Starting /dee2/code/volunteer_pipeline.sh ERR3450080 current disk space = 1542818152448 free memory = 1591133032 ERR3450080 SRAfilesize e728addcd1544089dd9a4c51290f5f9a ERR3450080.sra ERR3450080.sra file validated ERR3450080 is paired end ERR3450080 is conventional basespace ERR3450080 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3450080_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 101 %GC 52 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.08425 37.0 37.0 37.0 37.0 37.0 2 36.304 37.0 37.0 37.0 37.0 37.0 3 36.4335 37.0 37.0 37.0 37.0 37.0 4 36.4775 37.0 37.0 37.0 37.0 37.0 5 36.545 37.0 37.0 37.0 37.0 37.0 6 36.553 37.0 37.0 37.0 37.0 37.0 7 36.437 37.0 37.0 37.0 37.0 37.0 8 36.503 37.0 37.0 37.0 37.0 37.0 9 36.4905 37.0 37.0 37.0 37.0 37.0 10-11 36.52725 37.0 37.0 37.0 37.0 37.0 12-13 36.50425 37.0 37.0 37.0 37.0 37.0 14-15 36.43625 37.0 37.0 37.0 37.0 37.0 16-17 36.40525 37.0 37.0 37.0 37.0 37.0 18-19 36.530249999999995 37.0 37.0 37.0 37.0 37.0 20-21 36.5015 37.0 37.0 37.0 37.0 37.0 22-23 36.48175 37.0 37.0 37.0 37.0 37.0 24-25 36.48075 37.0 37.0 37.0 37.0 37.0 26-27 36.445499999999996 37.0 37.0 37.0 37.0 37.0 28-29 36.442499999999995 37.0 37.0 37.0 37.0 37.0 30-31 36.41675 37.0 37.0 37.0 37.0 37.0 32-33 36.393 37.0 37.0 37.0 37.0 37.0 34-35 36.411249999999995 37.0 37.0 37.0 37.0 37.0 36-37 36.34375 37.0 37.0 37.0 37.0 37.0 38-39 36.34975 37.0 37.0 37.0 37.0 37.0 40-41 36.342 37.0 37.0 37.0 37.0 37.0 42-43 36.2845 37.0 37.0 37.0 37.0 37.0 44-45 36.2495 37.0 37.0 37.0 37.0 37.0 46-47 36.30875 37.0 37.0 37.0 37.0 37.0 48-49 36.1695 37.0 37.0 37.0 37.0 37.0 50-51 36.27325 37.0 37.0 37.0 37.0 37.0 52-53 36.19775 37.0 37.0 37.0 37.0 37.0 54-55 36.144999999999996 37.0 37.0 37.0 37.0 37.0 56-57 36.0955 37.0 37.0 37.0 37.0 37.0 58-59 36.12025 37.0 37.0 37.0 37.0 37.0 60-61 36.071749999999994 37.0 37.0 37.0 37.0 37.0 62-63 36.02525 37.0 37.0 37.0 37.0 37.0 64-65 36.08925 37.0 37.0 37.0 37.0 37.0 66-67 36.059 37.0 37.0 37.0 37.0 37.0 68-69 36.008250000000004 37.0 37.0 37.0 37.0 37.0 70-71 36.07175 37.0 37.0 37.0 37.0 37.0 72-73 36.14175 37.0 37.0 37.0 37.0 37.0 74-75 36.15675 37.0 37.0 37.0 37.0 37.0 76-77 36.15875 37.0 37.0 37.0 37.0 37.0 78-79 36.0415 37.0 37.0 37.0 37.0 37.0 80-81 36.083749999999995 37.0 37.0 37.0 37.0 37.0 82-83 36.035 37.0 37.0 37.0 37.0 37.0 84-85 36.058 37.0 37.0 37.0 37.0 37.0 86-87 36.1075 37.0 37.0 37.0 37.0 37.0 88-89 36.039500000000004 37.0 37.0 37.0 37.0 37.0 90-91 35.980000000000004 37.0 37.0 37.0 37.0 37.0 92-93 36.02525 37.0 37.0 37.0 37.0 37.0 94-95 35.9595 37.0 37.0 37.0 37.0 37.0 96-97 35.92275 37.0 37.0 37.0 37.0 37.0 98-99 35.929 37.0 37.0 37.0 37.0 37.0 100-101 35.91 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 23 1.0 24 5.0 25 5.0 26 9.0 27 16.0 28 21.0 29 37.0 30 28.0 31 53.0 32 91.0 33 85.0 34 121.0 35 178.0 36 1726.0 37 1624.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 40.87371328144614 9.666080843585236 10.946522721566659 38.513683153401956 2 21.625 13.175 29.099999999999998 36.1 3 22.0 15.125 25.525 37.35 4 27.900000000000002 21.55 17.7 32.85 5 26.05 26.325 22.7 24.925 6 22.425 31.15 24.875 21.55 7 20.25 22.35 36.475 20.925 8 21.55 21.0 29.45 28.000000000000004 9 23.775 20.175 30.475 25.575 10-11 24.3 28.575 22.400000000000002 24.725 12-13 23.5875 22.900000000000002 25.7125 27.800000000000004 14-15 23.25 23.8625 26.687499999999996 26.200000000000003 16-17 23.5125 24.1125 25.6 26.775 18-19 23.674999999999997 25.05 24.5375 26.737499999999997 20-21 24.575 24.212500000000002 25.637500000000003 25.575 22-23 25.1 24.175 24.6 26.125 24-25 23.425 24.025 25.412499999999998 27.1375 26-27 23.5625 23.724999999999998 25.5 27.212500000000002 28-29 24.8125 23.5125 24.2875 27.3875 30-31 23.8125 24.212500000000002 24.0375 27.9375 32-33 24.3875 23.575 24.775 27.2625 34-35 24.875 23.275000000000002 23.8125 28.037499999999998 36-37 23.875 24.0625 24.212500000000002 27.85 38-39 24.5 23.9125 23.95 27.6375 40-41 23.9125 23.4625 24.2375 28.3875 42-43 23.75 23.7 24.712500000000002 27.8375 44-45 24.6125 23.5875 24.7375 27.0625 46-47 25.837500000000002 23.95 23.35 26.8625 48-49 24.0125 23.775 23.8375 28.375 50-51 24.9375 22.7375 24.85 27.474999999999998 52-53 24.6 23.799999999999997 23.225 28.375 54-55 25.374999999999996 23.599999999999998 23.9375 27.0875 56-57 24.825 23.25 23.925 28.000000000000004 58-59 25.587500000000002 23.375 23.849999999999998 27.187499999999996 60-61 25.412499999999998 23.3875 23.7 27.500000000000004 62-63 24.775 22.75 25.275 27.200000000000003 64-65 24.2375 23.8625 23.9125 27.987499999999997 66-67 24.6875 23.3 23.4375 28.575 68-69 26.0 24.5375 23.2375 26.224999999999998 70-71 25.087500000000002 24.25 23.0625 27.6 72-73 25.525 23.875 23.5875 27.0125 74-75 25.924999999999997 24.6 23.0 26.474999999999998 76-77 26.400000000000002 23.3125 24.0 26.2875 78-79 25.337500000000002 23.4125 23.175 28.075 80-81 24.9375 24.2375 23.175 27.650000000000002 82-83 25.825 23.4625 24.325 26.387500000000003 84-85 25.587500000000002 23.5875 24.15 26.674999999999997 86-87 26.187500000000004 23.724999999999998 23.05 27.037499999999998 88-89 25.324999999999996 24.775 23.2375 26.6625 90-91 26.474999999999998 23.1875 22.675 27.6625 92-93 26.0375 23.425 24.2 26.337500000000002 94-95 25.337500000000002 24.325 23.225 27.1125 96-97 24.587500000000002 23.7375 23.6375 28.037499999999998 98-99 25.2125 23.2625 23.8375 27.6875 100-101 24.9125 25.0 23.400000000000002 26.687499999999996 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 8.0 1 5.5 2 2.5 3 1.0 4 0.5 5 2.0 6 2.0 7 0.5 8 0.0 9 1.5 10 1.5 11 0.5 12 1.0 13 0.5 14 1.0 15 1.5 16 1.0 17 1.0 18 1.0 19 0.5 20 0.0 21 0.5 22 1.0 23 0.5 24 0.0 25 0.0 26 1.0 27 3.0 28 2.0 29 0.0 30 1.0 31 5.5 32 10.0 33 9.5 34 10.5 35 19.5 36 27.0 37 38.5 38 41.5 39 46.0 40 71.5 41 91.0 42 97.0 43 111.5 44 137.5 45 149.5 46 166.0 47 181.5 48 183.5 49 182.0 50 168.0 51 153.0 52 158.5 53 164.5 54 164.0 55 155.5 56 146.5 57 131.0 58 100.5 59 90.0 60 95.0 61 85.5 62 72.0 63 66.5 64 64.0 65 59.0 66 65.0 67 68.0 68 55.5 69 43.5 70 38.0 71 44.0 72 39.5 73 33.0 74 29.5 75 24.0 76 19.0 77 13.5 78 8.0 79 4.5 80 5.5 81 6.0 82 4.5 83 4.5 84 2.5 85 0.5 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 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.42500000000000004 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-11 0.0 12-13 0.0 14-15 0.0 16-17 0.0 18-19 0.0 20-21 0.0 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.0 30-31 0.0 32-33 0.0 34-35 0.0 36-37 0.0 38-39 0.0 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0 54-55 0.0 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0 66-67 0.0 68-69 0.0 70-71 0.0 72-73 0.0 74-75 0.0 76-77 0.0 78-79 0.0 80-81 0.0 82-83 0.0 84-85 0.0 86-87 0.0 88-89 0.0 90-91 0.0 92-93 0.0 94-95 0.0 96-97 0.0 98-99 0.0 100-101 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 101 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 83.675 #Duplication Level Percentage of deduplicated Percentage of total 1 85.33014639976098 71.39999999999999 2 11.771735882880192 19.7 3 2.1810576635793244 5.475 4 0.23902001792650132 0.8 5 0.23902001792650132 1.0 6 0.089632506722438 0.44999999999999996 7 0.05975500448162533 0.35000000000000003 8 0.029877502240812665 0.2 9 0.0 0.0 >10 0.05975500448162533 0.625 >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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACCTGAAGCTATCTCGTAT 14 0.35000000000000003 TruSeq Adapter, Index 19 (97% over 38bp) AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 11 0.27499999999999997 No Hit CCCGACTGTCCCTATTAATCATTACTCCGATCCCGAAGGCCAACACAATA 8 0.2 No Hit GCTGGAATTACCGCGGCTGCTGGCACCAGACTTGCCCTCCAATGGATCCT 7 0.17500000000000002 No Hit CTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTG 7 0.17500000000000002 No Hit GTCACTACCTCCCCGTGTCAGGATTGGGTAATTTGCGCGCCTGCTGCCTT 6 0.15 No Hit ATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATA 6 0.15 No Hit CGGCATCGTTTATGGTTGAGACTAGGACGGTATCTGATCGTCTTCGAGCC 6 0.15 No Hit CTTCCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGA 5 0.125 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACCTGAAGCTATCGCGTAT 5 0.125 TruSeq Adapter, Index 19 (97% over 38bp) CCTAATTCTCCGTCACCCGTCACCACCATGGTAGGCCCCTATCCTACCAT 5 0.125 No Hit GCGGTCATTTAGGGGCCTTAGCTGGTGATCCGGGCTGTTTCCCTCTCGAC 5 0.125 No Hit GCAGAAATTTGAATGATGCGTCGCCGGCACGAGGGCCGTGCGATCCGTCG 5 0.125 No Hit GCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGC 5 0.125 No Hit CCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCT 5 0.125 No Hit GCGGTTATGAGTACGACCGGGCGTGAACGGTACTCGGTCCTCCGGATTTT 5 0.125 No Hit >>END_MODULE >>Adapter Content warn #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 0.0125 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.0625 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 0.1 0.0 0.0 0.0 0.0 40-41 0.1 0.0 0.0 0.0 0.0 42-43 0.15 0.0 0.0 0.0 0.0 44-45 0.2 0.0 0.0 0.0 0.0 46-47 0.2875 0.0 0.0 0.0 0.0 48-49 0.325 0.0 0.0 0.0 0.0 50-51 0.3375 0.0 0.0 0.0 0.0 52-53 0.45 0.0 0.0 0.0 0.0 54-55 0.5 0.0 0.0 0.0 0.0 56-57 0.5874999999999999 0.0 0.0 0.0 0.0 58-59 0.7125 0.0 0.0 0.0 0.0 60-61 0.85 0.0 0.0 0.0 0.0 62-63 1.0 0.0 0.0 0.0 0.0 64-65 1.1875 0.0 0.0 0.0 0.0 66-67 1.3375 0.0 0.0 0.0 0.0 68-69 1.475 0.0 0.0 0.0 0.0 70-71 1.675 0.0 0.0 0.0 0.0 72-73 1.8875000000000002 0.0 0.0 0.0 0.0 74-75 2.125 0.0 0.0 0.0 0.0 76-77 2.5250000000000004 0.0 0.0 0.0 0.0 78-79 2.9124999999999996 0.0 0.0 0.0 0.0 80-81 3.2625 0.0 0.0 0.0 0.0 82-83 3.85 0.0 0.0 0.0 0.0 84-85 4.2 0.0 0.0 0.0 0.0 86-87 4.75 0.0 0.0 0.0 0.0 88-89 5.325 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ATCAACT 15 0.009957196 47.5 58-59 >>END_MODULE ERR3450080 read2 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3450080_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 101 %GC 53 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.9895 37.0 37.0 37.0 37.0 37.0 2 35.881 37.0 37.0 37.0 37.0 37.0 3 35.9755 37.0 37.0 37.0 37.0 37.0 4 36.03 37.0 37.0 37.0 37.0 37.0 5 36.098 37.0 37.0 37.0 37.0 37.0 6 36.1565 37.0 37.0 37.0 37.0 37.0 7 36.0365 37.0 37.0 37.0 37.0 37.0 8 36.069 37.0 37.0 37.0 37.0 37.0 9 36.1515 37.0 37.0 37.0 37.0 37.0 10-11 36.08625 37.0 37.0 37.0 37.0 37.0 12-13 36.02825 37.0 37.0 37.0 37.0 37.0 14-15 35.998999999999995 37.0 37.0 37.0 37.0 37.0 16-17 36.0215 37.0 37.0 37.0 37.0 37.0 18-19 36.069500000000005 37.0 37.0 37.0 37.0 37.0 20-21 36.0525 37.0 37.0 37.0 37.0 37.0 22-23 35.9745 37.0 37.0 37.0 37.0 37.0 24-25 35.979749999999996 37.0 37.0 37.0 37.0 37.0 26-27 35.963499999999996 37.0 37.0 37.0 37.0 37.0 28-29 35.824749999999995 37.0 37.0 37.0 37.0 37.0 30-31 35.846500000000006 37.0 37.0 37.0 37.0 37.0 32-33 35.8225 37.0 37.0 37.0 37.0 37.0 34-35 35.78075 37.0 37.0 37.0 37.0 37.0 36-37 35.89325 37.0 37.0 37.0 37.0 37.0 38-39 35.858999999999995 37.0 37.0 37.0 37.0 37.0 40-41 35.82125 37.0 37.0 37.0 37.0 37.0 42-43 35.74625 37.0 37.0 37.0 37.0 37.0 44-45 35.8265 37.0 37.0 37.0 37.0 37.0 46-47 35.786249999999995 37.0 37.0 37.0 37.0 37.0 48-49 35.748999999999995 37.0 37.0 37.0 37.0 37.0 50-51 35.829750000000004 37.0 37.0 37.0 37.0 37.0 52-53 35.7405 37.0 37.0 37.0 37.0 37.0 54-55 35.8475 37.0 37.0 37.0 37.0 37.0 56-57 35.84375 37.0 37.0 37.0 37.0 37.0 58-59 35.750249999999994 37.0 37.0 37.0 37.0 37.0 60-61 35.724000000000004 37.0 37.0 37.0 37.0 37.0 62-63 35.777249999999995 37.0 37.0 37.0 37.0 37.0 64-65 35.8245 37.0 37.0 37.0 37.0 37.0 66-67 35.76875 37.0 37.0 37.0 37.0 37.0 68-69 35.7525 37.0 37.0 37.0 37.0 37.0 70-71 35.722 37.0 37.0 37.0 37.0 37.0 72-73 35.659 37.0 37.0 37.0 37.0 37.0 74-75 35.642250000000004 37.0 37.0 37.0 37.0 37.0 76-77 35.678 37.0 37.0 37.0 37.0 37.0 78-79 35.7035 37.0 37.0 37.0 37.0 37.0 80-81 35.781499999999994 37.0 37.0 37.0 37.0 37.0 82-83 35.709500000000006 37.0 37.0 37.0 37.0 37.0 84-85 35.652249999999995 37.0 37.0 37.0 37.0 37.0 86-87 35.682 37.0 37.0 37.0 37.0 37.0 88-89 35.64375 37.0 37.0 37.0 37.0 37.0 90-91 35.687 37.0 37.0 37.0 37.0 37.0 92-93 35.54325 37.0 37.0 37.0 37.0 37.0 94-95 35.647 37.0 37.0 37.0 37.0 37.0 96-97 35.51575 37.0 37.0 37.0 37.0 37.0 98-99 35.497 37.0 37.0 37.0 37.0 37.0 100-101 35.551249999999996 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 1.0 14 3.0 15 10.0 16 7.0 17 4.0 18 4.0 19 9.0 20 9.0 21 12.0 22 8.0 23 13.0 24 17.0 25 16.0 26 17.0 27 19.0 28 22.0 29 17.0 30 39.0 31 46.0 32 53.0 33 65.0 34 118.0 35 241.0 36 2133.0 37 1117.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 41.4 16.675 11.95 29.975 2 27.05 22.95 25.775 24.224999999999998 3 25.8 23.35 26.650000000000002 24.2 4 29.425 26.924999999999997 17.05 26.6 5 31.474999999999998 27.85 17.825 22.85 6 24.375 32.6 20.674999999999997 22.35 7 26.650000000000002 19.55 31.0 22.8 8 26.825 19.650000000000002 23.425 30.099999999999998 9 27.400000000000002 22.6 24.05 25.95 10-11 29.812499999999996 26.7125 18.3 25.174999999999997 12-13 28.9 21.475 22.400000000000002 27.224999999999998 14-15 28.15 25.45 22.05 24.349999999999998 16-17 28.962500000000002 23.25 22.287499999999998 25.5 18-19 29.099999999999998 24.125 21.6 25.174999999999997 20-21 27.6875 25.45 22.4375 24.425 22-23 28.4125 23.3625 21.775 26.450000000000003 24-25 27.5125 23.575 23.7625 25.15 26-27 28.1625 24.087500000000002 22.575 25.174999999999997 28-29 29.175 24.1625 21.475 25.1875 30-31 27.675 24.3625 21.5 26.4625 32-33 27.762500000000003 24.474999999999998 22.6375 25.124999999999996 34-35 27.975 24.7 21.8 25.525 36-37 26.9625 24.75 22.125 26.1625 38-39 28.000000000000004 24.4375 21.775 25.7875 40-41 28.475 24.2875 20.925 26.3125 42-43 27.925 24.349999999999998 23.0125 24.712500000000002 44-45 27.6875 25.637500000000003 22.5 24.175 46-47 27.6 24.5375 21.9625 25.900000000000002 48-49 27.5875 24.224999999999998 22.9625 25.224999999999998 50-51 26.224999999999998 24.025 22.7 27.05 52-53 27.212500000000002 24.5375 22.287499999999998 25.9625 54-55 28.3375 24.2375 22.725 24.7 56-57 27.875 24.2 22.525000000000002 25.4 58-59 29.037499999999998 24.0375 22.0 24.925 60-61 27.737499999999997 25.087500000000002 22.925 24.25 62-63 28.575 24.4375 22.8 24.1875 64-65 29.575000000000003 24.7375 22.1 23.5875 66-67 28.375 24.125 22.4625 25.0375 68-69 28.1375 25.1 22.3125 24.45 70-71 28.6875 24.55 21.837500000000002 24.925 72-73 28.537499999999998 25.025 22.5 23.9375 74-75 28.3625 25.087500000000002 21.8 24.75 76-77 29.2375 24.425 21.2875 25.05 78-79 27.4125 24.6875 23.275000000000002 24.625 80-81 26.8375 24.875 22.537499999999998 25.75 82-83 28.199999999999996 24.65 21.8875 25.2625 84-85 27.8875 24.212500000000002 23.875 24.025 86-87 29.025000000000002 23.3625 23.225 24.3875 88-89 28.3875 24.837500000000002 21.762500000000003 25.0125 90-91 29.3375 24.6625 22.1875 23.8125 92-93 28.599999999999998 26.150000000000002 21.337500000000002 23.9125 94-95 28.6625 24.925 21.7375 24.675 96-97 28.9875 24.95 22.650000000000002 23.4125 98-99 28.9375 25.3 21.8625 23.9 100-101 28.799999999999997 24.4375 23.2375 23.525 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.5 2 1.0 3 0.5 4 0.0 5 1.0 6 3.5 7 3.0 8 1.5 9 1.5 10 1.0 11 2.5 12 3.0 13 1.5 14 0.5 15 0.5 16 0.5 17 1.0 18 3.0 19 2.0 20 1.0 21 1.5 22 0.5 23 0.5 24 2.5 25 5.0 26 3.5 27 1.5 28 3.0 29 4.0 30 3.5 31 4.5 32 5.5 33 5.5 34 7.5 35 9.5 36 15.0 37 26.5 38 37.5 39 49.5 40 62.0 41 82.0 42 102.0 43 129.0 44 141.0 45 129.5 46 140.0 47 160.5 48 179.5 49 165.5 50 153.0 51 164.0 52 164.0 53 156.5 54 154.0 55 141.0 56 131.0 57 123.5 58 106.5 59 92.0 60 83.5 61 95.0 62 79.5 63 68.0 64 86.5 65 83.5 66 64.0 67 64.5 68 66.5 69 60.5 70 58.0 71 47.5 72 36.5 73 39.5 74 40.0 75 28.0 76 16.5 77 14.0 78 16.0 79 9.5 80 6.0 81 6.0 82 4.0 83 2.5 84 0.5 85 0.0 86 0.5 87 0.5 88 1.0 89 1.5 90 1.0 91 1.0 92 0.5 93 1.0 94 2.0 95 1.0 96 0.0 97 3.0 98 3.5 99 2.5 100 7.5 >>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 10-11 0.0 12-13 0.0 14-15 0.0 16-17 0.0 18-19 0.0 20-21 0.0 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.0 30-31 0.0 32-33 0.0 34-35 0.0 36-37 0.0 38-39 0.0 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0 54-55 0.0 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0 66-67 0.0 68-69 0.0 70-71 0.0 72-73 0.0 74-75 0.0 76-77 0.0 78-79 0.0 80-81 0.0 82-83 0.0 84-85 0.0 86-87 0.0 88-89 0.0 90-91 0.0 92-93 0.0 94-95 0.0 96-97 0.0 98-99 0.0 100-101 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 101 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 84.65 #Duplication Level Percentage of deduplicated Percentage of total 1 86.00118133490845 72.8 2 11.311281748375665 19.15 3 1.919669226225635 4.875 4 0.5611340815121088 1.9 5 0.08860011813349085 0.375 6 0.0 0.0 7 0.08860011813349085 0.525 8 0.0 0.0 9 0.0 0.0 >10 0.029533372711163616 0.375 >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 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 15 0.375 No Hit CCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGCAA 7 0.17500000000000002 No Hit CTTTGGGCCGGGTCGGCCGGTCCGCCTCACGGCGAGCACCGACCTACTCG 7 0.17500000000000002 No Hit GGGAAACTTACCAGGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTC 7 0.17500000000000002 No Hit GAGCGATTTGTCTGGTTAATTCCGTTAACGAACGAGACCTCAGCCTGCTA 5 0.125 No Hit GTAATTCTAGAGCTAATACGTGCAACAAACCCCGACTTCTGGGAGGGGCG 5 0.125 No Hit TCGCCGTTTAGGCGACGGAAGTTTGAGGCAATAACAGGTCTGTGATGCCC 5 0.125 No Hit >>END_MODULE >>Adapter Content warn #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 0.0125 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.0625 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 0.1 0.0 0.0 0.0 0.0 40-41 0.1 0.0 0.0 0.0 0.0 42-43 0.125 0.0 0.0 0.0 0.0 44-45 0.175 0.0 0.0 0.0 0.0 46-47 0.2625 0.0 0.0 0.0 0.0 48-49 0.3 0.0 0.0 0.0 0.0 50-51 0.3375 0.0 0.0 0.0 0.0 52-53 0.45 0.0 0.0 0.0 0.0 54-55 0.5 0.0 0.0 0.0 0.0 56-57 0.5874999999999999 0.0 0.0 0.0 0.0 58-59 0.7125 0.0 0.0 0.0 0.0 60-61 0.85 0.0 0.0 0.0 0.0 62-63 1.0125 0.0 0.0 0.0 0.0 64-65 1.2125 0.0 0.0 0.0 0.0 66-67 1.3624999999999998 0.0 0.0 0.0 0.0 68-69 1.5 0.0 0.0 0.0 0.0 70-71 1.7 0.0 0.0 0.0 0.0 72-73 1.9125 0.0 0.0 0.0 0.0 74-75 2.1500000000000004 0.0 0.0 0.0 0.0 76-77 2.575 0.0 0.0 0.0 0.0 78-79 2.9625000000000004 0.0 0.0 0.0 0.0 80-81 3.3 0.0 0.0 0.0 0.0 82-83 3.8625 0.0 0.0 0.0 0.0 84-85 4.2 0.0 0.0 0.0 0.0 86-87 4.75 0.0 0.0 0.0 0.0 88-89 5.325 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1460331 spots for ERR3450080.sra Written 1460331 spots for ERR3450080.sra Read 1460331 spots for ERR3450080.sra Written 1460331 spots for ERR3450080.sra Read 1460332 spots for ERR3450080.sra Written 1460332 spots for ERR3450080.sra Read 1460331 spots for ERR3450080.sra Written 1460331 spots for ERR3450080.sra Read 1460331 spots for ERR3450080.sra Written 1460331 spots for ERR3450080.sra Read 1460331 spots for ERR3450080.sra Written 1460331 spots for ERR3450080.sra Read 1460331 spots for ERR3450080.sra Written 1460331 spots for ERR3450080.sra Read 1460331 spots for ERR3450080.sra Written 1460331 spots for ERR3450080.sra Read 1460331 spots for ERR3450080.sra Written 1460331 spots for ERR3450080.sra Read 1460331 spots for ERR3450080.sra Written 1460331 spots for ERR3450080.sra Read 1460331 spots for ERR3450080.sra Written 1460331 spots for ERR3450080.sra Read 1460331 spots for ERR3450080.sra Written 1460331 spots for ERR3450080.sra Read 1460331 spots for ERR3450080.sra Written 1460331 spots for ERR3450080.sra Read 1460331 spots for ERR3450080.sra Written 1460331 spots for ERR3450080.sra Read 1460331 spots for ERR3450080.sra Written 1460331 spots for ERR3450080.sra Read 1460331 spots for ERR3450080.sra Written 1460331 spots for ERR3450080.sra Read 1460331 spots for ERR3450080.sra Written 1460331 spots for ERR3450080.sra Read 1460331 spots for ERR3450080.sra Written 1460331 spots for ERR3450080.sra Read 1460331 spots for ERR3450080.sra Written 1460331 spots for ERR3450080.sra Read 1460331 spots for ERR3450080.sra Written 1460331 spots for ERR3450080.sra SRR ids: ['ERR3450080.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_ift9mw76 ERR3450080.sra spots: 29206621 blocks: [[1, 1460331], [1460332, 2920662], [2920663, 4380993], [4380994, 5841324], [5841325, 7301655], [7301656, 8761986], [8761987, 10222317], [10222318, 11682648], [11682649, 13142979], [13142980, 14603310], [14603311, 16063641], [16063642, 17523972], [17523973, 18984303], [18984304, 20444634], [20444635, 21904965], [21904966, 23365296], [23365297, 24825627], [24825628, 26285958], [26285959, 27746289], [27746290, 29206621]] ERR3450080 file size 7023256 ERR3450080 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 ERR3450080 ERR3450080_1.fastq ERR3450080_2.fastq Input file: ERR3450080_1.fastq Paired file: ERR3450080_2.fastq trimmed: ERR3450080-trimmed-pair1.fastq, ERR3450080-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 14:52:24 2024 >> started Sat Dec 7 14:53:14 2024 >> done (50.083s) 29206621 read pairs processed; of these: 148 ( 0.00%) short read pairs filtered out after trimming by size control 119505 ( 0.41%) empty read pairs filtered out after trimming by size control 29086968 (99.59%) read pairs available; of these: 2802733 ( 9.64%) trimmed read pairs available after processing 26284235 (90.36%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 55 0.00% 19 89 0.00% 20 251 0.00% 21 576 0.00% 22 715 0.00% 23 341 0.00% 24 372 0.00% 25 472 0.00% 26 723 0.00% 27 970 0.00% 28 1394 0.00% 29 1711 0.01% 30 2087 0.01% 31 2442 0.01% 32 2625 0.01% 33 2554 0.01% 34 2517 0.01% 35 2615 0.01% 36 2771 0.01% 37 3241 0.01% 38 3745 0.01% 39 4186 0.01% 40 5052 0.02% 41 5625 0.02% 42 6447 0.02% 43 6943 0.02% 44 6647 0.02% 45 6452 0.02% 46 6780 0.02% 47 7445 0.03% 48 8323 0.03% 49 9023 0.03% 50 10447 0.04% 51 11268 0.04% 52 12327 0.04% 53 13424 0.05% 54 13890 0.05% 55 14338 0.05% 56 15060 0.05% 57 15942 0.05% 58 17457 0.06% 59 18603 0.06% 60 20483 0.07% 61 22470 0.08% 62 24243 0.08% 63 26429 0.09% 64 27669 0.10% 65 28776 0.10% 66 29598 0.10% 67 31222 0.11% 68 32906 0.11% 69 33867 0.12% 70 35869 0.12% 71 38346 0.13% 72 41692 0.14% 73 44120 0.15% 74 46293 0.16% 75 47958 0.16% 76 49492 0.17% 77 50822 0.17% 78 53464 0.18% 79 55630 0.19% 80 57931 0.20% 81 60339 0.21% 82 64065 0.22% 83 66203 0.23% 84 68956 0.24% 85 71488 0.25% 86 73274 0.25% 87 75947 0.26% 88 78171 0.27% 89 81168 0.28% 90 83564 0.29% 91 88195 0.30% 92 92005 0.32% 93 94377 0.32% 94 98252 0.34% 95 101311 0.35% 96 103922 0.36% 97 106842 0.37% 98 108722 0.37% 99 109454 0.38% 100 129253 0.44% 101 26284235 90.36% 29086968 reads passed initial QC criterion=sequence-density sequence-density=0.25 sequence-density-rank=1 fanout-score=2.26 fanout-score-rank=29 prefix-density=0.27 prefix-fanout=2.1 sequence=TTTCCTCTGGCTTCGCCCCGCTCAGGCATAGTTCACCATCTTTCGGGTCCCGACAGGCGTGCTCCAACTCGAACCCTTCACAGAAGATCAGGGTCGGCCAGCGGTGCGGCCCGTGAGGGCCTCCCGCTCGTCAGCTTCCTTGCGCATCCCAGGTTTCAGAACCCGTCGACTCGCACGCATGTCAGACTCCTTGGTCCGTGTT criterion=fanout-score sequence-density=0.07 sequence-density-rank=28 fanout-score=187.07 fanout-score-rank=1 prefix-density=0.54 prefix-fanout=22.4 sequence=CGCCGCCGCCGC criterion=sequence-density sequence-density=0.24 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=30 prefix-density=0.24 prefix-fanout=2.0 sequence=CAAGTGTTGGATT criterion=fanout-score sequence-density=0.07 sequence-density-rank=24 fanout-score=219.57 fanout-score-rank=1 prefix-density=1.23 prefix-fanout=13.2 sequence=CGCCGCCGCCAT ERR3450080 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 14:53:45 Started mapping on | Dec 07 14:53:46 Finished on | Dec 07 14:56:12 Mapping speed, Million of reads per hour | 717.21 Number of input reads | 29086968 Average input read length | 198 UNIQUE READS: Uniquely mapped reads number | 20881177 Uniquely mapped reads % | 71.79% Average mapped length | 197.95 Number of splices: Total | 13189806 Number of splices: Annotated (sjdb) | 12494126 Number of splices: GT/AG | 13014589 Number of splices: GC/AG | 151860 Number of splices: AT/AC | 8361 Number of splices: Non-canonical | 14996 Mismatch rate per base, % | 0.23% Deletion rate per base | 0.01% Deletion average length | 2.08 Insertion rate per base | 0.01% Insertion average length | 1.94 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1665340 % of reads mapped to multiple loci | 5.73% Number of reads mapped to too many loci | 1073034 % of reads mapped to too many loci | 3.69% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.74% % of reads unmapped: other | 15.06% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 6540451 6540451 6540451 N_multimapping 1665340 1665340 1665340 N_noFeature 794753 20073187 1280877 N_ambiguous 389705 3336 71103 UnstrandedReadsAssigned:19696719 PositiveStrandReadsAssigned:804654 NegativeStrandReadsAssigned:19529197 Dataset is classified negative stranded MeadianReadLen=101 20thPercentileLength=101 echo kmer=97 ERR3450080 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: ERR3450080-trimmed-pair1.fastq ERR3450080-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 29,086,968 reads, 20,742,401 reads pseudoaligned [quant] estimated average fragment length: 185.811 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,162 rounds 52973 ERR3450080.ke.tsv 35125 ERR3450080.se.tsv 88098 total ==> ERR3450080.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 751.459 0 0 PNS24247 1044 859.189 47.0034 3.88301 PNS24249 1928 1743.19 302.754 12.3275 PNS24246 1044 859.189 47.0034 3.88301 PNS24248 1044 859.189 47.0034 3.88301 PNS24244 1471 1286.19 45.2359 2.49636 PNS24243 293 128.92 1 0.550563 KQK14069 1603 1418.19 1448.17 72.4793 KQK14071 474 293.089 78.2385 18.9474 ==> ERR3450080.se.tsv <== BRADI_1g14170v3 1533 BRADI_1g53295v3 19 BRADI_1g59795v3 254 BRADI_1g07683v3 0 BRADI_1g00485v3 47 BRADI_1g20270v3 3925 BRADI_1g74790v3 178 BRADI_1g09890v3 35 BRADI_1g77505v3 304 BRADI_1g48960v3 0 ERR3450080 completed mapping pipeline successfully