Starting /dee2/code/volunteer_pipeline.sh SRR13347976 current disk space = 3051388809216 free memory = 1436001120 SRR13347976 SRAfilesize 5822c9b6ccc1ad2ebef7d13bbe8665b8 SRR13347976.sra SRR13347976.sra file validated SRR13347976 is paired end SRR13347976 is conventional basespace SRR13347976 read1 length is 51-150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR13347976_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 51-150 %GC 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.5135 37.0 37.0 37.0 37.0 37.0 2 36.491 37.0 37.0 37.0 37.0 37.0 3 36.612 37.0 37.0 37.0 37.0 37.0 4 36.595 37.0 37.0 37.0 37.0 37.0 5 36.54125 37.0 37.0 37.0 37.0 37.0 6 36.5575 37.0 37.0 37.0 37.0 37.0 7 36.572 37.0 37.0 37.0 37.0 37.0 8 36.468 37.0 37.0 37.0 37.0 37.0 9 36.559 37.0 37.0 37.0 37.0 37.0 10-14 36.4254 37.0 37.0 37.0 37.0 37.0 15-19 36.555600000000005 37.0 37.0 37.0 37.0 37.0 20-24 36.4653 37.0 37.0 37.0 37.0 37.0 25-29 36.486000000000004 37.0 37.0 37.0 37.0 37.0 30-34 36.459 37.0 37.0 37.0 37.0 37.0 35-39 36.3827 37.0 37.0 37.0 37.0 37.0 40-44 36.3803 37.0 37.0 37.0 37.0 37.0 45-49 36.2 37.0 37.0 37.0 37.0 37.0 50-54 36.03640623681524 37.0 37.0 37.0 34.6 37.0 55-59 36.10650296011045 37.0 37.0 37.0 37.0 37.0 60-64 35.520721692902626 37.0 37.0 37.0 34.6 37.0 65-69 36.200280933451836 37.0 37.0 37.0 37.0 37.0 70-74 36.276472710369895 37.0 37.0 37.0 37.0 37.0 75-79 36.09785891333601 37.0 37.0 37.0 34.6 37.0 80-84 36.22128847279703 37.0 37.0 37.0 37.0 37.0 85-89 36.07200036479837 37.0 37.0 37.0 37.0 37.0 90-94 36.03558333644243 37.0 37.0 37.0 37.0 37.0 95-99 36.13942270178149 37.0 37.0 37.0 37.0 37.0 100-104 35.55935191912026 37.0 37.0 37.0 31.8 37.0 105-109 35.91622973949179 37.0 37.0 37.0 34.6 37.0 110-114 36.039743704994024 37.0 37.0 37.0 37.0 37.0 115-119 36.058854964573214 37.0 37.0 37.0 37.0 37.0 120-124 35.7245004088508 37.0 37.0 37.0 34.6 37.0 125-129 35.88522209911284 37.0 37.0 37.0 34.6 37.0 130-134 36.14054847772214 37.0 37.0 37.0 37.0 37.0 135-139 34.69973266894967 37.0 34.6 37.0 29.4 37.0 140-144 35.51646467376205 37.0 37.0 37.0 34.6 37.0 145-149 35.857619304531305 37.0 37.0 37.0 37.0 37.0 150 36.51599443671766 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 28 4.0 29 15.0 30 23.0 31 32.0 32 55.0 33 71.0 34 141.0 35 667.0 36 2857.0 37 135.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 39.2 12.1 12.15 36.55 2 23.7 8.35 30.675 37.275000000000006 3 22.400000000000002 11.425 25.124999999999996 41.05 4 26.900000000000002 14.7 22.25 36.15 5 28.307076769192296 19.454863715928983 25.081270317579396 27.156789197299325 6 25.1 28.4 23.799999999999997 22.7 7 15.2 27.825 39.85 17.125 8 17.45 25.924999999999997 33.4 23.225 9 17.775 24.425 34.775 23.025000000000002 10-14 19.355 29.62 28.615000000000002 22.41 15-19 20.474999999999998 27.150000000000002 28.599999999999998 23.775 20-24 20.605 27.744999999999997 27.815 23.835 25-29 21.11 28.02 27.6 23.27 30-34 20.78 28.035 27.51 23.674999999999997 35-39 20.825 27.41 27.815 23.95 40-44 20.4 27.765 27.83 24.005000000000003 45-49 20.78 26.96 28.03 24.23 50-54 20.901270381114333 27.943383014904473 27.39821946583975 23.757127138141442 55-59 20.990436132391967 27.66511441590306 27.38971508687597 23.954734364829005 60-64 20.311323123273915 28.6115992970123 27.44162691438614 23.635450665327642 65-69 20.575757575757574 28.510101010101007 27.24242424242424 23.671717171717173 70-74 20.877335499593826 28.031072298943947 26.96994313566206 24.121649065800163 75-79 20.377840183814143 28.200153178452897 27.224917028338012 24.197089609394943 80-84 20.52550231839258 27.73312725399279 28.02163833075734 23.71973209685729 85-89 20.573540126990736 27.984802747996252 27.82346205891538 23.618195066097634 90-94 20.717173308132512 28.098913214679477 27.78915314747729 23.394760329710714 95-99 20.78191489361702 27.404255319148934 27.8031914893617 24.01063829787234 100-104 21.01308249540491 28.284138825819007 27.143474970267057 23.559303708509027 105-109 21.061888534681763 28.360998131252064 27.250742002858086 23.32637133120809 110-114 20.862784696510715 28.59867609110288 27.44867048131942 23.089868731066982 115-119 20.869465341985872 27.85275368977201 28.105438465514272 23.172342502727847 120-124 21.27634591674984 27.922268537544763 27.352785768801734 23.44859977690366 125-129 20.648700789775127 27.202025682763608 28.347501055043107 23.801772472418158 130-134 20.60745627684073 27.889462874214228 28.21310761187527 23.28997323706977 135-139 20.836029506923772 27.636857771450757 27.772744920408954 23.754367801216514 140-144 20.5017534394389 28.702454815214455 27.623415160507147 23.172376584839494 145-149 21.070965098012433 28.72071579810122 27.101973908886006 23.10634519500034 150 21.835883171070932 27.88595271210014 26.112656467315716 24.165507649513213 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 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 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.5 25 1.5 26 3.0 27 5.5 28 4.5 29 6.0 30 15.5 31 21.0 32 25.5 33 31.5 34 38.0 35 54.5 36 68.5 37 77.5 38 104.5 39 130.0 40 172.5 41 215.0 42 235.0 43 257.5 44 271.5 45 282.0 46 299.0 47 283.0 48 257.0 49 236.0 50 195.5 51 148.5 52 113.5 53 110.5 54 87.0 55 65.5 56 52.5 57 35.0 58 34.5 59 26.0 60 19.5 61 17.5 62 11.5 63 8.0 64 6.0 65 6.5 66 5.0 67 2.0 68 2.0 69 2.0 70 1.0 71 1.0 72 2.5 73 3.5 74 2.0 75 1.0 76 1.5 77 1.0 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 0.0 2 0.0 3 0.0 4 0.0 5 0.025 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 0.0 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 warn #Length Count 50-51 1.0 52-53 2.0 54-55 2.0 56-57 2.0 58-59 2.0 60-61 9.0 62-63 7.0 64-65 10.0 66-67 9.0 68-69 9.0 70-71 6.0 72-73 15.0 74-75 5.0 76-77 6.0 78-79 20.0 80-81 12.0 82-83 16.0 84-85 15.0 86-87 18.0 88-89 14.0 90-91 10.0 92-93 14.0 94-95 21.0 96-97 29.0 98-99 24.0 100-101 22.0 102-103 24.0 104-105 28.0 106-107 20.0 108-109 33.0 110-111 31.0 112-113 31.0 114-115 38.0 116-117 23.0 118-119 31.0 120-121 33.0 122-123 37.0 124-125 38.0 126-127 33.0 128-129 42.0 130-131 48.0 132-133 36.0 134-135 65.0 136-137 41.0 138-139 49.0 140-141 64.0 142-143 24.0 144-145 2.0 146-147 1.0 148-149 52.0 150-151 2876.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 92.10000000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 92.18241042345277 84.89999999999999 2 7.057546145494029 13.0 3 0.760043431053203 2.1 4 0.0 0.0 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >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 pass >>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 0.0 0.0 0.0 0.0 0.0 82-83 0.0 0.0 0.0 0.0 0.0 84-85 0.0 0.0 0.0 0.0 0.0 86-87 0.0 0.0 0.0 0.0 0.0 88-89 0.0 0.0 0.0 0.0 0.0 90-91 0.0 0.0 0.0 0.0 0.0 92-93 0.0 0.0 0.0 0.0 0.0 94-95 0.0 0.0 0.0 0.0 0.0 96-97 0.0 0.0 0.0 0.0 0.0 98-99 0.0 0.0 0.0 0.0 0.0 100-101 0.0 0.0 0.0 0.0 0.0 102-103 0.0 0.0 0.0 0.0 0.0 104-105 0.0 0.0 0.0 0.0 0.0 106-107 0.0 0.0 0.0 0.0 0.0 108-109 0.0 0.0 0.0 0.0 0.0 110-111 0.0 0.0 0.0 0.0 0.0 112-113 0.0 0.0 0.0 0.0 0.0 114-115 0.0 0.0 0.0 0.0 0.0 116-117 0.0 0.0 0.0 0.0 0.0 118-119 0.0 0.0 0.0 0.0 0.0 120-121 0.0 0.0 0.0 0.0 0.0 122-123 0.0 0.0 0.0 0.0 0.0 124-125 0.0 0.0 0.0 0.0 0.0 126-127 0.0 0.0 0.0 0.0 0.0 128-129 0.0 0.0 0.0 0.0 0.0 130-131 0.0 0.0 0.0 0.0 0.0 132-133 0.0 0.0 0.0 0.0 0.0 134-135 0.0 0.0 0.0 0.0 0.0 136-137 0.0 0.0 0.0 0.0 0.0 138 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR13347976 read2 length is 51-150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR13347976_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 51-150 %GC 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.3635 37.0 37.0 37.0 25.0 37.0 2 35.908 37.0 37.0 37.0 37.0 37.0 3 32.007 37.0 37.0 37.0 11.0 37.0 4 36.241 37.0 37.0 37.0 37.0 37.0 5 36.143 37.0 37.0 37.0 37.0 37.0 6 36.2215 37.0 37.0 37.0 37.0 37.0 7 33.8445 37.0 37.0 37.0 25.0 37.0 8 36.2805 37.0 37.0 37.0 37.0 37.0 9 36.197 37.0 37.0 37.0 37.0 37.0 10-14 34.43499999999999 37.0 37.0 37.0 27.0 37.0 15-19 35.85699999999999 37.0 37.0 37.0 37.0 37.0 20-24 35.8443 37.0 37.0 37.0 34.6 37.0 25-29 35.8837 37.0 37.0 37.0 34.6 37.0 30-34 35.5255 37.0 37.0 37.0 34.6 37.0 35-39 34.159299999999995 37.0 34.6 37.0 24.2 37.0 40-44 36.0303 37.0 37.0 37.0 37.0 37.0 45-49 35.5851 37.0 37.0 37.0 34.6 37.0 50-54 35.43909444081313 37.0 37.0 37.0 34.6 37.0 55-59 35.64191546535661 37.0 37.0 37.0 34.6 37.0 60-64 34.323556301978115 37.0 34.6 37.0 29.4 37.0 65-69 35.876000056508424 37.0 37.0 37.0 37.0 37.0 70-74 35.05844875845206 37.0 37.0 37.0 32.2 37.0 75-79 35.50315632546342 37.0 37.0 37.0 34.6 37.0 80-84 35.95383570169556 37.0 37.0 37.0 37.0 37.0 85-89 35.8415143456521 37.0 37.0 37.0 37.0 37.0 90-94 34.87842761686575 37.0 37.0 37.0 27.4 37.0 95-99 35.04224106177291 37.0 34.6 37.0 31.8 37.0 100-104 35.44677934448803 37.0 37.0 37.0 32.2 37.0 105-109 35.58563255890522 37.0 37.0 37.0 37.0 37.0 110-114 35.243388760094355 37.0 37.0 37.0 29.8 37.0 115-119 35.50105170805943 37.0 37.0 37.0 34.6 37.0 120-124 35.30439385834268 37.0 37.0 37.0 32.2 37.0 125-129 35.63116540354197 37.0 37.0 37.0 32.2 37.0 130-134 35.39103710330895 37.0 37.0 37.0 32.2 37.0 135-139 35.105863872307204 37.0 37.0 37.0 32.2 37.0 140-144 35.58290064426745 37.0 37.0 37.0 37.0 37.0 145-149 35.615359514924634 37.0 37.0 37.0 34.6 37.0 150 36.13949339992865 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 26 2.0 27 3.0 28 7.0 29 20.0 30 31.0 31 62.0 32 95.0 33 216.0 34 626.0 35 1400.0 36 1500.0 37 38.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 31.95 27.925 13.875000000000002 26.25 2 21.975 30.925000000000004 30.45 16.650000000000002 3 20.4 28.15 33.625 17.825 4 23.875 29.7 24.55 21.875 5 24.425 33.1 24.775 17.7 6 20.7 37.45 23.0 18.85 7 21.425 23.849999999999998 35.325 19.400000000000002 8 22.0 25.0 29.7 23.3 9 22.7 23.474999999999998 31.3 22.525000000000002 10-14 22.695 29.375 26.290000000000003 21.64 15-19 23.35 28.134999999999998 27.71 20.805 20-24 22.994999999999997 27.82 28.075 21.11 25-29 23.544999999999998 28.444999999999997 27.800000000000004 20.21 30-34 23.06 27.98 28.105000000000004 20.855 35-39 22.065 29.005 27.215 21.715 40-44 23.73 27.73 27.275 21.265 45-49 23.35 27.655 28.455000000000002 20.54 50-54 23.770696813566104 27.827522385073284 27.69746385873643 20.70431694262418 55-59 23.67682437850842 27.390737770649558 27.61627906976744 21.316158781074577 60-64 22.749005989229452 28.63757612360964 27.29880718707534 21.31461070008556 65-69 23.44359454941492 28.291373284028165 27.607517349678336 20.657514816878578 70-74 23.944809327427322 28.124840894048162 27.126928364136244 20.80342141438827 75-79 23.93766979342867 27.894817776410886 27.536009021477266 20.631503408683173 80-84 23.806568399275925 27.551073183346265 27.887251099043187 20.755107318334627 85-89 24.02214214841506 27.17113165178338 27.860462687346597 20.94626351245496 90-94 23.547706905640485 27.701634159198736 27.68581971534001 21.06483921982077 95-99 24.187339606501283 27.790846877673225 27.58233532934132 20.439478186484177 100-104 23.938685655269882 27.03701690493015 27.374028374191443 21.650269065608523 105-109 23.53916744983139 27.923047155730004 27.364696777046827 21.173088617391787 110-114 24.092371972220654 27.598667494777256 27.084862514821296 21.224098018180793 115-119 24.06410924029393 27.796100214083204 27.17699473471041 20.962795810912457 120-124 24.091393394104415 27.483130105362854 27.506807150467623 20.918669350065112 125-129 23.62630683199611 27.741308047653778 27.820325796255773 20.812059324094335 130-134 24.25935224704996 27.366306803916647 27.46673361787597 20.90760733115742 135-139 24.014360313315926 27.63054830287206 27.134464751958227 21.220626631853786 140-144 24.450493365090168 28.057162300102075 26.655324940455937 20.83701939435182 145-149 24.81239242685026 29.067125645438896 26.216867469879517 19.903614457831324 150 26.2575811630396 28.11273635390653 24.331073849447023 21.29860863360685 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 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 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.5 20 1.0 21 0.5 22 0.0 23 0.5 24 1.0 25 0.5 26 3.0 27 4.5 28 3.0 29 7.5 30 12.0 31 16.5 32 28.0 33 39.0 34 50.0 35 58.0 36 82.5 37 117.5 38 143.0 39 177.0 40 220.5 41 249.0 42 270.0 43 284.0 44 284.5 45 274.5 46 253.0 47 251.0 48 225.0 49 190.5 50 169.5 51 140.0 52 105.5 53 76.0 54 69.0 55 61.5 56 43.5 57 29.0 58 27.5 59 22.5 60 15.5 61 11.5 62 7.5 63 4.5 64 3.0 65 2.5 66 3.0 67 4.5 68 4.5 69 2.5 70 1.0 71 1.5 72 1.0 73 1.0 74 1.5 75 2.5 76 2.5 77 1.5 78 2.0 79 1.0 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 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 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 warn #Length Count 50-51 1.0 52-53 4.0 54-55 4.0 56-57 1.0 58-59 5.0 60-61 12.0 62-63 8.0 64-65 11.0 66-67 11.0 68-69 4.0 70-71 10.0 72-73 16.0 74-75 6.0 76-77 9.0 78-79 19.0 80-81 11.0 82-83 14.0 84-85 16.0 86-87 16.0 88-89 14.0 90-91 13.0 92-93 17.0 94-95 21.0 96-97 30.0 98-99 25.0 100-101 23.0 102-103 23.0 104-105 26.0 106-107 24.0 108-109 32.0 110-111 33.0 112-113 34.0 114-115 38.0 116-117 24.0 118-119 32.0 120-121 34.0 122-123 34.0 124-125 38.0 126-127 35.0 128-129 41.0 130-131 47.0 132-133 38.0 134-135 63.0 136-137 44.0 138-139 47.0 140-141 64.0 142-143 22.0 144-145 0.0 146-147 1.0 148-149 102.0 150-151 2803.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 95.0 #Duplication Level Percentage of deduplicated Percentage of total 1 95.13157894736842 90.375 2 4.473684210526316 8.5 3 0.39473684210526316 1.125 4 0.0 0.0 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >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 pass >>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 0.0 0.0 0.0 0.0 0.0 82-83 0.0 0.0 0.0 0.0 0.0 84-85 0.0 0.0 0.0 0.0 0.0 86-87 0.0 0.0 0.0 0.0 0.0 88-89 0.0 0.0 0.0 0.0 0.0 90-91 0.0 0.0 0.0 0.0 0.0 92-93 0.0 0.0 0.0 0.0 0.0 94-95 0.0 0.0 0.0 0.0 0.0 96-97 0.0 0.0 0.0 0.0 0.0 98-99 0.0 0.0 0.0 0.0 0.0 100-101 0.0 0.0 0.0 0.0 0.0 102-103 0.0 0.0 0.0 0.0 0.0 104-105 0.0 0.0 0.0 0.0 0.0 106-107 0.0 0.0 0.0 0.0 0.0 108-109 0.0 0.0 0.0 0.0 0.0 110-111 0.0 0.0 0.0 0.0 0.0 112-113 0.0 0.0 0.0 0.0 0.0 114-115 0.0 0.0 0.0 0.0 0.0 116-117 0.0 0.0 0.0 0.0 0.0 118-119 0.0 0.0 0.0 0.0 0.0 120-121 0.0 0.0 0.0 0.0 0.0 122-123 0.0 0.0 0.0 0.0 0.0 124-125 0.0 0.0 0.0 0.0 0.0 126-127 0.0 0.0 0.0 0.0 0.0 128-129 0.0 0.0 0.0 0.0 0.0 130-131 0.0 0.0 0.0 0.0 0.0 132-133 0.0 0.0 0.0 0.0 0.0 134-135 0.0 0.0 0.0 0.0 0.0 136-137 0.0 0.0 0.0 0.0 0.0 138 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ATTTCTT 10 0.008295993 135.875 4 >>END_MODULE Read 1068353 spots for SRR13347976.sra Written 1068353 spots for SRR13347976.sra Read 1068353 spots for SRR13347976.sra Written 1068353 spots for SRR13347976.sra Read 1068353 spots for SRR13347976.sra Written 1068353 spots for SRR13347976.sra Read 1068353 spots for SRR13347976.sra Written 1068353 spots for SRR13347976.sra Read 1068353 spots for SRR13347976.sra Written 1068353 spots for SRR13347976.sra Read 1068353 spots for SRR13347976.sra Written 1068353 spots for SRR13347976.sra Read 1068353 spots for SRR13347976.sra Written 1068353 spots for SRR13347976.sra Read 1068353 spots for SRR13347976.sra Written 1068353 spots for SRR13347976.sra Read 1068353 spots for SRR13347976.sra Written 1068353 spots for SRR13347976.sra Read 1068353 spots for SRR13347976.sra Written 1068353 spots for SRR13347976.sra Read 1068353 spots for SRR13347976.sra Written 1068353 spots for SRR13347976.sra Read 1068353 spots for SRR13347976.sra Written 1068353 spots for SRR13347976.sra Read 1068353 spots for SRR13347976.sra Written 1068353 spots for SRR13347976.sra Read 1068353 spots for SRR13347976.sra Written 1068353 spots for SRR13347976.sra Read 1068353 spots for SRR13347976.sra Written 1068353 spots for SRR13347976.sra Read 1068357 spots for SRR13347976.sra Written 1068357 spots for SRR13347976.sra Read 1068353 spots for SRR13347976.sra Written 1068353 spots for SRR13347976.sra Read 1068353 spots for SRR13347976.sra Written 1068353 spots for SRR13347976.sra Read 1068353 spots for SRR13347976.sra Written 1068353 spots for SRR13347976.sra Read 1068353 spots for SRR13347976.sra Written 1068353 spots for SRR13347976.sra SRR ids: ['SRR13347976.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_8btyogf2 SRR13347976.sra spots: 21367064 blocks: [[1, 1068353], [1068354, 2136706], [2136707, 3205059], [3205060, 4273412], [4273413, 5341765], [5341766, 6410118], [6410119, 7478471], [7478472, 8546824], [8546825, 9615177], [9615178, 10683530], [10683531, 11751883], [11751884, 12820236], [12820237, 13888589], [13888590, 14956942], [14956943, 16025295], [16025296, 17093648], [17093649, 18162001], [18162002, 19230354], [19230355, 20298707], [20298708, 21367064]] SRR13347976 file size 6793013 SRR13347976 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 SRR13347976 SRR13347976_1.fastq SRR13347976_2.fastq Input file: SRR13347976_1.fastq Paired file: SRR13347976_2.fastq trimmed: SRR13347976-trimmed-pair1.fastq, SRR13347976-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 00:32:28 2025 >> started Wed Feb 12 00:32:50 2025 >> done (21.709s) 21367064 read pairs processed; of these: 0 ( 0.00%) short read pairs filtered out after trimming by size control 1 ( 0.00%) empty read pairs filtered out after trimming by size control 21367063 (100.00%) read pairs available; of these: 995847 ( 4.66%) trimmed read pairs available after processing 20371216 (95.34%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 42 1 0.00% 43 0 0.00% 44 0 0.00% 45 0 0.00% 46 1 0.00% 47 0 0.00% 48 2 0.00% 49 7 0.00% 50 5728 0.03% 51 6606 0.03% 52 7279 0.03% 53 7730 0.04% 54 7868 0.04% 55 8126 0.04% 56 8572 0.04% 57 9460 0.04% 58 10830 0.05% 59 11910 0.06% 60 13189 0.06% 61 14923 0.07% 62 16031 0.08% 63 16971 0.08% 64 17322 0.08% 65 17811 0.08% 66 18456 0.09% 67 18507 0.09% 68 19362 0.09% 69 20783 0.10% 70 22370 0.10% 71 24887 0.12% 72 26686 0.12% 73 28349 0.13% 74 29130 0.14% 75 29743 0.14% 76 29613 0.14% 77 29976 0.14% 78 30381 0.14% 79 31582 0.15% 80 33008 0.15% 81 34619 0.16% 82 37276 0.17% 83 38873 0.18% 84 40435 0.19% 85 41535 0.19% 86 41750 0.20% 87 41942 0.20% 88 41677 0.20% 89 42219 0.20% 90 43814 0.21% 91 45710 0.21% 92 47813 0.22% 93 49792 0.23% 94 52254 0.24% 95 53307 0.25% 96 53654 0.25% 97 54574 0.26% 98 54014 0.25% 99 54762 0.26% 100 62541 0.29% 101 64046 0.30% 102 67002 0.31% 103 68919 0.32% 104 70414 0.33% 105 72469 0.34% 106 73727 0.35% 107 73834 0.35% 108 73998 0.35% 109 74486 0.35% 110 75089 0.35% 111 76501 0.36% 112 79037 0.37% 113 80856 0.38% 114 83742 0.39% 115 86531 0.40% 116 87745 0.41% 117 89305 0.42% 118 89085 0.42% 119 89373 0.42% 120 90808 0.42% 121 92447 0.43% 122 95207 0.45% 123 97830 0.46% 124 100994 0.47% 125 103195 0.48% 126 106281 0.50% 127 107754 0.50% 128 109431 0.51% 129 109227 0.51% 130 111702 0.52% 131 112359 0.53% 132 114589 0.54% 133 118992 0.56% 134 121794 0.57% 135 124793 0.58% 136 127784 0.60% 137 130233 0.61% 138 133323 0.62% 139 133977 0.63% 140 134812 0.63% 141 135433 0.63% 142 134079 0.63% 143 139768 0.65% 144 142760 0.67% 145 147304 0.69% 146 149981 0.70% 147 152538 0.71% 148 159891 0.75% 149 828854 3.88% 150 14017003 65.60% 21367063 reads passed initial QC criterion=sequence-density sequence-density=0.55 sequence-density-rank=1 fanout-score=2.33 fanout-score-rank=30 prefix-density=0.56 prefix-fanout=2.3 sequence=CCACACTTGCAG criterion=fanout-score sequence-density=0.01 sequence-density-rank=34 fanout-score=16.10 fanout-score-rank=1 prefix-density=0.03 prefix-fanout=4.0 sequence=ACCTTGTTACGACTTCTCCTTCCTCTAAATGATAAGGTTCAGTGGACTTCTCGCGACGTCGCCGGCGGCGAACCGCCCACGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAGACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACC criterion=sequence-density sequence-density=0.57 sequence-density-rank=1 fanout-score=2.89 fanout-score-rank=25 prefix-density=0.81 prefix-fanout=2.0 sequence=CTGCAAGTGTGG criterion=fanout-score sequence-density=0.10 sequence-density-rank=17 fanout-score=132.65 fanout-score-rank=1 prefix-density=0.62 prefix-fanout=21.9 sequence=GAAGAAGATCTC SRR13347976 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 12 00:33:35 Started mapping on | Feb 12 00:33:35 Finished on | Feb 12 00:36:13 Mapping speed, Million of reads per hour | 486.84 Number of input reads | 21367063 Average input read length | 280 UNIQUE READS: Uniquely mapped reads number | 19750579 Uniquely mapped reads % | 92.43% Average mapped length | 279.67 Number of splices: Total | 18924119 Number of splices: Annotated (sjdb) | 18551504 Number of splices: GT/AG | 18629234 Number of splices: GC/AG | 243884 Number of splices: AT/AC | 16182 Number of splices: Non-canonical | 34819 Mismatch rate per base, % | 0.29% Deletion rate per base | 0.02% Deletion average length | 2.35 Insertion rate per base | 0.01% Insertion average length | 1.83 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 601234 % of reads mapped to multiple loci | 2.81% Number of reads mapped to too many loci | 329434 % of reads mapped to too many loci | 1.54% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.86% % of reads unmapped: other | 0.35% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1017833 1017833 1017833 N_multimapping 601234 601234 601234 N_noFeature 674510 19548439 794642 N_ambiguous 160654 1421 77663 UnstrandedReadsAssigned:18915415 PositiveStrandReadsAssigned:200719 NegativeStrandReadsAssigned:18878274 Dataset is classified negative stranded MeadianReadLen=150 20thPercentileLength=133 echo kmer=129 SRR13347976 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: SRR13347976-trimmed-pair1.fastq SRR13347976-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 21,367,063 reads, 19,333,216 reads pseudoaligned [quant] estimated average fragment length: 168.1 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,109 rounds 52401 SRR13347976.ke.tsv 34699 SRR13347976.se.tsv 87100 total ==> SRR13347976.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1850.9 2387 71.1218 Potri.005G024800.1.v4.1 1035 867.9 414 26.3066 Potri.004G059700.1.v4.1 961 793.905 111 7.7106 Potri.007G009000.2.v4.1 1416 1248.9 0 0 Potri.003G141000.2.v4.1 2943 2775.9 922.254 18.3223 Potri.016G087400.1.v4.1 270 106.233 1158 601.147 Potri.015G069301.1.v4.1 564 396.961 0 0 Potri.010G195200.1.v4.1 1773 1605.9 749.875 25.7516 Potri.012G127500.1.v4.1 977 809.905 5327 362.729 ==> SRR13347976.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 48 Potri.001G233950.v4.1 1 Potri.001G122700.v4.1 345 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 10 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 677 SRR13347976 completed mapping pipeline successfully