Starting /dee2/code/volunteer_pipeline.sh SRR7169994 current disk space = 3049651322880 free memory = 1581796516 SRR7169994 SRAfilesize a914ff5b7d9a6a9a484f5ac8a8a0ee24 SRR7169994.sra SRR7169994.sra file validated SRR7169994 is paired end SRR7169994 is conventional basespace SRR7169994 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7169994_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 41 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.445 34.0 34.0 34.0 33.0 34.0 2 33.549 34.0 34.0 34.0 33.0 34.0 3 33.65475 34.0 34.0 34.0 33.0 34.0 4 33.69925 34.0 34.0 34.0 33.0 34.0 5 33.72225 34.0 34.0 34.0 33.0 34.0 6 37.2475 38.0 37.0 38.0 36.0 38.0 7 37.5965 38.0 38.0 38.0 37.0 38.0 8 37.67375 38.0 38.0 38.0 38.0 38.0 9 37.69125 38.0 38.0 38.0 38.0 38.0 10-14 37.68905 38.0 38.0 38.0 38.0 38.0 15-19 37.67614999999999 38.0 38.0 38.0 38.0 38.0 20-24 37.63235 38.0 38.0 38.0 38.0 38.0 25-29 37.59715 38.0 38.0 38.0 38.0 38.0 30-34 37.501549999999995 38.0 38.0 38.0 38.0 38.0 35-39 37.388400000000004 38.0 38.0 38.0 37.6 38.0 40-44 36.434749999999994 38.0 38.0 38.0 32.4 38.0 45-49 36.965199999999996 38.0 38.0 38.0 35.8 38.0 50-54 36.92115 38.0 38.0 38.0 35.6 38.0 55-59 36.911500000000004 38.0 38.0 38.0 35.6 38.0 60-64 36.810300000000005 38.0 38.0 38.0 35.4 38.0 65-69 36.696650000000005 38.0 38.0 38.0 34.8 38.0 70-74 36.3945 38.0 38.0 38.0 34.2 38.0 75-79 32.9151 38.0 36.2 38.0 4.6 38.0 80-84 32.53465 38.0 36.0 38.0 2.0 38.0 85-89 32.357299999999995 38.0 36.0 38.0 2.0 38.0 90-94 32.16705 38.0 35.6 38.0 2.0 38.0 95-99 31.998400000000004 38.0 35.0 38.0 2.0 38.0 100-104 32.013149999999996 38.0 34.8 38.0 2.0 38.0 105-109 31.90855 38.0 34.4 38.0 2.0 38.0 110-114 31.5813 38.0 34.0 38.0 2.0 38.0 115-119 31.18775 38.0 33.6 38.0 2.0 38.0 120-124 30.905849999999997 38.0 32.4 38.0 2.0 38.0 125-129 30.52575 38.0 31.0 38.0 2.0 38.0 130-134 30.137350000000005 38.0 30.0 38.0 2.0 38.0 135-139 29.461400000000005 36.8 26.8 38.0 2.0 38.0 140-144 29.044 36.0 24.8 38.0 2.0 38.0 145-149 28.10865 36.0 21.0 38.0 2.0 38.0 150-151 23.985 32.5 2.0 37.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 8 1.0 9 1.0 10 2.0 11 1.0 12 6.0 13 1.0 14 8.0 15 10.0 16 27.0 17 27.0 18 133.0 19 251.0 20 22.0 21 7.0 22 9.0 23 9.0 24 28.0 25 25.0 26 23.0 27 21.0 28 32.0 29 36.0 30 40.0 31 40.0 32 62.0 33 92.0 34 169.0 35 305.0 36 906.0 37 1706.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 45.36990437845999 14.016104680422748 10.920986411675894 29.693004529441367 2 21.349999999999998 22.95 27.474999999999998 28.225 3 17.474999999999998 17.424999999999997 33.025 32.074999999999996 4 18.9 22.95 21.925 36.225 5 30.099999999999998 27.474999999999998 22.5 19.925 6 28.9 29.925 22.775000000000002 18.4 7 13.450000000000001 37.5 34.125 14.924999999999999 8 15.35 36.675000000000004 27.650000000000002 20.325 9 25.025 26.25 29.599999999999998 19.125 10-14 18.595 33.095 24.565 23.745 15-19 18.805 29.830000000000002 27.334999999999997 24.03 20-24 18.865000000000002 32.379999999999995 26.584999999999997 22.17 25-29 19.005 29.67 26.655 24.67 30-34 16.735 32.0 26.900000000000002 24.365000000000002 35-39 21.245 29.9 26.150000000000002 22.705000000000002 40-44 17.355 29.225 28.785 24.635 45-49 21.69 28.83 29.26 20.22 50-54 19.62 26.82 26.595000000000002 26.965 55-59 19.555 26.825 30.855 22.765 60-64 19.105 28.634999999999998 29.099999999999998 23.16 65-69 17.205000000000002 38.565 24.19 20.04 70-74 16.900000000000002 38.475 23.974999999999998 20.65 75-79 17.675 36.95 24.125 21.25 80-84 19.035 33.635 25.355 21.975 85-89 20.28 31.314999999999998 25.215 23.189999999999998 90-94 19.217099664614306 30.394954197326925 26.510487060119136 23.87745907793963 95-99 18.31105771637383 32.377233818891725 26.345297091655407 22.96641137307904 100-104 17.885 37.13 24.055 20.93 105-109 17.635 37.614999999999995 23.9 20.849999999999998 110-114 17.89 36.5 23.95 21.66 115-119 17.904999999999998 36.515 23.82 21.759999999999998 120-124 18.360000000000003 36.265 23.64 21.735 125-129 18.61 35.47 23.544999999999998 22.375 130-134 18.993547096193286 34.91070981941874 23.81071482166975 22.285028262718225 135-139 18.682472989195677 35.04401760704282 23.82452981192477 22.448979591836736 140-144 19.628832974838677 34.63558601370617 23.505577509879448 22.23000350157571 145-149 18.790334684076242 35.1693431387263 23.472910100555307 22.567412076642153 150-151 18.589823727965996 35.60445055631954 23.47793474184273 22.327790973871732 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 3.0 1 2.0 2 1.5 3 1.0 4 0.5 5 1.0 6 1.0 7 0.5 8 0.0 9 0.0 10 0.5 11 1.0 12 0.5 13 0.0 14 0.0 15 1.0 16 1.5 17 1.0 18 1.5 19 1.5 20 0.5 21 0.0 22 2.0 23 4.0 24 3.5 25 6.5 26 8.0 27 12.5 28 19.5 29 22.0 30 30.5 31 50.5 32 61.0 33 76.5 34 98.0 35 113.5 36 141.0 37 160.5 38 186.5 39 210.5 40 229.0 41 245.5 42 241.5 43 241.5 44 253.5 45 237.5 46 192.5 47 176.0 48 172.0 49 143.5 50 111.5 51 93.0 52 79.0 53 68.0 54 74.0 55 61.0 56 31.0 57 30.0 58 29.5 59 15.5 60 9.0 61 9.5 62 11.0 63 7.0 64 2.5 65 2.0 66 1.0 67 2.5 68 2.5 69 1.5 70 1.0 71 0.0 72 0.0 73 0.5 74 0.5 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 0.65 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 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 0.11499999999999999 95-99 0.11499999999999999 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 0.045 135-139 0.04 140-144 0.045 145-149 0.055 150-151 0.0125 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 87.35000000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 97.79622209502004 85.425 2 1.7458500286204923 3.05 3 0.22896393817973668 0.6 4 0.028620492272467084 0.1 5 0.05724098454493417 0.25 6 0.028620492272467084 0.15 7 0.0 0.0 8 0.028620492272467084 0.2 9 0.0 0.0 >10 0.05724098454493417 0.7250000000000001 >50 0.0 0.0 >100 0.028620492272467084 9.5 >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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACATACGGATCTCGTATGC 380 9.5 TruSeq Adapter, Index 27 (97% over 37bp) ATCGGAAGAGCACACGTCTGAACTCCAGTCACATACGGATCTCGTATGCC 18 0.44999999999999996 TruSeq Adapter, Index 27 (97% over 36bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACATACGGATATCGTATGC 11 0.27499999999999997 TruSeq Adapter, Index 27 (97% over 37bp) AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATACGGATCTCGTATG 8 0.2 TruSeq Adapter, Index 27 (97% over 37bp) CGGAAGAGCACACGTCTGAACTCCAGTCACATACGGATCTCGTATGCCGT 6 0.15 TruSeq Adapter, Index 27 (97% over 34bp) CCCCACTGCTGCCTCCCGTAGGAGTCTGGACCGTGTCTCAGTTCCAGTGT 5 0.125 No Hit CGGTGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACATACGGATCTC 5 0.125 TruSeq Adapter, Index 27 (97% over 37bp) >>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 0.275 0.0 0.0 0.0 0.0 2 0.3 0.0 0.0 0.0 0.0 3 0.3 0.0 0.0 0.0 0.0 4 0.3 0.0 0.0 0.0 0.0 5 0.3 0.0 0.0 0.0 0.0 6 0.675 0.0 0.0 0.0 0.0 7 0.675 0.0 0.0 0.0 0.0 8 0.675 0.0 0.0 0.0 0.0 9 0.675 0.0 0.0 0.0 0.0 10-11 0.675 0.0 0.0 0.0 0.0 12-13 0.7124999999999999 0.0 0.0 0.0 0.0 14-15 0.725 0.0 0.0 0.0 0.0 16-17 0.725 0.0 0.0 0.0 0.0 18-19 0.75 0.0 0.0 0.0 0.0 20-21 0.75 0.0 0.0 0.0 0.0 22-23 0.75 0.0 0.0 0.0 0.0 24-25 0.75 0.0 0.0 0.0 0.0 26-27 0.75 0.0 0.0 0.0 0.0 28-29 0.75 0.0 0.0 0.0 0.0 30-31 0.775 0.0 0.0 0.0 0.0 32-33 0.775 0.0 0.0 0.0 0.0 34-35 0.775 0.0 0.0 0.0 0.0 36-37 0.775 0.0 0.0 0.0 0.0 38-39 0.775 0.0 0.0 0.0 0.0 40-41 0.775 0.0 0.0 0.0 0.0 42-43 0.775 0.0 0.0 0.0 0.0 44-45 0.775 0.0 0.0 0.0 0.0 46-47 0.775 0.0 0.0 0.0 0.0 48-49 0.775 0.0 0.0 0.0 0.0 50-51 0.775 0.0 0.0 0.0 0.0 52-53 0.775 0.0 0.0 0.0 0.0 54-55 0.7875000000000001 0.0 0.0 0.0 0.0 56-57 0.8 0.0 0.0 0.0 0.0 58-59 0.8 0.0 0.0 0.0 0.0 60-61 0.8125 0.0 0.0 0.0 0.0 62-63 0.8374999999999999 0.0 0.0 0.0 0.0 64-65 0.85 0.0 0.0 0.0 0.0 66-67 0.85 0.0 0.0 0.0 0.0 68-69 0.85 0.0 0.0 0.0 0.0 70-71 0.85 0.0 0.0 0.0 0.0 72-73 0.8625 0.0 0.0 0.0 0.0 74-75 0.875 0.0 0.0 0.0 0.0 76-77 0.9 0.0 0.0 0.0 0.0 78-79 0.9 0.0 0.0 0.0 0.0 80-81 0.925 0.0 0.0 0.0 0.0 82-83 0.9375 0.0 0.0 0.0 0.0 84-85 0.9624999999999999 0.0 0.0 0.0 0.0 86-87 1.0125 0.0 0.0 0.0 0.0 88-89 1.1 0.0 0.0 0.0 0.0 90-91 1.2625000000000002 0.0 0.0 0.0 0.0 92-93 1.3375 0.0 0.0 0.0 0.0 94-95 1.4 0.0 0.0 0.0 0.0 96-97 1.4625 0.0 0.0 0.0 0.0 98-99 1.6125 0.0 0.0 0.0 0.0 100-101 1.7625000000000002 0.0 0.0 0.0 0.0 102-103 2.1125 0.0 0.0 0.0 0.0 104-105 2.325 0.0 0.0 0.0 0.0 106-107 2.675 0.0 0.0 0.0 0.0 108-109 2.9125 0.0 0.0 0.0 0.0 110-111 3.2 0.0 0.0 0.0 0.0 112-113 3.4875 0.0 0.0 0.0 0.0 114-115 3.7375 0.0 0.0 0.0 0.0 116-117 4.125 0.0 0.0 0.0 0.0 118-119 4.487500000000001 0.0 0.0 0.0 0.0 120-121 4.762499999999999 0.0 0.0 0.0 0.0 122-123 5.300000000000001 0.0 0.0 0.0 0.0 124-125 5.7 0.0 0.0 0.0 0.0 126-127 5.9875 0.0 0.0 0.0 0.0 128-129 6.3125 0.0 0.0 0.0 0.0 130-131 6.9 0.0 0.0 0.0 0.0 132-133 7.387499999999999 0.0 0.0 0.0 0.0 134-135 7.975 0.0 0.0 0.0 0.0 136-137 8.5125 0.0 0.0 0.0 0.0 138-139 9.175 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TAGTTAT 10 0.006830828 145.0 9 TTTAGTT 10 0.006830828 145.0 7 TTAGTTA 10 0.006830828 145.0 8 CCATTTT 25 8.7132835E-4 87.0 2 GATCGGA 80 6.366463E-11 72.5 1 AGAGCAC 80 6.366463E-11 72.5 8 TCGGAAG 85 1.07320375E-10 68.2353 3 GAGCACA 85 1.07320375E-10 68.2353 9 CGGAAGA 85 1.07320375E-10 68.2353 4 ATCGGAA 85 1.07320375E-10 68.2353 2 GAAGAGC 90 1.8007995E-10 64.44444 6 GGAAGAG 90 1.8007995E-10 64.44444 5 CATTTTT 35 0.0033124194 62.14286 3 AAGAGCA 100 4.5838533E-10 58.0 7 TGGGAAG 20 0.00593511 29.0 105-109 TGCCGTC 50 7.0600436E-8 26.1 45-49 TATGCCG 50 7.0600436E-8 26.1 45-49 GGATCTC 50 7.0600436E-8 26.1 35-39 CGGATCT 50 7.0600436E-8 26.1 35-39 TCTCGTA 50 7.0600436E-8 26.1 40-44 >>END_MODULE SRR7169994 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7169994_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 42 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.97075 34.0 33.0 34.0 33.0 34.0 2 32.995 34.0 33.0 34.0 33.0 34.0 3 32.9045 34.0 33.0 34.0 33.0 34.0 4 32.754 34.0 33.0 34.0 33.0 34.0 5 32.89475 34.0 33.0 34.0 33.0 34.0 6 37.0 38.0 38.0 38.0 37.0 38.0 7 37.06 38.0 38.0 38.0 38.0 38.0 8 37.0185 38.0 38.0 38.0 38.0 38.0 9 37.02875 38.0 38.0 38.0 38.0 38.0 10-14 36.840650000000004 38.0 38.0 38.0 37.8 38.0 15-19 36.771249999999995 38.0 38.0 38.0 37.2 38.0 20-24 36.818599999999996 38.0 38.0 38.0 37.6 38.0 25-29 36.79344999999999 38.0 38.0 38.0 37.2 38.0 30-34 36.83445 38.0 38.0 38.0 37.2 38.0 35-39 36.7355 38.0 38.0 38.0 37.0 38.0 40-44 36.60015 38.0 38.0 38.0 37.0 38.0 45-49 36.46785 38.0 38.0 38.0 36.2 38.0 50-54 36.57705 38.0 38.0 38.0 36.6 38.0 55-59 36.70245 38.0 38.0 38.0 37.0 38.0 60-64 36.645500000000006 38.0 38.0 38.0 36.8 38.0 65-69 35.6289 38.0 38.0 38.0 28.4 38.0 70-74 33.085300000000004 38.0 38.0 38.0 2.0 38.0 75-79 32.766999999999996 38.0 38.0 38.0 2.0 38.0 80-84 32.57535 38.0 38.0 38.0 2.0 38.0 85-89 32.23215 38.0 37.6 38.0 2.0 38.0 90-94 32.1533 38.0 37.0 38.0 2.0 38.0 95-99 32.2586 38.0 37.0 38.0 2.0 38.0 100-104 32.28035 38.0 37.0 38.0 2.0 38.0 105-109 32.1083 38.0 36.4 38.0 2.0 38.0 110-114 31.9603 38.0 36.0 38.0 2.0 38.0 115-119 31.781299999999998 38.0 35.6 38.0 2.0 38.0 120-124 31.5539 38.0 34.8 38.0 2.0 38.0 125-129 31.27 38.0 34.6 38.0 2.0 38.0 130-134 30.4669 38.0 33.6 38.0 2.0 38.0 135-139 29.623399999999997 38.0 29.8 38.0 2.0 38.0 140-144 28.97565 38.0 27.2 38.0 2.0 38.0 145-149 28.5525 38.0 23.8 38.0 2.0 38.0 150-151 24.7755 34.5 2.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 39.0 3 20.0 4 2.0 5 1.0 6 5.0 7 2.0 8 1.0 9 0.0 10 2.0 11 1.0 12 4.0 13 8.0 14 4.0 15 14.0 16 37.0 17 228.0 18 138.0 19 39.0 20 16.0 21 8.0 22 7.0 23 12.0 24 7.0 25 10.0 26 10.0 27 27.0 28 30.0 29 20.0 30 44.0 31 39.0 32 68.0 33 102.0 34 103.0 35 141.0 36 383.0 37 2428.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 44.53907815631262 19.06312625250501 14.253507014028056 22.14428857715431 2 24.799398194583752 34.52858575727182 24.37311935807422 16.29889669007021 3 20.82177968237963 25.661709100075626 35.9465591126796 17.569952104865138 4 23.06329113924051 29.924050632911392 20.911392405063292 26.101265822784807 5 33.55991943605237 30.815709969788518 20.54380664652568 15.080563947633435 6 30.005030181086518 33.07344064386318 21.705231388329977 15.216297786720324 7 19.497487437185928 30.22613065326633 33.89447236180905 16.381909547738694 8 21.66164658634538 32.8062248995984 24.17168674698795 21.360441767068274 9 29.813976872800403 23.95676219205631 27.828054298642535 18.401206636500756 10-14 26.33412429949008 28.015348109254308 24.849800575554095 20.80072701570152 15-19 25.943539411109988 25.827177982394012 28.270767985429522 19.958514621066477 20-24 28.233987785797204 29.88441932064806 23.918639277242214 17.96295361631252 25-29 25.45959595959596 31.6010101010101 24.70707070707071 18.232323232323232 30-34 25.56626141350956 27.538717651213236 29.067245119305856 17.827775815971346 35-39 22.004654928152195 26.52803076300344 29.10848006476422 22.358834244080146 40-44 30.513119829467595 24.899761457646044 26.579708673806017 18.007410039080344 45-49 23.86916835699797 24.893509127789045 26.86612576064909 24.371196754563897 50-54 23.19769789983845 27.35258481421648 28.685379644588043 20.764337641357027 55-59 21.064055322800463 31.013073545000253 29.44323860481551 18.479632527383778 60-64 21.24216063119563 35.56038842808012 25.404612583451346 17.79283835727291 65-69 20.890929270507517 35.86923620219958 25.8097063868429 17.430128140450005 70-74 21.902132998745294 35.43789209535759 24.511919698870766 18.14805520702635 75-79 21.075625188309733 34.44812694586723 26.047002109068995 18.429245756754042 80-84 22.0063581773225 33.1836302164808 26.472220820507648 18.337790785689055 85-89 23.156176680607977 32.19932673671325 25.986942772620626 18.657553810058143 90-94 23.542909591555762 31.55881903013615 26.30666462699505 18.591606751313037 95-99 22.567485898468977 31.59246575342466 26.96414182111201 18.87590652699436 100-104 21.8564381355079 33.24775999194604 26.150206382764523 18.745595489781536 105-109 21.504130566189804 33.67418899858956 26.077977030022165 18.74370340519847 110-114 21.318514776458702 33.88734528921445 26.046981561000255 18.7471583733266 115-119 22.06629445198934 33.25285448418088 26.06005734118002 18.62079372264977 120-124 21.791718946047677 32.9435382685069 26.193224592220826 19.071518193224595 125-129 22.345233863186227 33.44167386115484 25.950942054745823 18.262150220913107 130-134 22.74347713769052 33.22138982175149 25.51795401704986 18.517179023508138 135-139 22.6048611475668 32.852118221428945 26.211349677148405 18.331670953855845 140-144 23.13286267848612 32.443335633526196 25.983332448643772 18.440469239343916 145-149 23.304758482624095 32.072275550536425 25.97402597402597 18.64893999281351 150-151 23.134422906372734 33.85278094514126 24.95882427467376 18.053971873812237 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 1.0 1 3.5 2 5.0 3 3.0 4 2.5 5 2.0 6 2.0 7 2.5 8 3.5 9 3.0 10 1.5 11 2.0 12 2.0 13 1.0 14 0.5 15 2.0 16 1.5 17 0.5 18 0.5 19 1.0 20 1.5 21 1.5 22 1.5 23 2.5 24 3.0 25 2.0 26 3.0 27 5.5 28 7.0 29 12.0 30 19.5 31 32.0 32 41.0 33 56.5 34 87.5 35 113.0 36 144.5 37 160.0 38 169.5 39 197.5 40 225.5 41 233.5 42 226.0 43 245.0 44 250.0 45 222.0 46 208.5 47 209.5 48 191.0 49 159.0 50 142.0 51 128.0 52 102.5 53 83.5 54 69.0 55 49.5 56 42.0 57 32.5 58 22.5 59 16.0 60 11.0 61 8.5 62 6.5 63 5.5 64 2.5 65 1.5 66 1.0 67 1.5 68 1.5 69 0.5 70 1.0 71 1.0 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 0.0 >>END_MODULE >>Per base N content warn #Base N-Count 1 0.2 2 0.3 3 0.8250000000000001 4 1.25 5 0.7000000000000001 6 0.6 7 0.5 8 0.4 9 0.5499999999999999 10-14 0.9650000000000001 15-19 1.17 20-24 0.935 25-29 1.0 30-34 0.885 35-39 1.18 40-44 1.485 45-49 1.4000000000000001 50-54 0.96 55-59 0.9450000000000001 60-64 1.1400000000000001 65-69 0.89 70-74 0.375 75-79 0.43 80-84 0.915 85-89 1.97 90-94 1.9449999999999998 95-99 0.72 100-104 0.67 105-109 0.74 110-114 1.0250000000000001 115-119 0.5950000000000001 120-124 0.375 125-129 1.545 130-134 3.225 135-139 4.755 140-144 5.805 145-149 2.595 150-151 1.3375 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 87.47500000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 97.9994284081166 85.725 2 1.6576164618462417 2.9000000000000004 3 0.11431837667905116 0.3 4 0.11431837667905116 0.4 5 0.02857959416976279 0.125 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.05715918833952558 0.8250000000000001 >50 0.0 0.0 >100 0.02857959416976279 9.725 >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 389 9.725 Illumina Single End PCR Primer 1 (100% over 50bp) ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT 22 0.5499999999999999 Illumina Single End PCR Primer 1 (100% over 50bp) AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC 11 0.27499999999999997 Illumina Single End PCR Primer 1 (100% over 50bp) CACCGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGG 5 0.125 Illumina Single End PCR Primer 1 (100% over 45bp) >>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 0.275 0.0 0.0 0.0 0.0 2 0.3 0.0 0.0 0.0 0.0 3 0.3 0.0 0.0 0.0 0.0 4 0.3 0.0 0.0 0.0 0.0 5 0.3 0.0 0.0 0.0 0.0 6 0.675 0.0 0.0 0.0 0.0 7 0.675 0.0 0.0 0.0 0.0 8 0.675 0.0 0.0 0.0 0.0 9 0.675 0.0 0.0 0.0 0.0 10-11 0.675 0.0 0.0 0.0 0.0 12-13 0.7124999999999999 0.0 0.0 0.0 0.0 14-15 0.725 0.0 0.0 0.0 0.0 16-17 0.725 0.0 0.0 0.0 0.0 18-19 0.75 0.0 0.0 0.0 0.0 20-21 0.75 0.0 0.0 0.0 0.0 22-23 0.75 0.0 0.0 0.0 0.0 24-25 0.75 0.0 0.0 0.0 0.0 26-27 0.75 0.0 0.0 0.0 0.0 28-29 0.75 0.0 0.0 0.0 0.0 30-31 0.775 0.0 0.0 0.0 0.0 32-33 0.775 0.0 0.0 0.0 0.0 34-35 0.775 0.0 0.0 0.0 0.0 36-37 0.775 0.0 0.0 0.0 0.0 38-39 0.775 0.0 0.0 0.0 0.0 40-41 0.775 0.0 0.0 0.0 0.0 42-43 0.775 0.0 0.0 0.0 0.0 44-45 0.775 0.0 0.0 0.0 0.0 46-47 0.775 0.0 0.0 0.0 0.0 48-49 0.775 0.0 0.0 0.0 0.0 50-51 0.7875000000000001 0.0 0.0 0.0 0.0 52-53 0.8 0.0 0.0 0.0 0.0 54-55 0.8 0.0 0.0 0.0 0.0 56-57 0.8 0.0 0.0 0.0 0.0 58-59 0.8 0.0 0.0 0.0 0.0 60-61 0.8125 0.0 0.0 0.0 0.0 62-63 0.8374999999999999 0.0 0.0 0.0 0.0 64-65 0.85 0.0 0.0 0.0 0.0 66-67 0.85 0.0 0.0 0.0 0.0 68-69 0.85 0.0 0.0 0.0 0.0 70-71 0.85 0.0 0.0 0.0 0.0 72-73 0.8625 0.0 0.0 0.0 0.0 74-75 0.875 0.0 0.0 0.0 0.0 76-77 0.9 0.0 0.0 0.0 0.0 78-79 0.9 0.0 0.0 0.0 0.0 80-81 0.925 0.0 0.0 0.0 0.0 82-83 0.9375 0.0 0.0 0.0 0.0 84-85 0.9875 0.0 0.0 0.0 0.0 86-87 1.0375 0.0 0.0 0.0 0.0 88-89 1.125 0.0 0.0 0.0 0.0 90-91 1.2875 0.0 0.0 0.0 0.0 92-93 1.3625 0.0 0.0 0.0 0.0 94-95 1.45 0.0 0.0 0.0 0.0 96-97 1.5 0.0 0.0 0.0 0.0 98-99 1.6375 0.0 0.0 0.0 0.0 100-101 1.775 0.0 0.0 0.0 0.0 102-103 2.075 0.0 0.0 0.0 0.0 104-105 2.325 0.0 0.0 0.0 0.0 106-107 2.725 0.0 0.0 0.0 0.0 108-109 2.9875 0.0 0.0 0.0 0.0 110-111 3.2375 0.0 0.0 0.0 0.0 112-113 3.5125 0.0 0.0 0.0 0.0 114-115 3.7750000000000004 0.0 0.0 0.0 0.0 116-117 4.175 0.0 0.0 0.0 0.0 118-119 4.550000000000001 0.0 0.0 0.0 0.0 120-121 4.8125 0.0 0.0 0.0 0.0 122-123 5.3125 0.0 0.0 0.0 0.0 124-125 5.75 0.0 0.0 0.0 0.0 126-127 5.987500000000001 0.0 0.0 0.0 0.0 128-129 6.275 0.0 0.0 0.0 0.0 130-131 6.7625 0.0 0.0 0.0 0.0 132-133 7.2125 0.0 0.0 0.0 0.0 134-135 7.75 0.0 0.0 0.0 0.0 136-137 8.25 0.0 0.0 0.0 0.0 138-139 8.85 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GAGCGTC 80 6.548362E-11 72.18125 9 AGAGCGT 80 6.548362E-11 72.18125 8 GGAAGAG 90 1.8189894E-12 72.18125 5 AAGAGCG 85 1.1277734E-10 67.935295 7 GAAGAGC 85 1.1277734E-10 67.935295 6 TCGGAAG 85 1.1277734E-10 67.935295 3 CGGAAGA 85 1.1277734E-10 67.935295 4 GATCGGA 90 1.8735591E-10 64.16111 1 ATCGGAA 95 3.0195224E-10 60.784206 2 TGGTCGC 50 7.3681804E-8 25.985249 40-44 GTCGCCG 50 7.3681804E-8 25.985249 40-44 CCGTATC 50 7.3681804E-8 25.985249 45-49 CGTATCA 50 7.3681804E-8 25.985249 45-49 GTGGTCG 50 7.3681804E-8 25.985249 40-44 GCCGTAT 50 7.3681804E-8 25.985249 45-49 CGCCGTA 50 7.3681804E-8 25.985249 45-49 TTAAAAA 50 7.3681804E-8 25.985249 55-59 GGTCGCC 50 7.3681804E-8 25.985249 40-44 CATTAAA 55 1.853441E-7 23.622953 50-54 TCTCGGT 55 1.853441E-7 23.622953 35-39 >>END_MODULE Read 582576 spots for SRR7169994.sra Written 582576 spots for SRR7169994.sra Read 582576 spots for SRR7169994.sra Written 582576 spots for SRR7169994.sra Read 582576 spots for SRR7169994.sra Written 582576 spots for SRR7169994.sra Read 582576 spots for SRR7169994.sra Written 582576 spots for SRR7169994.sra Read 582576 spots for SRR7169994.sra Written 582576 spots for SRR7169994.sra Read 582576 spots for SRR7169994.sra Written 582576 spots for SRR7169994.sra Read 582576 spots for SRR7169994.sra Written 582576 spots for SRR7169994.sra Read 582576 spots for SRR7169994.sra Written 582576 spots for SRR7169994.sra Read 582576 spots for SRR7169994.sra Written 582576 spots for SRR7169994.sra Read 582576 spots for SRR7169994.sra Written 582576 spots for SRR7169994.sra Read 582576 spots for SRR7169994.sra Written 582576 spots for SRR7169994.sra Read 582576 spots for SRR7169994.sra Written 582576 spots for SRR7169994.sra Read 582576 spots for SRR7169994.sra Written 582576 spots for SRR7169994.sra Read 582576 spots for SRR7169994.sra Written 582576 spots for SRR7169994.sra Read 582576 spots for SRR7169994.sra Written 582576 spots for SRR7169994.sra Read 582576 spots for SRR7169994.sra Written 582576 spots for SRR7169994.sra Read 582576 spots for SRR7169994.sra Written 582576 spots for SRR7169994.sra Read 582576 spots for SRR7169994.sra Written 582576 spots for SRR7169994.sra Read 582576 spots for SRR7169994.sra Written 582576 spots for SRR7169994.sra Read 582587 spots for SRR7169994.sra Written 582587 spots for SRR7169994.sra SRR ids: ['SRR7169994.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_wghpdf2t SRR7169994.sra spots: 11651531 blocks: [[1, 582576], [582577, 1165152], [1165153, 1747728], [1747729, 2330304], [2330305, 2912880], [2912881, 3495456], [3495457, 4078032], [4078033, 4660608], [4660609, 5243184], [5243185, 5825760], [5825761, 6408336], [6408337, 6990912], [6990913, 7573488], [7573489, 8156064], [8156065, 8738640], [8738641, 9321216], [9321217, 9903792], [9903793, 10486368], [10486369, 11068944], [11068945, 11651531]] SRR7169994 file size 3926621 SRR7169994 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 SRR7169994 SRR7169994_1.fastq SRR7169994_2.fastq Input file: SRR7169994_1.fastq Paired file: SRR7169994_2.fastq trimmed: SRR7169994-trimmed-pair1.fastq, SRR7169994-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 Wed Feb 12 08:45:45 2025 >> started Wed Feb 12 08:45:57 2025 >> done (12.954s) 11651531 read pairs processed; of these: 95299 ( 0.82%) short read pairs filtered out after trimming by size control 1157125 ( 9.93%) empty read pairs filtered out after trimming by size control 10399107 (89.25%) read pairs available; of these: 6087624 (58.54%) trimmed read pairs available after processing 4311483 (41.46%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 155 0.00% 19 86 0.00% 20 31 0.00% 21 31 0.00% 22 55 0.00% 23 89 0.00% 24 46 0.00% 25 19 0.00% 26 50 0.00% 27 42 0.00% 28 35 0.00% 29 59 0.00% 30 31 0.00% 31 48 0.00% 32 37 0.00% 33 45 0.00% 34 48 0.00% 35 69 0.00% 36 54 0.00% 37 43 0.00% 38 70 0.00% 39 45 0.00% 40 84 0.00% 41 101 0.00% 42 105 0.00% 43 186 0.00% 44 188 0.00% 45 282 0.00% 46 358 0.00% 47 418 0.00% 48 398 0.00% 49 373 0.00% 50 437 0.00% 51 474 0.00% 52 612 0.01% 53 553 0.01% 54 516 0.00% 55 490 0.00% 56 480 0.00% 57 471 0.00% 58 552 0.01% 59 536 0.01% 60 555 0.01% 61 630 0.01% 62 1093 0.01% 63 1231 0.01% 64 1150 0.01% 65 1436 0.01% 66 2293 0.02% 67 2425 0.02% 68 3597 0.03% 69 9857 0.09% 70 19925 0.19% 71 10521 0.10% 72 5503 0.05% 73 4046 0.04% 74 3432 0.03% 75 3100 0.03% 76 3067 0.03% 77 3009 0.03% 78 2897 0.03% 79 3084 0.03% 80 3285 0.03% 81 3576 0.03% 82 4157 0.04% 83 4757 0.05% 84 6194 0.06% 85 6905 0.07% 86 7697 0.07% 87 8275 0.08% 88 8788 0.08% 89 9389 0.09% 90 9747 0.09% 91 10272 0.10% 92 10509 0.10% 93 11352 0.11% 94 11975 0.12% 95 12896 0.12% 96 13271 0.13% 97 13604 0.13% 98 14300 0.14% 99 14803 0.14% 100 15519 0.15% 101 16179 0.16% 102 17391 0.17% 103 18034 0.17% 104 19320 0.19% 105 20731 0.20% 106 21552 0.21% 107 22240 0.21% 108 23413 0.23% 109 24165 0.23% 110 23719 0.23% 111 23986 0.23% 112 24838 0.24% 113 26175 0.25% 114 27783 0.27% 115 28738 0.28% 116 29592 0.28% 117 29953 0.29% 118 30143 0.29% 119 30485 0.29% 120 31194 0.30% 121 31831 0.31% 122 33416 0.32% 123 34617 0.33% 124 36781 0.35% 125 37669 0.36% 126 39600 0.38% 127 41120 0.40% 128 42299 0.41% 129 43227 0.42% 130 44801 0.43% 131 45772 0.44% 132 48367 0.47% 133 50633 0.49% 134 53045 0.51% 135 55780 0.54% 136 59770 0.57% 137 62836 0.60% 138 66929 0.64% 139 71348 0.69% 140 75203 0.72% 141 80635 0.78% 142 87820 0.84% 143 97673 0.94% 144 110268 1.06% 145 128295 1.23% 146 159872 1.54% 147 219032 2.11% 148 321633 3.09% 149 606180 5.83% 150 2518617 24.22% 151 4311483 41.46% 10399107 reads passed initial QC criterion=sequence-density sequence-density=0.15 sequence-density-rank=1 fanout-score=3.74 fanout-score-rank=29 prefix-density=0.20 prefix-fanout=2.9 sequence=GGCTTCTCCCATTTGAGGGGCTTGACAAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=39 fanout-score=220.44 fanout-score-rank=1 prefix-density=0.27 prefix-fanout=11.8 sequence=ATCATCAACTATGAACATTTAATACATGAAGCGCAACCCAAAAAACAGACAATGGAGGAGGCAAATCGATGTAGAGATCTAGGCATTCACATGTATAGGATGGTCACATCACACATTAAAGCAAGCTCACTTGTAGGTCCCCATACCCACACCAACATCTCCACCGTATGGCTGGAAGCTGTCACTGGCCTTGGAATAGCAAA criterion=sequence-density sequence-density=0.29 sequence-density-rank=1 fanout-score=5.21 fanout-score-rank=22 prefix-density=0.43 prefix-fanout=3.5 sequence=GCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATG criterion=fanout-score sequence-density=0.07 sequence-density-rank=23 fanout-score=67.70 fanout-score-rank=1 prefix-density=0.37 prefix-fanout=13.5 sequence=AGAAGGAGAAAGAAAAGGAGAGTGCTTCCCAGTAGGGCAGCAGGCAGTATTCTTGTGTTCTATAGAACGGTGATGATGATGCTTGATGTGTGGCTTGTTTGGTTATGTCCATCTACTGTTTTTCTTCCTTTTTAGAAAA SRR7169994 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 12 08:46:46 Started mapping on | Feb 12 08:46:46 Finished on | Feb 12 08:49:19 Mapping speed, Million of reads per hour | 244.68 Number of input reads | 10399107 Average input read length | 289 UNIQUE READS: Uniquely mapped reads number | 9075557 Uniquely mapped reads % | 87.27% Average mapped length | 290.08 Number of splices: Total | 6619041 Number of splices: Annotated (sjdb) | 6477771 Number of splices: GT/AG | 6515126 Number of splices: GC/AG | 77597 Number of splices: AT/AC | 6001 Number of splices: Non-canonical | 20317 Mismatch rate per base, % | 0.39% Deletion rate per base | 0.04% Deletion average length | 2.63 Insertion rate per base | 0.03% Insertion average length | 2.35 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 173090 % of reads mapped to multiple loci | 1.66% Number of reads mapped to too many loci | 26680 % of reads mapped to too many loci | 0.26% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 10.74% % of reads unmapped: other | 0.07% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1169682 1169682 1169682 N_multimapping 173090 173090 173090 N_noFeature 253229 8924857 314573 N_ambiguous 127926 623 38255 UnstrandedReadsAssigned:8694402 PositiveStrandReadsAssigned:150077 NegativeStrandReadsAssigned:8722729 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=145 echo kmer=141 SRR7169994 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: SRR7169994-trimmed-pair1.fastq SRR7169994-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 10,399,107 reads, 8,730,481 reads pseudoaligned [quant] estimated average fragment length: 218.22 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,045 rounds 52401 SRR7169994.ke.tsv 34699 SRR7169994.se.tsv 87100 total ==> SRR7169994.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1800.78 159 9.06688 Potri.005G024800.1.v4.1 1035 817.78 20 2.51139 Potri.004G059700.1.v4.1 961 743.804 8 1.10447 Potri.007G009000.2.v4.1 1416 1198.78 0 0 Potri.003G141000.2.v4.1 2943 2725.78 108 4.06869 Potri.016G087400.1.v4.1 270 86.9366 1161 1371.36 Potri.015G069301.1.v4.1 564 348.533 0 0 Potri.010G195200.1.v4.1 1773 1555.78 37 2.44216 Potri.012G127500.1.v4.1 977 759.794 2953 399.106 ==> SRR7169994.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 1013 Potri.001G233950.v4.1 1 Potri.001G122700.v4.1 247 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 16 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 0 SRR7169994 completed mapping pipeline successfully