Starting /dee2/code/volunteer_pipeline.sh ERR3450074 current disk space = 1542963961856 free memory = 1594279220 ERR3450074 SRAfilesize 4ab147ab184508a0431bc577735ef511 ERR3450074.sra ERR3450074.sra file validated ERR3450074 is paired end ERR3450074 is conventional basespace ERR3450074 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3450074_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 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.13425 37.0 37.0 37.0 37.0 37.0 2 36.235 37.0 37.0 37.0 37.0 37.0 3 36.384 37.0 37.0 37.0 37.0 37.0 4 36.409 37.0 37.0 37.0 37.0 37.0 5 36.4155 37.0 37.0 37.0 37.0 37.0 6 36.5245 37.0 37.0 37.0 37.0 37.0 7 36.3975 37.0 37.0 37.0 37.0 37.0 8 36.4275 37.0 37.0 37.0 37.0 37.0 9 36.462 37.0 37.0 37.0 37.0 37.0 10-11 36.50625 37.0 37.0 37.0 37.0 37.0 12-13 36.40475 37.0 37.0 37.0 37.0 37.0 14-15 36.46575 37.0 37.0 37.0 37.0 37.0 16-17 36.499750000000006 37.0 37.0 37.0 37.0 37.0 18-19 36.47 37.0 37.0 37.0 37.0 37.0 20-21 36.4095 37.0 37.0 37.0 37.0 37.0 22-23 36.38875 37.0 37.0 37.0 37.0 37.0 24-25 36.3455 37.0 37.0 37.0 37.0 37.0 26-27 36.3785 37.0 37.0 37.0 37.0 37.0 28-29 36.275999999999996 37.0 37.0 37.0 37.0 37.0 30-31 36.34025 37.0 37.0 37.0 37.0 37.0 32-33 36.376999999999995 37.0 37.0 37.0 37.0 37.0 34-35 36.27525 37.0 37.0 37.0 37.0 37.0 36-37 36.294250000000005 37.0 37.0 37.0 37.0 37.0 38-39 36.313500000000005 37.0 37.0 37.0 37.0 37.0 40-41 36.216499999999996 37.0 37.0 37.0 37.0 37.0 42-43 36.18925 37.0 37.0 37.0 37.0 37.0 44-45 36.17400000000001 37.0 37.0 37.0 37.0 37.0 46-47 36.10025 37.0 37.0 37.0 37.0 37.0 48-49 36.16875 37.0 37.0 37.0 37.0 37.0 50-51 36.14149999999999 37.0 37.0 37.0 37.0 37.0 52-53 36.0865 37.0 37.0 37.0 37.0 37.0 54-55 36.07875 37.0 37.0 37.0 37.0 37.0 56-57 36.02175 37.0 37.0 37.0 37.0 37.0 58-59 35.980000000000004 37.0 37.0 37.0 37.0 37.0 60-61 35.969 37.0 37.0 37.0 37.0 37.0 62-63 36.0005 37.0 37.0 37.0 37.0 37.0 64-65 36.02475 37.0 37.0 37.0 37.0 37.0 66-67 35.97725 37.0 37.0 37.0 37.0 37.0 68-69 36.028999999999996 37.0 37.0 37.0 37.0 37.0 70-71 35.91075 37.0 37.0 37.0 37.0 37.0 72-73 35.9805 37.0 37.0 37.0 37.0 37.0 74-75 36.07225 37.0 37.0 37.0 37.0 37.0 76-77 36.024249999999995 37.0 37.0 37.0 37.0 37.0 78-79 35.98725 37.0 37.0 37.0 37.0 37.0 80-81 35.903999999999996 37.0 37.0 37.0 37.0 37.0 82-83 35.915499999999994 37.0 37.0 37.0 37.0 37.0 84-85 35.864 37.0 37.0 37.0 37.0 37.0 86-87 35.9105 37.0 37.0 37.0 37.0 37.0 88-89 35.968 37.0 37.0 37.0 37.0 37.0 90-91 35.8805 37.0 37.0 37.0 37.0 37.0 92-93 35.83725 37.0 37.0 37.0 37.0 37.0 94-95 35.79525 37.0 37.0 37.0 37.0 37.0 96-97 35.79875 37.0 37.0 37.0 37.0 37.0 98-99 35.751 37.0 37.0 37.0 37.0 37.0 100-101 35.786 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 22 3.0 23 1.0 24 6.0 25 12.0 26 14.0 27 22.0 28 22.0 29 28.0 30 42.0 31 74.0 32 75.0 33 79.0 34 130.0 35 193.0 36 1738.0 37 1561.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 40.326223337515685 10.439146800501883 11.794228356336262 37.44040150564618 2 21.349999999999998 13.425 28.9 36.325 3 21.575 16.675 24.775 36.975 4 28.375 22.775000000000002 20.05 28.799999999999997 5 29.175 26.400000000000002 21.6 22.825 6 22.375 31.45 24.349999999999998 21.825 7 20.825 23.65 36.25 19.275000000000002 8 21.475 20.825 32.475 25.224999999999998 9 22.775000000000002 21.2 30.425 25.6 10-11 24.6125 28.762500000000003 22.8625 23.7625 12-13 23.9375 23.400000000000002 25.900000000000002 26.7625 14-15 23.0375 24.8 25.85 26.3125 16-17 24.975 23.5 25.337500000000002 26.187500000000004 18-19 23.7875 25.374999999999996 24.8625 25.974999999999998 20-21 25.0 24.25 25.112499999999997 25.637500000000003 22-23 24.5625 22.912499999999998 25.224999999999998 27.3 24-25 24.2 23.625 25.4875 26.687499999999996 26-27 24.4 24.2375 24.5125 26.85 28-29 23.7875 24.2375 24.9875 26.987499999999997 30-31 23.7375 23.2125 24.1625 28.8875 32-33 24.275 22.9625 24.349999999999998 28.4125 34-35 24.8125 24.462500000000002 24.075 26.650000000000002 36-37 23.8875 24.9 23.8875 27.325 38-39 24.175 24.25 24.212500000000002 27.3625 40-41 24.75 24.5125 23.95 26.787499999999998 42-43 24.3 23.8625 25.387500000000003 26.450000000000003 44-45 24.275 24.6625 24.2625 26.8 46-47 25.5375 23.7625 24.1375 26.5625 48-49 23.9125 23.7875 24.825 27.474999999999998 50-51 24.15 23.474999999999998 24.887500000000003 27.487499999999997 52-53 25.637500000000003 23.2625 24.087500000000002 27.0125 54-55 24.675 24.337500000000002 24.4125 26.575 56-57 23.325000000000003 23.9875 24.837500000000002 27.85 58-59 25.3 23.9375 24.1625 26.6 60-61 24.4375 24.25 24.425 26.887499999999996 62-63 24.3125 24.2 25.0 26.487500000000004 64-65 23.150000000000002 24.337500000000002 25.35 27.1625 66-67 24.5375 24.0375 23.575 27.85 68-69 24.175 24.637500000000003 24.837500000000002 26.35 70-71 24.525 24.349999999999998 24.5375 26.5875 72-73 24.7 24.5125 24.625 26.1625 74-75 24.9375 24.224999999999998 23.849999999999998 26.987499999999997 76-77 25.387500000000003 24.1875 23.3875 27.037499999999998 78-79 24.95 24.587500000000002 23.875 26.5875 80-81 24.4875 23.7 24.2375 27.575 82-83 25.8 23.799999999999997 24.087500000000002 26.3125 84-85 24.725 23.5625 24.9 26.8125 86-87 25.162499999999998 23.7375 24.025 27.075 88-89 25.2875 25.124999999999996 23.525 26.0625 90-91 24.4125 24.9 24.1375 26.55 92-93 26.2875 23.6625 23.7625 26.2875 94-95 25.3 24.9 24.0 25.8 96-97 24.625 23.8875 24.4 27.0875 98-99 24.587500000000002 24.9 23.175 27.3375 100-101 24.625 24.9 23.7375 26.737499999999997 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 11.0 1 7.0 2 2.0 3 0.5 4 1.0 5 1.5 6 1.0 7 0.5 8 1.0 9 1.5 10 1.0 11 1.5 12 1.0 13 0.5 14 0.5 15 1.0 16 1.0 17 0.0 18 0.0 19 0.0 20 0.5 21 1.5 22 1.5 23 0.5 24 0.5 25 0.5 26 0.5 27 2.0 28 2.0 29 2.0 30 5.5 31 4.5 32 6.0 33 10.0 34 11.0 35 15.5 36 31.0 37 45.0 38 49.0 39 64.0 40 75.0 41 93.5 42 134.0 43 148.5 44 143.5 45 155.0 46 176.5 47 181.5 48 184.5 49 194.5 50 178.5 51 161.5 52 155.0 53 160.0 54 153.5 55 147.5 56 144.5 57 118.5 58 93.0 59 72.0 60 68.5 61 59.5 62 53.0 63 61.0 64 66.5 65 60.5 66 47.5 67 42.0 68 50.5 69 59.0 70 47.0 71 44.0 72 43.0 73 33.0 74 28.5 75 22.5 76 15.5 77 12.5 78 11.5 79 7.5 80 5.5 81 3.5 82 2.0 83 2.5 84 1.5 85 0.5 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 0.375 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 83.275 #Duplication Level Percentage of deduplicated Percentage of total 1 85.25968177724407 71.0 2 11.61813269288502 19.35 3 2.2215550885619937 5.55 4 0.45031522065445817 1.5 5 0.12008405884118883 0.5 6 0.18012608826178325 0.8999999999999999 7 0.06004202942059442 0.35000000000000003 8 0.03002101471029721 0.2 9 0.0 0.0 >10 0.06004202942059442 0.65 >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 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 13 0.325 No Hit GTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCAT 13 0.325 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACTCTCGCGCATCTCGTAT 8 0.2 TruSeq Adapter, Index 8 (97% over 36bp) GTCACTACCTCCCCGTGTCAGGATTGGGTAATTTGCGCGCCTGCTGCCTT 7 0.17500000000000002 No Hit CCCGACTGTCCCTATTAATCATTACTCCGATCCCGAAGGCCAACACAATA 7 0.17500000000000002 No Hit CTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGG 6 0.15 No Hit CTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATT 6 0.15 No Hit GCAGAAATTTGAATGATGCGTCGCCGGCACGAGGGCCGTGCGATCCGTCG 6 0.15 No Hit GCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGC 6 0.15 No Hit GCCGCAGGCTCCACGCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTT 6 0.15 No Hit CCCCGACTGTCCCTATTAATCATTACTCCGATCCCGAAGGCCAACACAAT 6 0.15 No Hit GCTGGAATTACCGCGGCTGCTGGCACCAGACTTGCCCTCCAATGGATCCT 5 0.125 No Hit CCTTCCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGG 5 0.125 No Hit CCCATGCTAATGTATCCAGAGCGATGGCTTGCTTTGAGCACTCTAATTTC 5 0.125 No Hit CCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCT 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 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.07500000000000001 0.0 0.0 0.0 0.0 34-35 0.1125 0.0 0.0 0.0 0.0 36-37 0.125 0.0 0.0 0.0 0.0 38-39 0.125 0.0 0.0 0.0 0.0 40-41 0.125 0.0 0.0 0.0 0.0 42-43 0.1375 0.0 0.0 0.0 0.0 44-45 0.16249999999999998 0.0 0.0 0.0 0.0 46-47 0.175 0.0 0.0 0.0 0.0 48-49 0.275 0.0 0.0 0.0 0.0 50-51 0.4 0.0 0.0 0.0 0.0 52-53 0.425 0.0 0.0 0.0 0.0 54-55 0.5375 0.0 0.0 0.0 0.0 56-57 0.6375 0.0 0.0 0.0 0.0 58-59 0.7875000000000001 0.0 0.0 0.0 0.0 60-61 0.8999999999999999 0.0 0.0 0.0 0.0 62-63 1.05 0.0 0.0 0.0 0.0 64-65 1.1875 0.0 0.0 0.0 0.0 66-67 1.3 0.0 0.0 0.0 0.0 68-69 1.6 0.0 0.0 0.0 0.0 70-71 1.7374999999999998 0.0 0.0 0.0 0.0 72-73 2.1875 0.0 0.0 0.0 0.0 74-75 2.45 0.0 0.0 0.0 0.0 76-77 2.7375 0.0 0.0 0.0 0.0 78-79 3.0625 0.0 0.0 0.0 0.0 80-81 3.45 0.0 0.0 0.0 0.0 82-83 3.9375 0.0 0.0 0.0 0.0 84-85 4.3625 0.0 0.0 0.0 0.0 86-87 4.8375 0.0 0.0 0.0 0.0 88-89 5.35 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTGTTCC 15 0.009957196 47.5 56-57 >>END_MODULE ERR3450074 read2 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3450074_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 52 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.9795 37.0 37.0 37.0 37.0 37.0 2 35.764 37.0 37.0 37.0 37.0 37.0 3 35.878 37.0 37.0 37.0 37.0 37.0 4 36.0445 37.0 37.0 37.0 37.0 37.0 5 35.975 37.0 37.0 37.0 37.0 37.0 6 35.9825 37.0 37.0 37.0 37.0 37.0 7 36.117 37.0 37.0 37.0 37.0 37.0 8 36.076 37.0 37.0 37.0 37.0 37.0 9 36.0845 37.0 37.0 37.0 37.0 37.0 10-11 36.059749999999994 37.0 37.0 37.0 37.0 37.0 12-13 36.0415 37.0 37.0 37.0 37.0 37.0 14-15 36.04375 37.0 37.0 37.0 37.0 37.0 16-17 35.987750000000005 37.0 37.0 37.0 37.0 37.0 18-19 36.0255 37.0 37.0 37.0 37.0 37.0 20-21 36.07425 37.0 37.0 37.0 37.0 37.0 22-23 35.96825 37.0 37.0 37.0 37.0 37.0 24-25 35.9155 37.0 37.0 37.0 37.0 37.0 26-27 36.0325 37.0 37.0 37.0 37.0 37.0 28-29 35.95625 37.0 37.0 37.0 37.0 37.0 30-31 35.9035 37.0 37.0 37.0 37.0 37.0 32-33 35.922250000000005 37.0 37.0 37.0 37.0 37.0 34-35 35.943 37.0 37.0 37.0 37.0 37.0 36-37 35.897 37.0 37.0 37.0 37.0 37.0 38-39 35.9375 37.0 37.0 37.0 37.0 37.0 40-41 35.841 37.0 37.0 37.0 37.0 37.0 42-43 35.80175 37.0 37.0 37.0 37.0 37.0 44-45 35.838 37.0 37.0 37.0 37.0 37.0 46-47 35.88525 37.0 37.0 37.0 37.0 37.0 48-49 35.84675 37.0 37.0 37.0 37.0 37.0 50-51 35.879000000000005 37.0 37.0 37.0 37.0 37.0 52-53 35.87425 37.0 37.0 37.0 37.0 37.0 54-55 35.8575 37.0 37.0 37.0 37.0 37.0 56-57 35.8825 37.0 37.0 37.0 37.0 37.0 58-59 35.87325 37.0 37.0 37.0 37.0 37.0 60-61 35.763 37.0 37.0 37.0 37.0 37.0 62-63 35.834500000000006 37.0 37.0 37.0 37.0 37.0 64-65 35.8915 37.0 37.0 37.0 37.0 37.0 66-67 35.8395 37.0 37.0 37.0 37.0 37.0 68-69 35.866 37.0 37.0 37.0 37.0 37.0 70-71 35.721000000000004 37.0 37.0 37.0 37.0 37.0 72-73 35.712 37.0 37.0 37.0 37.0 37.0 74-75 35.697 37.0 37.0 37.0 37.0 37.0 76-77 35.734 37.0 37.0 37.0 37.0 37.0 78-79 35.6635 37.0 37.0 37.0 37.0 37.0 80-81 35.66775 37.0 37.0 37.0 37.0 37.0 82-83 35.69175 37.0 37.0 37.0 37.0 37.0 84-85 35.77875 37.0 37.0 37.0 37.0 37.0 86-87 35.701499999999996 37.0 37.0 37.0 37.0 37.0 88-89 35.652 37.0 37.0 37.0 37.0 37.0 90-91 35.768 37.0 37.0 37.0 37.0 37.0 92-93 35.6725 37.0 37.0 37.0 37.0 37.0 94-95 35.6785 37.0 37.0 37.0 37.0 37.0 96-97 35.659000000000006 37.0 37.0 37.0 37.0 37.0 98-99 35.607 37.0 37.0 37.0 37.0 37.0 100-101 35.604749999999996 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 5.0 16 5.0 17 5.0 18 3.0 19 10.0 20 5.0 21 11.0 22 19.0 23 11.0 24 14.0 25 16.0 26 16.0 27 13.0 28 26.0 29 27.0 30 35.0 31 39.0 32 54.0 33 87.0 34 113.0 35 212.0 36 2030.0 37 1240.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 41.4 16.650000000000002 12.325 29.625 2 26.5 23.375 25.650000000000002 24.474999999999998 3 26.450000000000003 22.475 27.575 23.5 4 30.725 26.275 18.224999999999998 24.775 5 30.075000000000003 30.425 18.6 20.9 6 23.775 32.525 21.45 22.25 7 26.85 18.675 29.25 25.224999999999998 8 25.575 20.674999999999997 24.325 29.425 9 26.674999999999997 22.425 24.55 26.35 10-11 28.812500000000004 26.700000000000003 19.7375 24.75 12-13 29.2875 22.037499999999998 22.425 26.25 14-15 27.4125 24.9375 22.775000000000002 24.875 16-17 28.275 24.887500000000003 22.2125 24.625 18-19 27.6375 24.925 22.7625 24.675 20-21 27.250000000000004 24.4125 23.1375 25.2 22-23 27.450000000000003 24.975 22.575 25.0 24-25 27.725 24.975 23.225 24.075 26-27 27.2625 25.087500000000002 23.474999999999998 24.175 28-29 28.262500000000003 25.174999999999997 22.0125 24.55 30-31 27.6375 25.337500000000002 22.412499999999998 24.6125 32-33 27.3625 24.962500000000002 22.8375 24.837500000000002 34-35 28.1125 25.7375 22.425 23.724999999999998 36-37 26.8125 24.825 21.975 26.387500000000003 38-39 26.700000000000003 24.7375 23.1375 25.424999999999997 40-41 27.500000000000004 25.5625 21.825 25.112499999999997 42-43 26.724999999999998 25.2875 22.7625 25.224999999999998 44-45 26.575 25.45 23.125 24.85 46-47 27.8125 25.4875 21.912499999999998 24.7875 48-49 27.250000000000004 25.224999999999998 22.650000000000002 24.875 50-51 26.7125 25.6 23.2625 24.425 52-53 27.474999999999998 24.887500000000003 22.825 24.8125 54-55 27.650000000000002 24.325 22.1875 25.837500000000002 56-57 26.450000000000003 25.662499999999998 23.45 24.4375 58-59 27.775 25.2 22.55 24.474999999999998 60-61 28.3125 24.25 23.325000000000003 24.1125 62-63 28.5625 23.775 23.2125 24.45 64-65 28.15 25.124999999999996 22.375 24.349999999999998 66-67 26.75 26.437500000000004 22.7625 24.05 68-69 28.175 25.337500000000002 22.112499999999997 24.375 70-71 28.475 24.6125 23.0625 23.849999999999998 72-73 27.2625 24.575 22.650000000000002 25.5125 74-75 28.4 23.8625 23.35 24.3875 76-77 28.962500000000002 24.575 22.9375 23.525 78-79 27.4125 25.025 22.9625 24.6 80-81 27.250000000000004 24.887500000000003 23.1 24.762500000000003 82-83 27.474999999999998 25.5125 23.0625 23.95 84-85 27.200000000000003 24.962500000000002 23.5375 24.3 86-87 27.3125 24.7 23.400000000000002 24.587500000000002 88-89 28.449999999999996 24.775 22.4375 24.337500000000002 90-91 27.975 24.962500000000002 22.75 24.3125 92-93 27.5875 25.05 23.25 24.1125 94-95 27.8625 25.324999999999996 22.05 24.762500000000003 96-97 28.3375 24.4875 23.3625 23.8125 98-99 28.0625 25.05 23.3375 23.549999999999997 100-101 28.249999999999996 25.687500000000004 22.537499999999998 23.525 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 1.0 4 1.5 5 1.5 6 1.5 7 1.5 8 1.0 9 0.5 10 1.0 11 0.5 12 0.5 13 0.5 14 2.0 15 3.5 16 2.0 17 1.0 18 1.0 19 1.0 20 1.5 21 3.0 22 4.0 23 2.5 24 1.5 25 2.0 26 4.0 27 5.5 28 4.0 29 1.5 30 2.5 31 5.0 32 6.5 33 6.5 34 6.0 35 13.0 36 29.5 37 41.5 38 58.0 39 81.0 40 82.0 41 86.5 42 117.5 43 139.5 44 138.5 45 143.0 46 151.5 47 171.5 48 178.0 49 171.5 50 153.5 51 147.0 52 159.0 53 162.5 54 167.5 55 148.0 56 119.5 57 105.5 58 90.5 59 76.5 60 75.5 61 75.5 62 67.5 63 57.0 64 58.0 65 60.5 66 66.0 67 62.0 68 57.5 69 61.0 70 57.0 71 50.0 72 42.0 73 34.0 74 33.0 75 28.0 76 20.0 77 16.0 78 10.5 79 11.5 80 9.0 81 4.5 82 3.5 83 2.0 84 1.0 85 0.0 86 0.0 87 0.5 88 1.5 89 2.5 90 3.5 91 2.5 92 1.5 93 1.5 94 1.0 95 0.5 96 1.0 97 1.5 98 1.5 99 1.0 100 4.0 >>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 10-11 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 84.625 #Duplication Level Percentage of deduplicated Percentage of total 1 85.96750369276218 72.75 2 11.137370753323486 18.85 3 2.3042836041358936 5.8500000000000005 4 0.29542097488921715 1.0 5 0.11816838995568685 0.5 6 0.08862629246676515 0.44999999999999996 7 0.029542097488921712 0.17500000000000002 8 0.029542097488921712 0.2 9 0.029542097488921712 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 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 9 0.22499999999999998 No Hit CCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGCAA 8 0.2 No Hit GGAGAATTAGGGTTCGATTCCGGAGAGGGAGCCTGAGAAACGGCTACCAC 7 0.17500000000000002 No Hit CTTGGATTTATGAAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTT 6 0.15 No Hit GGTCGGCCGGTCCGCCTCACGGCGAGCACCGACCTACTCGACCCTTCAGC 6 0.15 No Hit CAACCATAAACGATGCCGACCAGGGATCGGCGGATGTTGCTTATAGGACT 6 0.15 No Hit TGCTTGTCTCAAAGATTAAGCCATGCATGTGCAAGTATGAACTAATTTGA 5 0.125 No Hit GCGATTTGTCTGGTTAATTCCGTTAACGAACGAGACCTCAGCCTGCTAAC 5 0.125 No Hit ACTTACCAGGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCT 5 0.125 No Hit CTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGTTAACGAACGAGACC 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 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.07500000000000001 0.0 0.0 0.0 0.0 34-35 0.1125 0.0 0.0 0.0 0.0 36-37 0.125 0.0 0.0 0.0 0.0 38-39 0.125 0.0 0.0 0.0 0.0 40-41 0.125 0.0 0.0 0.0 0.0 42-43 0.1375 0.0 0.0 0.0 0.0 44-45 0.16249999999999998 0.0 0.0 0.0 0.0 46-47 0.175 0.0 0.0 0.0 0.0 48-49 0.275 0.0 0.0 0.0 0.0 50-51 0.4 0.0 0.0 0.0 0.0 52-53 0.425 0.0 0.0 0.0 0.0 54-55 0.5375 0.0 0.0 0.0 0.0 56-57 0.6375 0.0 0.0 0.0 0.0 58-59 0.7875000000000001 0.0 0.0 0.0 0.0 60-61 0.8999999999999999 0.0 0.0 0.0 0.0 62-63 1.05 0.0 0.0 0.0 0.0 64-65 1.1875 0.0 0.0 0.0 0.0 66-67 1.3 0.0 0.0 0.0 0.0 68-69 1.6 0.0 0.0 0.0 0.0 70-71 1.7374999999999998 0.0 0.0 0.0 0.0 72-73 2.1875 0.0 0.0 0.0 0.0 74-75 2.4749999999999996 0.0 0.0 0.0 0.0 76-77 2.7625 0.0 0.0 0.0 0.0 78-79 3.0875 0.0 0.0 0.0 0.0 80-81 3.475 0.0 0.0 0.0 0.0 82-83 3.9625000000000004 0.0 0.0 0.0 0.0 84-85 4.3875 0.0 0.0 0.0 0.0 86-87 4.8625 0.0 0.0 0.0 0.0 88-89 5.35 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1261684 spots for ERR3450074.sra Written 1261684 spots for ERR3450074.sra Read 1261693 spots for ERR3450074.sra Written 1261693 spots for ERR3450074.sra Read 1261684 spots for ERR3450074.sra Written 1261684 spots for ERR3450074.sra Read 1261684 spots for ERR3450074.sra Written 1261684 spots for ERR3450074.sra Read 1261684 spots for ERR3450074.sra Written 1261684 spots for ERR3450074.sra Read 1261684 spots for ERR3450074.sra Written 1261684 spots for ERR3450074.sra Read 1261684 spots for ERR3450074.sra Written 1261684 spots for ERR3450074.sra Read 1261684 spots for ERR3450074.sra Written 1261684 spots for ERR3450074.sra Read 1261684 spots for ERR3450074.sra Written 1261684 spots for ERR3450074.sra Read 1261684 spots for ERR3450074.sra Written 1261684 spots for ERR3450074.sra Read 1261684 spots for ERR3450074.sra Written 1261684 spots for ERR3450074.sra Read 1261684 spots for ERR3450074.sra Written 1261684 spots for ERR3450074.sra Read 1261684 spots for ERR3450074.sra Written 1261684 spots for ERR3450074.sra Read 1261684 spots for ERR3450074.sra Written 1261684 spots for ERR3450074.sra Read 1261684 spots for ERR3450074.sra Written 1261684 spots for ERR3450074.sra Read 1261684 spots for ERR3450074.sra Written 1261684 spots for ERR3450074.sra Read 1261684 spots for ERR3450074.sra Written 1261684 spots for ERR3450074.sra Read 1261684 spots for ERR3450074.sra Written 1261684 spots for ERR3450074.sra Read 1261684 spots for ERR3450074.sra Written 1261684 spots for ERR3450074.sra Read 1261684 spots for ERR3450074.sra Written 1261684 spots for ERR3450074.sra SRR ids: ['ERR3450074.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_ip9xswk_ ERR3450074.sra spots: 25233689 blocks: [[1, 1261684], [1261685, 2523368], [2523369, 3785052], [3785053, 5046736], [5046737, 6308420], [6308421, 7570104], [7570105, 8831788], [8831789, 10093472], [10093473, 11355156], [11355157, 12616840], [12616841, 13878524], [13878525, 15140208], [15140209, 16401892], [16401893, 17663576], [17663577, 18925260], [18925261, 20186944], [20186945, 21448628], [21448629, 22710312], [22710313, 23971996], [23971997, 25233689]] ERR3450074 file size 6064941 ERR3450074 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 ERR3450074 ERR3450074_1.fastq ERR3450074_2.fastq Input file: ERR3450074_1.fastq Paired file: ERR3450074_2.fastq trimmed: ERR3450074-trimmed-pair1.fastq, ERR3450074-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 14:38:14 2024 >> started Sat Dec 7 14:38:36 2024 >> done (21.809s) 25233689 read pairs processed; of these: 155 ( 0.00%) short read pairs filtered out after trimming by size control 64889 ( 0.26%) empty read pairs filtered out after trimming by size control 25168645 (99.74%) read pairs available; of these: 2244212 ( 8.92%) trimmed read pairs available after processing 22924433 (91.08%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 46 0.00% 19 81 0.00% 20 203 0.00% 21 464 0.00% 22 615 0.00% 23 284 0.00% 24 285 0.00% 25 380 0.00% 26 527 0.00% 27 750 0.00% 28 1053 0.00% 29 1384 0.01% 30 1721 0.01% 31 1968 0.01% 32 2199 0.01% 33 1912 0.01% 34 1948 0.01% 35 1935 0.01% 36 2193 0.01% 37 2487 0.01% 38 2939 0.01% 39 3239 0.01% 40 3945 0.02% 41 4441 0.02% 42 5013 0.02% 43 5262 0.02% 44 5048 0.02% 45 4944 0.02% 46 5237 0.02% 47 5724 0.02% 48 6397 0.03% 49 6857 0.03% 50 7842 0.03% 51 8887 0.04% 52 9520 0.04% 53 10124 0.04% 54 10327 0.04% 55 10787 0.04% 56 11437 0.05% 57 11831 0.05% 58 13157 0.05% 59 13737 0.05% 60 15025 0.06% 61 16600 0.07% 62 18415 0.07% 63 19680 0.08% 64 20793 0.08% 65 21396 0.09% 66 22281 0.09% 67 23782 0.09% 68 24914 0.10% 69 25621 0.10% 70 27916 0.11% 71 29294 0.12% 72 32234 0.13% 73 34093 0.14% 74 35554 0.14% 75 37109 0.15% 76 38477 0.15% 77 39667 0.16% 78 41586 0.17% 79 43627 0.17% 80 45681 0.18% 81 47114 0.19% 82 50362 0.20% 83 52730 0.21% 84 54909 0.22% 85 57113 0.23% 86 59550 0.24% 87 61890 0.25% 88 63598 0.25% 89 66418 0.26% 90 68552 0.27% 91 72566 0.29% 92 76078 0.30% 93 78330 0.31% 94 81348 0.32% 95 83930 0.33% 96 86458 0.34% 97 88974 0.35% 98 90357 0.36% 99 92539 0.37% 100 108521 0.43% 101 22924433 91.08% 25168645 reads passed initial QC criterion=sequence-density sequence-density=0.41 sequence-density-rank=1 fanout-score=2.13 fanout-score-rank=27 prefix-density=0.42 prefix-fanout=2.1 sequence=TTCGCTATCGGTC criterion=fanout-score sequence-density=0.08 sequence-density-rank=15 fanout-score=165.30 fanout-score-rank=1 prefix-density=0.58 prefix-fanout=21.4 sequence=CGCCGCCGCCGC criterion=sequence-density sequence-density=0.24 sequence-density-rank=1 fanout-score=2.03 fanout-score-rank=33 prefix-density=0.25 prefix-fanout=2.0 sequence=AGCCAGAGGAAA criterion=fanout-score sequence-density=0.08 sequence-density-rank=31 fanout-score=225.75 fanout-score-rank=1 prefix-density=0.76 prefix-fanout=22.7 sequence=CGGCGGCGGCGC ERR3450074 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 14:39:08 Started mapping on | Dec 07 14:39:09 Finished on | Dec 07 14:41:03 Mapping speed, Million of reads per hour | 794.80 Number of input reads | 25168645 Average input read length | 198 UNIQUE READS: Uniquely mapped reads number | 18503898 Uniquely mapped reads % | 73.52% Average mapped length | 198.28 Number of splices: Total | 11322972 Number of splices: Annotated (sjdb) | 10700281 Number of splices: GT/AG | 11170358 Number of splices: GC/AG | 131836 Number of splices: AT/AC | 6922 Number of splices: Non-canonical | 13856 Mismatch rate per base, % | 0.24% Deletion rate per base | 0.01% Deletion average length | 2.13 Insertion rate per base | 0.01% Insertion average length | 1.91 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1066558 % of reads mapped to multiple loci | 4.24% Number of reads mapped to too many loci | 946191 % of reads mapped to too many loci | 3.76% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.27% % of reads unmapped: other | 15.21% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 5598189 5598189 5598189 N_multimapping 1066558 1066558 1066558 N_noFeature 633733 17810037 1042660 N_ambiguous 348504 2729 66771 UnstrandedReadsAssigned:17521661 PositiveStrandReadsAssigned:691132 NegativeStrandReadsAssigned:17394467 Dataset is classified negative stranded MeadianReadLen=101 20thPercentileLength=101 echo kmer=97 ERR3450074 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: ERR3450074-trimmed-pair1.fastq ERR3450074-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 25,168,645 reads, 18,309,153 reads pseudoaligned [quant] estimated average fragment length: 186.843 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,265 rounds 52973 ERR3450074.ke.tsv 35125 ERR3450074.se.tsv 88098 total ==> ERR3450074.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 750.469 0 0 PNS24247 1044 858.157 37.447 3.72987 PNS24249 1928 1742.16 263.545 12.9304 PNS24246 1044 858.157 37.447 3.72987 PNS24248 1044 858.157 37.447 3.72987 PNS24244 1471 1285.16 76.1143 5.06237 PNS24243 293 127.931 1 0.66814 KQK14069 1603 1417.16 7472.1 450.68 KQK14071 474 291.96 265.747 77.8017 ==> ERR3450074.se.tsv <== BRADI_1g14170v3 7899 BRADI_1g53295v3 116 BRADI_1g59795v3 204 BRADI_1g07683v3 0 BRADI_1g00485v3 6 BRADI_1g20270v3 811 BRADI_1g74790v3 251 BRADI_1g09890v3 6 BRADI_1g77505v3 257 BRADI_1g48960v3 0 ERR3450074 completed mapping pipeline successfully