Starting /dee2/code/volunteer_pipeline.sh SRR12951311 current disk space = 1543002075136 free memory = 1598636064 SRR12951311 SRAfilesize 2f2cdaaee8be3a3d74d87d214a839f1d SRR12951311.sra SRR12951311.sra file validated SRR12951311 is paired end SRR12951311 is conventional basespace SRR12951311 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12951311_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 52 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.434 37.0 37.0 37.0 37.0 37.0 2 36.1375 37.0 37.0 37.0 37.0 37.0 3 36.462 37.0 37.0 37.0 37.0 37.0 4 36.5175 37.0 37.0 37.0 37.0 37.0 5 36.528 37.0 37.0 37.0 37.0 37.0 6 36.519 37.0 37.0 37.0 37.0 37.0 7 36.414 37.0 37.0 37.0 37.0 37.0 8 36.5635 37.0 37.0 37.0 37.0 37.0 9 36.615 37.0 37.0 37.0 37.0 37.0 10-14 36.555 37.0 37.0 37.0 37.0 37.0 15-19 36.5418 37.0 37.0 37.0 37.0 37.0 20-24 36.4807 37.0 37.0 37.0 37.0 37.0 25-29 36.4809 37.0 37.0 37.0 37.0 37.0 30-34 36.4414 37.0 37.0 37.0 37.0 37.0 35-39 36.4185 37.0 37.0 37.0 37.0 37.0 40-44 36.4303 37.0 37.0 37.0 37.0 37.0 45-49 36.3558 37.0 37.0 37.0 37.0 37.0 50-54 36.351600000000005 37.0 37.0 37.0 37.0 37.0 55-59 36.3168 37.0 37.0 37.0 37.0 37.0 60-64 36.326499999999996 37.0 37.0 37.0 37.0 37.0 65-69 36.266600000000004 37.0 37.0 37.0 37.0 37.0 70-74 36.2087 37.0 37.0 37.0 37.0 37.0 75-79 36.1933 37.0 37.0 37.0 37.0 37.0 80-84 36.2319 37.0 37.0 37.0 37.0 37.0 85-89 36.244299999999996 37.0 37.0 37.0 37.0 37.0 90-94 36.203199999999995 37.0 37.0 37.0 37.0 37.0 95-99 36.215700000000005 37.0 37.0 37.0 37.0 37.0 100-104 36.22019999999999 37.0 37.0 37.0 37.0 37.0 105-109 36.1733 37.0 37.0 37.0 37.0 37.0 110-114 36.1481 37.0 37.0 37.0 37.0 37.0 115-119 36.15070000000001 37.0 37.0 37.0 37.0 37.0 120-124 36.139 37.0 37.0 37.0 37.0 37.0 125-129 36.0124 37.0 37.0 37.0 37.0 37.0 130-134 36.037 37.0 37.0 37.0 37.0 37.0 135-139 36.0241 37.0 37.0 37.0 37.0 37.0 140-144 35.964299999999994 37.0 37.0 37.0 37.0 37.0 145-149 35.8904 37.0 37.0 37.0 37.0 37.0 150-151 35.653 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 2.0 22 1.0 23 1.0 24 6.0 25 1.0 26 2.0 27 4.0 28 13.0 29 16.0 30 36.0 31 37.0 32 39.0 33 70.0 34 131.0 35 299.0 36 2852.0 37 489.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 48.975 10.7 5.575 34.75 2 23.190954773869347 9.874371859296483 31.984924623115578 34.949748743718594 3 20.375 15.75 25.674999999999997 38.2 4 25.874999999999996 19.825 21.05 33.25 5 26.125 25.324999999999996 22.475 26.075 6 25.924999999999997 29.975 22.675 21.425 7 19.7 25.05 35.825 19.425 8 21.349999999999998 22.15 28.299999999999997 28.199999999999996 9 22.875 19.925 32.425 24.775 10-14 24.21 25.71 24.09 25.990000000000002 15-19 25.324999999999996 23.380000000000003 24.185000000000002 27.11 20-24 24.425 25.224999999999998 23.605 26.745 25-29 24.175 24.19 23.84 27.794999999999998 30-34 24.215 23.880000000000003 24.415 27.49 35-39 24.355 24.355 24.375 26.915 40-44 24.279999999999998 24.245 24.16 27.315 45-49 24.505 24.18 24.154999999999998 27.16 50-54 23.98 24.255 23.695 28.07 55-59 23.87 23.485 24.33 28.315 60-64 24.05 23.365 24.535 28.050000000000004 65-69 24.365000000000002 24.09 24.255 27.29 70-74 25.035 23.965 24.09 26.91 75-79 25.064999999999998 23.669999999999998 23.685000000000002 27.58 80-84 25.55 23.14 23.849999999999998 27.46 85-89 25.465 23.59 23.765 27.18 90-94 25.085 24.235 23.235 27.445000000000004 95-99 24.345 23.445 24.29 27.92 100-104 25.629999999999995 23.365 23.294999999999998 27.71 105-109 26.11 23.79 23.05 27.05 110-114 25.385 24.925 22.56 27.13 115-119 25.44 23.74 23.32 27.500000000000004 120-124 25.55 24.12 23.195 27.134999999999998 125-129 25.595000000000002 24.005000000000003 22.91 27.49 130-134 26.07 23.365 22.755 27.810000000000002 135-139 25.705 23.905 22.564999999999998 27.825 140-144 25.88 23.835 21.97 28.315 145-149 26.05 23.875 22.67 27.405 150-151 26.7625 23.150000000000002 21.825 28.262500000000003 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 1.0 1 0.5 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.5 10 0.5 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.5 20 0.5 21 0.5 22 0.5 23 0.0 24 0.0 25 0.0 26 0.0 27 0.0 28 1.5 29 1.5 30 2.5 31 3.5 32 4.5 33 8.5 34 14.0 35 20.5 36 26.5 37 43.0 38 58.0 39 66.0 40 82.5 41 110.5 42 121.5 43 130.5 44 140.0 45 139.0 46 159.0 47 186.0 48 189.5 49 190.0 50 178.5 51 160.5 52 164.0 53 164.0 54 145.5 55 134.0 56 123.0 57 103.0 58 97.0 59 84.5 60 79.0 61 68.5 62 62.0 63 74.5 64 79.0 65 71.5 66 65.5 67 63.0 68 50.5 69 39.5 70 44.5 71 44.5 72 37.0 73 31.5 74 26.0 75 26.0 76 22.0 77 18.5 78 15.5 79 11.5 80 6.0 81 1.5 82 2.0 83 2.5 84 1.5 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 0.5 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 76.225 #Duplication Level Percentage of deduplicated Percentage of total 1 79.37028533945556 60.5 2 14.430960970810103 22.0 3 4.099704821252869 9.375 4 1.1479173499508035 3.5000000000000004 5 0.42636930141029844 1.625 6 0.3279763857002296 1.5 7 0.09839291571006888 0.525 8 0.0 0.0 9 0.032797638570022956 0.22499999999999998 >10 0.06559527714004591 0.75 >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 GTGCGACGTGGGGCTGGATCTCAGTGGATCGTGGCAGCAAGGCCACTCTG 18 0.44999999999999996 No Hit GCCGCAGGCTCCACGCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTT 12 0.3 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACTGACATCTCGTAT 9 0.22499999999999998 TruSeq Adapter, Index 4 (97% over 37bp) GCAACAACTTAAATATACGCTATTGGAGCTGGAATTACCGCGGCTGCTGG 7 0.17500000000000002 No Hit CGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACT 7 0.17500000000000002 No Hit GTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCAT 7 0.17500000000000002 No Hit GTCGGATGGGGAGCCCGCAGGCCGTTGCAGCGCAGTGCCCCGAGGGACAC 6 0.15 No Hit ATCGAAAGTTGATAGGGCAGAAATTTGAATGATGCGTCGCCGGCACGAGG 6 0.15 No Hit CCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCT 6 0.15 No Hit GCGGCGCCCAACAACGGAGGCAGTGGCAGCAGTTCTTTCTCAGGCCTTGA 6 0.15 No Hit GCCCTTCCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCC 6 0.15 No Hit GTTTTTTCTTAAGGTCATTTCTACTTAATAATATACAGACGGCAGCAAAG 6 0.15 No Hit CCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAG 6 0.15 No Hit GTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTA 6 0.15 No Hit GGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGC 6 0.15 No Hit ATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATA 6 0.15 No Hit GTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCT 5 0.125 No Hit CCGGCAATTTCAAGCACTCTTTGACTCTCTTTTCAAAGTCCTTTTCATCT 5 0.125 No Hit GGGGCTAGTTGATTCGGCAGGTGAGTTGTTACACACTCCTTAGCGGATTT 5 0.125 No Hit GTCCATGTTCATGTCGGTGATCAGCTGCAGATCTTCCTTGTAGCGATGGT 5 0.125 No Hit GTCCGTACCAGTTCTGAGTCGACTGTTCAGCGCTCGGGGAAAGCCCCCGA 5 0.125 No Hit GTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGAACCCA 5 0.125 No Hit GTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGC 5 0.125 No Hit CCTTCCAGGTGTGCTGATTCTTGGGTATTTTGGGTCCCTGGCCTTCTTGA 5 0.125 No Hit TGATAGAACTCGTAATGGGCTCCAGCTATCCTGAGGGAAACTTCGGAGGG 5 0.125 No Hit CCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCT 5 0.125 No Hit CCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTATA 5 0.125 No Hit GTCCAACTACGAGCTTTTTAACTGCAACAACTTAAATATACGCTATTGGA 5 0.125 No Hit CTATGATGTTATCCCATGCTAATGTATCCAGAGCGATGGCTTGCTTTGAG 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 0.0125 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.025 0.0 0.0 0.0 0.0 68-69 0.025 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 0.075 0.0 0.0 0.0 0.0 76-77 0.1375 0.0 0.0 0.0 0.0 78-79 0.1875 0.0 0.0 0.0 0.0 80-81 0.225 0.0 0.0 0.0 0.0 82-83 0.35 0.0 0.0 0.0 0.0 84-85 0.4375 0.0 0.0 0.0 0.0 86-87 0.575 0.0 0.0 0.0 0.0 88-89 0.825 0.0 0.0 0.0 0.0 90-91 1.3375 0.0 0.0 0.0 0.0 92-93 1.5 0.0 0.0 0.0 0.0 94-95 1.7625 0.0 0.0 0.0 0.0 96-97 2.0375 0.0 0.0 0.0 0.0 98-99 2.3 0.0 0.0 0.0 0.0 100-101 2.625 0.0 0.0 0.0 0.0 102-103 2.9875 0.0 0.0 0.0 0.0 104-105 3.4125 0.0 0.0 0.0 0.0 106-107 3.8 0.0 0.0 0.0 0.0 108-109 4.2125 0.0 0.0 0.0 0.0 110-111 4.4625 0.0 0.0 0.0 0.0 112-113 4.8625 0.0 0.0 0.0 0.0 114-115 5.362500000000001 0.0 0.0 0.0 0.0 116-117 5.9625 0.0 0.0 0.0 0.0 118-119 6.425000000000001 0.0 0.0 0.0 0.0 120-121 6.9 0.0 0.0 0.0 0.0 122-123 7.425 0.0 0.0 0.0 0.0 124-125 8.1125 0.0 0.0 0.0 0.0 126-127 8.8125 0.0 0.0 0.0 0.0 128-129 9.45 0.0 0.0 0.0 0.0 130-131 10.0625 0.0 0.0 0.0 0.0 132-133 10.875 0.0 0.0 0.0 0.0 134-135 11.6 0.0 0.0 0.0 0.0 136-137 12.4875 0.0 0.0 0.0 0.0 138-139 13.2 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR12951311 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12951311_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 53 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.084 37.0 37.0 37.0 37.0 37.0 2 36.1305 37.0 37.0 37.0 37.0 37.0 3 36.0995 37.0 37.0 37.0 37.0 37.0 4 36.1895 37.0 37.0 37.0 37.0 37.0 5 36.113 37.0 37.0 37.0 37.0 37.0 6 36.062 37.0 37.0 37.0 37.0 37.0 7 36.0685 37.0 37.0 37.0 37.0 37.0 8 36.1835 37.0 37.0 37.0 37.0 37.0 9 36.02 37.0 37.0 37.0 37.0 37.0 10-14 36.094100000000005 37.0 37.0 37.0 37.0 37.0 15-19 36.152100000000004 37.0 37.0 37.0 37.0 37.0 20-24 36.008500000000005 37.0 37.0 37.0 37.0 37.0 25-29 36.017 37.0 37.0 37.0 37.0 37.0 30-34 35.9206 37.0 37.0 37.0 37.0 37.0 35-39 36.0017 37.0 37.0 37.0 37.0 37.0 40-44 35.9405 37.0 37.0 37.0 37.0 37.0 45-49 35.9521 37.0 37.0 37.0 37.0 37.0 50-54 35.864799999999995 37.0 37.0 37.0 37.0 37.0 55-59 35.8222 37.0 37.0 37.0 37.0 37.0 60-64 35.8444 37.0 37.0 37.0 37.0 37.0 65-69 35.8977 37.0 37.0 37.0 37.0 37.0 70-74 35.84160000000001 37.0 37.0 37.0 37.0 37.0 75-79 35.757999999999996 37.0 37.0 37.0 37.0 37.0 80-84 35.7311 37.0 37.0 37.0 37.0 37.0 85-89 35.7513 37.0 37.0 37.0 37.0 37.0 90-94 35.7903 37.0 37.0 37.0 37.0 37.0 95-99 35.715500000000006 37.0 37.0 37.0 37.0 37.0 100-104 35.668600000000005 37.0 37.0 37.0 37.0 37.0 105-109 35.688 37.0 37.0 37.0 37.0 37.0 110-114 35.7149 37.0 37.0 37.0 37.0 37.0 115-119 35.717600000000004 37.0 37.0 37.0 37.0 37.0 120-124 35.5744 37.0 37.0 37.0 37.0 37.0 125-129 35.4657 37.0 37.0 37.0 37.0 37.0 130-134 35.363 37.0 37.0 37.0 34.6 37.0 135-139 35.2746 37.0 37.0 37.0 34.6 37.0 140-144 35.18820000000001 37.0 37.0 37.0 32.2 37.0 145-149 34.982800000000005 37.0 37.0 37.0 27.4 37.0 150-151 34.553 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 4.0 13 6.0 14 3.0 15 2.0 16 2.0 17 2.0 18 2.0 19 5.0 20 4.0 21 12.0 22 5.0 23 16.0 24 5.0 25 13.0 26 14.0 27 12.0 28 8.0 29 18.0 30 26.0 31 32.0 32 51.0 33 96.0 34 204.0 35 557.0 36 2578.0 37 323.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 45.824999999999996 20.45 7.3 26.424999999999997 2 30.55 22.575 22.45 24.425 3 26.525 23.400000000000002 27.1 22.975 4 27.950000000000003 30.049999999999997 18.925 23.075000000000003 5 29.15 31.15 18.9 20.8 6 26.424999999999997 33.475 18.125 21.975 7 24.6 19.2 31.974999999999998 24.224999999999998 8 25.224999999999998 21.275 23.150000000000002 30.349999999999998 9 28.225 21.825 24.725 25.224999999999998 10-14 27.765 24.97 21.990000000000002 25.275 15-19 27.665 23.855 23.34 25.14 20-24 26.88 24.63 22.825 25.665 25-29 27.865000000000002 24.25 22.595000000000002 25.290000000000003 30-34 27.395000000000003 24.990000000000002 22.745 24.87 35-39 27.08 24.875 22.125 25.919999999999998 40-44 28.42 24.51 22.13 24.94 45-49 27.339999999999996 24.345 23.064999999999998 25.25 50-54 27.725 24.925 22.755 24.595 55-59 27.63 24.69 22.305 25.374999999999996 60-64 27.675 23.72 23.24 25.365 65-69 28.199999999999996 24.39 22.185 25.224999999999998 70-74 28.42 24.5 22.11 24.97 75-79 27.860000000000003 23.630000000000003 23.205000000000002 25.305 80-84 28.42 23.625 23.13 24.825 85-89 28.17 23.544999999999998 23.425 24.86 90-94 28.84 23.14 23.544999999999998 24.474999999999998 95-99 29.654999999999998 23.94 22.74 23.665 100-104 29.14 24.529999999999998 22.585 23.745 105-109 28.725 24.41 22.8 24.065 110-114 28.895 24.64 22.33 24.135 115-119 29.835 24.779999999999998 21.42 23.965 120-124 28.939999999999998 24.59 22.06 24.41 125-129 29.659999999999997 25.285000000000004 21.665 23.39 130-134 29.675 24.29 22.295 23.74 135-139 30.23 24.13 22.125 23.515 140-144 30.955 24.065 22.025 22.955000000000002 145-149 31.445 23.775 22.0 22.78 150-151 31.724999999999998 24.8 21.575 21.9 >>END_MODULE >>Per sequence GC content fail #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 1.0 8 1.0 9 0.5 10 0.5 11 1.5 12 1.5 13 1.0 14 1.5 15 1.0 16 1.5 17 1.0 18 0.5 19 0.5 20 0.5 21 1.0 22 1.5 23 1.5 24 0.5 25 1.5 26 2.0 27 0.5 28 0.5 29 2.5 30 3.5 31 4.0 32 6.0 33 7.0 34 10.5 35 22.0 36 33.0 37 42.5 38 52.5 39 64.0 40 82.5 41 89.5 42 100.5 43 118.5 44 130.0 45 139.5 46 155.0 47 157.5 48 160.0 49 182.5 50 154.5 51 151.0 52 164.5 53 150.0 54 149.0 55 132.0 56 115.5 57 112.5 58 109.0 59 88.5 60 74.5 61 73.0 62 65.0 63 69.5 64 81.0 65 82.0 66 79.5 67 78.5 68 83.0 69 73.5 70 50.0 71 40.5 72 40.5 73 40.0 74 34.5 75 27.5 76 26.5 77 21.0 78 11.5 79 4.0 80 2.0 81 1.5 82 2.0 83 2.5 84 0.5 85 0.5 86 0.5 87 1.5 88 2.0 89 0.5 90 1.0 91 2.0 92 2.0 93 2.5 94 2.0 95 1.0 96 1.0 97 1.0 98 1.5 99 1.5 100 2.0 >>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 78.175 #Duplication Level Percentage of deduplicated Percentage of total 1 80.81228014070994 63.175000000000004 2 13.751199232491206 21.5 3 3.6456667732651105 8.55 4 1.0233450591621363 3.2 5 0.4157339302846178 1.625 6 0.1598976654940838 0.75 7 0.12791813239526703 0.7000000000000001 8 0.0 0.0 9 0.03197953309881676 0.22499999999999998 >10 0.03197953309881676 0.27499999999999997 >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 CTTACCAGGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTT 11 0.27499999999999997 No Hit AGCGATTTGTCTGGTTAATTCCGTTAACGAACGAGACCTCAGCCTGCTAA 9 0.22499999999999998 No Hit GCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGTTAACGAAC 7 0.17500000000000002 No Hit GGTCAGGCGGGACTACCCGCTGAGTTTAAGCATATAAATAAGCGGAGGAG 7 0.17500000000000002 No Hit CAGCAGGCGCGCAAATTACCCAATCCTGACACGGGGAGGTAGTGACAATA 7 0.17500000000000002 No Hit GTTAGTTTTACCCTACTGATGACCGTGCCGCGATAGTAATTCAACCTAGT 7 0.17500000000000002 No Hit CAACAATCGAGCAAAGCCTCCTCCTCCTGGCTGCTGCCATATGTTTGGTG 6 0.15 No Hit AGCAGAACAAGAAGGAGCTCTCCCGCGCCAGTCTCGGCGGCGACGAGGAC 6 0.15 No Hit GTCTGACATGCGTGCGAGTCGACGGGTTCTGAAACCTGGGATGCGCAAGG 6 0.15 No Hit TAAAAAGCTCGTAGTTGGACTTTGGGCCGGGTCGGCCGGTCCGCCTCACG 6 0.15 No Hit GTGAAATTCTTGGATTTATGAAAGACGAACAACTGCGAAAGCATTTGCCA 6 0.15 No Hit GCAGAGGTAAGTTTGGGAGGTCGTACTCAGAAGCTCCAATGGCTCCTAAA 5 0.125 No Hit CCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGCAA 5 0.125 No Hit TACCAGGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGA 5 0.125 No Hit TGTAAATGAAATTACCTATGTTCGATCAAAGGAGATGTTGCATGTGATTC 5 0.125 No Hit CGGGCACATTAGTGTCTGGTAATTGGAATGAGTACAATCTAAATCCCTTA 5 0.125 No Hit CGGGGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAA 5 0.125 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 5 0.125 No Hit AGCTAATACGTGTAACAAACCCCGACTTCTGGGAGGGGCGCATTTATTAG 5 0.125 No Hit GTCACAGCAAGCCGGGGTTCGAGAGAAGAACCATCCAATCCAGGCTCGAC 5 0.125 No Hit GCGCTCCTAGCCTTAATTGGCCGGGTCGTGCCTCCGGCATCGTTACTTTG 5 0.125 No Hit AGGAGTCTGACATGCGTGCGAGTCGACGGGTTCTGAAACCTGGGATGCGC 5 0.125 No Hit ATATGCTTGTCTCAAAGATTAAGCCATGCATGTGCAAGTATGAACTAATT 5 0.125 No Hit CAGATACCGTCCTAGTCTCAACCATAAACGATGCCGACCAGGGATCGGCG 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 0.0125 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.025 0.0 0.0 0.0 0.0 68-69 0.025 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 0.075 0.0 0.0 0.0 0.0 76-77 0.1375 0.0 0.0 0.0 0.0 78-79 0.1875 0.0 0.0 0.0 0.0 80-81 0.225 0.0 0.0 0.0 0.0 82-83 0.35 0.0 0.0 0.0 0.0 84-85 0.4375 0.0 0.0 0.0 0.0 86-87 0.575 0.0 0.0 0.0 0.0 88-89 0.825 0.0 0.0 0.0 0.0 90-91 1.3375 0.0 0.0 0.0 0.0 92-93 1.5 0.0 0.0 0.0 0.0 94-95 1.7625 0.0 0.0 0.0 0.0 96-97 2.0375 0.0 0.0 0.0 0.0 98-99 2.3 0.0 0.0 0.0 0.0 100-101 2.625 0.0 0.0 0.0 0.0 102-103 2.9875 0.0 0.0 0.0 0.0 104-105 3.4125 0.0 0.0 0.0 0.0 106-107 3.8 0.0 0.0 0.0 0.0 108-109 4.2125 0.0 0.0 0.0 0.0 110-111 4.4625 0.0 0.0 0.0 0.0 112-113 4.9 0.0 0.0 0.0 0.0 114-115 5.4125 0.0 0.0 0.0 0.0 116-117 6.025 0.0 0.0 0.0 0.0 118-119 6.525 0.0 0.0 0.0 0.0 120-121 6.9875 0.0 0.0 0.0 0.0 122-123 7.5 0.0 0.0 0.0 0.0 124-125 8.1875 0.0 0.0 0.0 0.0 126-127 8.875 0.0 0.0 0.0 0.0 128-129 9.4625 0.0 0.0 0.0 0.0 130-131 10.075 0.0 0.0 0.0 0.0 132-133 10.8875 0.0 0.0 0.0 0.0 134-135 11.575 0.0 0.0 0.0 0.0 136-137 12.4375 0.0 0.0 0.0 0.0 138-139 13.125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CGTTCGA 10 0.006830828 145.0 4 TGCGTGC 10 0.006830828 145.0 3 GCGTGCT 10 0.006830828 145.0 4 >>END_MODULE Read 1699040 spots for SRR12951311.sra Written 1699040 spots for SRR12951311.sra Read 1699040 spots for SRR12951311.sra Written 1699040 spots for SRR12951311.sra Read 1699040 spots for SRR12951311.sra Written 1699040 spots for SRR12951311.sra Read 1699040 spots for SRR12951311.sra Written 1699040 spots for SRR12951311.sra Read 1699040 spots for SRR12951311.sra Written 1699040 spots for SRR12951311.sra Read 1699040 spots for SRR12951311.sra Written 1699040 spots for SRR12951311.sra Read 1699040 spots for SRR12951311.sra Written 1699040 spots for SRR12951311.sra Read 1699040 spots for SRR12951311.sra Written 1699040 spots for SRR12951311.sra Read 1699040 spots for SRR12951311.sra Written 1699040 spots for SRR12951311.sra Read 1699040 spots for SRR12951311.sra Written 1699040 spots for SRR12951311.sra Read 1699040 spots for SRR12951311.sra Written 1699040 spots for SRR12951311.sra Read 1699040 spots for SRR12951311.sra Written 1699040 spots for SRR12951311.sra Read 1699056 spots for SRR12951311.sra Written 1699056 spots for SRR12951311.sra Read 1699040 spots for SRR12951311.sra Written 1699040 spots for SRR12951311.sra Read 1699040 spots for SRR12951311.sra Written 1699040 spots for SRR12951311.sra Read 1699040 spots for SRR12951311.sra Written 1699040 spots for SRR12951311.sra Read 1699040 spots for SRR12951311.sra Written 1699040 spots for SRR12951311.sra Read 1699040 spots for SRR12951311.sra Written 1699040 spots for SRR12951311.sra Read 1699040 spots for SRR12951311.sra Written 1699040 spots for SRR12951311.sra Read 1699040 spots for SRR12951311.sra Written 1699040 spots for SRR12951311.sra SRR ids: ['SRR12951311.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_x5gklzj8 SRR12951311.sra spots: 33980816 blocks: [[1, 1699040], [1699041, 3398080], [3398081, 5097120], [5097121, 6796160], [6796161, 8495200], [8495201, 10194240], [10194241, 11893280], [11893281, 13592320], [13592321, 15291360], [15291361, 16990400], [16990401, 18689440], [18689441, 20388480], [20388481, 22087520], [22087521, 23786560], [23786561, 25485600], [25485601, 27184640], [27184641, 28883680], [28883681, 30582720], [30582721, 32281760], [32281761, 33980816]] SRR12951311 file size 11526467 SRR12951311 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 SRR12951311 SRR12951311_1.fastq SRR12951311_2.fastq Input file: SRR12951311_1.fastq Paired file: SRR12951311_2.fastq trimmed: SRR12951311-trimmed-pair1.fastq, SRR12951311-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 Sat Dec 7 11:26:29 2024 >> started Sat Dec 7 11:27:07 2024 >> done (38.471s) 33980816 read pairs processed; of these: 169 ( 0.00%) short read pairs filtered out after trimming by size control 169008 ( 0.50%) empty read pairs filtered out after trimming by size control 33811639 (99.50%) read pairs available; of these: 5883722 (17.40%) trimmed read pairs available after processing 27927917 (82.60%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 21 0.00% 19 23 0.00% 20 30 0.00% 21 29 0.00% 22 23 0.00% 23 63 0.00% 24 63 0.00% 25 51 0.00% 26 61 0.00% 27 54 0.00% 28 80 0.00% 29 71 0.00% 30 78 0.00% 31 83 0.00% 32 90 0.00% 33 82 0.00% 34 108 0.00% 35 96 0.00% 36 104 0.00% 37 111 0.00% 38 149 0.00% 39 126 0.00% 40 158 0.00% 41 186 0.00% 42 160 0.00% 43 170 0.00% 44 186 0.00% 45 215 0.00% 46 247 0.00% 47 286 0.00% 48 337 0.00% 49 376 0.00% 50 397 0.00% 51 474 0.00% 52 471 0.00% 53 524 0.00% 54 669 0.00% 55 668 0.00% 56 707 0.00% 57 784 0.00% 58 1025 0.00% 59 1092 0.00% 60 1261 0.00% 61 1621 0.00% 62 1716 0.01% 63 1992 0.01% 64 2099 0.01% 65 2263 0.01% 66 2527 0.01% 67 2865 0.01% 68 3323 0.01% 69 3552 0.01% 70 4200 0.01% 71 4783 0.01% 72 5729 0.02% 73 6728 0.02% 74 7109 0.02% 75 7841 0.02% 76 8210 0.02% 77 8822 0.03% 78 9958 0.03% 79 11398 0.03% 80 12415 0.04% 81 14302 0.04% 82 16144 0.05% 83 17601 0.05% 84 19453 0.06% 85 21040 0.06% 86 24403 0.07% 87 24602 0.07% 88 26027 0.08% 89 27011 0.08% 90 28866 0.09% 91 31570 0.09% 92 34423 0.10% 93 38143 0.11% 94 38715 0.11% 95 42496 0.13% 96 44306 0.13% 97 45942 0.14% 98 48138 0.14% 99 51162 0.15% 100 51465 0.15% 101 53408 0.16% 102 54661 0.16% 103 58307 0.17% 104 60863 0.18% 105 61971 0.18% 106 64270 0.19% 107 65874 0.19% 108 66287 0.20% 109 68421 0.20% 110 69109 0.20% 111 74179 0.22% 112 77187 0.23% 113 77790 0.23% 114 82665 0.24% 115 85741 0.25% 116 88476 0.26% 117 86632 0.26% 118 87714 0.26% 119 90319 0.27% 120 94522 0.28% 121 93313 0.28% 122 98254 0.29% 123 103044 0.30% 124 105978 0.31% 125 107237 0.32% 126 110864 0.33% 127 110040 0.33% 128 109481 0.32% 129 113815 0.34% 130 111086 0.33% 131 111976 0.33% 132 116245 0.34% 133 119441 0.35% 134 120089 0.36% 135 123585 0.37% 136 125577 0.37% 137 124382 0.37% 138 128972 0.38% 139 126640 0.37% 140 129623 0.38% 141 129844 0.38% 142 132234 0.39% 143 133023 0.39% 144 139104 0.41% 145 137502 0.41% 146 138549 0.41% 147 137877 0.41% 148 136356 0.40% 149 137964 0.41% 150 136282 0.40% 151 27927917 82.60% 33811639 reads passed initial QC criterion=sequence-density sequence-density=0.38 sequence-density-rank=1 fanout-score=2.73 fanout-score-rank=35 prefix-density=1.04 prefix-fanout=1.0 sequence=CTTGGATGTGGCAGCCGTTTCTC criterion=fanout-score sequence-density=0.03 sequence-density-rank=35 fanout-score=349.86 fanout-score-rank=1 prefix-density=0.49 prefix-fanout=19.5 sequence=CCGCCGCCGCGTAGCTTCTGGTGGACGGGGCCAGCAGCTGGGCCAGCGCGCGGGCAGCAGCCGAGGAACCGGAGAGAGCGAGAGCCATCGGATTGATCTGTGTGTTTTGATCGGATGGCTGGTGGCGCTCCGGCTCTCTGCTGCTGCTCCAACGTGGGTTGCTGGT criterion=sequence-density sequence-density=0.43 sequence-density-rank=1 fanout-score=2.06 fanout-score-rank=34 prefix-density=0.44 prefix-fanout=2.0 sequence=CGGTTCCGGTTC criterion=fanout-score sequence-density=0.08 sequence-density-rank=23 fanout-score=264.54 fanout-score-rank=1 prefix-density=0.75 prefix-fanout=26.9 sequence=GCGGCGGCGGCG SRR12951311 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 11:27:45 Started mapping on | Dec 07 11:27:45 Finished on | Dec 07 11:31:22 Mapping speed, Million of reads per hour | 560.93 Number of input reads | 33811639 Average input read length | 292 UNIQUE READS: Uniquely mapped reads number | 23932011 Uniquely mapped reads % | 70.78% Average mapped length | 291.94 Number of splices: Total | 20561567 Number of splices: Annotated (sjdb) | 19082654 Number of splices: GT/AG | 20286072 Number of splices: GC/AG | 234809 Number of splices: AT/AC | 13164 Number of splices: Non-canonical | 27522 Mismatch rate per base, % | 0.13% Deletion rate per base | 0.01% Deletion average length | 1.48 Insertion rate per base | 0.00% Insertion average length | 1.14 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 234882 % of reads mapped to multiple loci | 0.69% Number of reads mapped to too many loci | 1308399 % of reads mapped to too many loci | 3.87% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.61% % of reads unmapped: other | 21.04% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 9644746 9644746 9644746 N_multimapping 234882 234882 234882 N_noFeature 897435 23248205 1127634 N_ambiguous 539823 3389 85750 UnstrandedReadsAssigned:22494753 PositiveStrandReadsAssigned:680417 NegativeStrandReadsAssigned:22718627 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12951311 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: 52,972 [index] number of k-mers: 66,720,672 [index] number of equivalence classes: 111,837 [quant] running in paired-end mode [quant] will process pair 1: SRR12951311-trimmed-pair1.fastq SRR12951311-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 33,811,639 reads, 23,282,922 reads pseudoaligned [quant] estimated average fragment length: 241.779 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,146 rounds 52973 SRR12951311.ke.tsv 35125 SRR12951311.se.tsv 88098 total ==> SRR12951311.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 695.595 0 0 PNS24247 1044 803.221 143.959 10.3407 PNS24249 1928 1687.22 268.039 9.1658 PNS24246 1044 803.221 143.959 10.3407 PNS24248 1044 803.221 143.959 10.3407 PNS24244 1471 1230.22 159.082 7.46076 PNS24243 293 107.517 0 0 KQK14069 1603 1362.22 33385.8 1414.03 KQK14071 474 250.868 66.2416 15.2345 ==> SRR12951311.se.tsv <== BRADI_1g14170v3 33033 BRADI_1g53295v3 143 BRADI_1g59795v3 378 BRADI_1g07683v3 0 BRADI_1g00485v3 15 BRADI_1g20270v3 933 BRADI_1g74790v3 2753 BRADI_1g09890v3 0 BRADI_1g77505v3 233 BRADI_1g48960v3 0 SRR12951311 completed mapping pipeline successfully