999997 25.019999999999996 140-144 21.365000000000002 27.694999999999997 25.555 25.385 145-149 22.015 27.365000000000002 24.834999999999997 25.785000000000004 150-151 21.712500000000002 27.3625 26.625 24.3 >>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 0.5 6 0.5 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 0.5 19 1.5 20 1.0 21 1.0 22 3.0 23 5.0 24 3.5 25 1.5 26 2.5 27 5.5 28 8.5 29 9.5 30 14.5 31 20.0 32 24.0 33 28.5 34 49.5 35 62.0 36 79.0 37 115.0 38 129.5 39 145.0 40 176.0 41 201.0 42 218.0 43 233.0 44 264.0 45 284.5 46 265.0 47 250.5 48 223.0 49 190.5 50 187.5 51 180.0 52 138.5 53 95.0 54 71.0 55 65.5 56 72.0 57 53.5 58 33.5 59 27.5 60 17.0 61 9.0 62 8.5 63 7.0 64 4.5 65 4.0 66 2.5 67 2.5 68 2.0 69 1.0 70 0.5 71 0.5 72 0.5 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 0.075 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 80.85 #Duplication Level Percentage of deduplicated Percentage of total 1 81.94186765615336 66.25 2 14.131106988249845 22.85 3 2.782931354359926 6.75 4 0.8348794063079777 2.7 5 0.15460729746444032 0.625 6 0.06184291898577613 0.3 7 0.0927643784786642 0.525 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 CTTTCTGGTACTGACTGGGAAAGCTGCGGCAGACTTGAGACCATTGAATG 7 0.17500000000000002 No Hit AGCACGATCCACACGATCCCTGGTCTTTGACGCTAGTAACGGCACCGTGG 7 0.17500000000000002 No Hit CCCCACTCAGCATCACACAGTCACTACCATCAAGAACTGCATTGGCAACA 7 0.17500000000000002 No Hit AGTTGTTGCATTGTAGCAAATTTAGTAGCAAAGCTCCTTCCCTTGACGAG 6 0.15 No Hit CTGGAAAGGTCTCTCCATGCAGTAAGCACCTGACACTCAAATCAAGAGTT 6 0.15 No Hit CCACCATCACTCTCTTGGGAAAACAATAAAGACTTGTACTTTTGAGCTTG 5 0.125 No Hit CTCTTCAAGTTGTCCCACTCAAAATCATTCTTACAGTACGCAGATCGAAC 5 0.125 No Hit GCCAAGAACTGTAATCGCAAGTATGCATCACAAATTTAAATGCCATGATG 5 0.125 No Hit CCCATTTAGCAGGATCCAGGCGAAATGCTTCCAGAGCACGCTTCTGACAT 5 0.125 No Hit GACCGGTCCAAGAGCCCATCCGGCAAGAAGATTCTTCTGTCAGGACCGTA 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.037500000000000006 0.0 0.0 0.0 0.0 60-61 0.0625 0.0 0.0 0.0 0.0 62-63 0.11249999999999999 0.0 0.0 0.0 0.0 64-65 0.175 0.0 0.0 0.0 0.0 66-67 0.2 0.0 0.0 0.0 0.0 68-69 0.32499999999999996 0.0 0.0 0.0 0.0 70-71 0.425 0.0 0.0 0.0 0.0 72-73 0.5 0.0 0.0 0.0 0.0 74-75 0.85 0.0 0.0 0.0 0.0 76-77 1.1125 0.0 0.0 0.0 0.0 78-79 1.3875 0.0 0.0 0.0 0.0 80-81 1.575 0.0 0.0 0.0 0.0 82-83 1.9125 0.0 0.0 0.0 0.0 84-85 2.3 0.0 0.0 0.0 0.0 86-87 2.625 0.0 0.0 0.0 0.0 88-89 3.05 0.0 0.0 0.0 0.0 90-91 3.4625 0.0 0.0 0.0 0.0 92-93 4.1375 0.0 0.0 0.0 0.0 94-95 4.825 0.0 0.0 0.0 0.0 96-97 5.512499999999999 0.0 0.0 0.0 0.0 98-99 6.300000000000001 0.0 0.0 0.0 0.0 100-101 6.887499999999999 0.0 0.0 0.0 0.0 102-103 7.9750000000000005 0.0 0.0 0.0 0.0 104-105 9.125 0.0 0.0 0.0 0.0 106-107 9.9 0.0 0.0 0.0 0.0 108-109 10.525 0.0 0.0 0.0 0.0 110-111 11.475000000000001 0.0 0.0 0.0 0.0 112-113 12.4 0.0 0.0 0.0 0.0 114-115 13.6 0.0 0.0 0.0 0.0 116-117 14.8 0.0 0.0 0.0 0.0 118-119 15.662500000000001 0.0 0.0 0.0 0.0 120-121 16.6875 0.0 0.0 0.0 0.0 122-123 17.674999999999997 0.0 0.0 0.0 0.0 124-125 18.75 0.0 0.0 0.0 0.0 126-127 19.6375 0.0 0.0 0.0 0.0 128-129 20.75 0.0 0.0 0.0 0.0 130-131 21.95 0.0 0.0 0.0 0.0 132-133 22.7875 0.0 0.0 0.0 0.0 134-135 23.65 0.0 0.0 0.0 0.0 136-137 24.5125 0.0 0.0 0.0 0.0 138-139 25.6875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR12670141 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670141_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 36.212 37.0 37.0 37.0 37.0 37.0 2 36.168 37.0 37.0 37.0 37.0 37.0 3 36.1655 37.0 37.0 37.0 37.0 37.0 4 36.2915 37.0 37.0 37.0 37.0 37.0 5 36.394 37.0 37.0 37.0 37.0 37.0 6 36.1605 37.0 37.0 37.0 37.0 37.0 7 36.3005 37.0 37.0 37.0 37.0 37.0 8 36.2925 37.0 37.0 37.0 37.0 37.0 9 36.3275 37.0 37.0 37.0 37.0 37.0 10-14 36.3362 37.0 37.0 37.0 37.0 37.0 15-19 36.349000000000004 37.0 37.0 37.0 37.0 37.0 20-24 36.2901 37.0 37.0 37.0 37.0 37.0 25-29 36.2999 37.0 37.0 37.0 37.0 37.0 30-34 36.2423 37.0 37.0 37.0 37.0 37.0 35-39 36.211 37.0 37.0 37.0 37.0 37.0 40-44 36.1395 37.0 37.0 37.0 37.0 37.0 45-49 36.1888 37.0 37.0 37.0 37.0 37.0 50-54 36.1466 37.0 37.0 37.0 37.0 37.0 55-59 36.101800000000004 37.0 37.0 37.0 37.0 37.0 60-64 36.1186 37.0 37.0 37.0 37.0 37.0 65-69 36.066500000000005 37.0 37.0 37.0 37.0 37.0 70-74 36.00580000000001 37.0 37.0 37.0 37.0 37.0 75-79 35.948 37.0 37.0 37.0 37.0 37.0 80-84 35.9645 37.0 37.0 37.0 37.0 37.0 85-89 35.962599999999995 37.0 37.0 37.0 37.0 37.0 90-94 35.9827 37.0 37.0 37.0 37.0 37.0 95-99 35.848099999999995 37.0 37.0 37.0 37.0 37.0 100-104 35.7965 37.0 37.0 37.0 37.0 37.0 105-109 35.7841 37.0 37.0 37.0 37.0 37.0 110-114 35.7116 37.0 37.0 37.0 37.0 37.0 115-119 35.6849 37.0 37.0 37.0 37.0 37.0 120-124 35.54600000000001 37.0 37.0 37.0 37.0 37.0 125-129 35.4477 37.0 37.0 37.0 37.0 37.0 130-134 35.26270000000001 37.0 37.0 37.0 34.6 37.0 135-139 35.119299999999996 37.0 37.0 37.0 29.8 37.0 140-144 34.7853 37.0 37.0 37.0 25.0 37.0 145-149 34.4632 37.0 37.0 37.0 25.0 37.0 150-151 34.260999999999996 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 2.0 14 4.0 15 2.0 16 2.0 17 1.0 18 0.0 19 1.0 20 2.0 21 1.0 22 2.0 23 4.0 24 6.0 25 7.0 26 6.0 27 13.0 28 14.0 29 17.0 30 33.0 31 37.0 32 72.0 33 118.0 34 227.0 35 580.0 36 2580.0 37 268.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 40.425 24.625 9.475 25.474999999999998 2 28.349999999999998 26.224999999999998 30.099999999999998 15.325 3 20.0 28.65 32.925 18.425 4 25.3 31.7 23.474999999999998 19.525000000000002 5 25.924999999999997 36.9 20.225 16.950000000000003 6 19.525000000000002 40.8 22.725 16.950000000000003 7 20.1 22.6 37.824999999999996 19.475 8 20.599999999999998 26.25 29.45 23.7 9 21.025 26.150000000000002 29.599999999999998 23.225 10-14 24.044999999999998 28.854999999999997 25.985000000000003 21.115000000000002 15-19 23.799999999999997 27.825 27.894999999999996 20.48 20-24 23.66 28.26 27.175 20.905 25-29 22.78 28.685 27.455000000000002 21.08 30-34 23.305 28.305000000000003 27.37 21.02 35-39 23.865 27.97 27.389999999999997 20.775 40-44 23.599999999999998 28.294999999999998 27.3 20.805 45-49 22.57 28.57 27.555000000000003 21.305 50-54 23.555 27.555000000000003 27.625 21.265 55-59 23.68 27.22 27.229999999999997 21.87 60-64 23.28 28.54 27.605 20.575 65-69 23.175 28.310000000000002 27.48 21.035 70-74 23.53 27.700000000000003 27.400000000000002 21.37 75-79 23.674999999999997 27.85 27.16 21.315 80-84 24.255 27.875 27.29 20.580000000000002 85-89 23.955000000000002 28.34 27.18 20.525 90-94 24.625 28.165000000000003 26.784999999999997 20.424999999999997 95-99 25.355 28.82 25.580000000000002 20.244999999999997 100-104 25.25 28.189999999999998 26.195 20.365 105-109 25.490000000000002 27.634999999999998 26.810000000000002 20.064999999999998 110-114 26.235000000000003 28.57 25.624999999999996 19.57 115-119 27.015 28.044999999999998 25.525 19.415 120-124 27.224999999999998 28.134999999999998 25.590000000000003 19.05 125-129 28.48 27.834999999999997 24.474999999999998 19.21 130-134 27.779999999999998 28.275 24.905 19.040000000000003 135-139 28.87 27.43 25.34 18.360000000000003 140-144 31.064999999999998 26.51 24.265 18.16 145-149 32.29 26.985 23.46 17.265 150-151 34.0 25.0125 23.5875 17.4 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.5 2 0.5 3 0.5 4 0.5 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.5 11 1.5 12 1.5 13 0.5 14 0.0 15 0.5 16 0.5 17 1.0 18 2.0 19 2.0 20 1.0 21 0.5 22 1.0 23 1.0 24 1.0 25 2.0 26 2.5 27 4.0 28 7.5 29 9.0 30 10.0 31 18.0 32 22.5 33 29.0 34 43.5 35 64.0 36 85.0 37 99.5 38 125.0 39 150.5 40 188.5 41 229.5 42 261.5 43 278.5 44 264.0 45 266.0 46 272.5 47 255.0 48 222.0 49 197.5 50 174.5 51 136.5 52 106.0 53 94.5 54 85.0 55 63.5 56 48.0 57 40.0 58 26.0 59 20.0 60 22.0 61 13.0 62 8.5 63 7.0 64 2.5 65 1.5 66 2.0 67 1.0 68 0.0 69 1.0 70 1.5 71 1.5 72 2.0 73 3.0 74 2.5 75 0.5 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 0.5 87 0.5 88 0.5 89 0.5 90 0.0 91 0.5 92 0.5 93 0.0 94 0.5 95 1.5 96 1.5 97 0.5 98 0.0 99 1.5 100 3.0 >>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 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 81.15 #Duplication Level Percentage of deduplicated Percentage of total 1 82.56315465187923 67.0 2 13.555144793592113 22.0 3 2.7418361059765863 6.675000000000001 4 0.7393715341959335 2.4 5 0.21565003080714723 0.8750000000000001 6 0.030807147258163897 0.15 7 0.12322858903265559 0.7000000000000001 8 0.030807147258163897 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 CATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAATCAA 8 0.2 No Hit GTAGAAATGACCGATATGTTGATAACCACAAAAGGAAATTTGCAGAGCAG 7 0.17500000000000002 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 7 0.17500000000000002 No Hit ATTCGGCAAAAATTATGCGACTCAAGAGGAACATGATTACCGATTTAGTG 7 0.17500000000000002 No Hit GAAAGTGATGATCTACAAGTGCAACATCCAAGGAAAACCAGTTGTCACTG 7 0.17500000000000002 No Hit GATGGCTTCCTCCTCTATGATCTCATCGGCAGCCGTTGCCACCGTCAACC 6 0.15 No Hit AAGAGATATGGCTTCCCTGGCAGCATCCAGAGCAGCTGCCTCCCTTGGAG 5 0.125 No Hit AGGCTTACACGACCGAGTTGGAACTTAAAGTTGCTCTGTTAGGAGAGGAG 5 0.125 No Hit GGCTTGAGCTTATACCCTCAGAGAACTTCACCTCCGTATCAGTGATGCAA 5 0.125 No Hit GAATCTTCTAGGCATAAGGGTTTGGCTATGCGAATCTTAGAGCTGCTGTA 5 0.125 No Hit AGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAA 5 0.125 No Hit GTCCTTTTATCCATGGCTACCTCTTTATCTCTCCCAAACTTCCTCTCCTT 5 0.125 No Hit GGAGGATGGAGTTGGAGGCTGAGTTGACTCGAATGATGCTGCAGACTCGG 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.037500000000000006 0.0 0.0 0.0 0.0 60-61 0.0625 0.0 0.0 0.0 0.0 62-63 0.11249999999999999 0.0 0.0 0.0 0.0 64-65 0.175 0.0 0.0 0.0 0.0 66-67 0.2 0.0 0.0 0.0 0.0 68-69 0.32499999999999996 0.0 0.0 0.0 0.0 70-71 0.425 0.0 0.0 0.0 0.0 72-73 0.5 0.0 0.0 0.0 0.0 74-75 0.85 0.0 0.0 0.0 0.0 76-77 1.125 0.0 0.0 0.0 0.0 78-79 1.4375 0.0 0.0 0.0 0.0 80-81 1.675 0.0 0.0 0.0 0.0 82-83 2.0125 0.0 0.0 0.0 0.0 84-85 2.4 0.0 0.0 0.0 0.0 86-87 2.7375 0.0 0.0 0.0 0.0 88-89 3.175 0.0 0.0 0.0 0.0 90-91 3.5875 0.0 0.0 0.0 0.0 92-93 4.275 0.0 0.0 0.0 0.0 94-95 4.975 0.0 0.0 0.0 0.0 96-97 5.625 0.0 0.0 0.0 0.0 98-99 6.4125 0.0 0.0 0.0 0.0 100-101 6.987500000000001 0.0 0.0 0.0 0.0 102-103 8.075 0.0 0.0 0.0 0.0 104-105 9.225000000000001 0.0 0.0 0.0 0.0 106-107 10.0125 0.0 0.0 0.0 0.0 108-109 10.6375 0.0 0.0 0.0 0.0 110-111 11.600000000000001 0.0 0.0 0.0 0.0 112-113 12.5375 0.0 0.0 0.0 0.0 114-115 13.787500000000001 0.0 0.0 0.0 0.0 116-117 15.0625 0.0 0.0 0.0 0.0 118-119 15.9375 0.0 0.0 0.0 0.0 120-121 16.9625 0.0 0.0 0.0 0.0 122-123 17.9375 0.0 0.0 0.0 0.0 124-125 19.0125 0.0 0.0 0.0 0.0 126-127 19.9375 0.0 0.0 0.0 0.0 128-129 21.0875 0.0 0.0 0.0 0.0 130-131 22.3875 0.0 0.0 0.0 0.0 132-133 23.299999999999997 0.0 0.0 0.0 0.0 134-135 24.175 0.0 0.0 0.0 0.0 136-137 25.0375 0.0 0.0 0.0 0.0 138-139 26.2125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ATCCTAC 10 0.006830828 145.0 9 ATTAGCA 10 0.006830828 145.0 1 AAGATCG 10 0.006830828 145.0 145 GGGGGGG 170 6.849629E-5 9.382353 140-144 >>END_MODULE Read 546799 spots for SRR12670141.sra Written 546799 spots for SRR12670141.sra Read 546799 spots for SRR12670141.sra Written 546799 spots for SRR12670141.sra Read 546799 spots for SRR12670141.sra Written 546799 spots for SRR12670141.sra Read 546799 spots for SRR12670141.sra Written 546799 spots for SRR12670141.sra Read 546799 spots for SRR12670141.sra Written 546799 spots for SRR12670141.sra Read 546799 spots for SRR12670141.sra Written 546799 spots for SRR12670141.sra Read 546799 spots for SRR12670141.sra Written 546799 spots for SRR12670141.sra Read 546799 spots for SRR12670141.sra Written 546799 spots for SRR12670141.sra Read 546799 spots for SRR12670141.sra Written 546799 spots for SRR12670141.sra Read 546799 spots for SRR12670141.sra Written 546799 spots for SRR12670141.sra Read 546799 spots for SRR12670141.sra Written 546799 spots for SRR12670141.sra Read 546799 spots for SRR12670141.sra Written 546799 spots for SRR12670141.sra Read 546799 spots for SRR12670141.sra Written 546799 spots for SRR12670141.sra Read 546799 spots for SRR12670141.sra Written 546799 spots for SRR12670141.sra Read 546804 spots for SRR12670141.sra Written 546804 spots for SRR12670141.sra Read 546799 spots for SRR12670141.sra Written 546799 spots for SRR12670141.sra Read 546799 spots for SRR12670141.sra Written 546799 spots for SRR12670141.sra Read 546799 spots for SRR12670141.sra Written 546799 spots for SRR12670141.sra Read 546799 spots for SRR12670141.sra Written 546799 spots for SRR12670141.sra Read 546799 spots for SRR12670141.sra Written 546799 spots for SRR12670141.sra SRR ids: ['SRR12670141.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_mcv00f7y SRR12670141.sra spots: 10935985 blocks: [[1, 546799], [546800, 1093598], [1093599, 1640397], [1640398, 2187196], [2187197, 2733995], [2733996, 3280794], [3280795, 3827593], [3827594, 4374392], [4374393, 4921191], [4921192, 5467990], [5467991, 6014789], [6014790, 6561588], [6561589, 7108387], [7108388, 7655186], [7655187, 8201985], [8201986, 8748784], [8748785, 9295583], [9295584, 9842382], [9842383, 10389181], [10389182, 10935985]] SRR12670141 file size 3694825 SRR12670141 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 SRR12670141 SRR12670141_1.fastq SRR12670141_2.fastq Input file: SRR12670141_1.fastq Paired file: SRR12670141_2.fastq trimmed: SRR12670141-trimmed-pair1.fastq, SRR12670141-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 01:25:20 2025 >> started Tue Feb 11 01:25:32 2025 >> done (12.282s) 10935985 read pairs processed; of these: 57 ( 0.00%) short read pairs filtered out after trimming by size control 4796 ( 0.04%) empty read pairs filtered out after trimming by size control 10931132 (99.96%) read pairs available; of these: 3384422 (30.96%) trimmed read pairs available after processing 7546710 (69.04%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 2 0.00% 19 3 0.00% 20 5 0.00% 21 7 0.00% 22 13 0.00% 23 17 0.00% 24 16 0.00% 25 30 0.00% 26 31 0.00% 27 29 0.00% 28 33 0.00% 29 54 0.00% 30 51 0.00% 31 53 0.00% 32 81 0.00% 33 59 0.00% 34 63 0.00% 35 89 0.00% 36 80 0.00% 37 91 0.00% 38 117 0.00% 39 138 0.00% 40 181 0.00% 41 149 0.00% 42 188 0.00% 43 190 0.00% 44 218 0.00% 45 209 0.00% 46 267 0.00% 47 314 0.00% 48 371 0.00% 49 455 0.00% 50 574 0.01% 51 539 0.00% 52 663 0.01% 53 641 0.01% 54 683 0.01% 55 804 0.01% 56 891 0.01% 57 1103 0.01% 58 1274 0.01% 59 1385 0.01% 60 1796 0.02% 61 1913 0.02% 62 2218 0.02% 63 2503 0.02% 64 2599 0.02% 65 2853 0.03% 66 3252 0.03% 67 3563 0.03% 68 3921 0.04% 69 4566 0.04% 70 5036 0.05% 71 5796 0.05% 72 6850 0.06% 73 7477 0.07% 74 8336 0.08% 75 9044 0.08% 76 9802 0.09% 77 10451 0.10% 78 11457 0.10% 79 12394 0.11% 80 13516 0.12% 81 15383 0.14% 82 17106 0.16% 83 18545 0.17% 84 20247 0.19% 85 22217 0.20% 86 22977 0.21% 87 24446 0.22% 88 25490 0.23% 89 26349 0.24% 90 27808 0.25% 91 29868 0.27% 92 31378 0.29% 93 33730 0.31% 94 35392 0.32% 95 37703 0.34% 96 38074 0.35% 97 39602 0.36% 98 39811 0.36% 99 40968 0.37% 100 41768 0.38% 101 42200 0.39% 102 43784 0.40% 103 45135 0.41% 104 46883 0.43% 105 47794 0.44% 106 48875 0.45% 107 49578 0.45% 108 49730 0.45% 109 49669 0.45% 110 49237 0.45% 111 49862 0.46% 112 50951 0.47% 113 51694 0.47% 114 52525 0.48% 115 53385 0.49% 116 54472 0.50% 117 55141 0.50% 118 55257 0.51% 119 54596 0.50% 120 54769 0.50% 121 54708 0.50% 122 55040 0.50% 123 55053 0.50% 124 55749 0.51% 125 55456 0.51% 126 56796 0.52% 127 56921 0.52% 128 56609 0.52% 129 56077 0.51% 130 56008 0.51% 131 55122 0.50% 132 54232 0.50% 133 55023 0.50% 134 54907 0.50% 135 55251 0.51% 136 55135 0.50% 137 54391 0.50% 138 55315 0.51% 139 55731 0.51% 140 54983 0.50% 141 54925 0.50% 142 54160 0.50% 143 53785 0.49% 144 54470 0.50% 145 54038 0.49% 146 53636 0.49% 147 53923 0.49% 148 54112 0.50% 149 53365 0.49% 150 53598 0.49% 151 7546710 69.04% 10931132 reads passed initial QC criterion=sequence-density sequence-density=0.31 sequence-density-rank=1 fanout-score=2.01 fanout-score-rank=25 prefix-density=0.31 prefix-fanout=2.0 sequence=CGGTAGACCCAACCTTTCTCCAACTCGAATTCCAAGCAAGGAACCCACTT criterion=fanout-score sequence-density=0.03 sequence-density-rank=32 fanout-score=33.35 fanout-score-rank=1 prefix-density=0.12 prefix-fanout=8.5 sequence=AATGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGTTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGGAGTATGAATGTGTTCTCTGTGT criterion=sequence-density sequence-density=0.43 sequence-density-rank=1 fanout-score=2.03 fanout-score-rank=34 prefix-density=0.43 prefix-fanout=2.0 sequence=TGTAAGAGATGGCTTCCTC criterion=fanout-score sequence-density=0.13 sequence-density-rank=26 fanout-score=29.47 fanout-score-rank=1 prefix-density=0.34 prefix-fanout=11.0 sequence=AAAGAAAAGAAAA SRR12670141 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 01:26:13 Started mapping on | Feb 11 01:26:13 Finished on | Feb 11 01:27:26 Mapping speed, Million of reads per hour | 539.07 Number of input reads | 10931132 Average input read length | 281 UNIQUE READS: Uniquely mapped reads number | 10128926 Uniquely mapped reads % | 92.66% Average mapped length | 280.16 Number of splices: Total | 9501265 Number of splices: Annotated (sjdb) | 9268475 Number of splices: GT/AG | 9306294 Number of splices: GC/AG | 153212 Number of splices: AT/AC | 6309 Number of splices: Non-canonical | 35450 Mismatch rate per base, % | 0.37% Deletion rate per base | 0.03% Deletion average length | 2.92 Insertion rate per base | 0.02% Insertion average length | 2.41 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 259404 % of reads mapped to multiple loci | 2.37% Number of reads mapped to too many loci | 195518 % of reads mapped to too many loci | 1.79% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.90% % of reads unmapped: other | 0.28% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 542802 542802 542802 N_multimapping 259404 259404 259404 N_noFeature 464191 9972738 536643 N_ambiguous 149357 715 65179 UnstrandedReadsAssigned:9515378 PositiveStrandReadsAssigned:155473 NegativeStrandReadsAssigned:9527104 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=128 echo kmer=123 SRR12670141 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: SRR12670141-trimmed-pair1.fastq SRR12670141-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 10,931,132 reads, 9,660,829 reads pseudoaligned [quant] estimated average fragment length: 199.658 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,045 rounds 52401 SRR12670141.ke.tsv 34699 SRR12670141.se.tsv 87100 total ==> SRR12670141.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1819.34 427 24.0721 Potri.005G024800.1.v4.1 1035 836.342 158 19.3764 Potri.004G059700.1.v4.1 961 762.388 9 1.21079 Potri.007G009000.2.v4.1 1416 1217.34 0 0 Potri.003G141000.2.v4.1 2943 2744.34 548.485 20.4987 Potri.016G087400.1.v4.1 270 112.74 397 361.172 Potri.015G069301.1.v4.1 564 372.593 0 0 Potri.010G195200.1.v4.1 1773 1574.34 89 5.79818 Potri.012G127500.1.v4.1 977 778.384 73 9.619 ==> SRR12670141.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 161 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 176 Potri.001G212900.v4.1 16 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 19 Potri.001G416900.v4.1 4 Potri.001G452600.v4.1 0 SRR12670141 completed mapping pipeline successfully