Starting /dee2/code/volunteer_pipeline.sh SRR11389842 current disk space = 1544480108544 free memory = 1601466324 SRR11389842 SRAfilesize 33e3d81e5e80680987758e4118f3f39c SRR11389842.sra SRR11389842.sra file validated SRR11389842 is paired end SRR11389842 is conventional basespace SRR11389842 read1 length is 50-76 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11389842_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 50-76 %GC 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.99725 32.0 32.0 32.0 32.0 32.0 2 31.0945 32.0 32.0 32.0 32.0 32.0 3 31.11375 32.0 32.0 32.0 32.0 32.0 4 31.112 32.0 32.0 32.0 32.0 32.0 5 31.18875 32.0 32.0 32.0 32.0 32.0 6 33.96575 36.0 36.0 36.0 32.0 36.0 7 34.00675 36.0 36.0 36.0 32.0 36.0 8 33.90825 36.0 36.0 36.0 32.0 36.0 9 34.06825 36.0 36.0 36.0 32.0 36.0 10-11 34.0095 36.0 36.0 36.0 32.0 36.0 12-13 34.187250000000006 36.0 36.0 36.0 32.0 36.0 14-15 34.02275 36.0 36.0 36.0 32.0 36.0 16-17 33.967 36.0 36.0 36.0 32.0 36.0 18-19 34.016125 36.0 36.0 36.0 32.0 36.0 20-21 34.025875 36.0 36.0 36.0 32.0 36.0 22-23 33.843 36.0 36.0 36.0 32.0 36.0 24-25 33.785625 36.0 36.0 36.0 32.0 36.0 26-27 33.645375 36.0 36.0 36.0 29.5 36.0 28-29 33.504125 36.0 36.0 36.0 24.0 36.0 30-31 33.565375 36.0 36.0 36.0 29.5 36.0 32-33 33.438125 36.0 36.0 36.0 24.0 36.0 34-35 33.34675 36.0 36.0 36.0 24.0 36.0 36-37 33.409875 36.0 36.0 36.0 24.0 36.0 38-39 33.2425 36.0 36.0 36.0 17.5 36.0 40-41 33.22275 36.0 36.0 36.0 17.5 36.0 42-43 33.099374999999995 36.0 36.0 36.0 17.5 36.0 44-45 33.112375 36.0 36.0 36.0 21.0 36.0 46-47 33.072125 36.0 36.0 36.0 17.5 36.0 48-49 32.863625 36.0 36.0 36.0 14.0 36.0 50-51 32.765573893473366 36.0 34.0 36.0 14.0 36.0 52-53 32.4569077174246 36.0 32.0 36.0 14.0 36.0 54-55 32.519139354515886 36.0 32.0 36.0 14.0 36.0 56-57 32.290801565019336 36.0 32.0 36.0 14.0 36.0 58-59 32.091140472046355 36.0 32.0 36.0 14.0 36.0 60-61 32.20513450517363 36.0 32.0 36.0 14.0 36.0 62-63 32.00689050363317 36.0 32.0 36.0 14.0 36.0 64-65 32.15478018812385 36.0 32.0 36.0 14.0 36.0 66-67 32.00288890665636 36.0 32.0 36.0 14.0 36.0 68-69 31.98155542708116 36.0 32.0 36.0 14.0 36.0 70-71 31.95905728132227 36.0 32.0 36.0 14.0 36.0 72-73 31.899372453496973 36.0 32.0 36.0 14.0 36.0 74-75 31.694586695173374 36.0 32.0 36.0 14.0 36.0 76 30.59184409960303 36.0 27.0 36.0 14.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 3.0 22 6.0 23 15.0 24 17.0 25 34.0 26 66.0 27 99.0 28 144.0 29 193.0 30 245.0 31 323.0 32 397.0 33 599.0 34 953.0 35 905.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 36.1 10.625 15.049999999999999 38.224999999999994 2 24.55 13.675 29.825000000000003 31.95 3 24.474999999999998 17.224999999999998 22.6 35.699999999999996 4 29.549999999999997 23.875 21.325 25.25 5 27.125 26.950000000000003 23.724999999999998 22.2 6 22.1 31.95 26.450000000000003 19.5 7 18.825 25.85 34.525 20.8 8 21.0 23.674999999999997 30.925000000000004 24.4 9 18.775 21.575 35.175 24.474999999999998 10-11 23.7625 28.8375 24.4 23.0 12-13 23.3 24.0 26.974999999999998 25.724999999999998 14-15 22.2125 25.900000000000002 26.637499999999996 25.25 16-17 22.6 26.0 26.2625 25.137500000000003 18-19 22.900000000000002 25.5125 26.450000000000003 25.137500000000003 20-21 23.4875 25.900000000000002 25.912499999999998 24.7 22-23 23.45 26.187500000000004 25.525 24.837500000000002 24-25 23.05 25.25 26.5375 25.162499999999998 26-27 22.875 25.2375 26.724999999999998 25.162499999999998 28-29 23.8125 25.662499999999998 25.6 24.925 30-31 23.5375 25.4625 25.0125 25.9875 32-33 22.5125 25.162499999999998 27.0125 25.3125 34-35 23.775 25.0625 26.150000000000002 25.0125 36-37 22.900000000000002 24.525 26.325 26.25 38-39 22.825 25.887500000000003 26.025 25.2625 40-41 23.525 24.9875 26.1625 25.324999999999996 42-43 22.225 25.2 26.637499999999996 25.937500000000004 44-45 23.1625 24.375 26.05 26.4125 46-47 24.5125 25.162499999999998 25.6 24.725 48-49 23.5625 24.1125 26.4625 25.8625 50-51 23.65295661957745 24.30303787973497 26.103262907863485 25.9407425928241 52-53 23.783918969613605 24.684256596223584 25.30949105914718 26.222333375015634 54-55 23.29246935201401 24.355766825118838 26.10708031023267 26.244683512634477 56-57 23.413840570641973 25.4411212614191 25.678888749843576 25.46614941809536 58-59 23.109664496745115 24.349023535302955 26.752628943415125 25.78868302453681 60-61 22.617407639323734 25.109580463368818 26.261740763932373 26.01127113337508 62-63 23.44024054121774 24.95615134051616 26.196441994487596 25.407166123778502 64-65 23.11066549692944 24.714876550946233 26.055896728913396 26.11856122321093 66-67 23.547860996110902 23.87404340735165 26.734412244385897 25.843683352151547 68-69 23.54713191916656 24.890171959332246 25.442450106690096 26.120246014811094 70-71 23.64321608040201 25.100502512562816 25.99246231155779 25.263819095477384 72-73 23.568810817641854 24.390243902439025 26.538607354985466 25.502337924933656 74-75 23.651342014350252 22.229604039330322 27.265479670475685 26.85357427584374 76 25.18946228798268 0.0 36.66546373150487 38.14507398051245 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 25.0 1 15.5 2 4.0 3 2.0 4 2.0 5 1.5 6 1.0 7 1.0 8 1.0 9 1.5 10 2.5 11 1.5 12 0.0 13 0.0 14 0.0 15 0.5 16 1.5 17 2.5 18 8.5 19 14.0 20 15.0 21 18.0 22 15.0 23 10.5 24 10.0 25 8.5 26 6.0 27 10.0 28 14.0 29 14.5 30 17.0 31 28.5 32 38.0 33 35.0 34 48.5 35 69.5 36 83.0 37 100.0 38 135.5 39 158.5 40 158.0 41 175.5 42 195.0 43 209.5 44 222.5 45 235.0 46 225.5 47 212.0 48 211.5 49 191.5 50 176.5 51 161.0 52 141.0 53 120.5 54 111.5 55 129.5 56 137.5 57 116.0 58 100.0 59 106.0 60 95.5 61 89.0 62 93.5 63 81.0 64 66.0 65 69.5 66 70.5 67 60.0 68 59.5 69 48.0 70 40.5 71 41.0 72 35.5 73 34.0 74 35.0 75 33.5 76 27.5 77 18.0 78 11.0 79 11.0 80 10.0 81 7.0 82 5.0 83 3.5 84 3.0 85 2.0 86 0.5 87 0.0 88 1.0 89 1.5 90 1.0 91 0.5 92 0.0 93 0.0 94 0.0 95 0.5 96 1.0 97 0.5 98 0.0 99 0.0 100 0.0 >>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 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 50 1.0 51 0.0 52 1.0 53 1.0 54 0.0 55 1.0 56 1.0 57 0.0 58 2.0 59 0.0 60 1.0 61 1.0 62 0.0 63 1.0 64 1.0 65 3.0 66 1.0 67 1.0 68 1.0 69 2.0 70 2.0 71 14.0 72 17.0 73 58.0 74 254.0 75 865.0 76 2771.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 96.42500000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 97.89992221934146 94.39999999999999 2 1.5037593984962405 2.9000000000000004 3 0.4148301788955146 1.2 4 0.10370754472387865 0.4 5 0.0 0.0 6 0.025926886180969663 0.15 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.051853772361939325 0.95 >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 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 28 0.7000000000000001 No Hit GTCAATTAGAAGAATAAAGAAGAATTACTGCATTTCGTAACTTATTTTTT 10 0.25 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACCTGAAGCTATCTCGTAT 6 0.15 TruSeq Adapter, Index 19 (97% over 38bp) >>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 0.0 0.0 0.0 0.0 0.0 11 0.0 0.0 0.0 0.0 0.0 12 0.0 0.0 0.0 0.0 0.0 13 0.0 0.0 0.0 0.0 0.0 14 0.0 0.0 0.0 0.0 0.0 15 0.0 0.0 0.0 0.0 0.0 16 0.0 0.0 0.0 0.0 0.0 17 0.0 0.0 0.0 0.0 0.0 18 0.0 0.0 0.0 0.0 0.0 19 0.0 0.0 0.0 0.0 0.0 20 0.0 0.0 0.0 0.0 0.0 21 0.0 0.0 0.0 0.0 0.0 22 0.0 0.0 0.0 0.0 0.0 23 0.0 0.0 0.0 0.0 0.0 24 0.0 0.0 0.0 0.0 0.0 25 0.0 0.0 0.0 0.0 0.0 26 0.0 0.0 0.0 0.0 0.0 27 0.0 0.0 0.0 0.0 0.0 28 0.0 0.0 0.0 0.0 0.0 29 0.0 0.0 0.0 0.0 0.0 30 0.0 0.0 0.0 0.0 0.0 31 0.0 0.0 0.0 0.0 0.0 32 0.0 0.0 0.0 0.0 0.0 33 0.0 0.0 0.0 0.0 0.0 34 0.0 0.0 0.0 0.0 0.0 35 0.0 0.0 0.0 0.0 0.0 36 0.0 0.0 0.0 0.0 0.0 37 0.0 0.0 0.0 0.0 0.0 38 0.0 0.0 0.0 0.0 0.0 39 0.0 0.0 0.0 0.0 0.0 40 0.0 0.0 0.0 0.0 0.0 41 0.0 0.0 0.0 0.0 0.0 42 0.0 0.0 0.0 0.0 0.0 43 0.0 0.0 0.0 0.0 0.0 44 0.0 0.0 0.0 0.0 0.0 45 0.0 0.0 0.0 0.0 0.0 46 0.0 0.0 0.0 0.0 0.0 47 0.0 0.0 0.0 0.0 0.0 48 0.0 0.0 0.0 0.0 0.0 49 0.0 0.0 0.0 0.0 0.0 50 0.0 0.0 0.0 0.0 0.0 51 0.0 0.0 0.0 0.0 0.0 52 0.0 0.0 0.0 0.0 0.0 53 0.0 0.0 0.0 0.0 0.0 54 0.0 0.0 0.0 0.0 0.0 55 0.0 0.0 0.0 0.0 0.0 56 0.0 0.0 0.0 0.0 0.0 57 0.0 0.0 0.0 0.0 0.0 58 0.0 0.0 0.0 0.0 0.0 59 0.0 0.0 0.0 0.0 0.0 60 0.0 0.0 0.0 0.0 0.0 61 0.0 0.0 0.0 0.0 0.0 62 0.0 0.0 0.0 0.0 0.0 63 0.0 0.0 0.0 0.0 0.0 64 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR11389842 read2 length is 50-76 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11389842_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 50-76 %GC 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.5425 32.0 32.0 32.0 32.0 32.0 2 30.19775 32.0 32.0 32.0 21.0 32.0 3 30.3445 32.0 32.0 32.0 21.0 32.0 4 30.488 32.0 32.0 32.0 32.0 32.0 5 30.37625 32.0 32.0 32.0 21.0 32.0 6 33.58875 36.0 36.0 36.0 21.0 36.0 7 33.49725 36.0 36.0 36.0 21.0 36.0 8 33.2325 36.0 36.0 36.0 21.0 36.0 9 32.99125 36.0 36.0 36.0 14.0 36.0 10-11 33.372375000000005 36.0 36.0 36.0 21.0 36.0 12-13 33.437375 36.0 36.0 36.0 21.0 36.0 14-15 33.318 36.0 36.0 36.0 21.0 36.0 16-17 33.294875000000005 36.0 36.0 36.0 21.0 36.0 18-19 33.068375 36.0 36.0 36.0 14.0 36.0 20-21 33.040875 36.0 36.0 36.0 14.0 36.0 22-23 32.908375 36.0 36.0 36.0 14.0 36.0 24-25 33.021 36.0 36.0 36.0 14.0 36.0 26-27 32.897875 36.0 36.0 36.0 14.0 36.0 28-29 32.88375 36.0 36.0 36.0 14.0 36.0 30-31 32.654375 36.0 36.0 36.0 14.0 36.0 32-33 32.815 36.0 36.0 36.0 14.0 36.0 34-35 32.59225 36.0 36.0 36.0 14.0 36.0 36-37 32.605125 36.0 36.0 36.0 14.0 36.0 38-39 32.660125 36.0 36.0 36.0 14.0 36.0 40-41 32.434 36.0 34.0 36.0 14.0 36.0 42-43 32.331875 36.0 34.0 36.0 14.0 36.0 44-45 32.4795 36.0 36.0 36.0 14.0 36.0 46-47 32.25425 36.0 34.0 36.0 14.0 36.0 48-49 32.247375000000005 36.0 32.0 36.0 14.0 36.0 50-51 32.16664200425106 36.0 32.0 36.0 14.0 36.0 52-53 32.043895478622034 36.0 32.0 36.0 14.0 36.0 54-55 32.028521391043284 36.0 32.0 36.0 14.0 36.0 56-57 31.79675626815802 36.0 32.0 36.0 14.0 36.0 58-59 31.747704221663156 36.0 32.0 36.0 14.0 36.0 60-61 31.67342260943837 36.0 32.0 36.0 14.0 36.0 62-63 31.769298245614035 36.0 32.0 36.0 14.0 36.0 64-65 31.74397212097502 36.0 32.0 36.0 14.0 36.0 66-67 31.647949572977975 36.0 32.0 36.0 14.0 36.0 68-69 31.58678723938709 36.0 32.0 36.0 14.0 36.0 70-71 31.57349289014106 36.0 32.0 36.0 14.0 36.0 72-73 31.341597723328803 36.0 32.0 36.0 14.0 36.0 74-75 31.15667624123293 36.0 32.0 36.0 14.0 36.0 76 29.713076923076922 32.0 27.0 36.0 14.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 14 8.0 15 31.0 16 32.0 17 15.0 18 14.0 19 22.0 20 9.0 21 11.0 22 16.0 23 24.0 24 30.0 25 52.0 26 64.0 27 94.0 28 128.0 29 185.0 30 233.0 31 291.0 32 407.0 33 575.0 34 906.0 35 853.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 35.925000000000004 17.175 12.425 34.475 2 30.2 25.324999999999996 23.549999999999997 20.925 3 29.675 28.599999999999998 19.075 22.650000000000002 4 30.95 32.625 16.8 19.625 5 30.3 32.725 19.8 17.175 6 24.5 34.925 21.099999999999998 19.475 7 25.3 18.275 32.1 24.325 8 27.675 21.675 24.099999999999998 26.55 9 23.200000000000003 23.425 27.775 25.6 10-11 27.5125 28.212500000000002 20.025000000000002 24.25 12-13 27.0 24.075 23.5 25.424999999999997 14-15 27.037499999999998 24.7875 24.349999999999998 23.825 16-17 27.987499999999997 25.05 22.5625 24.4 18-19 26.487500000000004 24.4375 24.5375 24.5375 20-21 27.3 25.7625 23.8125 23.125 22-23 28.299999999999997 24.762500000000003 22.7375 24.2 24-25 26.5 26.775 23.1 23.625 26-27 26.8375 26.0125 23.875 23.275000000000002 28-29 28.075 24.175 22.8125 24.9375 30-31 26.5875 25.687500000000004 23.75 23.974999999999998 32-33 26.0125 25.587500000000002 24.25 24.15 34-35 26.8 25.937500000000004 22.75 24.5125 36-37 26.1625 25.9625 23.1375 24.7375 38-39 26.450000000000003 26.150000000000002 23.05 24.349999999999998 40-41 26.474999999999998 25.412499999999998 23.3375 24.775 42-43 26.200000000000003 25.9875 23.2875 24.525 44-45 26.187500000000004 25.924999999999997 23.6125 24.275 46-47 26.525 25.8125 23.175 24.4875 48-49 25.887500000000003 25.174999999999997 24.4375 24.5 50-51 26.878359794974372 24.965620702587824 24.52806600825103 23.627953494186773 52-53 26.910091284231584 25.597098912092036 23.471301738151805 24.02150806552457 54-55 26.55741806354766 26.032024018013512 23.705278959219413 23.705278959219413 56-57 27.130521837066702 26.279564510073833 23.764234764109624 22.82567888874984 58-59 26.646631605309288 25.694966190833963 23.816679188580014 23.841723015276735 60-61 26.2557935613178 26.39358637103846 23.236878366528874 24.11374170111487 62-63 26.36591478696742 24.93734335839599 24.486215538847116 24.210526315789473 64-65 26.792878635907723 25.764794383149447 23.106820461384153 24.335506519558674 66-67 26.17702448210923 26.001255492780917 23.904582548650346 23.91713747645951 68-69 26.124089424767643 25.84777694046722 24.026626475759862 24.001507159005275 70-71 26.39255626807494 26.128504966679237 22.87187224946561 24.60706651578021 72-73 26.059992406024552 26.07264903176813 24.186811795975196 23.680546766232123 74-75 27.059297021733297 22.726053125838476 25.51650120740542 24.69814864502281 76 29.5 0.0 33.34615384615385 37.15384615384615 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 16.0 1 8.0 2 0.5 3 0.5 4 0.0 5 1.0 6 2.0 7 2.0 8 2.0 9 1.5 10 0.5 11 0.5 12 1.0 13 1.5 14 2.0 15 2.0 16 2.5 17 2.5 18 6.0 19 8.5 20 7.5 21 6.5 22 4.5 23 4.5 24 8.5 25 10.5 26 11.0 27 13.0 28 15.5 29 16.0 30 17.5 31 24.5 32 30.0 33 34.5 34 43.0 35 67.5 36 95.5 37 109.0 38 132.5 39 144.0 40 150.0 41 157.0 42 165.0 43 175.5 44 188.0 45 193.0 46 180.5 47 188.0 48 190.0 49 178.5 50 174.5 51 148.5 52 118.5 53 130.0 54 144.0 55 130.5 56 111.5 57 110.0 58 116.0 59 125.5 60 132.5 61 125.0 62 118.0 63 109.0 64 94.5 65 87.5 66 83.0 67 79.0 68 71.0 69 64.0 70 56.5 71 53.5 72 59.0 73 51.0 74 37.5 75 32.5 76 29.0 77 23.0 78 15.5 79 11.5 80 11.5 81 9.5 82 5.5 83 3.0 84 2.5 85 2.0 86 2.0 87 2.0 88 1.0 89 1.5 90 3.0 91 1.5 92 0.0 93 0.5 94 1.5 95 1.0 96 0.0 97 1.5 98 2.5 99 5.0 100 8.0 >>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 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 50 1.0 51 0.0 52 1.0 53 1.0 54 0.0 55 1.0 56 1.0 57 1.0 58 2.0 59 0.0 60 1.0 61 1.0 62 0.0 63 1.0 64 2.0 65 4.0 66 1.0 67 1.0 68 0.0 69 3.0 70 3.0 71 12.0 72 25.0 73 68.0 74 286.0 75 984.0 76 2600.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 96.2 #Duplication Level Percentage of deduplicated Percentage of total 1 97.5051975051975 93.8 2 1.8191268191268193 3.5000000000000004 3 0.36382536382536385 1.05 4 0.12993762993762994 0.5 5 0.10395010395010396 0.5 6 0.0 0.0 7 0.02598752598752599 0.17500000000000002 8 0.0 0.0 9 0.02598752598752599 0.22499999999999998 >10 0.02598752598752599 0.25 >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 10 0.25 No Hit AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 9 0.22499999999999998 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACA 7 0.17500000000000002 No Hit TTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGG 5 0.125 No Hit CTTGATTTTACCAAAGATGATGAAAACGTAAACTCACAACCATTTATGCG 5 0.125 No Hit AAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTCG 5 0.125 No Hit TGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTT 5 0.125 No Hit >>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 0.0 0.0 0.0 0.0 0.0 11 0.0 0.0 0.0 0.0 0.0 12 0.0 0.0 0.0 0.0 0.0 13 0.0 0.0 0.0 0.0 0.0 14 0.0 0.0 0.0 0.0 0.0 15 0.0 0.0 0.0 0.0 0.0 16 0.0 0.0 0.0 0.0 0.0 17 0.0 0.0 0.0 0.0 0.0 18 0.0 0.0 0.0 0.0 0.0 19 0.0 0.0 0.0 0.0 0.0 20 0.0 0.0 0.0 0.0 0.0 21 0.0 0.0 0.0 0.0 0.0 22 0.0 0.0 0.0 0.0 0.0 23 0.0 0.0 0.0 0.0 0.0 24 0.0 0.0 0.0 0.0 0.0 25 0.0 0.0 0.0 0.0 0.0 26 0.0 0.0 0.0 0.0 0.0 27 0.0 0.0 0.0 0.0 0.0 28 0.0 0.0 0.0 0.0 0.0 29 0.0 0.0 0.0 0.0 0.0 30 0.0 0.0 0.0 0.0 0.0 31 0.0 0.0 0.0 0.0 0.0 32 0.0 0.0 0.0 0.0 0.0 33 0.0 0.0 0.0 0.0 0.0 34 0.0 0.0 0.0 0.0 0.0 35 0.0 0.0 0.0 0.0 0.0 36 0.0 0.0 0.0 0.0 0.0 37 0.0 0.0 0.0 0.0 0.0 38 0.0 0.0 0.0 0.0 0.0 39 0.0 0.0 0.0 0.0 0.0 40 0.0 0.0 0.0 0.0 0.0 41 0.0 0.0 0.0 0.0 0.0 42 0.0 0.0 0.0 0.0 0.0 43 0.0 0.0 0.0 0.0 0.0 44 0.0 0.0 0.0 0.0 0.0 45 0.0 0.0 0.0 0.0 0.0 46 0.0 0.0 0.0 0.0 0.0 47 0.0 0.0 0.0 0.0 0.0 48 0.0 0.0 0.0 0.0 0.0 49 0.0 0.0 0.0 0.0 0.0 50 0.0 0.0 0.0 0.0 0.0 51 0.0 0.0 0.0 0.0 0.0 52 0.0 0.0 0.0 0.0 0.0 53 0.0 0.0 0.0 0.0 0.0 54 0.0 0.0 0.0 0.0 0.0 55 0.0 0.0 0.0 0.0 0.0 56 0.0 0.0 0.0 0.0 0.0 57 0.0 0.0 0.0 0.0 0.0 58 0.0 0.0 0.0 0.0 0.0 59 0.0 0.0 0.0 0.0 0.0 60 0.0 0.0 0.0 0.0 0.0 61 0.0 0.0 0.0 0.0 0.0 62 0.0 0.0 0.0 0.0 0.0 63 0.0 0.0 0.0 0.0 0.0 64 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 694799 spots for SRR11389842.sra Written 694799 spots for SRR11389842.sra Read 694799 spots for SRR11389842.sra Written 694799 spots for SRR11389842.sra Read 694799 spots for SRR11389842.sra Written 694799 spots for SRR11389842.sra Read 694799 spots for SRR11389842.sra Written 694799 spots for SRR11389842.sra Read 694799 spots for SRR11389842.sra Written 694799 spots for SRR11389842.sra Read 694799 spots for SRR11389842.sra Written 694799 spots for SRR11389842.sra Read 694799 spots for SRR11389842.sra Written 694799 spots for SRR11389842.sra Read 694799 spots for SRR11389842.sra Written 694799 spots for SRR11389842.sra Read 694799 spots for SRR11389842.sra Written 694799 spots for SRR11389842.sra Read 694799 spots for SRR11389842.sra Written 694799 spots for SRR11389842.sra Read 694799 spots for SRR11389842.sra Written 694799 spots for SRR11389842.sra Read 694799 spots for SRR11389842.sra Written 694799 spots for SRR11389842.sra Read 694799 spots for SRR11389842.sra Written 694799 spots for SRR11389842.sra Read 694799 spots for SRR11389842.sra Written 694799 spots for SRR11389842.sra Read 694799 spots for SRR11389842.sra Written 694799 spots for SRR11389842.sra Read 694799 spots for SRR11389842.sra Written 694799 spots for SRR11389842.sra Read 694799 spots for SRR11389842.sra Written 694799 spots for SRR11389842.sra Read 694799 spots for SRR11389842.sra Written 694799 spots for SRR11389842.sra Read 694799 spots for SRR11389842.sra Written 694799 spots for SRR11389842.sra Read 694812 spots for SRR11389842.sra Written 694812 spots for SRR11389842.sra SRR ids: ['SRR11389842.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_1t6_sz5u SRR11389842.sra spots: 13895993 blocks: [[1, 694799], [694800, 1389598], [1389599, 2084397], [2084398, 2779196], [2779197, 3473995], [3473996, 4168794], [4168795, 4863593], [4863594, 5558392], [5558393, 6253191], [6253192, 6947990], [6947991, 7642789], [7642790, 8337588], [8337589, 9032387], [9032388, 9727186], [9727187, 10421985], [10421986, 11116784], [11116785, 11811583], [11811584, 12506382], [12506383, 13201181], [13201182, 13895993]] SRR11389842 file size 2635726 SRR11389842 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 SRR11389842 SRR11389842_1.fastq SRR11389842_2.fastq Input file: SRR11389842_1.fastq Paired file: SRR11389842_2.fastq trimmed: SRR11389842-trimmed-pair1.fastq, SRR11389842-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 07:59:03 2024 >> started Sat Dec 7 07:59:21 2024 >> done (18.750s) 13895993 read pairs processed; of these: 2 ( 0.00%) short read pairs filtered out after trimming by size control 66116 ( 0.48%) empty read pairs filtered out after trimming by size control 13829875 (99.52%) read pairs available; of these: 63839 ( 0.46%) trimmed read pairs available after processing 13766036 (99.54%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 25 1 0.00% 26 0 0.00% 27 0 0.00% 28 0 0.00% 29 2 0.00% 30 4 0.00% 31 4 0.00% 32 6 0.00% 33 9 0.00% 34 3 0.00% 35 197 0.00% 36 251 0.00% 37 322 0.00% 38 406 0.00% 39 493 0.00% 40 604 0.00% 41 716 0.01% 42 840 0.01% 43 936 0.01% 44 1002 0.01% 45 1183 0.01% 46 1275 0.01% 47 1374 0.01% 48 1543 0.01% 49 1759 0.01% 50 1915 0.01% 51 2181 0.02% 52 2502 0.02% 53 2835 0.02% 54 3057 0.02% 55 3528 0.03% 56 3875 0.03% 57 4336 0.03% 58 4687 0.03% 59 5235 0.04% 60 5721 0.04% 61 6241 0.05% 62 6845 0.05% 63 7708 0.06% 64 8534 0.06% 65 9349 0.07% 66 10031 0.07% 67 11251 0.08% 68 11487 0.08% 69 12688 0.09% 70 14239 0.10% 71 17080 0.12% 72 27681 0.20% 73 128087 0.93% 74 1016818 7.35% 75 6149123 44.46% 76 6339911 45.84% 13829875 reads passed initial QC criterion=sequence-density sequence-density=0.75 sequence-density-rank=1 fanout-score=2.02 fanout-score-rank=20 prefix-density=0.73 prefix-fanout=2.0 sequence=TTCAAATGTACA criterion=fanout-score sequence-density=0.01 sequence-density-rank=28 fanout-score=45.63 fanout-score-rank=1 prefix-density=0.05 prefix-fanout=6.6 sequence=AAAAAAAAGTATGTTTGCATCAATGATAATCCCAAAGTAGGAAGTGTGTACGTAGTAGCAAGTGTTATACATACATAAAATTAAGCGATGCGTTTCGATCAAGTACTTGGCATCATCGATCACATACGTACATTTCACAGCAGGTAGCTACGTACATTACAGGCATACGTACATGCAGAGAGATACCCGGCCCTGTGTTGTGTTTGCAATTGCATAGATGAGAATGAGATGACTTGATTCTTAATTAGCCGGCGAGAGCGCTGGTGTTGTAGACGAGGAGGGCGCCGCCGCCGAGGAGGCCGGCCAGGGTGACGGCCCAGATCAGGAGCCCCGTCGTCCCACCGGCGTAGCGGTCGCCAGATTCGGACCATACCTCCGGCGTGTAGATCGGGCTGTAGCCGTCGACGTTGGCGCCGTACTTGTCAACAAACTGGTACACACCCTTTCCCGTGCCCTTCCTGCCGTTGGCGTCGATGTCCACCGTCAAGCCACCTCCGATCCCGAGGGGCTT criterion=sequence-density sequence-density=0.68 sequence-density-rank=1 fanout-score=1.99 fanout-score-rank=28 prefix-density=0.67 prefix-fanout=2.0 sequence=GACGCCTATGTCCGCATCATCGGCTTCGACAACACCCGGCAGGTGCAGTGCATCAGCTTCATCGCCTTCAAGCCACCGGG criterion=fanout-score sequence-density=0.02 sequence-density-rank=32 fanout-score=6.93 fanout-score-rank=1 prefix-density=0.05 prefix-fanout=2.2 sequence=CCTCAAGCCAAAGCCTCTTGCTAAGCGTACCACACTATACAGACGTGCGCGCGCAGCCATGGCACCCACCGTGATGGCTTCCTCCGCCACCTCCGTGGCTCCTTTCCA SRR11389842 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 07:59:46 Started mapping on | Dec 07 07:59:47 Finished on | Dec 07 08:00:51 Mapping speed, Million of reads per hour | 777.93 Number of input reads | 13829875 Average input read length | 150 UNIQUE READS: Uniquely mapped reads number | 11506994 Uniquely mapped reads % | 83.20% Average mapped length | 149.92 Number of splices: Total | 5168272 Number of splices: Annotated (sjdb) | 4922582 Number of splices: GT/AG | 5097674 Number of splices: GC/AG | 62445 Number of splices: AT/AC | 1554 Number of splices: Non-canonical | 6599 Mismatch rate per base, % | 0.72% Deletion rate per base | 0.01% Deletion average length | 1.68 Insertion rate per base | 0.01% Insertion average length | 1.68 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1374265 % of reads mapped to multiple loci | 9.94% Number of reads mapped to too many loci | 28844 % of reads mapped to too many loci | 0.21% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 5.67% % of reads unmapped: other | 0.98% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 948616 948616 948616 N_multimapping 1374265 1374265 1374265 N_noFeature 394018 11126751 558931 N_ambiguous 296253 1958 88456 UnstrandedReadsAssigned:10816723 PositiveStrandReadsAssigned:378285 NegativeStrandReadsAssigned:10859607 Dataset is classified negative stranded MeadianReadLen=76 20thPercentileLength=75 echo kmer=71 SRR11389842 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: SRR11389842-trimmed-pair1.fastq SRR11389842-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 13,829,875 reads, 12,367,278 reads pseudoaligned [quant] estimated average fragment length: 195.92 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,095 rounds 52973 SRR11389842.ke.tsv 35125 SRR11389842.se.tsv 88098 total ==> SRR11389842.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 741.337 0 0 PNS24247 1044 849.08 16.734 2.19631 PNS24249 1928 1733.08 79.3372 5.10153 PNS24246 1044 849.08 16.734 2.19631 PNS24248 1044 849.08 16.734 2.19631 PNS24244 1471 1276.08 14.4607 1.26285 PNS24243 293 125.03 0 0 KQK14069 1603 1408.08 1068.33 84.5516 KQK14071 474 283.097 100.988 39.7535 ==> SRR11389842.se.tsv <== BRADI_1g14170v3 1363 BRADI_1g53295v3 13 BRADI_1g59795v3 208 BRADI_1g07683v3 0 BRADI_1g00485v3 1 BRADI_1g20270v3 140 BRADI_1g74790v3 247 BRADI_1g09890v3 0 BRADI_1g77505v3 132 BRADI_1g48960v3 0 SRR11389842 completed mapping pipeline successfully