Starting /dee2/code/volunteer_pipeline.sh SRR12670109 current disk space = 3057553707008 free memory = 1217392048 SRR12670109 SRAfilesize 4569804220cebda41c5e2ff86ed23603 SRR12670109.sra SRR12670109.sra file validated SRR12670109 is paired end SRR12670109 is conventional basespace SRR12670109 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670109_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 36.5695 37.0 37.0 37.0 37.0 37.0 2 36.5555 37.0 37.0 37.0 37.0 37.0 3 36.696 37.0 37.0 37.0 37.0 37.0 4 36.716 37.0 37.0 37.0 37.0 37.0 5 36.649 37.0 37.0 37.0 37.0 37.0 6 36.704 37.0 37.0 37.0 37.0 37.0 7 36.6535 37.0 37.0 37.0 37.0 37.0 8 36.733 37.0 37.0 37.0 37.0 37.0 9 36.666 37.0 37.0 37.0 37.0 37.0 10-14 36.6637 37.0 37.0 37.0 37.0 37.0 15-19 36.6391 37.0 37.0 37.0 37.0 37.0 20-24 36.6447 37.0 37.0 37.0 37.0 37.0 25-29 36.6128 37.0 37.0 37.0 37.0 37.0 30-34 36.5856 37.0 37.0 37.0 37.0 37.0 35-39 36.5548 37.0 37.0 37.0 37.0 37.0 40-44 36.5705 37.0 37.0 37.0 37.0 37.0 45-49 36.5287 37.0 37.0 37.0 37.0 37.0 50-54 36.50789999999999 37.0 37.0 37.0 37.0 37.0 55-59 36.497 37.0 37.0 37.0 37.0 37.0 60-64 36.500600000000006 37.0 37.0 37.0 37.0 37.0 65-69 36.4899 37.0 37.0 37.0 37.0 37.0 70-74 36.4416 37.0 37.0 37.0 37.0 37.0 75-79 36.4349 37.0 37.0 37.0 37.0 37.0 80-84 36.4559 37.0 37.0 37.0 37.0 37.0 85-89 36.3891 37.0 37.0 37.0 37.0 37.0 90-94 36.360699999999994 37.0 37.0 37.0 37.0 37.0 95-99 36.358799999999995 37.0 37.0 37.0 37.0 37.0 100-104 36.382 37.0 37.0 37.0 37.0 37.0 105-109 36.35329999999999 37.0 37.0 37.0 37.0 37.0 110-114 36.2678 37.0 37.0 37.0 37.0 37.0 115-119 36.2945 37.0 37.0 37.0 37.0 37.0 120-124 36.280499999999996 37.0 37.0 37.0 37.0 37.0 125-129 36.1774 37.0 37.0 37.0 37.0 37.0 130-134 36.1735 37.0 37.0 37.0 37.0 37.0 135-139 36.1022 37.0 37.0 37.0 37.0 37.0 140-144 36.0308 37.0 37.0 37.0 37.0 37.0 145-149 35.9846 37.0 37.0 37.0 37.0 37.0 150-151 35.848749999999995 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 22 1.0 23 1.0 24 1.0 25 1.0 26 2.0 27 5.0 28 8.0 29 10.0 30 15.0 31 23.0 32 38.0 33 54.0 34 75.0 35 251.0 36 3069.0 37 446.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 37.1 12.55 6.45 43.9 2 18.828242363545318 12.99449173760641 36.12919379068603 32.048072108162245 3 17.474999999999998 16.35 26.150000000000002 40.025 4 20.599999999999998 23.25 23.625 32.525 5 21.875 30.65 25.275 22.2 6 19.525000000000002 34.4 24.775 21.3 7 16.6 26.075 40.875 16.45 8 19.475 24.825 32.875 22.825 9 18.224999999999998 24.725 34.25 22.8 10-14 19.259999999999998 29.515 27.99 23.235 15-19 19.885 28.34 27.560000000000002 24.215 20-24 20.294999999999998 28.715000000000003 27.775 23.215 25-29 19.415 27.325 28.345 24.915000000000003 30-34 19.725 28.389999999999997 27.584999999999997 24.3 35-39 19.935 28.225 27.41 24.43 40-44 20.24 28.389999999999997 27.35 24.02 45-49 19.765 28.17 27.41 24.654999999999998 50-54 19.555 27.91 27.279999999999998 25.255 55-59 19.955000000000002 28.015 27.905 24.125 60-64 19.994999999999997 28.01 27.605 24.39 65-69 19.99 28.349999999999998 27.51 24.15 70-74 20.26 28.535 27.36 23.845 75-79 19.93 27.775 27.655 24.64 80-84 20.474999999999998 27.675 27.73 24.12 85-89 19.825 27.63 28.255000000000003 24.29 90-94 20.8 27.625 27.315 24.26 95-99 19.595000000000002 28.105000000000004 27.55 24.75 100-104 20.424999999999997 28.01 27.445000000000004 24.12 105-109 20.555 28.105000000000004 27.284999999999997 24.055 110-114 20.580000000000002 28.355000000000004 27.36 23.705000000000002 115-119 20.95 27.944999999999997 27.155 23.95 120-124 20.805 28.199999999999996 26.85 24.145 125-129 20.865000000000002 28.904999999999998 25.96 24.27 130-134 21.715 28.23 25.91 24.145 135-139 20.665 28.705000000000002 26.205000000000002 24.425 140-144 21.475 28.53 26.125 23.87 145-149 21.765 27.67 26.455000000000002 24.11 150-151 20.8875 27.85 26.35 24.9125 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.5 19 0.5 20 1.0 21 2.0 22 2.0 23 1.0 24 0.0 25 0.5 26 1.5 27 5.0 28 8.0 29 10.0 30 10.0 31 9.5 32 18.0 33 27.5 34 42.5 35 70.0 36 90.0 37 107.5 38 131.5 39 161.5 40 189.5 41 217.0 42 238.0 43 230.5 44 246.0 45 281.0 46 256.0 47 237.5 48 250.5 49 225.0 50 184.0 51 152.0 52 125.0 53 103.0 54 89.5 55 71.0 56 60.5 57 52.0 58 30.5 59 20.0 60 13.0 61 9.5 62 8.0 63 4.0 64 2.5 65 1.5 66 1.0 67 0.0 68 0.0 69 0.0 70 0.0 71 0.0 72 1.0 73 1.0 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 0.15 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 79.725 #Duplication Level Percentage of deduplicated Percentage of total 1 81.4989024772656 64.97500000000001 2 13.48385073690812 21.5 3 3.6375039197240513 8.7 4 1.0034493571652556 3.2 5 0.3449357165255566 1.375 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.03135779241141424 0.25 >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 GTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACC 10 0.25 No Hit GTCGCGTTCTTCAAAGGGGAAAATACCAGACGCATTCCAGGAAACAACAG 5 0.125 No Hit GGTTCACATCCATGGGAGTACTGCCACAAGTGCTGGTGGTGTAAACTCCT 5 0.125 No Hit GGGAATTCTGATGTCCTCTCTGAACACAGTTGAAGAGCTTGGCATCTTTG 5 0.125 No Hit CTCTGATCAGGAGCTATTTCAGTTCTTGCACGAAATTGGCCCGGTTCATT 5 0.125 No Hit CCCTCTGTTCCGGGCCAGTGAAGAGCCCGCACATAAAAGCATGCGCCTTA 5 0.125 No Hit ACCCAATGAAGACAAGAATCAACCACGATCTTCCATGATAACTAGGTAGA 5 0.125 No Hit GCCATCATTTCCAAAACATCAAGGCGCTCGAGCAACAAGCAACAAACAAC 5 0.125 No Hit CCACACCAGAGGCCACAGACATGGCCAATACATAACAATGAAGAAGACAC 5 0.125 No Hit GCTCCAAGTCAGAAATATCACCTTGATAACGCTTCAGGAAAATAAGGTGG 5 0.125 No Hit GGCTGCTCAAAAGTTGGGGGTCCTTCCCTTGAGTTCACAAGTTTCTTTCC 5 0.125 No Hit GAAAACATCATCCAAGAGTAGTTTTGGAACACTTGCCCTGATCACATCAA 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 0.0 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 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.025 0.0 0.0 0.0 0.0 72-73 0.037500000000000006 0.0 0.0 0.0 0.0 74-75 0.125 0.0 0.0 0.0 0.0 76-77 0.1375 0.0 0.0 0.0 0.0 78-79 0.175 0.0 0.0 0.0 0.0 80-81 0.21250000000000002 0.0 0.0 0.0 0.0 82-83 0.3125 0.0 0.0 0.0 0.0 84-85 0.425 0.0 0.0 0.0 0.0 86-87 0.6375 0.0 0.0 0.0 0.0 88-89 0.8374999999999999 0.0 0.0 0.0 0.0 90-91 0.8875 0.0 0.0 0.0 0.0 92-93 1.0375 0.0 0.0 0.0 0.0 94-95 1.3375 0.0 0.0 0.0 0.0 96-97 1.7125 0.0 0.0 0.0 0.0 98-99 2.1500000000000004 0.0 0.0 0.0 0.0 100-101 2.3875 0.0 0.0 0.0 0.0 102-103 2.7249999999999996 0.0 0.0 0.0 0.0 104-105 3.05 0.0 0.0 0.0 0.0 106-107 3.5875 0.0 0.0 0.0 0.0 108-109 4.0 0.0 0.0 0.0 0.0 110-111 4.4625 0.0 0.0 0.0 0.0 112-113 4.987500000000001 0.0 0.0 0.0 0.0 114-115 5.512499999999999 0.0 0.0 0.0 0.0 116-117 5.9875 0.0 0.0 0.0 0.0 118-119 6.5375 0.0 0.0 0.0 0.0 120-121 7.375 0.0 0.0 0.0 0.0 122-123 7.824999999999999 0.0 0.0 0.0 0.0 124-125 8.412500000000001 0.0 0.0 0.0 0.0 126-127 8.975000000000001 0.0 0.0 0.0 0.0 128-129 9.5 0.0 0.0 0.0 0.0 130-131 10.325 0.0 0.0 0.0 0.0 132-133 11.100000000000001 0.0 0.0 0.0 0.0 134-135 11.7875 0.0 0.0 0.0 0.0 136-137 12.675 0.0 0.0 0.0 0.0 138-139 13.45 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ATCTGAT 10 0.006830828 145.0 1 TTTTTTT 25 4.977651E-4 29.0 135-139 >>END_MODULE SRR12670109 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670109_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 36.4085 37.0 37.0 37.0 37.0 37.0 2 36.21 37.0 37.0 37.0 37.0 37.0 3 36.336 37.0 37.0 37.0 37.0 37.0 4 36.4305 37.0 37.0 37.0 37.0 37.0 5 36.4235 37.0 37.0 37.0 37.0 37.0 6 36.419 37.0 37.0 37.0 37.0 37.0 7 36.4075 37.0 37.0 37.0 37.0 37.0 8 36.47 37.0 37.0 37.0 37.0 37.0 9 36.48 37.0 37.0 37.0 37.0 37.0 10-14 36.4276 37.0 37.0 37.0 37.0 37.0 15-19 36.383799999999994 37.0 37.0 37.0 37.0 37.0 20-24 36.3514 37.0 37.0 37.0 37.0 37.0 25-29 36.291599999999995 37.0 37.0 37.0 37.0 37.0 30-34 36.325300000000006 37.0 37.0 37.0 37.0 37.0 35-39 36.2791 37.0 37.0 37.0 37.0 37.0 40-44 36.2369 37.0 37.0 37.0 37.0 37.0 45-49 36.2632 37.0 37.0 37.0 37.0 37.0 50-54 36.2091 37.0 37.0 37.0 37.0 37.0 55-59 36.1314 37.0 37.0 37.0 37.0 37.0 60-64 36.144400000000005 37.0 37.0 37.0 37.0 37.0 65-69 36.1337 37.0 37.0 37.0 37.0 37.0 70-74 36.0997 37.0 37.0 37.0 37.0 37.0 75-79 36.1356 37.0 37.0 37.0 37.0 37.0 80-84 36.055600000000005 37.0 37.0 37.0 37.0 37.0 85-89 36.089800000000004 37.0 37.0 37.0 37.0 37.0 90-94 36.053399999999996 37.0 37.0 37.0 37.0 37.0 95-99 36.0256 37.0 37.0 37.0 37.0 37.0 100-104 35.9872 37.0 37.0 37.0 37.0 37.0 105-109 35.9678 37.0 37.0 37.0 37.0 37.0 110-114 35.92880000000001 37.0 37.0 37.0 37.0 37.0 115-119 35.998799999999996 37.0 37.0 37.0 37.0 37.0 120-124 35.8819 37.0 37.0 37.0 37.0 37.0 125-129 35.770599999999995 37.0 37.0 37.0 37.0 37.0 130-134 35.6292 37.0 37.0 37.0 37.0 37.0 135-139 35.552800000000005 37.0 37.0 37.0 37.0 37.0 140-144 35.43 37.0 37.0 37.0 37.0 37.0 145-149 35.248000000000005 37.0 37.0 37.0 32.2 37.0 150-151 34.971999999999994 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 3.0 14 4.0 15 3.0 16 1.0 17 0.0 18 1.0 19 0.0 20 0.0 21 1.0 22 3.0 23 2.0 24 6.0 25 4.0 26 2.0 27 10.0 28 17.0 29 14.0 30 16.0 31 18.0 32 46.0 33 75.0 34 183.0 35 497.0 36 2825.0 37 269.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 36.8 25.025 9.65 28.525 2 27.0 27.500000000000004 30.85 14.649999999999999 3 19.6 29.575000000000003 32.550000000000004 18.275 4 24.275 32.375 24.875 18.475 5 25.424999999999997 35.725 23.375 15.475 6 23.825 39.425 20.875 15.875 7 21.075 22.75 37.225 18.95 8 19.650000000000002 25.724999999999998 28.749999999999996 25.874999999999996 9 22.650000000000002 25.900000000000002 28.999999999999996 22.45 10-14 24.060000000000002 28.715000000000003 26.06 21.165 15-19 23.64 27.55 28.105000000000004 20.705000000000002 20-24 23.294999999999998 28.299999999999997 28.59 19.814999999999998 25-29 23.75 27.644999999999996 28.655 19.950000000000003 30-34 23.32 27.85 27.750000000000004 21.08 35-39 22.525000000000002 29.020000000000003 27.315 21.14 40-44 22.36 28.84 27.755000000000003 21.044999999999998 45-49 23.525 27.889999999999997 27.950000000000003 20.635 50-54 22.985 27.625 27.755000000000003 21.634999999999998 55-59 23.880000000000003 28.12 27.445000000000004 20.555 60-64 23.415 28.78 27.12 20.685000000000002 65-69 24.195 27.77 27.115000000000002 20.919999999999998 70-74 24.64 27.534999999999997 27.639999999999997 20.185 75-79 24.58 28.28 26.784999999999997 20.355 80-84 24.385 28.4 26.279999999999998 20.935000000000002 85-89 24.37 27.644999999999996 27.265 20.72 90-94 24.525 27.779999999999998 27.0 20.695 95-99 24.18 28.634999999999998 27.02 20.165 100-104 24.505 28.23 26.775 20.49 105-109 24.59 28.125 26.85 20.435 110-114 24.94 27.474999999999998 27.405 20.18 115-119 25.185000000000002 27.810000000000002 26.779999999999998 20.225 120-124 25.650000000000002 28.02 26.375 19.955000000000002 125-129 26.235000000000003 28.005000000000003 26.365 19.395 130-134 26.52 27.79 26.75 18.94 135-139 27.02 28.384999999999998 26.435 18.16 140-144 28.285 27.29 25.845000000000002 18.58 145-149 28.365000000000002 27.62 25.45 18.565 150-151 29.3375 27.537499999999998 24.95 18.175 >>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 0.5 8 0.5 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 2.0 19 2.5 20 0.5 21 0.0 22 0.5 23 1.5 24 1.5 25 0.5 26 0.5 27 3.0 28 5.0 29 7.5 30 9.5 31 11.5 32 23.5 33 31.0 34 37.0 35 55.0 36 81.0 37 108.0 38 140.5 39 174.0 40 200.0 41 230.0 42 255.5 43 269.0 44 273.5 45 295.0 46 277.5 47 225.0 48 215.0 49 203.0 50 179.5 51 142.0 52 109.0 53 95.5 54 81.5 55 72.5 56 55.5 57 38.0 58 27.5 59 18.0 60 10.5 61 7.0 62 5.5 63 3.0 64 1.0 65 1.5 66 1.5 67 2.0 68 1.5 69 0.0 70 0.5 71 1.0 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 0.5 87 0.5 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 0.5 100 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 80.125 #Duplication Level Percentage of deduplicated Percentage of total 1 81.8408736349454 65.575 2 13.541341653666148 21.7 3 3.2761310452418098 7.875 4 0.8424336973478939 2.7 5 0.40561622464898595 1.625 6 0.062402496099843996 0.3 7 0.0 0.0 8 0.0 0.0 9 0.031201248049921998 0.22499999999999998 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source AGAGAACACATTCATACCCCAAGTCTTTTAGTTCATCCATTTAAGCTTAA 9 0.22499999999999998 No Hit AGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATC 6 0.15 No Hit TATTTACCATGAATATTCAGTTATATAATCACAATATCACGGTTTCACGA 6 0.15 No Hit CTTTTAGTTCATCCATTTAAGCTTAATCAATCAATCATCATGTCTAGCAC 5 0.125 No Hit AGTTTGGAGAAATAAAGAATTTGCATTTGAATCTTGATCGCCGCACCGGT 5 0.125 No Hit GTTGATTCTAGTAATGCTGGTGATGCTGCTACTCTGAGTGGCAGAGTTTT 5 0.125 No Hit AAATGGATGCCCCTTGTTGAGTTTGTGGCGCAGCCGCTAATCCAAGAAGA 5 0.125 No Hit GTAGAGATGTTCCCTAAAGAATATGGTTACGTAGTTTTTGTTCTTGTTGC 5 0.125 No Hit GCCCAAAATTGCTCTGCAACCACAAGGGGCAATCACAAGCTTACGAACGC 5 0.125 No Hit CATCTCTTCAAGCAAGGAGTGCGTCCAGAGTGGGAAGACAAGCAAAACCA 5 0.125 No Hit GTTGGGACAGCTGAGAAGTCCATGGCTCAAGAGAACTTGAATAATGGGGG 5 0.125 No Hit TGAAGGCTATGGGATTTTCTGTTGATGTGAGTGCCAGTGATGTTTTAATG 5 0.125 No Hit AGAACACATTCATACCCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATC 5 0.125 No Hit CTTCGATTGCAGCAGTTGGATGTTCGTTGCGAGACAAAGACAAAGGATAA 5 0.125 No Hit GTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAA 5 0.125 No Hit AAAAAGCATTCCACTTATCTTAGTTTTATTTCTTGTTCAATGTCTTTATG 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 0.0 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 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.025 0.0 0.0 0.0 0.0 72-73 0.037500000000000006 0.0 0.0 0.0 0.0 74-75 0.125 0.0 0.0 0.0 0.0 76-77 0.1375 0.0 0.0 0.0 0.0 78-79 0.175 0.0 0.0 0.0 0.0 80-81 0.21250000000000002 0.0 0.0 0.0 0.0 82-83 0.3125 0.0 0.0 0.0 0.0 84-85 0.425 0.0 0.0 0.0 0.0 86-87 0.6375 0.0 0.0 0.0 0.0 88-89 0.8374999999999999 0.0 0.0 0.0 0.0 90-91 0.8875 0.0 0.0 0.0 0.0 92-93 1.0375 0.0 0.0 0.0 0.0 94-95 1.3375 0.0 0.0 0.0 0.0 96-97 1.7125 0.0 0.0 0.0 0.0 98-99 2.1500000000000004 0.0 0.0 0.0 0.0 100-101 2.3875 0.0 0.0 0.0 0.0 102-103 2.7249999999999996 0.0 0.0 0.0 0.0 104-105 3.025 0.0 0.0 0.0 0.0 106-107 3.5625 0.0 0.0 0.0 0.0 108-109 3.975 0.0 0.0 0.0 0.0 110-111 4.4 0.0 0.0 0.0 0.0 112-113 4.9125 0.0 0.0 0.0 0.0 114-115 5.4625 0.0 0.0 0.0 0.0 116-117 5.9375 0.0 0.0 0.0 0.0 118-119 6.487500000000001 0.0 0.0 0.0 0.0 120-121 7.3 0.0 0.0 0.0 0.0 122-123 7.7125 0.0 0.0 0.0 0.0 124-125 8.287500000000001 0.0 0.0 0.0 0.0 126-127 8.850000000000001 0.0 0.0 0.0 0.0 128-129 9.3625 0.0 0.0 0.0 0.0 130-131 10.175 0.0 0.0 0.0 0.0 132-133 10.95 0.0 0.0 0.0 0.0 134-135 11.5875 0.0 0.0 0.0 0.0 136-137 12.475000000000001 0.0 0.0 0.0 0.0 138-139 13.2625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTTTTAC 10 0.006830828 145.0 2 CTTGTTG 10 0.006830828 145.0 1 GGGGGGG 40 0.0076550315 18.125 140-144 >>END_MODULE Read 380981 spots for SRR12670109.sra Written 380981 spots for SRR12670109.sra Read 380981 spots for SRR12670109.sra Written 380981 spots for SRR12670109.sra Read 380981 spots for SRR12670109.sra Written 380981 spots for SRR12670109.sra Read 380981 spots for SRR12670109.sra Written 380981 spots for SRR12670109.sra Read 380981 spots for SRR12670109.sra Written 380981 spots for SRR12670109.sra Read 380981 spots for SRR12670109.sra Written 380981 spots for SRR12670109.sra Read 380981 spots for SRR12670109.sra Written 380981 spots for SRR12670109.sra Read 380981 spots for SRR12670109.sra Written 380981 spots for SRR12670109.sra Read 380981 spots for SRR12670109.sra Written 380981 spots for SRR12670109.sra Read 380981 spots for SRR12670109.sra Written 380981 spots for SRR12670109.sra Read 380981 spots for SRR12670109.sra Written 380981 spots for SRR12670109.sra Read 380981 spots for SRR12670109.sra Written 380981 spots for SRR12670109.sra Read 380998 spots for SRR12670109.sra Written 380998 spots for SRR12670109.sra Read 380981 spots for SRR12670109.sra Written 380981 spots for SRR12670109.sra Read 380981 spots for SRR12670109.sra Written 380981 spots for SRR12670109.sra Read 380981 spots for SRR12670109.sra Written 380981 spots for SRR12670109.sra Read 380981 spots for SRR12670109.sra Written 380981 spots for SRR12670109.sra Read 380981 spots for SRR12670109.sra Written 380981 spots for SRR12670109.sra Read 380981 spots for SRR12670109.sra Written 380981 spots for SRR12670109.sra Read 380981 spots for SRR12670109.sra Written 380981 spots for SRR12670109.sra SRR ids: ['SRR12670109.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_wdhvnpmu SRR12670109.sra spots: 7619637 blocks: [[1, 380981], [380982, 761962], [761963, 1142943], [1142944, 1523924], [1523925, 1904905], [1904906, 2285886], [2285887, 2666867], [2666868, 3047848], [3047849, 3428829], [3428830, 3809810], [3809811, 4190791], [4190792, 4571772], [4571773, 4952753], [4952754, 5333734], [5333735, 5714715], [5714716, 6095696], [6095697, 6476677], [6476678, 6857658], [6857659, 7238639], [7238640, 7619637]] SRR12670109 file size 2572434 SRR12670109 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 SRR12670109 SRR12670109_1.fastq SRR12670109_2.fastq Input file: SRR12670109_1.fastq Paired file: SRR12670109_2.fastq trimmed: SRR12670109-trimmed-pair1.fastq, SRR12670109-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 23:03:19 2025 >> started Mon Feb 10 23:03:32 2025 >> done (12.550s) 7619637 read pairs processed; of these: 23 ( 0.00%) short read pairs filtered out after trimming by size control 1817 ( 0.02%) empty read pairs filtered out after trimming by size control 7617797 (99.98%) read pairs available; of these: 1331378 (17.48%) trimmed read pairs available after processing 6286419 (82.52%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 5 0.00% 19 3 0.00% 20 1 0.00% 21 6 0.00% 22 9 0.00% 23 14 0.00% 24 17 0.00% 25 16 0.00% 26 18 0.00% 27 18 0.00% 28 16 0.00% 29 17 0.00% 30 19 0.00% 31 37 0.00% 32 31 0.00% 33 31 0.00% 34 40 0.00% 35 46 0.00% 36 32 0.00% 37 39 0.00% 38 62 0.00% 39 70 0.00% 40 54 0.00% 41 65 0.00% 42 55 0.00% 43 70 0.00% 44 60 0.00% 45 76 0.00% 46 109 0.00% 47 103 0.00% 48 119 0.00% 49 142 0.00% 50 164 0.00% 51 162 0.00% 52 205 0.00% 53 162 0.00% 54 189 0.00% 55 220 0.00% 56 218 0.00% 57 229 0.00% 58 307 0.00% 59 351 0.00% 60 381 0.01% 61 476 0.01% 62 504 0.01% 63 574 0.01% 64 659 0.01% 65 692 0.01% 66 714 0.01% 67 820 0.01% 68 851 0.01% 69 967 0.01% 70 1165 0.02% 71 1386 0.02% 72 1533 0.02% 73 1755 0.02% 74 1841 0.02% 75 2057 0.03% 76 2183 0.03% 77 2374 0.03% 78 2580 0.03% 79 2915 0.04% 80 3097 0.04% 81 3682 0.05% 82 4107 0.05% 83 4221 0.06% 84 4840 0.06% 85 5231 0.07% 86 5693 0.07% 87 5826 0.08% 88 6142 0.08% 89 6547 0.09% 90 7110 0.09% 91 7627 0.10% 92 7757 0.10% 93 8634 0.11% 94 9384 0.12% 95 10026 0.13% 96 10459 0.14% 97 11015 0.14% 98 11263 0.15% 99 11442 0.15% 100 12016 0.16% 101 12251 0.16% 102 12982 0.17% 103 13370 0.18% 104 14294 0.19% 105 14896 0.20% 106 15327 0.20% 107 15806 0.21% 108 16187 0.21% 109 16102 0.21% 110 16354 0.21% 111 16543 0.22% 112 17430 0.23% 113 17871 0.23% 114 18317 0.24% 115 19111 0.25% 116 19734 0.26% 117 20124 0.26% 118 20922 0.27% 119 20647 0.27% 120 21273 0.28% 121 21456 0.28% 122 21841 0.29% 123 22104 0.29% 124 22894 0.30% 125 23379 0.31% 126 24077 0.32% 127 24469 0.32% 128 24425 0.32% 129 24767 0.33% 130 25077 0.33% 131 25114 0.33% 132 24895 0.33% 133 25741 0.34% 134 25907 0.34% 135 26355 0.35% 136 26732 0.35% 137 27171 0.36% 138 27627 0.36% 139 28792 0.38% 140 28556 0.37% 141 29213 0.38% 142 29264 0.38% 143 28753 0.38% 144 29911 0.39% 145 30266 0.40% 146 31015 0.41% 147 30718 0.40% 148 31783 0.42% 149 31239 0.41% 150 32143 0.42% 151 6286419 82.52% 7617797 reads passed initial QC criterion=sequence-density sequence-density=0.37 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=21 prefix-density=0.37 prefix-fanout=2.0 sequence=CGGTAGACCCAACCTTTCTCCAACTCGAATTCCAAGCAAGGAACCCACTT criterion=fanout-score sequence-density=0.09 sequence-density-rank=28 fanout-score=9.67 fanout-score-rank=1 prefix-density=0.25 prefix-fanout=3.4 sequence=TCCAAGAGCTCCAAGCATGGCCCACCTGGAATGGATGACTTCAAGCTCACGGTTCTTGGCAAAGGTCTCTGGGTCAGCAGAGAGGCCAGCAGTGTCCCAGCCGTAGTCACCAGGGAACTCACCAGTCAAGTAGGATGGGGGCTCACCAGAGAACGGGCCCAAGTATTTAACACGGTCTGGTCCGTACCATGGGCTCCCGGAGGGAACAGGCTTGGTGGTTTTCCTCATGGAGACACGGCCATTGCCCATGATCTCAGAGGAGGAGGGGTTGAGCTTCACCGCCTTTCCGGCTAGCGAAGGGGAGGAGAGGGCCATTGTTGCTGCTGCCATTG criterion=sequence-density sequence-density=1.26 sequence-density-rank=1 fanout-score=2.13 fanout-score-rank=28 prefix-density=1.27 prefix-fanout=2.1 sequence=CCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAATCAATCATCATGTCTAGCACCTGCGACACCTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCATT criterion=fanout-score sequence-density=0.23 sequence-density-rank=17 fanout-score=11.84 fanout-score-rank=1 prefix-density=0.43 prefix-fanout=6.3 sequence=AAGAAAGCTTACCCTAAC SRR12670109 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 10 23:04:15 Started mapping on | Feb 10 23:04:16 Finished on | Feb 10 23:05:36 Mapping speed, Million of reads per hour | 342.80 Number of input reads | 7617797 Average input read length | 292 UNIQUE READS: Uniquely mapped reads number | 7068718 Uniquely mapped reads % | 92.79% Average mapped length | 291.25 Number of splices: Total | 7275632 Number of splices: Annotated (sjdb) | 7119802 Number of splices: GT/AG | 7135860 Number of splices: GC/AG | 112380 Number of splices: AT/AC | 4563 Number of splices: Non-canonical | 22829 Mismatch rate per base, % | 0.34% Deletion rate per base | 0.03% Deletion average length | 2.91 Insertion rate per base | 0.02% Insertion average length | 2.41 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 176059 % of reads mapped to multiple loci | 2.31% Number of reads mapped to too many loci | 20340 % of reads mapped to too many loci | 0.27% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.51% % of reads unmapped: other | 0.11% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 373020 373020 373020 N_multimapping 176059 176059 176059 N_noFeature 191391 6926100 234300 N_ambiguous 143510 405 43553 UnstrandedReadsAssigned:6733817 PositiveStrandReadsAssigned:142213 NegativeStrandReadsAssigned:6790865 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12670109 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: SRR12670109-trimmed-pair1.fastq SRR12670109-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 7,617,797 reads, 6,749,493 reads pseudoaligned [quant] estimated average fragment length: 228.675 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,004 rounds 52401 SRR12670109.ke.tsv 34699 SRR12670109.se.tsv 87100 total ==> SRR12670109.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1790.32 351 23.3512 Potri.005G024800.1.v4.1 1035 807.325 190 28.031 Potri.004G059700.1.v4.1 961 733.441 0 0 Potri.007G009000.2.v4.1 1416 1188.32 0 0 Potri.003G141000.2.v4.1 2943 2715.32 532.548 23.3599 Potri.016G087400.1.v4.1 270 94.5527 364 458.523 Potri.015G069301.1.v4.1 564 344.404 0 0 Potri.010G195200.1.v4.1 1773 1545.32 145 11.1759 Potri.012G127500.1.v4.1 977 749.368 67 10.6491 ==> SRR12670109.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 19 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 160 Potri.001G212900.v4.1 10 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 10 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 3 SRR12670109 completed mapping pipeline successfully