Starting /dee2/code/volunteer_pipeline.sh SRR6031391 current disk space = 3085166632960 free memory = 1466463652 SRR6031391 SRAfilesize 9beca8b9e080444a73c92980fca62c08 SRR6031391.sra SRR6031391.sra file validated SRR6031391 is paired end SRR6031391 is conventional basespace SRR6031391 read1 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6031391_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 42 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.997 34.0 33.0 34.0 33.0 34.0 2 33.37025 34.0 34.0 34.0 33.0 34.0 3 33.37975 34.0 33.0 34.0 33.0 34.0 4 33.436 34.0 34.0 34.0 33.0 34.0 5 33.5055 34.0 34.0 34.0 33.0 34.0 6 37.13875 38.0 38.0 38.0 36.0 38.0 7 37.31475 38.0 38.0 38.0 37.0 38.0 8 37.43675 38.0 38.0 38.0 37.0 38.0 9 37.4505 38.0 38.0 38.0 38.0 38.0 10-14 37.54535 38.0 38.0 38.0 38.0 38.0 15-19 37.570350000000005 38.0 38.0 38.0 37.8 38.0 20-24 37.4948 38.0 38.0 38.0 37.6 38.0 25-29 37.479600000000005 38.0 38.0 38.0 37.8 38.0 30-34 37.4096 38.0 38.0 38.0 37.4 38.0 35-39 37.390299999999996 38.0 38.0 38.0 37.6 38.0 40-44 36.5755 38.0 38.0 38.0 33.4 38.0 45-49 37.2962 38.0 38.0 38.0 37.0 38.0 50-54 37.27569999999999 38.0 38.0 38.0 37.0 38.0 55-59 37.1312 38.0 38.0 38.0 36.6 38.0 60-64 37.1391 38.0 38.0 38.0 36.4 38.0 65-69 36.9342 38.0 38.0 38.0 35.8 38.0 70-74 35.6945 38.0 37.6 38.0 29.2 38.0 75-79 31.38085 38.0 36.4 38.0 2.0 38.0 80-84 31.404200000000003 38.0 36.6 38.0 2.0 38.0 85-89 31.39685 38.0 36.2 38.0 2.0 38.0 90-94 31.3024 38.0 36.4 38.0 2.0 38.0 95-99 31.13975 38.0 36.0 38.0 2.0 38.0 100-104 30.86605 38.0 35.0 38.0 2.0 38.0 105-109 30.763799999999996 38.0 34.8 38.0 2.0 38.0 110-114 30.224700000000002 38.0 31.0 38.0 2.0 38.0 115-119 30.549449999999997 38.0 34.0 38.0 2.0 38.0 120-124 30.5708 38.0 34.0 38.0 2.0 38.0 125-129 30.510700000000003 38.0 34.0 38.0 2.0 38.0 130-134 30.2848 38.0 33.2 38.0 2.0 38.0 135-139 30.160400000000003 38.0 32.6 38.0 2.0 38.0 140-144 29.872500000000002 38.0 31.6 38.0 2.0 38.0 145-149 29.392900000000004 38.0 30.4 38.0 2.0 38.0 150 23.64475 33.0 2.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 3 1.0 4 0.0 5 1.0 6 0.0 7 1.0 8 0.0 9 0.0 10 1.0 11 4.0 12 1.0 13 3.0 14 3.0 15 8.0 16 9.0 17 35.0 18 187.0 19 386.0 20 22.0 21 28.0 22 10.0 23 12.0 24 14.0 25 11.0 26 9.0 27 26.0 28 18.0 29 24.0 30 24.0 31 30.0 32 36.0 33 49.0 34 54.0 35 125.0 36 300.0 37 2568.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 53.592282305153596 10.814927646610816 9.215536938309215 26.37725310992638 2 20.0 30.525000000000002 26.075 23.400000000000002 3 15.5 19.125 39.975 25.4 4 18.65 24.099999999999998 20.349999999999998 36.9 5 35.099999999999994 27.925 21.099999999999998 15.875 6 32.00800200050013 29.607401850462615 21.50537634408602 16.879219804951237 7 11.575000000000001 38.5 35.8 14.124999999999998 8 13.450000000000001 38.3 26.6 21.65 9 30.049999999999997 21.075 28.65 20.225 10-14 19.205 33.269999999999996 22.28 25.245 15-19 18.884999999999998 28.910000000000004 26.375 25.83 20-24 19.405 31.755 26.395000000000003 22.445 25-29 19.064999999999998 28.410000000000004 26.384999999999998 26.14 30-34 19.185 28.810000000000002 26.674999999999997 25.330000000000002 35-39 19.085 32.04 26.490000000000002 22.384999999999998 40-44 15.915000000000001 27.87 29.94 26.275 45-49 22.770000000000003 28.044999999999998 30.070000000000004 19.115 50-54 19.02 24.945 26.290000000000003 29.744999999999997 55-59 19.5 24.085 33.47 22.945 60-64 19.755 28.34 29.630000000000003 22.275 65-69 15.75 42.63 22.415 19.205 70-74 16.285 42.055 22.305 19.355 75-79 16.835 38.99 23.86 20.315 80-84 18.13 34.1 25.624999999999996 22.145 85-89 19.755 31.65 25.724999999999998 22.869999999999997 90-94 19.265 29.759999999999998 27.084999999999997 23.89 95-99 18.825 30.45 27.310000000000002 23.415 100-104 18.34 35.11 25.085 21.465 105-109 17.155 36.905 24.325 21.615000000000002 110-114 17.88 34.77 24.845 22.505 115-119 18.55 33.75 24.855 22.845 120-124 18.395 32.519999999999996 25.545 23.54 125-129 18.705 32.62 25.019999999999996 23.655 130-134 18.945 31.72 25.585 23.75 135-139 19.139999999999997 30.930000000000003 26.325 23.605 140-144 19.725 31.365 25.525 23.385 145-149 19.54 31.314999999999998 25.130000000000003 24.015 150 19.075 31.075000000000003 25.474999999999998 24.375 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 8.0 1 4.5 2 0.5 3 0.0 4 1.0 5 2.0 6 1.0 7 1.0 8 1.5 9 0.5 10 0.0 11 0.0 12 0.0 13 0.5 14 0.5 15 0.0 16 0.0 17 0.0 18 0.0 19 1.0 20 1.5 21 2.5 22 3.0 23 1.0 24 0.5 25 3.5 26 6.0 27 13.0 28 21.0 29 23.0 30 28.0 31 30.0 32 43.5 33 69.0 34 87.5 35 98.0 36 122.0 37 149.5 38 176.0 39 212.0 40 224.5 41 256.5 42 281.0 43 274.0 44 260.0 45 236.0 46 232.5 47 206.5 48 158.0 49 139.0 50 132.5 51 109.5 52 94.0 53 76.0 54 55.5 55 42.0 56 24.5 57 20.5 58 18.0 59 13.5 60 11.0 61 7.0 62 5.5 63 4.0 64 2.5 65 2.0 66 2.0 67 1.5 68 0.0 69 0.5 70 0.5 71 0.0 72 0.5 73 0.5 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 1.525 2 0.0 3 0.0 4 0.0 5 0.0 6 0.025 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 82.625 #Duplication Level Percentage of deduplicated Percentage of total 1 99.00151285930409 81.8 2 0.6959152798789713 1.15 3 0.0302571860816944 0.075 4 0.0907715582450832 0.3 5 0.0 0.0 6 0.0302571860816944 0.15 7 0.0 0.0 8 0.0907715582450832 0.6 9 0.0 0.0 >10 0.0302571860816944 0.25 >50 0.0 0.0 >100 0.0 0.0 >500 0.0302571860816944 15.675 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences fail #Sequence Count Percentage Possible Source GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGATCTCGTATGC 627 15.675 TruSeq Adapter, Index 9 (100% over 50bp) GATCGGAAGACACACGTCTGAACTCCAGTCACGATCAGATCTCGTATGCC 10 0.25 TruSeq Adapter, Index 9 (100% over 40bp) TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 8 0.2 No Hit NATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGATCTCGTATGC 8 0.2 TruSeq Adapter, Index 9 (98% over 50bp) GATCGGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGATCTCGTATG 8 0.2 TruSeq Adapter, Index 9 (100% over 45bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGAACTCGTATGC 6 0.15 TruSeq Adapter, Index 9 (98% over 50bp) >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.037500000000000006 0.0 0.0 0.0 0.0 82-83 0.0875 0.0 0.0 0.0 0.0 84-85 0.1 0.0 0.0 0.0 0.0 86-87 0.1 0.0 0.0 0.0 0.0 88-89 0.1375 0.0 0.0 0.0 0.0 90-91 0.2 0.0 0.0 0.0 0.0 92-93 0.225 0.0 0.0 0.0 0.0 94-95 0.2625 0.0 0.0 0.0 0.0 96-97 0.2875 0.0 0.0 0.0 0.0 98-99 0.3 0.0 0.0 0.0 0.0 100-101 0.3 0.0 0.0 0.0 0.0 102-103 0.32499999999999996 0.0 0.0 0.0 0.0 104-105 0.42500000000000004 0.0 0.0 0.0 0.0 106-107 0.4875 0.0 0.0 0.0 0.0 108-109 0.65 0.0 0.0 0.0 0.0 110-111 0.7 0.0 0.0 0.0 0.0 112-113 0.8125 0.0 0.0 0.0 0.0 114-115 1.0125 0.0 0.0 0.0 0.0 116-117 1.0875 0.0 0.0 0.0 0.0 118-119 1.2374999999999998 0.0 0.0 0.0 0.0 120-121 1.375 0.0 0.0 0.0 0.0 122-123 1.5125000000000002 0.0 0.0 0.0 0.0 124-125 1.7 0.0 0.0 0.0 0.0 126-127 1.825 0.0 0.0 0.0 0.0 128-129 2.0250000000000004 0.0 0.0 0.0 0.0 130-131 2.25 0.0 0.0 0.0 0.0 132-133 2.5875 0.0 0.0 0.0 0.0 134-135 2.8499999999999996 0.0 0.0 0.0 0.0 136-137 3.1 0.0 0.0 0.0 0.0 138 3.3 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AGAGCAC 60 0.0 108.0 8 GATCGGA 75 0.0 105.6 1 ATCGGAA 75 0.0 105.6 2 TCGGAAG 70 0.0 102.85714 3 CGGAAGA 70 0.0 102.85714 4 AAGAGCA 65 0.0 99.6923 7 GAAGAGC 65 0.0 99.6923 6 GAGCACA 65 0.0 99.6923 9 GGAAGAG 70 0.0 92.57143 5 GTCACGA 60 5.456968E-10 26.4 25-29 CAGTCAC 60 5.456968E-10 26.4 25-29 TGCCGTC 60 5.456968E-10 26.4 45-49 TATGCCG 60 5.456968E-10 26.4 45-49 CACGATC 60 5.456968E-10 26.4 30-34 TGCTTGA 60 5.456968E-10 26.4 55-59 TCAGATC 60 5.456968E-10 26.4 35-39 GATCTCG 60 5.456968E-10 26.4 35-39 ATGCCGT 60 5.456968E-10 26.4 45-49 GCTTGAA 60 5.456968E-10 26.4 55-59 GATCAGA 60 5.456968E-10 26.4 30-34 >>END_MODULE SRR6031391 read2 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6031391_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 42 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.64875 33.0 33.0 34.0 28.0 34.0 2 31.67 33.0 33.0 34.0 28.0 34.0 3 31.5435 33.0 33.0 34.0 28.0 34.0 4 31.36425 33.0 33.0 34.0 27.0 34.0 5 31.203 33.0 33.0 34.0 28.0 34.0 6 35.18275 38.0 38.0 38.0 29.0 38.0 7 35.1615 38.0 38.0 38.0 29.0 38.0 8 35.48475 38.0 38.0 38.0 31.0 38.0 9 35.12875 38.0 38.0 38.0 29.0 38.0 10-14 34.89185 38.0 37.4 38.0 28.0 38.0 15-19 34.57215 38.0 37.0 38.0 26.0 38.0 20-24 34.48715 38.0 37.0 38.0 23.4 38.0 25-29 34.29535 38.0 36.6 38.0 22.2 38.0 30-34 33.86325000000001 38.0 36.2 38.0 17.8 38.0 35-39 33.215849999999996 38.0 35.6 38.0 16.0 38.0 40-44 32.89105 38.0 35.4 38.0 14.6 38.0 45-49 32.41075000000001 38.0 34.0 38.0 14.4 38.0 50-54 32.196349999999995 38.0 33.4 38.0 14.6 38.0 55-59 32.27695 38.0 34.0 38.0 16.0 38.0 60-64 32.575500000000005 38.0 34.0 38.0 15.2 38.0 65-69 31.4301 38.0 32.6 38.0 6.8 38.0 70-74 29.5088 38.0 27.4 38.0 2.0 38.0 75-79 29.16635 38.0 25.8 38.0 2.0 38.0 80-84 28.945649999999993 38.0 24.4 38.0 2.0 38.0 85-89 28.70645 37.8 21.6 38.0 2.0 38.0 90-94 28.4409 37.4 15.0 38.0 2.0 38.0 95-99 28.1721 37.0 15.0 38.0 2.0 38.0 100-104 27.98055 37.0 15.0 38.0 2.0 38.0 105-109 27.71395 37.0 15.0 38.0 2.0 38.0 110-114 27.076599999999996 36.4 15.0 38.0 2.0 38.0 115-119 26.5551 35.2 14.8 38.0 2.0 38.0 120-124 25.910649999999997 34.6 13.6 38.0 2.0 38.0 125-129 25.348699999999997 34.0 13.0 38.0 2.0 38.0 130-134 24.636200000000002 34.0 2.0 38.0 2.0 38.0 135-139 23.81485 33.4 2.0 38.0 2.0 38.0 140-144 22.6302 31.0 2.0 38.0 2.0 38.0 145-149 20.611200000000004 27.2 2.0 36.6 2.0 38.0 150 15.3505 2.0 2.0 34.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 107.0 3 40.0 4 14.0 5 14.0 6 28.0 7 42.0 8 38.0 9 24.0 10 28.0 11 28.0 12 42.0 13 74.0 14 89.0 15 104.0 16 88.0 17 66.0 18 27.0 19 12.0 20 20.0 21 20.0 22 18.0 23 20.0 24 35.0 25 31.0 26 36.0 27 31.0 28 59.0 29 62.0 30 95.0 31 112.0 32 128.0 33 192.0 34 312.0 35 480.0 36 770.0 37 714.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 49.648594377510044 18.97590361445783 12.474899598393574 18.90060240963855 2 24.77295660948537 37.638748738647834 23.41069626639758 14.177598385469222 3 17.69755112345367 23.605150214592275 42.590254986114616 16.107043675839435 4 20.909090909090907 28.28282828282828 19.141414141414142 31.666666666666664 5 37.85353535353536 30.53030303030303 17.2979797979798 14.318181818181818 6 33.53550669699267 31.28632802628254 19.585544604498356 15.592620672226435 7 16.262626262626263 34.72222222222222 32.75252525252525 16.262626262626263 8 18.110633998484467 38.82293508461733 21.72265723667593 21.343773680222277 9 34.28499242041435 21.829206670035372 24.355735219807983 19.530065689742294 10-14 26.58649959579628 27.47574777687955 24.833265966046888 21.10448666127728 15-19 26.747182778311185 24.41760574056294 28.566375258982262 20.268836222143616 20-24 29.74939369442199 30.552748585286988 23.105295068714632 16.592562651576394 25-29 25.78689435659071 34.29495276107715 22.98287273278432 16.935280149547822 30-34 25.93565331582403 27.78423152684479 28.769129754027983 17.5109854033032 35-39 19.68066292759335 28.59380526501945 28.84139255217018 22.88413925521702 40-44 31.79360185980694 25.274169909536564 25.456107545358066 17.476120685298426 45-49 23.57756442647802 24.95199595755432 26.114199090449723 25.356240525517936 50-54 23.902833190242916 28.028887429927778 28.160193929599515 19.908085450229787 55-59 20.437550525464836 32.80113177041229 29.132983023443813 17.62833468067906 60-64 19.572468162522743 40.16575702445927 23.170608449565393 17.091166363452597 65-69 20.057610673135233 38.8619365271882 23.342429755407316 17.738023044269255 70-74 21.444090748319944 35.177605982517306 24.36966297812137 19.00864029104138 75-79 21.667508842849927 34.20414350682163 24.259727134916627 19.868620515411823 80-84 21.478036698175202 33.55406156801294 25.04170247181924 19.92619926199262 85-89 22.195824697973006 33.058686751251074 25.112470302785216 19.633018247990698 90-94 22.017282328566377 32.16433372075395 25.56470766587498 20.25367628480469 95-99 21.32854759617815 32.61715787877256 25.352611091451394 20.701683433597896 100-104 21.510864072764022 33.011622031328955 25.492673067205658 19.984840828701365 105-109 21.228655148024654 33.66676770738607 24.886329190663837 20.21824795392543 110-114 21.0627336094555 33.92261844630771 24.90655621779978 20.108091726437014 115-119 21.511569162372435 33.72234010306153 24.72971607557846 20.036374658987572 120-124 21.908323646838834 33.3097488249861 24.692980239551222 20.088947288623842 125-129 21.388860810674217 33.25583746083089 24.58303851207925 20.77226321641565 130-134 21.395372335051025 33.515206628271194 24.936849550368798 20.152571486308982 135-139 21.66506596572815 33.387251680735986 25.48652883789112 19.461153515644746 140-144 21.77627255724612 33.513622807460955 24.682808471920335 20.027296163372593 145-149 22.09754864796563 33.50012635835229 24.564063684609554 19.83826130907253 150 20.72800808897877 36.627906976744185 24.469160768452983 18.174924165824063 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 24.0 1 20.0 2 8.5 3 0.5 4 0.0 5 0.0 6 1.5 7 2.5 8 2.0 9 1.0 10 1.5 11 1.5 12 0.5 13 2.0 14 2.0 15 1.0 16 1.5 17 1.5 18 1.5 19 1.5 20 1.5 21 2.5 22 2.0 23 2.5 24 3.0 25 3.5 26 5.5 27 5.5 28 8.0 29 12.0 30 16.5 31 24.0 32 31.0 33 37.0 34 57.0 35 87.0 36 108.5 37 130.5 38 166.5 39 205.0 40 215.0 41 228.0 42 262.0 43 268.0 44 268.0 45 263.5 46 239.0 47 223.0 48 200.5 49 166.5 50 147.0 51 127.5 52 96.5 53 71.0 54 56.0 55 46.5 56 32.0 57 26.0 58 24.5 59 19.0 60 14.0 61 8.0 62 8.0 63 7.5 64 4.5 65 3.0 66 1.0 67 0.5 68 0.5 69 0.5 70 0.5 71 0.0 72 0.0 73 0.0 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.5 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.4 2 0.8999999999999999 3 0.975 4 1.0 5 1.0 6 1.075 7 1.0 8 1.0250000000000001 9 1.05 10-14 1.04 15-19 1.055 20-24 1.04 25-29 1.035 30-34 1.005 35-39 1.045 40-44 1.065 45-49 1.05 50-54 0.9950000000000001 55-59 1.04 60-64 1.06 65-69 1.06 70-74 1.045 75-79 1.05 80-84 1.085 85-89 1.085 90-94 1.055 95-99 1.095 100-104 1.05 105-109 1.03 110-114 1.01 115-119 1.03 120-124 1.065 125-129 1.0699999999999998 130-134 1.03 135-139 1.085 140-144 1.085 145-149 1.075 150 1.0999999999999999 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 90.9 #Duplication Level Percentage of deduplicated Percentage of total 1 99.0924092409241 90.075 2 0.44004400440044 0.8 3 0.1925192519251925 0.525 4 0.055005500550055 0.2 5 0.0275027502750275 0.125 6 0.0275027502750275 0.15 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.13751375137513752 1.4749999999999999 >50 0.0 0.0 >100 0.0275027502750275 6.65 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences fail #Sequence Count Percentage Possible Source GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG 266 6.65 Illumina Single End PCR Primer 1 (100% over 50bp) NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 16 0.4 No Hit GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATATCGGTGGTCGCCG 12 0.3 Illumina Single End PCR Primer 1 (98% over 50bp) GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTAGGTGGTCGCCG 11 0.27499999999999997 Illumina Single End PCR Primer 1 (98% over 50bp) GNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 10 0.25 No Hit GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTAGCCG 10 0.25 Illumina Single End PCR Primer 1 (98% over 50bp) GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGACG 6 0.15 Illumina Single End PCR Primer 1 (98% over 50bp) GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTGGCCG 5 0.125 Illumina Single End PCR Primer 1 (98% over 50bp) >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.037500000000000006 0.0 0.0 0.0 0.0 82-83 0.075 0.0 0.0 0.0 0.0 84-85 0.075 0.0 0.0 0.0 0.0 86-87 0.075 0.0 0.0 0.0 0.0 88-89 0.11249999999999999 0.0 0.0 0.0 0.0 90-91 0.16249999999999998 0.0 0.0 0.0 0.0 92-93 0.175 0.0 0.0 0.0 0.0 94-95 0.2 0.0 0.0 0.0 0.0 96-97 0.21250000000000002 0.0 0.0 0.0 0.0 98-99 0.225 0.0 0.0 0.0 0.0 100-101 0.225 0.0 0.0 0.0 0.0 102-103 0.25 0.0 0.0 0.0 0.0 104-105 0.3125 0.0 0.0 0.0 0.0 106-107 0.3625 0.0 0.0 0.0 0.0 108-109 0.525 0.0 0.0 0.0 0.0 110-111 0.525 0.0 0.0 0.0 0.0 112-113 0.6125 0.0 0.0 0.0 0.0 114-115 0.7125 0.0 0.0 0.0 0.0 116-117 0.775 0.0 0.0 0.0 0.0 118-119 0.8625 0.0 0.0 0.0 0.0 120-121 0.9375 0.0 0.0 0.0 0.0 122-123 1.0375 0.0 0.0 0.0 0.0 124-125 1.1875 0.0 0.0 0.0 0.0 126-127 1.2875 0.0 0.0 0.0 0.0 128-129 1.4125 0.0 0.0 0.0 0.0 130-131 1.6 0.0 0.0 0.0 0.0 132-133 1.825 0.0 0.0 0.0 0.0 134-135 2.0250000000000004 0.0 0.0 0.0 0.0 136-137 2.2375 0.0 0.0 0.0 0.0 138 2.325 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GCAGGCT 10 0.006973645 144.0 1 AGAGCGT 60 0.0 120.0 8 GAGCGTC 65 0.0 110.769226 9 AAGAGCG 65 0.0 110.769226 7 TCGGAAG 65 0.0 110.769226 3 CGGAAGA 65 0.0 110.769226 4 GATCGGA 75 0.0 105.6 1 ATCGGAA 75 0.0 105.6 2 GAAGAGC 70 0.0 102.85714 6 GGAAGAG 90 0.0 80.0 5 GTAGATC 30 4.3922482E-5 28.8 30-34 TGGTCGC 35 3.7333357E-6 28.8 40-44 ATCTCGG 30 4.3922482E-5 28.8 35-39 GTCGCCG 40 3.180794E-7 28.8 40-44 TCGGTGG 30 4.3922482E-5 28.8 35-39 CCGTATC 25 5.183459E-4 28.8 45-49 TCTCGGT 30 4.3922482E-5 28.8 35-39 TCGCCGT 30 4.3922482E-5 28.8 45-49 AGTGTAG 40 3.180794E-7 28.8 25-29 ATTAAAA 30 4.3922482E-5 28.8 55-59 >>END_MODULE Read 908553 spots for SRR6031391.sra Written 908553 spots for SRR6031391.sra Read 908553 spots for SRR6031391.sra Written 908553 spots for SRR6031391.sra Read 908553 spots for SRR6031391.sra Written 908553 spots for SRR6031391.sra Read 908571 spots for SRR6031391.sra Written 908571 spots for SRR6031391.sra Read 908553 spots for SRR6031391.sra Written 908553 spots for SRR6031391.sra Read 908553 spots for SRR6031391.sra Written 908553 spots for SRR6031391.sra Read 908553 spots for SRR6031391.sra Written 908553 spots for SRR6031391.sra Read 908553 spots for SRR6031391.sra Written 908553 spots for SRR6031391.sra Read 908553 spots for SRR6031391.sra Written 908553 spots for SRR6031391.sra Read 908553 spots for SRR6031391.sra Written 908553 spots for SRR6031391.sra Read 908553 spots for SRR6031391.sra Written 908553 spots for SRR6031391.sra Read 908553 spots for SRR6031391.sra Written 908553 spots for SRR6031391.sra Read 908553 spots for SRR6031391.sra Written 908553 spots for SRR6031391.sra Read 908553 spots for SRR6031391.sra Written 908553 spots for SRR6031391.sra Read 908553 spots for SRR6031391.sra Written 908553 spots for SRR6031391.sra Read 908553 spots for SRR6031391.sra Written 908553 spots for SRR6031391.sra Read 908553 spots for SRR6031391.sra Written 908553 spots for SRR6031391.sra Read 908553 spots for SRR6031391.sra Written 908553 spots for SRR6031391.sra Read 908553 spots for SRR6031391.sra Written 908553 spots for SRR6031391.sra Read 908553 spots for SRR6031391.sra Written 908553 spots for SRR6031391.sra SRR ids: ['SRR6031391.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_o_d7hqh9 SRR6031391.sra spots: 18171078 blocks: [[1, 908553], [908554, 1817106], [1817107, 2725659], [2725660, 3634212], [3634213, 4542765], [4542766, 5451318], [5451319, 6359871], [6359872, 7268424], [7268425, 8176977], [8176978, 9085530], [9085531, 9994083], [9994084, 10902636], [10902637, 11811189], [11811190, 12719742], [12719743, 13628295], [13628296, 14536848], [14536849, 15445401], [15445402, 16353954], [16353955, 17262507], [17262508, 18171078]] SRR6031391 file size 6100391 SRR6031391 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 SRR6031391 SRR6031391_1.fastq SRR6031391_2.fastq Input file: SRR6031391_1.fastq Paired file: SRR6031391_2.fastq trimmed: SRR6031391-trimmed-pair1.fastq, SRR6031391-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 Fri Feb 14 06:41:05 2025 >> started Fri Feb 14 06:41:36 2025 >> done (30.211s) 18171078 read pairs processed; of these: 62554 ( 0.34%) short read pairs filtered out after trimming by size control 3411943 (18.78%) empty read pairs filtered out after trimming by size control 14696581 (80.88%) read pairs available; of these: 7167110 (48.77%) trimmed read pairs available after processing 7529471 (51.23%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 5 0.00% 19 11 0.00% 20 7 0.00% 21 10 0.00% 22 8 0.00% 23 17 0.00% 24 27 0.00% 25 23 0.00% 26 15 0.00% 27 21 0.00% 28 12 0.00% 29 26 0.00% 30 14 0.00% 31 17 0.00% 32 22 0.00% 33 17 0.00% 34 26 0.00% 35 23 0.00% 36 27 0.00% 37 42 0.00% 38 47 0.00% 39 37 0.00% 40 49 0.00% 41 58 0.00% 42 111 0.00% 43 203 0.00% 44 388 0.00% 45 521 0.00% 46 556 0.00% 47 616 0.00% 48 768 0.01% 49 803 0.01% 50 832 0.01% 51 635 0.00% 52 796 0.01% 53 805 0.01% 54 896 0.01% 55 884 0.01% 56 911 0.01% 57 766 0.01% 58 704 0.00% 59 698 0.00% 60 681 0.00% 61 672 0.00% 62 604 0.00% 63 704 0.00% 64 766 0.01% 65 910 0.01% 66 1170 0.01% 67 1766 0.01% 68 3173 0.02% 69 10349 0.07% 70 12498 0.09% 71 7274 0.05% 72 5522 0.04% 73 3569 0.02% 74 2669 0.02% 75 2366 0.02% 76 2256 0.02% 77 2275 0.02% 78 2258 0.02% 79 2325 0.02% 80 2532 0.02% 81 2864 0.02% 82 3185 0.02% 83 3916 0.03% 84 6497 0.04% 85 6744 0.05% 86 7402 0.05% 87 8037 0.05% 88 8187 0.06% 89 8628 0.06% 90 8956 0.06% 91 9414 0.06% 92 9807 0.07% 93 9967 0.07% 94 10235 0.07% 95 10635 0.07% 96 10908 0.07% 97 11355 0.08% 98 11941 0.08% 99 12493 0.09% 100 13358 0.09% 101 14085 0.10% 102 15300 0.10% 103 15767 0.11% 104 16947 0.12% 105 17623 0.12% 106 18235 0.12% 107 19013 0.13% 108 19237 0.13% 109 20137 0.14% 110 20563 0.14% 111 21897 0.15% 112 23123 0.16% 113 24262 0.17% 114 25105 0.17% 115 26020 0.18% 116 27290 0.19% 117 27963 0.19% 118 28910 0.20% 119 29638 0.20% 120 31347 0.21% 121 32967 0.22% 122 35138 0.24% 123 37741 0.26% 124 39828 0.27% 125 41923 0.29% 126 43801 0.30% 127 46395 0.32% 128 48486 0.33% 129 50032 0.34% 130 52565 0.36% 131 56514 0.38% 132 60632 0.41% 133 66301 0.45% 134 71410 0.49% 135 77790 0.53% 136 82511 0.56% 137 88641 0.60% 138 93833 0.64% 139 99004 0.67% 140 106706 0.73% 141 117349 0.80% 142 128431 0.87% 143 146041 0.99% 144 170520 1.16% 145 203129 1.38% 146 264068 1.80% 147 376272 2.56% 148 690762 4.70% 149 3142536 21.38% 150 7529471 51.23% 14696581 reads passed initial QC criterion=sequence-density sequence-density=0.15 sequence-density-rank=1 fanout-score=4.64 fanout-score-rank=31 prefix-density=0.52 prefix-fanout=1.3 sequence=ATTCCTTTGCAGTTTGAACAGCATTACCAGCTTTG criterion=fanout-score sequence-density=0.07 sequence-density-rank=17 fanout-score=436.88 fanout-score-rank=1 prefix-density=0.95 prefix-fanout=34.0 sequence=CTTCTTCTTCTC criterion=sequence-density sequence-density=0.41 sequence-density-rank=1 fanout-score=4.72 fanout-score-rank=31 prefix-density=0.57 prefix-fanout=3.5 sequence=TGCAAAGGAATCAGT criterion=fanout-score sequence-density=0.08 sequence-density-rank=12 fanout-score=399.01 fanout-score-rank=1 prefix-density=1.09 prefix-fanout=28.2 sequence=AAGAAGAAGAAA SRR6031391 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 14 06:42:47 Started mapping on | Feb 14 06:42:48 Finished on | Feb 14 06:46:34 Mapping speed, Million of reads per hour | 234.10 Number of input reads | 14696581 Average input read length | 291 UNIQUE READS: Uniquely mapped reads number | 13704002 Uniquely mapped reads % | 93.25% Average mapped length | 291.32 Number of splices: Total | 11516679 Number of splices: Annotated (sjdb) | 11253932 Number of splices: GT/AG | 11324270 Number of splices: GC/AG | 160444 Number of splices: AT/AC | 7887 Number of splices: Non-canonical | 24078 Mismatch rate per base, % | 0.29% Deletion rate per base | 0.02% Deletion average length | 2.40 Insertion rate per base | 0.02% Insertion average length | 1.72 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 366313 % of reads mapped to multiple loci | 2.49% Number of reads mapped to too many loci | 77349 % of reads mapped to too many loci | 0.53% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.60% % of reads unmapped: other | 0.14% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 679638 679638 679638 N_multimapping 366313 366313 366313 N_noFeature 464682 13499156 539590 N_ambiguous 197312 1125 66936 UnstrandedReadsAssigned:13042008 PositiveStrandReadsAssigned:203721 NegativeStrandReadsAssigned:13097476 Dataset is classified negative stranded MeadianReadLen=150 20thPercentileLength=149 echo kmer=145 SRR6031391 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: 52,400 [index] number of k-mers: 62,057,036 [index] number of equivalence classes: 130,681 [quant] running in paired-end mode [quant] will process pair 1: SRR6031391-trimmed-pair1.fastq SRR6031391-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 14,696,581 reads, 13,270,392 reads pseudoaligned [quant] estimated average fragment length: 238.588 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,079 rounds 52401 SRR6031391.ke.tsv 34699 SRR6031391.se.tsv 87100 total ==> SRR6031391.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1780.41 178 5.91847 Potri.005G024800.1.v4.1 1035 797.412 78 5.79058 Potri.004G059700.1.v4.1 961 723.412 10 0.818322 Potri.007G009000.2.v4.1 1416 1178.41 2 0.100472 Potri.003G141000.2.v4.1 2943 2705.41 354 7.74604 Potri.016G087400.1.v4.1 270 74.9799 1088 859.002 Potri.015G069301.1.v4.1 564 328.8 0 0 Potri.010G195200.1.v4.1 1773 1535.41 50 1.92777 Potri.012G127500.1.v4.1 977 739.412 3489 279.334 ==> SRR6031391.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 15 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 305 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 4 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 198 Potri.001G416900.v4.1 1 Potri.001G452600.v4.1 6 SRR6031391 completed mapping pipeline successfully