Starting /dee2/code/volunteer_pipeline.sh ERR3450086 current disk space = 1542867681280 free memory = 1602362536 ERR3450086 SRAfilesize 5e9416adbc37998741398132ab0f07a6 ERR3450086.sra ERR3450086.sra file validated ERR3450086 is paired end ERR3450086 is conventional basespace ERR3450086 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3450086_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 36.2225 37.0 37.0 37.0 37.0 37.0 2 36.308 37.0 37.0 37.0 37.0 37.0 3 36.346 37.0 37.0 37.0 37.0 37.0 4 36.494 37.0 37.0 37.0 37.0 37.0 5 36.532 37.0 37.0 37.0 37.0 37.0 6 36.6035 37.0 37.0 37.0 37.0 37.0 7 36.4725 37.0 37.0 37.0 37.0 37.0 8 36.509 37.0 37.0 37.0 37.0 37.0 9 36.4625 37.0 37.0 37.0 37.0 37.0 10-11 36.52575 37.0 37.0 37.0 37.0 37.0 12-13 36.512 37.0 37.0 37.0 37.0 37.0 14-15 36.5165 37.0 37.0 37.0 37.0 37.0 16-17 36.4445 37.0 37.0 37.0 37.0 37.0 18-19 36.458 37.0 37.0 37.0 37.0 37.0 20-21 36.38825 37.0 37.0 37.0 37.0 37.0 22-23 36.3365 37.0 37.0 37.0 37.0 37.0 24-25 36.389250000000004 37.0 37.0 37.0 37.0 37.0 26-27 36.370999999999995 37.0 37.0 37.0 37.0 37.0 28-29 36.326750000000004 37.0 37.0 37.0 37.0 37.0 30-31 36.40775 37.0 37.0 37.0 37.0 37.0 32-33 36.328 37.0 37.0 37.0 37.0 37.0 34-35 36.28275 37.0 37.0 37.0 37.0 37.0 36-37 36.25775 37.0 37.0 37.0 37.0 37.0 38-39 36.24925 37.0 37.0 37.0 37.0 37.0 40-41 36.278999999999996 37.0 37.0 37.0 37.0 37.0 42-43 36.2275 37.0 37.0 37.0 37.0 37.0 44-45 36.147499999999994 37.0 37.0 37.0 37.0 37.0 46-47 36.165 37.0 37.0 37.0 37.0 37.0 48-49 36.13975 37.0 37.0 37.0 37.0 37.0 50-51 36.18325 37.0 37.0 37.0 37.0 37.0 52-53 36.104749999999996 37.0 37.0 37.0 37.0 37.0 54-55 36.1635 37.0 37.0 37.0 37.0 37.0 56-57 36.05775 37.0 37.0 37.0 37.0 37.0 58-59 36.057500000000005 37.0 37.0 37.0 37.0 37.0 60-61 36.073499999999996 37.0 37.0 37.0 37.0 37.0 62-63 36.0455 37.0 37.0 37.0 37.0 37.0 64-65 35.866 37.0 37.0 37.0 37.0 37.0 66-67 36.09975 37.0 37.0 37.0 37.0 37.0 68-69 35.9875 37.0 37.0 37.0 37.0 37.0 70-71 35.96725 37.0 37.0 37.0 37.0 37.0 72-73 36.00375 37.0 37.0 37.0 37.0 37.0 74-75 35.99675 37.0 37.0 37.0 37.0 37.0 76-77 35.927499999999995 37.0 37.0 37.0 37.0 37.0 78-79 35.97425 37.0 37.0 37.0 37.0 37.0 80-81 36.00025 37.0 37.0 37.0 37.0 37.0 82-83 35.8965 37.0 37.0 37.0 37.0 37.0 84-85 36.038 37.0 37.0 37.0 37.0 37.0 86-87 35.90725 37.0 37.0 37.0 37.0 37.0 88-89 35.893 37.0 37.0 37.0 37.0 37.0 90-91 35.813 37.0 37.0 37.0 37.0 37.0 92-93 35.873999999999995 37.0 37.0 37.0 37.0 37.0 94-95 35.752250000000004 37.0 37.0 37.0 37.0 37.0 96-97 35.84425 37.0 37.0 37.0 37.0 37.0 98-99 35.7475 37.0 37.0 37.0 37.0 37.0 100-101 35.69725 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 19 1.0 20 0.0 21 1.0 22 1.0 23 0.0 24 9.0 25 11.0 26 12.0 27 19.0 28 27.0 29 38.0 30 47.0 31 56.0 32 63.0 33 88.0 34 110.0 35 206.0 36 1710.0 37 1601.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 40.12531328320802 10.150375939849624 10.050125313283207 39.67418546365914 2 21.525 12.950000000000001 29.225 36.3 3 20.9 17.349999999999998 26.650000000000002 35.099999999999994 4 27.950000000000003 21.775 17.65 32.625 5 26.8 27.325 21.7 24.175 6 23.125 31.95 23.799999999999997 21.125 7 19.35 23.175 37.4 20.075000000000003 8 22.425 20.424999999999997 30.175 26.974999999999998 9 21.5 21.425 31.75 25.324999999999996 10-11 23.849999999999998 28.749999999999996 22.0125 25.387500000000003 12-13 23.599999999999998 22.650000000000002 25.6 28.15 14-15 22.925 23.8125 26.424999999999997 26.8375 16-17 23.9375 23.35 26.7125 26.0 18-19 24.5375 24.05 25.424999999999997 25.9875 20-21 25.825 24.462500000000002 24.45 25.2625 22-23 24.85 24.525 24.637500000000003 25.9875 24-25 23.724999999999998 23.825 24.7375 27.712500000000002 26-27 24.0125 23.75 24.8625 27.375 28-29 25.5375 23.7375 24.175 26.55 30-31 24.637500000000003 24.0125 23.4625 27.8875 32-33 23.8625 23.225 25.3 27.6125 34-35 24.5375 24.8125 23.25 27.400000000000002 36-37 24.0625 25.0375 24.837500000000002 26.0625 38-39 25.074999999999996 24.1125 24.1125 26.700000000000003 40-41 25.35 24.125 23.3375 27.187499999999996 42-43 24.1125 24.712500000000002 23.5375 27.6375 44-45 25.324999999999996 23.8625 23.9875 26.825 46-47 24.637500000000003 24.3625 24.675 26.325 48-49 25.662499999999998 23.962500000000002 23.575 26.8 50-51 23.974999999999998 24.075 24.825 27.125 52-53 24.875 22.3375 25.2875 27.500000000000004 54-55 24.9125 25.0125 23.1625 26.9125 56-57 23.8125 24.1375 24.474999999999998 27.575 58-59 24.9 24.075 23.9875 27.037499999999998 60-61 25.2125 23.2125 24.1625 27.4125 62-63 24.975 23.425 24.712500000000002 26.887499999999996 64-65 24.9875 23.5 24.55 26.9625 66-67 24.5125 24.4 23.799999999999997 27.287499999999998 68-69 25.474999999999998 24.5125 23.65 26.3625 70-71 24.1625 21.925 25.2125 28.7 72-73 25.5375 25.35 23.599999999999998 25.5125 74-75 26.0625 23.425 24.05 26.4625 76-77 25.15 24.325 23.4875 27.037499999999998 78-79 25.124999999999996 23.962500000000002 24.349999999999998 26.5625 80-81 25.087500000000002 23.7625 23.2125 27.9375 82-83 25.650000000000002 24.212500000000002 24.175 25.9625 84-85 25.874999999999996 23.525 23.0875 27.5125 86-87 25.7625 24.3875 23.724999999999998 26.125 88-89 24.4 24.3625 23.95 27.287499999999998 90-91 25.4875 24.349999999999998 23.125 27.037499999999998 92-93 25.474999999999998 25.4 22.425 26.700000000000003 94-95 25.95 24.2 23.0625 26.787499999999998 96-97 24.212500000000002 25.4875 23.5875 26.7125 98-99 24.3875 24.4 23.1 28.1125 100-101 24.9375 24.837500000000002 23.2375 26.987499999999997 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 10.0 1 6.0 2 2.0 3 1.5 4 1.0 5 1.0 6 0.5 7 0.0 8 0.0 9 0.5 10 0.5 11 0.5 12 1.5 13 1.0 14 0.5 15 0.5 16 0.0 17 0.5 18 0.5 19 1.0 20 1.0 21 0.0 22 1.0 23 1.0 24 0.0 25 0.0 26 2.0 27 3.0 28 2.0 29 2.5 30 3.0 31 4.5 32 5.5 33 6.5 34 12.5 35 16.0 36 26.5 37 39.5 38 44.5 39 61.0 40 80.0 41 97.0 42 115.0 43 115.5 44 141.5 45 179.0 46 168.0 47 172.0 48 189.5 49 180.0 50 163.0 51 155.0 52 157.5 53 160.5 54 161.5 55 161.5 56 144.0 57 116.0 58 108.0 59 107.0 60 87.0 61 66.0 62 60.0 63 62.5 64 61.0 65 54.5 66 57.5 67 59.5 68 52.5 69 51.0 70 46.0 71 37.0 72 35.5 73 27.5 74 26.0 75 19.5 76 10.0 77 11.5 78 14.0 79 12.5 80 7.0 81 3.5 82 1.5 83 1.5 84 1.0 85 1.5 86 2.0 87 1.0 88 0.5 89 0.5 90 0.5 91 0.0 92 0.5 93 0.5 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 0.25 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 82.825 #Duplication Level Percentage of deduplicated Percentage of total 1 84.5457289465741 70.025 2 12.28493812254754 20.349999999999998 3 2.233625113190462 5.55 4 0.5433142167220043 1.7999999999999998 5 0.18110473890733475 0.75 6 0.030184123151222455 0.15 7 0.06036824630244491 0.35000000000000003 8 0.0 0.0 9 0.030184123151222455 0.22499999999999998 >10 0.09055236945366738 0.8 >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 11 0.27499999999999997 No Hit CCCCGACTGTCCCTATTAATCATTACTCCGATCCCGAAGGCCAACACAAT 11 0.27499999999999997 No Hit GCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGC 10 0.25 No Hit TTACGACTTCTCCTTCCTCTAAATGATAAGGTTCAATGGACTTCTCGCGA 9 0.22499999999999998 No Hit GTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACT 7 0.17500000000000002 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACGAATTCGTATCTCGTAT 7 0.17500000000000002 TruSeq Adapter, Index 7 (97% over 35bp) TCGGCATCGTTTATGGTTGAGACTAGGACGGTATCTGATCGTCTTCGAGC 6 0.15 No Hit GTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAG 5 0.125 No Hit CGTCGAGTTATCATGAATCATCGGATCAGCGAGCAAAGCCCGCGTCAGCC 5 0.125 No Hit CCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGC 5 0.125 No Hit CTTTTATCTAATAAATGCGCCCCTCCCAGAAGTCGGGGTTTGTTGCACGT 5 0.125 No Hit CCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGAACC 5 0.125 No Hit GTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCAT 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 0.0125 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 0.0625 0.0 0.0 0.0 0.0 32-33 0.1 0.0 0.0 0.0 0.0 34-35 0.1375 0.0 0.0 0.0 0.0 36-37 0.16249999999999998 0.0 0.0 0.0 0.0 38-39 0.225 0.0 0.0 0.0 0.0 40-41 0.3125 0.0 0.0 0.0 0.0 42-43 0.35 0.0 0.0 0.0 0.0 44-45 0.4 0.0 0.0 0.0 0.0 46-47 0.4375 0.0 0.0 0.0 0.0 48-49 0.5125 0.0 0.0 0.0 0.0 50-51 0.5874999999999999 0.0 0.0 0.0 0.0 52-53 0.625 0.0 0.0 0.0 0.0 54-55 0.7124999999999999 0.0 0.0 0.0 0.0 56-57 0.7875 0.0 0.0 0.0 0.0 58-59 0.9375 0.0 0.0 0.0 0.0 60-61 1.1 0.0 0.0 0.0 0.0 62-63 1.25 0.0 0.0 0.0 0.0 64-65 1.4625 0.0 0.0 0.0 0.0 66-67 1.7 0.0 0.0 0.0 0.0 68-69 1.9 0.0 0.0 0.0 0.0 70-71 2.075 0.0 0.0 0.0 0.0 72-73 2.25 0.0 0.0 0.0 0.0 74-75 2.6625 0.0 0.0 0.0 0.0 76-77 3.0875 0.0 0.0 0.0 0.0 78-79 3.3125 0.0 0.0 0.0 0.0 80-81 3.6375 0.0 0.0 0.0 0.0 82-83 3.875 0.0 0.0 0.0 0.0 84-85 4.4125 0.0 0.0 0.0 0.0 86-87 5.1875 0.0 0.0 0.0 0.0 88-89 5.949999999999999 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE ERR3450086 read2 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3450086_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 36.0805 37.0 37.0 37.0 37.0 37.0 2 35.99 37.0 37.0 37.0 37.0 37.0 3 36.0535 37.0 37.0 37.0 37.0 37.0 4 36.228 37.0 37.0 37.0 37.0 37.0 5 36.2635 37.0 37.0 37.0 37.0 37.0 6 36.316 37.0 37.0 37.0 37.0 37.0 7 36.338 37.0 37.0 37.0 37.0 37.0 8 36.3585 37.0 37.0 37.0 37.0 37.0 9 36.2725 37.0 37.0 37.0 37.0 37.0 10-11 36.199749999999995 37.0 37.0 37.0 37.0 37.0 12-13 36.214749999999995 37.0 37.0 37.0 37.0 37.0 14-15 36.19375 37.0 37.0 37.0 37.0 37.0 16-17 36.22725 37.0 37.0 37.0 37.0 37.0 18-19 36.19725 37.0 37.0 37.0 37.0 37.0 20-21 36.2665 37.0 37.0 37.0 37.0 37.0 22-23 36.175 37.0 37.0 37.0 37.0 37.0 24-25 36.118750000000006 37.0 37.0 37.0 37.0 37.0 26-27 36.171 37.0 37.0 37.0 37.0 37.0 28-29 36.185 37.0 37.0 37.0 37.0 37.0 30-31 36.18125 37.0 37.0 37.0 37.0 37.0 32-33 36.122749999999996 37.0 37.0 37.0 37.0 37.0 34-35 36.14875 37.0 37.0 37.0 37.0 37.0 36-37 36.0645 37.0 37.0 37.0 37.0 37.0 38-39 36.07025 37.0 37.0 37.0 37.0 37.0 40-41 36.15375 37.0 37.0 37.0 37.0 37.0 42-43 36.07625 37.0 37.0 37.0 37.0 37.0 44-45 36.0595 37.0 37.0 37.0 37.0 37.0 46-47 36.08525 37.0 37.0 37.0 37.0 37.0 48-49 36.019999999999996 37.0 37.0 37.0 37.0 37.0 50-51 36.082499999999996 37.0 37.0 37.0 37.0 37.0 52-53 36.1435 37.0 37.0 37.0 37.0 37.0 54-55 36.08625 37.0 37.0 37.0 37.0 37.0 56-57 36.14375 37.0 37.0 37.0 37.0 37.0 58-59 36.126000000000005 37.0 37.0 37.0 37.0 37.0 60-61 36.076499999999996 37.0 37.0 37.0 37.0 37.0 62-63 36.110749999999996 37.0 37.0 37.0 37.0 37.0 64-65 36.04375 37.0 37.0 37.0 37.0 37.0 66-67 36.07375 37.0 37.0 37.0 37.0 37.0 68-69 36.068 37.0 37.0 37.0 37.0 37.0 70-71 36.03075 37.0 37.0 37.0 37.0 37.0 72-73 36.079750000000004 37.0 37.0 37.0 37.0 37.0 74-75 36.0115 37.0 37.0 37.0 37.0 37.0 76-77 35.963499999999996 37.0 37.0 37.0 37.0 37.0 78-79 35.8755 37.0 37.0 37.0 37.0 37.0 80-81 35.94925 37.0 37.0 37.0 37.0 37.0 82-83 35.9885 37.0 37.0 37.0 37.0 37.0 84-85 35.899249999999995 37.0 37.0 37.0 37.0 37.0 86-87 35.950500000000005 37.0 37.0 37.0 37.0 37.0 88-89 35.902 37.0 37.0 37.0 37.0 37.0 90-91 35.863749999999996 37.0 37.0 37.0 37.0 37.0 92-93 35.917500000000004 37.0 37.0 37.0 37.0 37.0 94-95 35.8695 37.0 37.0 37.0 37.0 37.0 96-97 35.89125 37.0 37.0 37.0 37.0 37.0 98-99 35.81325 37.0 37.0 37.0 37.0 37.0 100-101 35.787499999999994 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 14 1.0 15 6.0 16 9.0 17 4.0 18 4.0 19 3.0 20 4.0 21 8.0 22 14.0 23 11.0 24 6.0 25 10.0 26 12.0 27 10.0 28 17.0 29 23.0 30 31.0 31 25.0 32 49.0 33 54.0 34 115.0 35 205.0 36 1944.0 37 1435.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 39.875 16.650000000000002 12.3 31.175000000000004 2 26.25 22.775000000000002 26.275 24.7 3 26.55 22.5 27.05 23.9 4 30.55 27.675 16.900000000000002 24.875 5 28.9 30.425 18.224999999999998 22.45 6 24.15 31.900000000000002 19.425 24.525 7 24.9 19.0 30.975 25.124999999999996 8 25.275 20.825 22.900000000000002 31.0 9 26.450000000000003 21.349999999999998 25.1 27.1 10-11 27.6 28.050000000000004 19.575 24.775 12-13 27.787499999999998 22.1 22.8875 27.224999999999998 14-15 26.400000000000002 24.925 24.0625 24.6125 16-17 27.5625 23.5125 23.6375 25.2875 18-19 27.1375 24.4 23.3125 25.15 20-21 27.150000000000002 24.6 22.725 25.525 22-23 28.0625 24.3625 22.05 25.525 24-25 27.287499999999998 24.05 23.4625 25.2 26-27 27.800000000000004 24.5 23.1125 24.587500000000002 28-29 27.85 25.424999999999997 21.975 24.75 30-31 27.650000000000002 24.4375 22.8625 25.05 32-33 26.187500000000004 26.674999999999997 23.25 23.8875 34-35 28.95 24.349999999999998 22.625 24.075 36-37 27.962500000000002 24.95 21.712500000000002 25.374999999999996 38-39 26.937499999999996 25.2 22.8875 24.975 40-41 27.500000000000004 24.825 22.400000000000002 25.275 42-43 27.775 24.087500000000002 22.5 25.637500000000003 44-45 27.2625 24.337500000000002 22.675 25.724999999999998 46-47 26.887499999999996 24.875 22.4375 25.8 48-49 26.3 25.1875 22.5125 26.0 50-51 26.6125 25.6 22.375 25.412499999999998 52-53 27.8375 24.875 23.2375 24.05 54-55 27.987499999999997 24.325 21.912499999999998 25.775 56-57 27.787499999999998 26.0 22.0625 24.15 58-59 27.3875 25.112499999999997 23.1375 24.3625 60-61 27.487499999999997 25.162499999999998 22.575 24.775 62-63 27.787499999999998 24.3 22.6 25.3125 64-65 28.625 25.0625 22.3 24.0125 66-67 27.6125 25.25 22.5125 24.625 68-69 28.4125 24.224999999999998 23.150000000000002 24.212500000000002 70-71 27.775 25.174999999999997 22.5 24.55 72-73 27.875 25.4625 22.287499999999998 24.375 74-75 27.800000000000004 25.324999999999996 22.3625 24.5125 76-77 26.6625 25.662499999999998 23.0375 24.637500000000003 78-79 27.1375 24.45 23.7875 24.625 80-81 27.400000000000002 25.4625 22.3 24.837500000000002 82-83 27.575 25.650000000000002 22.8875 23.8875 84-85 28.3125 24.2375 22.3875 25.0625 86-87 28.775000000000002 24.212500000000002 22.8125 24.2 88-89 27.6125 24.625 23.4875 24.275 90-91 28.65 24.125 22.3875 24.837500000000002 92-93 28.4125 26.8625 21.224999999999998 23.5 94-95 28.075 25.2125 22.25 24.462500000000002 96-97 28.075 25.224999999999998 22.05 24.65 98-99 29.799999999999997 24.8 22.537499999999998 22.8625 100-101 28.9875 25.174999999999997 21.625 24.212500000000002 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.5 2 0.5 3 0.0 4 1.0 5 1.5 6 2.0 7 1.5 8 1.5 9 1.5 10 0.5 11 0.5 12 1.0 13 3.5 14 2.5 15 0.0 16 1.0 17 2.5 18 4.0 19 3.5 20 2.0 21 2.0 22 1.5 23 1.5 24 1.0 25 1.5 26 2.5 27 2.0 28 3.0 29 2.5 30 2.0 31 2.5 32 4.5 33 8.0 34 10.5 35 13.0 36 19.0 37 38.0 38 63.0 39 77.5 40 80.0 41 84.0 42 95.0 43 119.5 44 133.0 45 134.0 46 155.5 47 165.0 48 172.5 49 185.0 50 167.0 51 155.0 52 155.0 53 148.0 54 145.5 55 136.0 56 125.5 57 121.0 58 107.0 59 95.5 60 92.0 61 81.0 62 77.0 63 74.5 64 71.5 65 72.0 66 67.5 67 64.0 68 52.5 69 52.5 70 58.5 71 48.5 72 38.0 73 33.0 74 30.0 75 27.0 76 24.5 77 19.5 78 14.0 79 8.5 80 5.0 81 3.0 82 1.5 83 1.5 84 0.5 85 0.5 86 0.5 87 2.0 88 2.0 89 0.0 90 0.0 91 0.5 92 1.0 93 0.5 94 0.0 95 0.5 96 1.5 97 1.5 98 0.5 99 0.0 100 3.0 >>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 83.525 #Duplication Level Percentage of deduplicated Percentage of total 1 84.94462735707872 70.95 2 12.301706076025141 20.549999999999997 3 1.9155941334929663 4.8 4 0.32924274169410356 1.0999999999999999 5 0.26938042502244836 1.125 6 0.149655791679138 0.75 7 0.0 0.0 8 0.029931158335827598 0.2 9 0.029931158335827598 0.22499999999999998 >10 0.029931158335827598 0.3 >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 CCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGCAA 12 0.3 No Hit CTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGCAAG 9 0.22499999999999998 No Hit GCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGCAAGTA 8 0.2 No Hit AAGAAATTAGAGTGCTCAAAGCAAGCCATCGCTCTGGATACATTAGCATG 6 0.15 No Hit GATTAAGCCATGCATGTGCAAGTATGAACTAATTTGAACTGTGAAACTGC 6 0.15 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 6 0.15 No Hit ATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAGACGAACAACTG 6 0.15 No Hit CAATACCGGGCACATTAGTGTCTGGTAATTGGAATGAGTACAATCTAAAT 6 0.15 No Hit AGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTATGGGT 5 0.125 No Hit TACCAGGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGA 5 0.125 No Hit CTTTGGGCCGGGTCGGCCGGTCCGCCTCACGGCGAGCACCGACCTACTCG 5 0.125 No Hit TGCGAATGGCTCATTAAATCAGTTATAGTTTGTTTGATGGTACGTGCTAC 5 0.125 No Hit GTTGGATTTAAAGCTGGTGTTAAAGATTATAGATTGACTTACTACACCCC 5 0.125 No Hit TCGCCGTTTAGGCGACGGAAGTTTGAGGCAATAACAGGTCTGTGATGCCC 5 0.125 No Hit CGACCCTTCAGCCGGCGATGCGCTCCTAGCCTTAATTGGCCGGGTCGTGC 5 0.125 No Hit CTTACCAGGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTT 5 0.125 No Hit GTCGGGGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATG 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 0.0125 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 0.0625 0.0 0.0 0.0 0.0 32-33 0.1 0.0 0.0 0.0 0.0 34-35 0.1375 0.0 0.0 0.0 0.0 36-37 0.16249999999999998 0.0 0.0 0.0 0.0 38-39 0.225 0.0 0.0 0.0 0.0 40-41 0.3125 0.0 0.0 0.0 0.0 42-43 0.35 0.0 0.0 0.0 0.0 44-45 0.4 0.0 0.0 0.0 0.0 46-47 0.4375 0.0 0.0 0.0 0.0 48-49 0.4875 0.0 0.0 0.0 0.0 50-51 0.5625 0.0 0.0 0.0 0.0 52-53 0.6 0.0 0.0 0.0 0.0 54-55 0.6875 0.0 0.0 0.0 0.0 56-57 0.7625 0.0 0.0 0.0 0.0 58-59 0.9375 0.0 0.0 0.0 0.0 60-61 1.1 0.0 0.0 0.0 0.0 62-63 1.2375 0.0 0.0 0.0 0.0 64-65 1.4375 0.0 0.0 0.0 0.0 66-67 1.675 0.0 0.0 0.0 0.0 68-69 1.875 0.0 0.0 0.0 0.0 70-71 2.05 0.0 0.0 0.0 0.0 72-73 2.2125 0.0 0.0 0.0 0.0 74-75 2.6125 0.0 0.0 0.0 0.0 76-77 3.0375 0.0 0.0 0.0 0.0 78-79 3.2625 0.0 0.0 0.0 0.0 80-81 3.5875 0.0 0.0 0.0 0.0 82-83 3.8125 0.0 0.0 0.0 0.0 84-85 4.3625 0.0 0.0 0.0 0.0 86-87 5.1375 0.0 0.0 0.0 0.0 88-89 5.9 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTGGATT 15 6.142176E-4 95.0 2 >>END_MODULE Read 1367985 spots for ERR3450086.sra Written 1367985 spots for ERR3450086.sra Read 1367985 spots for ERR3450086.sra Written 1367985 spots for ERR3450086.sra Read 1367985 spots for ERR3450086.sra Written 1367985 spots for ERR3450086.sra Read 1367985 spots for ERR3450086.sra Written 1367985 spots for ERR3450086.sra Read 1367989 spots for ERR3450086.sra Written 1367989 spots for ERR3450086.sra Read 1367985 spots for ERR3450086.sra Written 1367985 spots for ERR3450086.sra Read 1367985 spots for ERR3450086.sra Written 1367985 spots for ERR3450086.sra Read 1367985 spots for ERR3450086.sra Written 1367985 spots for ERR3450086.sra Read 1367985 spots for ERR3450086.sra Written 1367985 spots for ERR3450086.sra Read 1367985 spots for ERR3450086.sra Written 1367985 spots for ERR3450086.sra Read 1367985 spots for ERR3450086.sra Written 1367985 spots for ERR3450086.sra Read 1367985 spots for ERR3450086.sra Written 1367985 spots for ERR3450086.sra Read 1367985 spots for ERR3450086.sra Written 1367985 spots for ERR3450086.sra Read 1367985 spots for ERR3450086.sra Written 1367985 spots for ERR3450086.sra Read 1367985 spots for ERR3450086.sra Written 1367985 spots for ERR3450086.sra Read 1367985 spots for ERR3450086.sra Written 1367985 spots for ERR3450086.sra Read 1367985 spots for ERR3450086.sra Written 1367985 spots for ERR3450086.sra Read 1367985 spots for ERR3450086.sra Written 1367985 spots for ERR3450086.sra Read 1367985 spots for ERR3450086.sra Written 1367985 spots for ERR3450086.sra Read 1367985 spots for ERR3450086.sra Written 1367985 spots for ERR3450086.sra SRR ids: ['ERR3450086.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_csii4eoq ERR3450086.sra spots: 27359704 blocks: [[1, 1367985], [1367986, 2735970], [2735971, 4103955], [4103956, 5471940], [5471941, 6839925], [6839926, 8207910], [8207911, 9575895], [9575896, 10943880], [10943881, 12311865], [12311866, 13679850], [13679851, 15047835], [15047836, 16415820], [16415821, 17783805], [17783806, 19151790], [19151791, 20519775], [20519776, 21887760], [21887761, 23255745], [23255746, 24623730], [24623731, 25991715], [25991716, 27359704]] ERR3450086 file size 6577759 ERR3450086 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 ERR3450086 ERR3450086_1.fastq ERR3450086_2.fastq Input file: ERR3450086_1.fastq Paired file: ERR3450086_2.fastq trimmed: ERR3450086-trimmed-pair1.fastq, ERR3450086-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 15:00:22 2024 >> started Sat Dec 7 15:00:47 2024 >> done (24.844s) 27359704 read pairs processed; of these: 153 ( 0.00%) short read pairs filtered out after trimming by size control 43407 ( 0.16%) empty read pairs filtered out after trimming by size control 27316144 (99.84%) read pairs available; of these: 2731101 (10.00%) trimmed read pairs available after processing 24585043 (90.00%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 43 0.00% 19 85 0.00% 20 208 0.00% 21 461 0.00% 22 662 0.00% 23 271 0.00% 24 306 0.00% 25 433 0.00% 26 667 0.00% 27 926 0.00% 28 1152 0.00% 29 1577 0.01% 30 1990 0.01% 31 2446 0.01% 32 2525 0.01% 33 2373 0.01% 34 2358 0.01% 35 2487 0.01% 36 2608 0.01% 37 2980 0.01% 38 3620 0.01% 39 4080 0.01% 40 4848 0.02% 41 5799 0.02% 42 6361 0.02% 43 6721 0.02% 44 6131 0.02% 45 6143 0.02% 46 6604 0.02% 47 7339 0.03% 48 8044 0.03% 49 8850 0.03% 50 9766 0.04% 51 11085 0.04% 52 11984 0.04% 53 12782 0.05% 54 13289 0.05% 55 13931 0.05% 56 14693 0.05% 57 15078 0.06% 58 16385 0.06% 59 18134 0.07% 60 19742 0.07% 61 22042 0.08% 62 23695 0.09% 63 25132 0.09% 64 26735 0.10% 65 27311 0.10% 66 29124 0.11% 67 30425 0.11% 68 31917 0.12% 69 33448 0.12% 70 35369 0.13% 71 37774 0.14% 72 41202 0.15% 73 43442 0.16% 74 44904 0.16% 75 47312 0.17% 76 48551 0.18% 77 49819 0.18% 78 52296 0.19% 79 54914 0.20% 80 57149 0.21% 81 59173 0.22% 82 62625 0.23% 83 64504 0.24% 84 66580 0.24% 85 70387 0.26% 86 72297 0.26% 87 74803 0.27% 88 76834 0.28% 89 79854 0.29% 90 82196 0.30% 91 86809 0.32% 92 90616 0.33% 93 93041 0.34% 94 95218 0.35% 95 98630 0.36% 96 99853 0.37% 97 103553 0.38% 98 105389 0.39% 99 106782 0.39% 100 121429 0.44% 101 24585043 90.00% 27316144 reads passed initial QC criterion=sequence-density sequence-density=0.35 sequence-density-rank=1 fanout-score=1.96 fanout-score-rank=34 prefix-density=0.35 prefix-fanout=1.9 sequence=GTATTTAGCCTTG criterion=fanout-score sequence-density=0.09 sequence-density-rank=20 fanout-score=47.70 fanout-score-rank=1 prefix-density=1.23 prefix-fanout=3.3 sequence=GGCGGCGGCGGCCTCGCCGTCGCTGGTGTACTTCCCCAGCTGCGCCAGGGAGTTTGCCTTGGCGCGCAGCAGCAGTGCCTCCTGGGCCGCCGCCACGTTCTCCGGCCGTCCTC criterion=sequence-density sequence-density=0.27 sequence-density-rank=1 fanout-score=1.99 fanout-score-rank=28 prefix-density=0.27 prefix-fanout=2.0 sequence=CAAGTGTTGGATT criterion=fanout-score sequence-density=0.08 sequence-density-rank=24 fanout-score=198.25 fanout-score-rank=1 prefix-density=0.70 prefix-fanout=22.5 sequence=CGGCGGCGGCGC ERR3450086 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 15:01:25 Started mapping on | Dec 07 15:01:25 Finished on | Dec 07 15:03:48 Mapping speed, Million of reads per hour | 687.68 Number of input reads | 27316144 Average input read length | 198 UNIQUE READS: Uniquely mapped reads number | 19464626 Uniquely mapped reads % | 71.26% Average mapped length | 197.83 Number of splices: Total | 12449039 Number of splices: Annotated (sjdb) | 11808212 Number of splices: GT/AG | 12284628 Number of splices: GC/AG | 143198 Number of splices: AT/AC | 7179 Number of splices: Non-canonical | 14034 Mismatch rate per base, % | 0.22% Deletion rate per base | 0.01% Deletion average length | 2.10 Insertion rate per base | 0.01% Insertion average length | 1.91 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1544454 % of reads mapped to multiple loci | 5.65% Number of reads mapped to too many loci | 1108900 % of reads mapped to too many loci | 4.06% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.87% % of reads unmapped: other | 16.16% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 6307064 6307064 6307064 N_multimapping 1544454 1544454 1544454 N_noFeature 713654 18752403 1135230 N_ambiguous 357345 2852 69570 UnstrandedReadsAssigned:18393627 PositiveStrandReadsAssigned:709371 NegativeStrandReadsAssigned:18259826 Dataset is classified negative stranded MeadianReadLen=101 20thPercentileLength=101 echo kmer=97 ERR3450086 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: ERR3450086-trimmed-pair1.fastq ERR3450086-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 27,316,144 reads, 19,318,197 reads pseudoaligned [quant] estimated average fragment length: 186.09 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,195 rounds 52973 ERR3450086.ke.tsv 35125 ERR3450086.se.tsv 88098 total ==> ERR3450086.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 751.133 0 0 PNS24247 1044 858.91 44.7831 4.02256 PNS24249 1928 1742.91 215.42 9.53558 PNS24246 1044 858.91 44.7831 4.02256 PNS24248 1044 858.91 44.7831 4.02256 PNS24244 1471 1285.91 52.2304 3.13364 PNS24243 293 129.694 0 0 KQK14069 1603 1417.91 5570.24 303.083 KQK14071 474 293.009 224.158 59.0212 ==> ERR3450086.se.tsv <== BRADI_1g14170v3 5910 BRADI_1g53295v3 26 BRADI_1g59795v3 149 BRADI_1g07683v3 0 BRADI_1g00485v3 38 BRADI_1g20270v3 2438 BRADI_1g74790v3 189 BRADI_1g09890v3 6 BRADI_1g77505v3 270 BRADI_1g48960v3 2 ERR3450086 completed mapping pipeline successfully