Starting /dee2/code/volunteer_pipeline.sh ERR3450063 current disk space = 1543119540224 free memory = 1600127580 ERR3450063 SRAfilesize f009e792738db1045946c9970e720a61 ERR3450063.sra ERR3450063.sra file validated ERR3450063 is paired end ERR3450063 is conventional basespace ERR3450063 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3450063_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 36.0055 37.0 37.0 37.0 37.0 37.0 2 36.347 37.0 37.0 37.0 37.0 37.0 3 36.365 37.0 37.0 37.0 37.0 37.0 4 36.537 37.0 37.0 37.0 37.0 37.0 5 36.552 37.0 37.0 37.0 37.0 37.0 6 36.4145 37.0 37.0 37.0 37.0 37.0 7 36.5475 37.0 37.0 37.0 37.0 37.0 8 36.4485 37.0 37.0 37.0 37.0 37.0 9 36.532 37.0 37.0 37.0 37.0 37.0 10-11 36.49 37.0 37.0 37.0 37.0 37.0 12-13 36.51625 37.0 37.0 37.0 37.0 37.0 14-15 36.60875 37.0 37.0 37.0 37.0 37.0 16-17 36.514250000000004 37.0 37.0 37.0 37.0 37.0 18-19 36.5625 37.0 37.0 37.0 37.0 37.0 20-21 36.5455 37.0 37.0 37.0 37.0 37.0 22-23 36.506 37.0 37.0 37.0 37.0 37.0 24-25 36.446749999999994 37.0 37.0 37.0 37.0 37.0 26-27 36.473 37.0 37.0 37.0 37.0 37.0 28-29 36.401250000000005 37.0 37.0 37.0 37.0 37.0 30-31 36.367000000000004 37.0 37.0 37.0 37.0 37.0 32-33 36.35575 37.0 37.0 37.0 37.0 37.0 34-35 36.252250000000004 37.0 37.0 37.0 37.0 37.0 36-37 36.32825 37.0 37.0 37.0 37.0 37.0 38-39 36.3925 37.0 37.0 37.0 37.0 37.0 40-41 36.359750000000005 37.0 37.0 37.0 37.0 37.0 42-43 36.32475 37.0 37.0 37.0 37.0 37.0 44-45 36.179 37.0 37.0 37.0 37.0 37.0 46-47 36.158249999999995 37.0 37.0 37.0 37.0 37.0 48-49 36.26125 37.0 37.0 37.0 37.0 37.0 50-51 36.13525 37.0 37.0 37.0 37.0 37.0 52-53 36.216750000000005 37.0 37.0 37.0 37.0 37.0 54-55 36.199 37.0 37.0 37.0 37.0 37.0 56-57 36.1665 37.0 37.0 37.0 37.0 37.0 58-59 36.086749999999995 37.0 37.0 37.0 37.0 37.0 60-61 36.06075 37.0 37.0 37.0 37.0 37.0 62-63 36.07475 37.0 37.0 37.0 37.0 37.0 64-65 35.917500000000004 37.0 37.0 37.0 37.0 37.0 66-67 35.976749999999996 37.0 37.0 37.0 37.0 37.0 68-69 36.00625 37.0 37.0 37.0 37.0 37.0 70-71 35.8755 37.0 37.0 37.0 37.0 37.0 72-73 35.71625 37.0 37.0 37.0 37.0 37.0 74-75 36.12475 37.0 37.0 37.0 37.0 37.0 76-77 36.12025 37.0 37.0 37.0 37.0 37.0 78-79 36.12625 37.0 37.0 37.0 37.0 37.0 80-81 36.065250000000006 37.0 37.0 37.0 37.0 37.0 82-83 36.064499999999995 37.0 37.0 37.0 37.0 37.0 84-85 36.0775 37.0 37.0 37.0 37.0 37.0 86-87 36.03675 37.0 37.0 37.0 37.0 37.0 88-89 36.02175 37.0 37.0 37.0 37.0 37.0 90-91 36.001000000000005 37.0 37.0 37.0 37.0 37.0 92-93 36.02375 37.0 37.0 37.0 37.0 37.0 94-95 35.9855 37.0 37.0 37.0 37.0 37.0 96-97 35.88125 37.0 37.0 37.0 37.0 37.0 98-99 35.90575 37.0 37.0 37.0 37.0 37.0 100-101 35.924 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 18 1.0 19 0.0 20 1.0 21 3.0 22 2.0 23 1.0 24 4.0 25 5.0 26 10.0 27 22.0 28 19.0 29 31.0 30 39.0 31 50.0 32 57.0 33 81.0 34 124.0 35 215.0 36 1799.0 37 1536.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 40.6469408224674 9.729187562688065 10.506519558676027 39.1173520561685 2 21.875 12.15 30.775000000000002 35.199999999999996 3 21.575 17.05 25.45 35.925000000000004 4 28.525 23.799999999999997 18.224999999999998 29.45 5 26.85 28.225 21.9 23.025000000000002 6 23.849999999999998 30.125 25.15 20.875 7 19.35 22.85 37.275000000000006 20.525 8 20.95 21.55 29.849999999999998 27.650000000000002 9 23.225 21.099999999999998 30.45 25.224999999999998 10-11 24.425 28.075 22.4875 25.0125 12-13 23.775 23.200000000000003 25.9625 27.0625 14-15 23.9375 24.4125 25.662499999999998 25.9875 16-17 23.7 23.974999999999998 25.924999999999997 26.400000000000002 18-19 24.2625 24.125 26.0 25.6125 20-21 24.1375 25.337500000000002 25.337500000000002 25.1875 22-23 25.5 24.575 23.6375 26.2875 24-25 24.7875 25.0625 23.825 26.325 26-27 24.175 24.4125 23.9 27.5125 28-29 24.15 24.325 24.087500000000002 27.437499999999996 30-31 24.15 23.1625 24.5 28.1875 32-33 24.625 24.675 23.375 27.325 34-35 25.0 24.5125 23.5125 26.974999999999998 36-37 23.6375 24.9875 23.6375 27.737499999999997 38-39 23.9125 24.55 24.4125 27.125 40-41 24.875 24.775 23.1 27.250000000000004 42-43 25.4375 24.1875 23.75 26.625 44-45 23.9875 23.3 25.025 27.6875 46-47 24.5625 24.3875 24.0375 27.0125 48-49 23.962500000000002 23.8125 24.9 27.325 50-51 24.224999999999998 23.849999999999998 24.0625 27.8625 52-53 24.975 24.4375 23.6625 26.924999999999997 54-55 24.1875 24.525 24.8 26.487500000000004 56-57 23.8125 23.75 24.5375 27.900000000000002 58-59 24.85 24.25 23.75 27.150000000000002 60-61 24.275 24.887500000000003 24.212500000000002 26.625 62-63 24.587500000000002 23.1625 24.962500000000002 27.287499999999998 64-65 25.0125 23.7125 23.9125 27.3625 66-67 25.0 24.8125 24.05 26.137500000000003 68-69 24.6125 24.7875 24.275 26.325 70-71 24.887500000000003 24.85 23.325000000000003 26.937499999999996 72-73 24.975 24.4375 23.8875 26.700000000000003 74-75 25.2375 24.25 23.375 27.1375 76-77 25.7875 25.162499999999998 23.1625 25.887500000000003 78-79 25.2875 25.2875 22.7625 26.6625 80-81 25.650000000000002 24.675 23.7375 25.937500000000004 82-83 26.7625 24.1875 22.4875 26.5625 84-85 25.8625 23.674999999999997 22.7125 27.750000000000004 86-87 25.837500000000002 25.2 22.05 26.9125 88-89 25.2125 24.75 23.1375 26.900000000000002 90-91 24.7 23.8375 23.9 27.5625 92-93 25.4875 25.424999999999997 22.7375 26.35 94-95 26.150000000000002 24.5125 22.787499999999998 26.55 96-97 25.05 25.674999999999997 22.8 26.474999999999998 98-99 24.525 24.7 23.5625 27.212500000000002 100-101 24.85 24.975 22.2625 27.9125 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 15.0 1 10.0 2 2.5 3 1.0 4 1.5 5 0.5 6 1.0 7 1.5 8 2.5 9 3.5 10 1.5 11 0.5 12 0.5 13 0.0 14 0.0 15 1.0 16 1.5 17 0.5 18 0.0 19 1.0 20 1.0 21 2.0 22 2.0 23 0.0 24 1.0 25 1.5 26 2.5 27 3.0 28 1.0 29 0.5 30 2.0 31 5.5 32 8.5 33 8.5 34 10.5 35 15.5 36 30.5 37 42.5 38 48.0 39 58.5 40 75.5 41 96.0 42 119.5 43 132.5 44 125.0 45 131.0 46 163.0 47 175.5 48 172.5 49 175.5 50 169.5 51 160.0 52 151.0 53 158.0 54 166.5 55 165.5 56 152.5 57 133.5 58 107.5 59 93.5 60 88.5 61 83.0 62 73.0 63 58.0 64 68.5 65 66.5 66 55.0 67 51.5 68 50.5 69 48.0 70 39.0 71 40.0 72 40.0 73 26.5 74 18.5 75 18.0 76 17.0 77 14.5 78 10.5 79 8.0 80 5.5 81 3.0 82 3.0 83 4.0 84 2.0 85 0.0 86 0.5 87 0.5 88 0.5 89 0.5 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 0.3 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 87.225 #Duplication Level Percentage of deduplicated Percentage of total 1 89.33791917454859 77.925 2 8.684436801375753 15.15 3 1.2897678417884781 3.375 4 0.3725995987388937 1.3 5 0.05732301519059903 0.25 6 0.11464603038119806 0.6 7 0.028661507595299514 0.17500000000000002 8 0.028661507595299514 0.2 9 0.0 0.0 >10 0.08598452278589853 1.0250000000000001 >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 19 0.475 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGATTCCATCTCGTAT 12 0.3 TruSeq Adapter, Index 7 (97% over 38bp) CCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCT 10 0.25 No Hit GCAGAAATTTGAATGATGCGTCGCCGGCACGAGGGCCGTGCGATCCGTCG 8 0.2 No Hit CCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAA 7 0.17500000000000002 No Hit CCCCGTGTCAGGATTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGT 6 0.15 No Hit GTCAGGATTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTGGTAGC 6 0.15 No Hit GTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACT 6 0.15 No Hit GTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCAT 6 0.15 No Hit GCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCC 5 0.125 No Hit CCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTATA 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 0.0 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 0.1 0.0 0.0 0.0 0.0 36-37 0.1125 0.0 0.0 0.0 0.0 38-39 0.125 0.0 0.0 0.0 0.0 40-41 0.15 0.0 0.0 0.0 0.0 42-43 0.225 0.0 0.0 0.0 0.0 44-45 0.3625 0.0 0.0 0.0 0.0 46-47 0.475 0.0 0.0 0.0 0.0 48-49 0.575 0.0 0.0 0.0 0.0 50-51 0.7375 0.0 0.0 0.0 0.0 52-53 0.8625 0.0 0.0 0.0 0.0 54-55 1.05 0.0 0.0 0.0 0.0 56-57 1.125 0.0 0.0 0.0 0.0 58-59 1.3250000000000002 0.0 0.0 0.0 0.0 60-61 1.6625 0.0 0.0 0.0 0.0 62-63 1.9375 0.0 0.0 0.0 0.0 64-65 2.2875 0.0 0.0 0.0 0.0 66-67 2.5125 0.0 0.0 0.0 0.0 68-69 2.875 0.0 0.0 0.0 0.0 70-71 3.1500000000000004 0.0 0.0 0.0 0.0 72-73 3.45 0.0 0.0 0.0 0.0 74-75 4.0 0.0 0.0 0.0 0.0 76-77 4.6875 0.0 0.0 0.0 0.0 78-79 5.2625 0.0 0.0 0.0 0.0 80-81 5.85 0.0 0.0 0.0 0.0 82-83 6.375 0.0 0.0 0.0 0.0 84-85 6.9 0.0 0.0 0.0 0.0 86-87 7.675000000000001 0.0 0.0 0.0 0.0 88-89 8.3875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE ERR3450063 read2 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3450063_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 36.3335 37.0 37.0 37.0 37.0 37.0 2 36.15925 37.0 37.0 37.0 37.0 37.0 3 36.2065 37.0 37.0 37.0 37.0 37.0 4 36.3325 37.0 37.0 37.0 37.0 37.0 5 36.3675 37.0 37.0 37.0 37.0 37.0 6 36.34925 37.0 37.0 37.0 37.0 37.0 7 36.293 37.0 37.0 37.0 37.0 37.0 8 36.3045 37.0 37.0 37.0 37.0 37.0 9 36.357 37.0 37.0 37.0 37.0 37.0 10-11 36.28975 37.0 37.0 37.0 37.0 37.0 12-13 36.19675 37.0 37.0 37.0 37.0 37.0 14-15 36.267250000000004 37.0 37.0 37.0 37.0 37.0 16-17 36.184749999999994 37.0 37.0 37.0 37.0 37.0 18-19 36.277125 37.0 37.0 37.0 37.0 37.0 20-21 36.15875 37.0 37.0 37.0 37.0 37.0 22-23 36.218374999999995 37.0 37.0 37.0 37.0 37.0 24-25 36.006625 37.0 37.0 37.0 37.0 37.0 26-27 36.072 37.0 37.0 37.0 37.0 37.0 28-29 35.9905 37.0 37.0 37.0 37.0 37.0 30-31 35.951499999999996 37.0 37.0 37.0 37.0 37.0 32-33 36.0345 37.0 37.0 37.0 37.0 37.0 34-35 35.83025 37.0 37.0 37.0 37.0 37.0 36-37 35.832750000000004 37.0 37.0 37.0 37.0 37.0 38-39 35.752250000000004 37.0 37.0 37.0 37.0 37.0 40-41 35.769 37.0 37.0 37.0 37.0 37.0 42-43 35.769625000000005 37.0 37.0 37.0 37.0 37.0 44-45 35.786249999999995 37.0 37.0 37.0 37.0 37.0 46-47 35.927375 37.0 37.0 37.0 37.0 37.0 48-49 35.852625 37.0 37.0 37.0 37.0 37.0 50-51 35.94375 37.0 37.0 37.0 37.0 37.0 52-53 35.82025 37.0 37.0 37.0 37.0 37.0 54-55 35.99675 37.0 37.0 37.0 37.0 37.0 56-57 35.914500000000004 37.0 37.0 37.0 37.0 37.0 58-59 35.972750000000005 37.0 37.0 37.0 37.0 37.0 60-61 35.99325 37.0 37.0 37.0 37.0 37.0 62-63 36.00425 37.0 37.0 37.0 37.0 37.0 64-65 36.01475 37.0 37.0 37.0 37.0 37.0 66-67 35.975 37.0 37.0 37.0 37.0 37.0 68-69 35.893249999999995 37.0 37.0 37.0 37.0 37.0 70-71 35.802499999999995 37.0 37.0 37.0 37.0 37.0 72-73 35.778499999999994 37.0 37.0 37.0 37.0 37.0 74-75 35.765125 37.0 37.0 37.0 37.0 37.0 76-77 35.783249999999995 37.0 37.0 37.0 37.0 37.0 78-79 35.766999999999996 37.0 37.0 37.0 37.0 37.0 80-81 35.564499999999995 37.0 37.0 37.0 37.0 37.0 82-83 35.628625 37.0 37.0 37.0 37.0 37.0 84-85 35.718 37.0 37.0 37.0 37.0 37.0 86-87 35.730500000000006 37.0 37.0 37.0 37.0 37.0 88-89 35.7095 37.0 37.0 37.0 37.0 37.0 90-91 35.741 37.0 37.0 37.0 37.0 37.0 92-93 35.65175 37.0 37.0 37.0 37.0 37.0 94-95 35.62825 37.0 37.0 37.0 37.0 37.0 96-97 35.58725 37.0 37.0 37.0 37.0 37.0 98-99 35.631875 37.0 37.0 37.0 37.0 37.0 100-101 35.562250000000006 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 16 1.0 17 1.0 18 4.0 19 3.0 20 10.0 21 7.0 22 10.0 23 11.0 24 10.0 25 15.0 26 13.0 27 16.0 28 17.0 29 21.0 30 23.0 31 46.0 32 55.0 33 90.0 34 144.0 35 348.0 36 2389.0 37 766.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 40.075 17.299999999999997 11.899999999999999 30.725 2 27.581895473868467 21.030257564391096 26.356589147286826 25.03125781445361 3 26.650000000000002 23.525 25.8 24.025 4 30.875000000000004 26.924999999999997 18.05 24.15 5 29.299999999999997 29.75 18.25 22.7 6 23.85596399099775 32.6081520380095 21.380345086271568 22.155538884721178 7 24.0 19.650000000000002 31.874999999999996 24.474999999999998 8 25.6 20.974999999999998 24.575 28.849999999999998 9 25.374999999999996 22.125 26.35 26.150000000000002 10-11 29.349999999999998 26.150000000000002 19.275000000000002 25.224999999999998 12-13 29.1125 21.837500000000002 21.9375 27.1125 14-15 28.025 24.825 23.25 23.9 16-17 28.825 23.2375 21.9375 26.0 18-19 28.653581697712216 24.803100387548444 22.677834729341168 23.865483185398176 20-21 27.525 24.349999999999998 23.1875 24.9375 22-23 27.440930116264532 24.50306288286036 22.95286910863858 25.103137892236532 24-25 27.028378547318415 24.50306288286036 22.42780347543443 26.040755094386796 26-27 26.5125 24.5625 23.7875 25.137500000000003 28-29 27.462500000000002 23.625 23.625 25.2875 30-31 27.950000000000003 23.674999999999997 23.0125 25.362499999999997 32-33 28.275 24.349999999999998 22.45 24.925 34-35 28.549999999999997 24.5625 22.5 24.3875 36-37 27.224999999999998 23.525 23.45 25.8 38-39 27.6125 24.1875 23.1125 25.087500000000002 40-41 27.8375 23.2875 22.650000000000002 26.224999999999998 42-43 28.078509813726715 23.65295661957745 22.82785348168521 25.440680085010626 44-45 28.069517379344838 24.76869217304326 23.168292073018254 23.99349837459365 46-47 28.92861607700963 23.6029503687961 22.290286285785722 25.17814726840855 48-49 28.053506688336043 24.32804100512564 22.677834729341168 24.94061757719715 50-51 28.175 24.5625 22.8625 24.4 52-53 28.3875 24.625 23.0 23.9875 54-55 27.6625 23.674999999999997 23.35 25.3125 56-57 28.599999999999998 24.0125 23.1125 24.275 58-59 28.449999999999996 23.9 23.025000000000002 24.625 60-61 28.425 24.3 22.7375 24.5375 62-63 27.5875 24.7 23.7625 23.95 64-65 28.299999999999997 24.325 22.287499999999998 25.087500000000002 66-67 28.975 24.125 22.0125 24.887500000000003 68-69 27.8125 24.762500000000003 23.1125 24.3125 70-71 29.394848712178046 24.618654663665918 21.767941985496375 24.218554638659665 72-73 28.394598649662417 24.8062015503876 22.605651412853213 24.193548387096776 74-75 28.166020752594072 24.74059257407176 22.890361295161895 24.20302537817227 76-77 29.462500000000002 23.674999999999997 22.3625 24.5 78-79 29.2875 24.0125 22.237499999999997 24.462500000000002 80-81 29.2875 24.575 22.237499999999997 23.9 82-83 28.391048881110137 24.353044130516317 23.377922240280036 23.87798474809351 84-85 29.9 22.875 23.1375 24.087500000000002 86-87 29.7875 23.925 22.237499999999997 24.05 88-89 29.812499999999996 24.525 22.35 23.3125 90-91 30.175 24.5375 22.2625 23.025000000000002 92-93 30.120030007501875 24.99374843710928 22.06801700425106 22.818204551137786 94-95 31.345336334083523 24.268567141785446 21.50537634408602 22.88072018004501 96-97 31.1875 24.087500000000002 21.825 22.900000000000002 98-99 30.078759844980624 24.953119139892486 22.115264408051004 22.852856607075882 100-101 29.932483120780194 24.981245311327832 22.355588897224308 22.73068267066767 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.5 2 0.5 3 0.5 4 0.5 5 1.5 6 2.0 7 1.0 8 1.0 9 0.5 10 0.5 11 0.5 12 0.5 13 1.0 14 0.5 15 2.0 16 2.5 17 2.0 18 2.5 19 1.0 20 1.5 21 1.5 22 0.0 23 0.0 24 0.5 25 2.5 26 2.5 27 1.5 28 2.0 29 3.5 30 2.5 31 2.0 32 4.5 33 6.5 34 7.5 35 15.0 36 23.5 37 37.0 38 45.0 39 52.5 40 72.0 41 83.0 42 99.5 43 122.0 44 147.5 45 146.0 46 153.0 47 171.0 48 157.0 49 160.0 50 165.5 51 160.5 52 142.0 53 138.0 54 159.5 55 157.0 56 142.5 57 125.0 58 110.0 59 97.0 60 83.5 61 84.0 62 80.5 63 75.0 64 75.5 65 74.0 66 65.5 67 65.0 68 66.5 69 52.5 70 38.5 71 36.5 72 44.0 73 42.0 74 35.5 75 32.0 76 21.5 77 15.5 78 15.0 79 9.0 80 5.0 81 2.5 82 2.0 83 2.5 84 1.0 85 0.5 86 1.0 87 2.0 88 2.5 89 1.0 90 0.0 91 0.0 92 0.5 93 0.5 94 0.5 95 0.5 96 1.0 97 1.5 98 1.5 99 3.5 100 10.5 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.025 3 0.0 4 0.0 5 0.0 6 0.025 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 0.0125 20-21 0.0 22-23 0.0125 24-25 0.0125 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 0.0125 44-45 0.025 46-47 0.0125 48-49 0.0125 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 0.025 72-73 0.025 74-75 0.0125 76-77 0.0 78-79 0.0 80-81 0.0 82-83 0.0125 84-85 0.0 86-87 0.0 88-89 0.0 90-91 0.0 92-93 0.025 94-95 0.025 96-97 0.0 98-99 0.0125 100-101 0.025 >>END_MODULE >>Sequence Length Distribution pass #Length Count 101 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 88.425 #Duplication Level Percentage of deduplicated Percentage of total 1 89.65224766751484 79.27499999999999 2 8.736217133163699 15.45 3 1.1874469889737065 3.15 4 0.2544529262086514 0.8999999999999999 5 0.05654509471303364 0.25 6 0.02827254735651682 0.15 7 0.0 0.0 8 0.05654509471303364 0.4 9 0.0 0.0 >10 0.02827254735651682 0.42500000000000004 >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 17 0.42500000000000004 No Hit CCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGCAA 8 0.2 No Hit CTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGCAAG 8 0.2 No Hit CTTGGATTTATGAAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTT 6 0.15 No Hit GCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGTTAACGAAC 5 0.125 No Hit AGTAATTCTAGAGCTAATACGTGCAACAAACCCCGACTTCTGGGAGGGGC 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 0.0 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 0.1 0.0 0.0 0.0 0.0 36-37 0.1125 0.0 0.0 0.0 0.0 38-39 0.125 0.0 0.0 0.0 0.0 40-41 0.15 0.0 0.0 0.0 0.0 42-43 0.2 0.0 0.0 0.0 0.0 44-45 0.3375 0.0 0.0 0.0 0.0 46-47 0.44999999999999996 0.0 0.0 0.0 0.0 48-49 0.55 0.0 0.0 0.0 0.0 50-51 0.7125 0.0 0.0 0.0 0.0 52-53 0.8375 0.0 0.0 0.0 0.0 54-55 1.025 0.0 0.0 0.0 0.0 56-57 1.1 0.0 0.0 0.0 0.0 58-59 1.2999999999999998 0.0 0.0 0.0 0.0 60-61 1.6625 0.0 0.0 0.0 0.0 62-63 1.9375 0.0 0.0 0.0 0.0 64-65 2.2750000000000004 0.0 0.0 0.0 0.0 66-67 2.4875 0.0 0.0 0.0 0.0 68-69 2.85 0.0 0.0 0.0 0.0 70-71 3.125 0.0 0.0 0.0 0.0 72-73 3.425 0.0 0.0 0.0 0.0 74-75 3.9499999999999997 0.0 0.0 0.0 0.0 76-77 4.637499999999999 0.0 0.0 0.0 0.0 78-79 5.225 0.0 0.0 0.0 0.0 80-81 5.825 0.0 0.0 0.0 0.0 82-83 6.325 0.0 0.0 0.0 0.0 84-85 6.862500000000001 0.0 0.0 0.0 0.0 86-87 7.625 0.0 0.0 0.0 0.0 88-89 8.3375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1080580 spots for ERR3450063.sra Written 1080580 spots for ERR3450063.sra Read 1080580 spots for ERR3450063.sra Written 1080580 spots for ERR3450063.sra Read 1080580 spots for ERR3450063.sra Written 1080580 spots for ERR3450063.sra Read 1080580 spots for ERR3450063.sra Written 1080580 spots for ERR3450063.sra Read 1080580 spots for ERR3450063.sra Written 1080580 spots for ERR3450063.sra Read 1080580 spots for ERR3450063.sra Written 1080580 spots for ERR3450063.sra Read 1080580 spots for ERR3450063.sra Written 1080580 spots for ERR3450063.sra Read 1080580 spots for ERR3450063.sra Written 1080580 spots for ERR3450063.sra Read 1080580 spots for ERR3450063.sra Written 1080580 spots for ERR3450063.sra Read 1080580 spots for ERR3450063.sra Written 1080580 spots for ERR3450063.sra Read 1080580 spots for ERR3450063.sra Written 1080580 spots for ERR3450063.sra Read 1080580 spots for ERR3450063.sra Written 1080580 spots for ERR3450063.sra Read 1080580 spots for ERR3450063.sra Written 1080580 spots for ERR3450063.sra Read 1080580 spots for ERR3450063.sra Written 1080580 spots for ERR3450063.sra Read 1080580 spots for ERR3450063.sra Written 1080580 spots for ERR3450063.sra Read 1080580 spots for ERR3450063.sra Written 1080580 spots for ERR3450063.sra Read 1080580 spots for ERR3450063.sra Written 1080580 spots for ERR3450063.sra Read 1080580 spots for ERR3450063.sra Written 1080580 spots for ERR3450063.sra Read 1080580 spots for ERR3450063.sra Written 1080580 spots for ERR3450063.sra Read 1080580 spots for ERR3450063.sra Written 1080580 spots for ERR3450063.sra SRR ids: ['ERR3450063.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_i8xv72vv ERR3450063.sra spots: 21611600 blocks: [[1, 1080580], [1080581, 2161160], [2161161, 3241740], [3241741, 4322320], [4322321, 5402900], [5402901, 6483480], [6483481, 7564060], [7564061, 8644640], [8644641, 9725220], [9725221, 10805800], [10805801, 11886380], [11886381, 12966960], [12966961, 14047540], [14047541, 15128120], [15128121, 16208700], [16208701, 17289280], [17289281, 18369860], [18369861, 19450440], [19450441, 20531020], [20531021, 21611600]] ERR3450063 file size 5191253 ERR3450063 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 ERR3450063 ERR3450063_1.fastq ERR3450063_2.fastq Input file: ERR3450063_1.fastq Paired file: ERR3450063_2.fastq trimmed: ERR3450063-trimmed-pair1.fastq, ERR3450063-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 14:21:27 2024 >> started Sat Dec 7 14:21:47 2024 >> done (20.143s) 21611600 read pairs processed; of these: 190 ( 0.00%) short read pairs filtered out after trimming by size control 74415 ( 0.34%) empty read pairs filtered out after trimming by size control 21536995 (99.65%) read pairs available; of these: 2805712 (13.03%) trimmed read pairs available after processing 18731283 (86.97%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 54 0.00% 19 76 0.00% 20 289 0.00% 21 791 0.00% 22 955 0.00% 23 463 0.00% 24 479 0.00% 25 716 0.00% 26 876 0.00% 27 1345 0.01% 28 1907 0.01% 29 2375 0.01% 30 2943 0.01% 31 3527 0.02% 32 3688 0.02% 33 3474 0.02% 34 3408 0.02% 35 3517 0.02% 36 3660 0.02% 37 4139 0.02% 38 4919 0.02% 39 5856 0.03% 40 6648 0.03% 41 7806 0.04% 42 8831 0.04% 43 9225 0.04% 44 8509 0.04% 45 8589 0.04% 46 8806 0.04% 47 9768 0.05% 48 10815 0.05% 49 11892 0.06% 50 13201 0.06% 51 14773 0.07% 52 15922 0.07% 53 16664 0.08% 54 17532 0.08% 55 17976 0.08% 56 18889 0.09% 57 19294 0.09% 58 21159 0.10% 59 22732 0.11% 60 24259 0.11% 61 26934 0.13% 62 29257 0.14% 63 31150 0.14% 64 31758 0.15% 65 32564 0.15% 66 33646 0.16% 67 34888 0.16% 68 36516 0.17% 69 37695 0.18% 70 40658 0.19% 71 42595 0.20% 72 45586 0.21% 73 47893 0.22% 74 49574 0.23% 75 50727 0.24% 76 51994 0.24% 77 53231 0.25% 78 54862 0.25% 79 57292 0.27% 80 58966 0.27% 81 61107 0.28% 82 63793 0.30% 83 65084 0.30% 84 66730 0.31% 85 69079 0.32% 86 70577 0.33% 87 73363 0.34% 88 74830 0.35% 89 76714 0.36% 90 78594 0.36% 91 81772 0.38% 92 85109 0.40% 93 86428 0.40% 94 88916 0.41% 95 89781 0.42% 96 91126 0.42% 97 93489 0.43% 98 94233 0.44% 99 95587 0.44% 100 108867 0.51% 101 18731283 86.97% 21536995 reads passed initial QC criterion=sequence-density sequence-density=0.34 sequence-density-rank=1 fanout-score=1.99 fanout-score-rank=32 prefix-density=0.34 prefix-fanout=2.0 sequence=GTATTTAGCCTTG criterion=fanout-score sequence-density=0.07 sequence-density-rank=25 fanout-score=170.15 fanout-score-rank=1 prefix-density=0.56 prefix-fanout=21.3 sequence=CGCCGCCGCCGC criterion=sequence-density sequence-density=0.21 sequence-density-rank=1 fanout-score=2.17 fanout-score-rank=28 prefix-density=0.22 prefix-fanout=2.1 sequence=AGCCAGAGGAAA criterion=fanout-score sequence-density=0.09 sequence-density-rank=16 fanout-score=178.82 fanout-score-rank=1 prefix-density=0.70 prefix-fanout=22.5 sequence=CGGCGGCGGCGA ERR3450063 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 14:22:19 Started mapping on | Dec 07 14:22:19 Finished on | Dec 07 14:24:25 Mapping speed, Million of reads per hour | 615.34 Number of input reads | 21536995 Average input read length | 196 UNIQUE READS: Uniquely mapped reads number | 15648272 Uniquely mapped reads % | 72.66% Average mapped length | 196.23 Number of splices: Total | 9747089 Number of splices: Annotated (sjdb) | 9230365 Number of splices: GT/AG | 9618187 Number of splices: GC/AG | 111627 Number of splices: AT/AC | 5850 Number of splices: Non-canonical | 11425 Mismatch rate per base, % | 0.24% Deletion rate per base | 0.01% Deletion average length | 2.12 Insertion rate per base | 0.01% Insertion average length | 1.87 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1288263 % of reads mapped to multiple loci | 5.98% Number of reads mapped to too many loci | 821039 % of reads mapped to too many loci | 3.81% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.14% % of reads unmapped: other | 14.41% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 4600460 4600460 4600460 N_multimapping 1288263 1288263 1288263 N_noFeature 572187 15007268 980535 N_ambiguous 285949 2577 56324 UnstrandedReadsAssigned:14790136 PositiveStrandReadsAssigned:638427 NegativeStrandReadsAssigned:14611413 Dataset is classified negative stranded MeadianReadLen=101 20thPercentileLength=101 echo kmer=97 ERR3450063 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: ERR3450063-trimmed-pair1.fastq ERR3450063-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 21,536,995 reads, 15,557,357 reads pseudoaligned [quant] estimated average fragment length: 181.097 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,156 rounds 52973 ERR3450063.ke.tsv 35125 ERR3450063.se.tsv 88098 total ==> ERR3450063.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 756.191 0 0 PNS24247 1044 863.903 34.4872 3.86959 PNS24249 1928 1747.9 167.512 9.28968 PNS24246 1044 863.903 34.4872 3.86959 PNS24248 1044 863.903 34.4872 3.86959 PNS24244 1471 1290.9 50.0264 3.75645 PNS24243 293 134.491 0 0 KQK14069 1603 1422.9 3530.59 240.516 KQK14071 474 297.902 199.92 65.051 ==> ERR3450063.se.tsv <== BRADI_1g14170v3 3881 BRADI_1g53295v3 22 BRADI_1g59795v3 200 BRADI_1g07683v3 0 BRADI_1g00485v3 39 BRADI_1g20270v3 1631 BRADI_1g74790v3 178 BRADI_1g09890v3 8 BRADI_1g77505v3 206 BRADI_1g48960v3 0 ERR3450063 completed mapping pipeline successfully