Starting /dee2/code/volunteer_pipeline.sh SRR5487670 current disk space = 3050316890112 free memory = 1297513840 SRR5487670 SRAfilesize f672484278f6bc43e5c9dd6cd79d4b0c SRR5487670.sra SRR5487670.sra file validated SRR5487670 is paired end SRR5487670 is conventional basespace SRR5487670 read1 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR5487670_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.60625 34.0 34.0 34.0 33.0 34.0 2 33.64225 34.0 34.0 34.0 33.0 34.0 3 33.35375 34.0 34.0 34.0 33.0 34.0 4 33.56425 34.0 34.0 34.0 33.0 34.0 5 33.613 34.0 34.0 34.0 33.0 34.0 6 37.48925 38.0 38.0 38.0 37.0 38.0 7 37.59075 38.0 38.0 38.0 38.0 38.0 8 37.6145 38.0 38.0 38.0 38.0 38.0 9 37.64225 38.0 38.0 38.0 38.0 38.0 10-14 37.4101 38.0 38.0 38.0 37.2 38.0 15-19 37.55884999999999 38.0 38.0 38.0 37.6 38.0 20-24 37.70935 38.0 38.0 38.0 38.0 38.0 25-29 37.666650000000004 38.0 38.0 38.0 38.0 38.0 30-34 37.66295 38.0 38.0 38.0 38.0 38.0 35-39 37.6423 38.0 38.0 38.0 38.0 38.0 40-44 37.577600000000004 38.0 38.0 38.0 38.0 38.0 45-49 37.56205 38.0 38.0 38.0 38.0 38.0 50-54 37.576100000000004 38.0 38.0 38.0 38.0 38.0 55-59 37.5392 38.0 38.0 38.0 38.0 38.0 60-64 37.561600000000006 38.0 38.0 38.0 38.0 38.0 65-69 37.54594999999999 38.0 38.0 38.0 38.0 38.0 70-74 37.5172 38.0 38.0 38.0 38.0 38.0 75-79 37.33710000000001 38.0 38.0 38.0 37.2 38.0 80-84 37.316700000000004 38.0 38.0 38.0 37.2 38.0 85-89 37.37695 38.0 38.0 38.0 38.0 38.0 90-94 37.35945 38.0 38.0 38.0 37.6 38.0 95-99 37.32215 38.0 38.0 38.0 37.2 38.0 100-104 37.26155 38.0 38.0 38.0 37.0 38.0 105-109 37.1922 38.0 38.0 38.0 36.8 38.0 110-114 37.13935 38.0 38.0 38.0 36.6 38.0 115-119 37.05915 38.0 38.0 38.0 36.0 38.0 120-124 36.958999999999996 38.0 38.0 38.0 36.0 38.0 125-129 36.84075 38.0 38.0 38.0 35.6 38.0 130-134 36.89399999999999 38.0 38.0 38.0 35.6 38.0 135-139 36.799350000000004 38.0 38.0 38.0 35.2 38.0 140-144 36.5656 38.0 38.0 38.0 35.0 38.0 145-149 36.4505 38.0 38.0 38.0 35.0 38.0 150 32.705 38.0 33.0 38.0 21.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 10 1.0 11 0.0 12 2.0 13 3.0 14 1.0 15 0.0 16 0.0 17 0.0 18 2.0 19 3.0 20 0.0 21 2.0 22 4.0 23 2.0 24 2.0 25 9.0 26 7.0 27 8.0 28 7.0 29 10.0 30 22.0 31 25.0 32 30.0 33 34.0 34 71.0 35 100.0 36 246.0 37 3409.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 42.85 11.799999999999999 8.825 36.525 2 23.05 14.924999999999999 33.2 28.825 3 20.277078085642316 21.05793450881612 26.322418136020154 32.34256926952141 4 23.0 26.125 23.925 26.950000000000003 5 23.775 33.1 24.025 19.1 6 19.175 36.325 25.2 19.3 7 14.625 25.25 41.425 18.7 8 18.925 25.45 30.25 25.374999999999996 9 17.175 24.025 33.85 24.95 10-14 19.935 29.970000000000002 26.424999999999997 23.669999999999998 15-19 20.34 27.865000000000002 27.38 24.415 20-24 20.669999999999998 28.09 27.095000000000002 24.145 25-29 20.064999999999998 28.99 27.24 23.705000000000002 30-34 20.215 28.565 27.325 23.895 35-39 20.41 28.095 27.339999999999996 24.154999999999998 40-44 20.89 27.810000000000002 27.565 23.735 45-49 20.419999999999998 28.144999999999996 27.245 24.19 50-54 20.61 28.345 26.805 24.240000000000002 55-59 20.380000000000003 27.83 27.555000000000003 24.235 60-64 20.655 27.765 27.665 23.915 65-69 20.595 27.634999999999998 27.139999999999997 24.63 70-74 20.794999999999998 27.889999999999997 27.16 24.154999999999998 75-79 20.66 28.29 26.365 24.685000000000002 80-84 20.54 27.805000000000003 27.055 24.6 85-89 21.125 27.665 27.045 24.165 90-94 20.835 27.57 27.215 24.38 95-99 20.075000000000003 28.255000000000003 26.950000000000003 24.72 100-104 21.11 28.205000000000002 26.825 23.86 105-109 21.33 27.529999999999998 27.235 23.905 110-114 21.05 27.83 26.99 24.13 115-119 21.245 27.685 26.865 24.205 120-124 21.665 27.665 26.41 24.26 125-129 21.349999999999998 28.215 26.43 24.005000000000003 130-134 21.36 28.07 26.16 24.41 135-139 21.05 27.79 26.384999999999998 24.775 140-144 21.525 27.474999999999998 26.47 24.529999999999998 145-149 21.404999999999998 27.87 26.16 24.565 150 21.175 26.974999999999998 26.950000000000003 24.9 >>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 1.0 19 1.0 20 0.5 21 0.5 22 2.0 23 4.5 24 4.5 25 3.5 26 3.5 27 3.0 28 7.0 29 15.0 30 20.5 31 29.5 32 40.0 33 50.5 34 64.5 35 83.5 36 99.0 37 113.5 38 145.5 39 171.5 40 166.0 41 179.5 42 194.5 43 186.0 44 214.0 45 240.5 46 233.5 47 216.5 48 214.5 49 207.0 50 166.0 51 128.0 52 117.5 53 121.5 54 98.0 55 71.0 56 67.0 57 60.5 58 47.5 59 40.0 60 33.0 61 26.5 62 24.0 63 15.5 64 11.0 65 9.5 66 5.5 67 8.5 68 10.0 69 5.0 70 4.5 71 4.0 72 2.5 73 3.0 74 2.5 75 1.0 76 0.5 77 0.5 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 0.75 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 pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 96.3 #Duplication Level Percentage of deduplicated Percentage of total 1 97.35202492211839 93.75 2 1.8691588785046727 3.5999999999999996 3 0.5192107995846313 1.5 4 0.1557632398753894 0.6 5 0.05192107995846314 0.25 6 0.05192107995846314 0.3 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 warn #Sequence Count Percentage Possible Source GATCGGAAGAGCACACGTCTGAACTCCAGTCACACGATAATCTCGTATGC 6 0.15 TruSeq Adapter, Index 15 (97% over 36bp) GTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACT 6 0.15 No Hit GTTCGATTAGTCTTTCGCCCCTATACCCAAGTCAGACGAACGATTTGCAC 5 0.125 No Hit GTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATT 5 0.125 No Hit >>END_MODULE >>Adapter Content warn #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 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 0.0125 0.0 0.0 0.0 0.0 78-79 0.025 0.0 0.0 0.0 0.0 80-81 0.037500000000000006 0.0 0.0 0.0 0.0 82-83 0.0625 0.0 0.0 0.0 0.0 84-85 0.0875 0.0 0.0 0.0 0.0 86-87 0.1125 0.0 0.0 0.0 0.0 88-89 0.2125 0.0 0.0 0.0 0.0 90-91 0.25 0.0 0.0 0.0 0.0 92-93 0.3125 0.0 0.0 0.0 0.0 94-95 0.4625 0.0 0.0 0.0 0.0 96-97 0.5875 0.0 0.0 0.0 0.0 98-99 0.7124999999999999 0.0 0.0 0.0 0.0 100-101 0.7625 0.0 0.0 0.0 0.0 102-103 0.95 0.0 0.0 0.0 0.0 104-105 1.0625 0.0 0.0 0.0 0.0 106-107 1.225 0.0 0.0 0.0 0.0 108-109 1.375 0.0 0.0 0.0 0.0 110-111 1.55 0.0 0.0 0.0 0.0 112-113 1.775 0.0 0.0 0.0 0.0 114-115 1.9125 0.0 0.0 0.0 0.0 116-117 2.05 0.0 0.0 0.0 0.0 118-119 2.3375 0.0 0.0 0.0 0.0 120-121 2.5875 0.0 0.0 0.0 0.0 122-123 2.825 0.0 0.0 0.0 0.0 124-125 3.1375 0.0 0.0 0.0 0.0 126-127 3.525 0.0 0.0 0.0 0.0 128-129 3.8875 0.0 0.0 0.0 0.0 130-131 4.2 0.0 0.0 0.0 0.0 132-133 4.5625 0.0 0.0 0.0 0.0 134-135 5.0375 0.0 0.0 0.0 0.0 136-137 5.3375 0.0 0.0 0.0 0.0 138 5.55 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR5487670 read2 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR5487670_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.77725 34.0 33.0 34.0 32.0 34.0 2 33.019 34.0 33.0 34.0 32.0 34.0 3 33.149 34.0 33.0 34.0 33.0 34.0 4 33.117 34.0 33.0 34.0 33.0 34.0 5 33.11325 34.0 33.0 34.0 33.0 34.0 6 37.3065 38.0 38.0 38.0 37.0 38.0 7 37.29375 38.0 38.0 38.0 37.0 38.0 8 37.21625 38.0 38.0 38.0 37.0 38.0 9 36.9275 38.0 38.0 38.0 37.0 38.0 10-14 37.2128 38.0 38.0 38.0 37.0 38.0 15-19 37.338 38.0 38.0 38.0 37.4 38.0 20-24 37.358549999999994 38.0 38.0 38.0 37.6 38.0 25-29 37.32165 38.0 38.0 38.0 37.6 38.0 30-34 37.106899999999996 38.0 38.0 38.0 37.6 38.0 35-39 36.1167 38.0 38.0 38.0 36.6 38.0 40-44 36.02335 38.0 38.0 38.0 36.4 38.0 45-49 36.2082 38.0 38.0 38.0 36.2 38.0 50-54 36.900099999999995 38.0 38.0 38.0 37.0 38.0 55-59 37.311 38.0 38.0 38.0 37.8 38.0 60-64 37.33225 38.0 38.0 38.0 38.0 38.0 65-69 37.26375 38.0 38.0 38.0 37.8 38.0 70-74 37.22625 38.0 38.0 38.0 37.4 38.0 75-79 37.133449999999996 38.0 38.0 38.0 37.4 38.0 80-84 36.4759 38.0 38.0 38.0 36.4 38.0 85-89 35.3328 38.0 38.0 38.0 30.8 38.0 90-94 35.536899999999996 38.0 38.0 38.0 34.6 38.0 95-99 36.268350000000005 38.0 38.0 38.0 35.4 38.0 100-104 37.026650000000004 38.0 38.0 38.0 37.0 38.0 105-109 36.89215 38.0 38.0 38.0 36.8 38.0 110-114 36.832800000000006 38.0 38.0 38.0 36.0 38.0 115-119 36.91185 38.0 38.0 38.0 36.4 38.0 120-124 36.767849999999996 38.0 38.0 38.0 36.0 38.0 125-129 36.27345 38.0 38.0 38.0 35.2 38.0 130-134 35.39475 38.0 38.0 38.0 32.6 38.0 135-139 34.6301 38.0 38.0 38.0 28.6 38.0 140-144 33.9615 38.0 38.0 38.0 18.8 38.0 145-149 33.7675 38.0 37.4 38.0 14.6 38.0 150 29.41375 36.0 28.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 1.0 3 2.0 4 0.0 5 1.0 6 3.0 7 1.0 8 0.0 9 4.0 10 2.0 11 1.0 12 2.0 13 5.0 14 4.0 15 2.0 16 3.0 17 5.0 18 5.0 19 4.0 20 7.0 21 19.0 22 22.0 23 24.0 24 28.0 25 30.0 26 28.0 27 19.0 28 25.0 29 22.0 30 30.0 31 38.0 32 52.0 33 52.0 34 79.0 35 117.0 36 288.0 37 3075.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 41.9647355163728 21.68765743073048 11.435768261964736 24.911838790931988 2 28.793189784677015 24.937406109163746 30.27040560841262 15.99899849774662 3 21.136989732031054 27.172551965940393 31.354871024292514 20.33558727773604 4 23.491109441522664 34.43526170798898 23.89181066867017 18.181818181818183 5 25.38808212318478 35.45317976965448 21.98297446169254 17.175763645468205 6 22.336168084042022 36.568284142071036 22.736368184092047 18.3591795897949 7 20.625 21.3 37.75 20.325 8 22.55 24.95 27.275 25.224999999999998 9 22.70093222474175 23.6079617031998 30.259511211892164 23.43159486016629 10-14 24.424309171005206 28.754505406487784 25.42551061273528 21.395674809771727 15-19 24.285 27.415 27.01 21.29 20-24 24.67 27.305 27.095000000000002 20.93 25-29 23.985 27.465 27.644999999999996 20.905 30-34 23.36034630291438 28.35858458750692 27.68409926007953 20.596969849499168 35-39 24.131683834567006 26.766395776178893 27.377193436513274 21.724726952740824 40-44 24.679503814812893 26.77635335028806 27.482223490943063 21.06191934395599 45-49 23.79111248582328 27.368800907310032 27.61624909784514 21.22383750902155 50-54 23.975224091046428 27.50528754154497 27.580823849330244 20.938664518078358 55-59 24.345 26.83 27.900000000000002 20.925 60-64 24.195 27.065 28.005000000000003 20.735 65-69 23.974589835934374 27.29591836734694 27.40096038415366 21.328531412565027 70-74 23.855 27.565 27.334999999999997 21.245 75-79 23.915 27.21 27.505000000000003 21.37 80-84 23.57992073976222 27.979880093486436 27.15171222436744 21.288486942383905 85-89 23.83772734420043 27.9050264688925 27.108339011478588 21.14890717542848 90-94 24.310371799551547 27.392188559211554 27.340042759555715 20.95739688168118 95-99 23.922304493356325 27.837508875139466 27.228927883152448 21.01125874835176 100-104 24.41 27.29 27.38 20.919999999999998 105-109 23.79 27.62 27.865000000000002 20.724999999999998 110-114 23.965 27.665 27.48 20.89 115-119 24.525 27.58 27.275 20.62 120-124 25.34 27.715 26.415 20.53 125-129 24.77697696688675 27.251650622448466 27.1004485661005 20.870923844564285 130-134 24.55978232968838 27.18825401714667 27.6810924585451 20.570871194619848 135-139 24.530467445742904 27.32679465776294 27.55634390651085 20.586393989983307 140-144 25.215022169987712 27.245045141300285 26.769592392756024 20.77034029595598 145-149 25.114249037227214 27.301668806161743 26.8395378690629 20.744544287548138 150 25.45 27.775 27.35 19.425 >>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 0.5 13 0.5 14 0.0 15 0.0 16 0.0 17 0.0 18 0.5 19 1.0 20 1.0 21 3.0 22 5.0 23 5.0 24 6.0 25 5.0 26 7.5 27 14.5 28 19.5 29 22.0 30 28.5 31 37.0 32 33.0 33 30.5 34 57.5 35 87.0 36 97.5 37 118.0 38 139.0 39 149.5 40 169.0 41 191.5 42 199.0 43 207.5 44 211.0 45 226.0 46 242.5 47 233.5 48 221.0 49 199.5 50 164.5 51 135.0 52 114.5 53 106.0 54 89.5 55 66.0 56 61.0 57 52.0 58 38.5 59 34.0 60 39.0 61 33.5 62 25.5 63 21.5 64 10.5 65 2.5 66 4.0 67 7.0 68 5.0 69 6.5 70 5.0 71 2.0 72 2.5 73 1.5 74 1.5 75 1.0 76 1.0 77 0.5 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 0.75 2 0.15 3 0.17500000000000002 4 0.17500000000000002 5 0.15 6 0.05 7 0.0 8 0.0 9 0.775 10-14 0.12 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.6649999999999999 35-39 3.405 40-44 3.665 45-49 3.01 50-54 0.7100000000000001 55-59 0.0 60-64 0.0 65-69 0.04 70-74 0.0 75-79 0.0 80-84 1.59 85-89 4.605 90-94 4.115 95-99 1.41 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.795 130-134 2.605 135-139 4.16 140-144 6.404999999999999 145-149 2.625 150 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 95.89999999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 96.8978102189781 92.925 2 2.3201251303441084 4.45 3 0.5995828988529718 1.725 4 0.026068821689259645 0.1 5 0.1303441084462982 0.625 6 0.0 0.0 7 0.026068821689259645 0.17500000000000002 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 warn #Sequence Count Percentage Possible Source CTTACCAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTT 7 0.17500000000000002 No Hit CATTAATTAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAAT 5 0.125 No Hit CCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAA 5 0.125 No Hit GGCGGGACTACCCGCTGAGTTTAAGCATATCAATAAGCGGAGGAAAAGAA 5 0.125 No Hit GTCTGACATGTGTGCGAGTCAACGGGCGAGTAAACCCGTAAGGCGCAAGG 5 0.125 No Hit GTTGGTTTATGCTCATCCCTACTCATAACCCCAGCACTTAGATATTTTAA 5 0.125 No Hit >>END_MODULE >>Adapter Content warn #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 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 0.0125 0.0 0.0 0.0 0.0 78-79 0.025 0.0 0.0 0.0 0.0 80-81 0.037500000000000006 0.0 0.0 0.0 0.0 82-83 0.0625 0.0 0.0 0.0 0.0 84-85 0.0875 0.0 0.0 0.0 0.0 86-87 0.1125 0.0 0.0 0.0 0.0 88-89 0.2125 0.0 0.0 0.0 0.0 90-91 0.25 0.0 0.0 0.0 0.0 92-93 0.3125 0.0 0.0 0.0 0.0 94-95 0.4375 0.0 0.0 0.0 0.0 96-97 0.5625 0.0 0.0 0.0 0.0 98-99 0.6625000000000001 0.0 0.0 0.0 0.0 100-101 0.7124999999999999 0.0 0.0 0.0 0.0 102-103 0.925 0.0 0.0 0.0 0.0 104-105 1.0625 0.0 0.0 0.0 0.0 106-107 1.25 0.0 0.0 0.0 0.0 108-109 1.4 0.0 0.0 0.0 0.0 110-111 1.575 0.0 0.0 0.0 0.0 112-113 1.8 0.0 0.0 0.0 0.0 114-115 1.9375 0.0 0.0 0.0 0.0 116-117 2.05 0.0 0.0 0.0 0.0 118-119 2.325 0.0 0.0 0.0 0.0 120-121 2.5625 0.0 0.0 0.0 0.0 122-123 2.7750000000000004 0.0 0.0 0.0 0.0 124-125 3.05 0.0 0.0 0.0 0.0 126-127 3.45 0.0 0.0 0.0 0.0 128-129 3.7874999999999996 0.0 0.0 0.0 0.0 130-131 4.0875 0.0 0.0 0.0 0.0 132-133 4.45 0.0 0.0 0.0 0.0 134-135 4.9 0.0 0.0 0.0 0.0 136-137 5.1 0.0 0.0 0.0 0.0 138 5.275 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 952467 spots for SRR5487670.sra Written 952467 spots for SRR5487670.sra Read 952467 spots for SRR5487670.sra Written 952467 spots for SRR5487670.sra Read 952467 spots for SRR5487670.sra Written 952467 spots for SRR5487670.sra Read 952467 spots for SRR5487670.sra Written 952467 spots for SRR5487670.sra Read 952467 spots for SRR5487670.sra Written 952467 spots for SRR5487670.sra Read 952467 spots for SRR5487670.sra Written 952467 spots for SRR5487670.sra Read 952467 spots for SRR5487670.sra Written 952467 spots for SRR5487670.sra Read 952467 spots for SRR5487670.sra Written 952467 spots for SRR5487670.sra Read 952467 spots for SRR5487670.sra Written 952467 spots for SRR5487670.sra Read 952467 spots for SRR5487670.sra Written 952467 spots for SRR5487670.sra Read 952467 spots for SRR5487670.sra Written 952467 spots for SRR5487670.sra Read 952485 spots for SRR5487670.sra Written 952485 spots for SRR5487670.sra Read 952467 spots for SRR5487670.sra Written 952467 spots for SRR5487670.sra Read 952467 spots for SRR5487670.sra Written 952467 spots for SRR5487670.sra Read 952467 spots for SRR5487670.sra Written 952467 spots for SRR5487670.sra Read 952467 spots for SRR5487670.sra Written 952467 spots for SRR5487670.sra Read 952467 spots for SRR5487670.sra Written 952467 spots for SRR5487670.sra Read 952467 spots for SRR5487670.sra Written 952467 spots for SRR5487670.sra Read 952467 spots for SRR5487670.sra Written 952467 spots for SRR5487670.sra Read 952467 spots for SRR5487670.sra Written 952467 spots for SRR5487670.sra SRR ids: ['SRR5487670.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd__ass_c_3 SRR5487670.sra spots: 19049358 blocks: [[1, 952467], [952468, 1904934], [1904935, 2857401], [2857402, 3809868], [3809869, 4762335], [4762336, 5714802], [5714803, 6667269], [6667270, 7619736], [7619737, 8572203], [8572204, 9524670], [9524671, 10477137], [10477138, 11429604], [11429605, 12382071], [12382072, 13334538], [13334539, 14287005], [14287006, 15239472], [15239473, 16191939], [16191940, 17144406], [17144407, 18096873], [18096874, 19049358]] SRR5487670 file size 6396296 SRR5487670 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 SRR5487670 SRR5487670_1.fastq SRR5487670_2.fastq Input file: SRR5487670_1.fastq Paired file: SRR5487670_2.fastq trimmed: SRR5487670-trimmed-pair1.fastq, SRR5487670-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 06:08:44 2025 >> started Wed Feb 12 06:09:04 2025 >> done (19.993s) 19049358 read pairs processed; of these: 12736 ( 0.07%) short read pairs filtered out after trimming by size control 47286 ( 0.25%) empty read pairs filtered out after trimming by size control 18989336 (99.68%) read pairs available; of these: 5264497 (27.72%) trimmed read pairs available after processing 13724839 (72.28%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 5 0.00% 19 3 0.00% 20 7 0.00% 21 6 0.00% 22 6 0.00% 23 8 0.00% 24 6 0.00% 25 9 0.00% 26 6 0.00% 27 10 0.00% 28 10 0.00% 29 6 0.00% 30 16 0.00% 31 9 0.00% 32 8 0.00% 33 6 0.00% 34 7 0.00% 35 15 0.00% 36 13 0.00% 37 19 0.00% 38 27 0.00% 39 21 0.00% 40 21 0.00% 41 23 0.00% 42 30 0.00% 43 33 0.00% 44 39 0.00% 45 25 0.00% 46 46 0.00% 47 45 0.00% 48 50 0.00% 49 56 0.00% 50 61 0.00% 51 71 0.00% 52 91 0.00% 53 89 0.00% 54 88 0.00% 55 92 0.00% 56 123 0.00% 57 117 0.00% 58 142 0.00% 59 165 0.00% 60 185 0.00% 61 202 0.00% 62 228 0.00% 63 262 0.00% 64 286 0.00% 65 359 0.00% 66 426 0.00% 67 580 0.00% 68 959 0.01% 69 2754 0.01% 70 4414 0.02% 71 3098 0.02% 72 1806 0.01% 73 1241 0.01% 74 1169 0.01% 75 1237 0.01% 76 1178 0.01% 77 1235 0.01% 78 1364 0.01% 79 1526 0.01% 80 1638 0.01% 81 1943 0.01% 82 2145 0.01% 83 2554 0.01% 84 3749 0.02% 85 4053 0.02% 86 4294 0.02% 87 4684 0.02% 88 5043 0.03% 89 5257 0.03% 90 5669 0.03% 91 6151 0.03% 92 6850 0.04% 93 7625 0.04% 94 7974 0.04% 95 8884 0.05% 96 9608 0.05% 97 9994 0.05% 98 10196 0.05% 99 10674 0.06% 100 11460 0.06% 101 12004 0.06% 102 13411 0.07% 103 14492 0.08% 104 15858 0.08% 105 16500 0.09% 106 17519 0.09% 107 17947 0.09% 108 18703 0.10% 109 19267 0.10% 110 19957 0.11% 111 21145 0.11% 112 23006 0.12% 113 24779 0.13% 114 26490 0.14% 115 28026 0.15% 116 28949 0.15% 117 29908 0.16% 118 30339 0.16% 119 30618 0.16% 120 31270 0.16% 121 32663 0.17% 122 33835 0.18% 123 35864 0.19% 124 37858 0.20% 125 39830 0.21% 126 41162 0.22% 127 42598 0.22% 128 43647 0.23% 129 44730 0.24% 130 45750 0.24% 131 46483 0.24% 132 48243 0.25% 133 50625 0.27% 134 53012 0.28% 135 55443 0.29% 136 58489 0.31% 137 60454 0.32% 138 64124 0.34% 139 68570 0.36% 140 69056 0.36% 141 73444 0.39% 142 78225 0.41% 143 83167 0.44% 144 92914 0.49% 145 106785 0.56% 146 129455 0.68% 147 172969 0.91% 148 308442 1.62% 149 2649888 13.95% 150 13724839 72.28% 18989336 reads passed initial QC criterion=sequence-density sequence-density=0.25 sequence-density-rank=1 fanout-score=2.30 fanout-score-rank=32 prefix-density=0.49 prefix-fanout=1.2 sequence=CGACGGTCTAAACCCAGCTCACGTTCCCTATTGGTGGGTGAACAATCCAACACTTGGTGAATTCTGCTTCACAATGATAGGAAGAGCCGACATCGAAGGATCAAAAAGCAACGTCGCTATGAACGCTTGGCTGCCACAAGCCAGTTATCCCTGTGGTAACTTTTCTGACACCTCTAGCTTCAAATTCCGAAGGTCTAAAGGATCGATAGGCCACGCTTTCACGGTTCGTATTCGTACTGGAAATCAGAATCAAACGAGCTTTTACCCTTTTGTTCCACACGAGATTTCTGTTCTCGTTGAGCTCATCTTAGGACACCTGCGTTATCTTTTAACAGATGTGCCGCCCCAGCCAAACTCCCCACCTGACAATGTCTTCCGCCCGGATCGGCCGCCGAAGCGGCCTTGGGTCCAAAAAGAGGGGCAGCGCCCCGCCTCCGATTCACGGAATAAGTAAAATAACGTTAAAAGTAGTGGTATTTCACCTTCGCCGAAGCTCCCACTTATCCTACAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=42 fanout-score=98.15 fanout-score-rank=1 prefix-density=0.08 prefix-fanout=6.3 sequence=TGGCAGCAAGGCCACTCTGCCACTTACAATACCCCGTCGCGTATTTAAGTCGTCTGCAAAGGATTCTACCCGCCGCTCGGTGGGAATTGTACTTCAAGGCGGCCCGCGCGGCTCTTTCACCGCGAGGGCTTGGCCAACGGCACGTGCCTCCGGGGCCAAGAGGCCCCTACTGCAGGTCGGCAATCGGACGGCGGGCGCACGCGTCGCATCTAGCCCGGATTCTGACTTAGAGGCGTTCAGTCATAATCCAACGCACGGTAGCTTCGCGCCACTGGCTTTTCAACCAAGCGCGATGACCAATTGTGCGAATCAACGGTTCCTCTCGTACTAGGTTGGATTACTATTGCGACACTGTCATCAGTAGGGTAAAACTAACCTGTCTCACGACGGTCTAA criterion=sequence-density sequence-density=0.37 sequence-density-rank=1 fanout-score=2.58 fanout-score-rank=26 prefix-density=0.38 prefix-fanout=2.5 sequence=TTAGACCGTCGTGAGACAGGTTAGTTTTACCCTACTGATGACAGTGTCGCAATAGTAATCCAACCTAGTACGAGAGGAACCGTTGATTCGCACAATTGGTCATCGCGCTTGGTTGAAAAGCCAGTGGCGCGAAGCTACCGTGCGTTGGATTATGACTGAACGCCTCTAAGTCAGAATCCGGGCTAGATGCGACGCGTGCGCCCGCCGTCCGATTGCCGACCTGCAGTAGGGGCCTCTTGGCCCCGGAGGCACGTGCCGTTGGCCAAGCCCTCGCGGTGAAAGAGCCGCGCGGGCCGCCTTGAAGTACAATTCCCACCGAGCGGCGGGTAGAATCCTTTGCAGACGACTTAAATACGCGACGGGGTATTGTAA criterion=fanout-score sequence-density=0.01 sequence-density-rank=36 fanout-score=17.28 fanout-score-rank=1 prefix-density=0.03 prefix-fanout=3.7 sequence=TGGAGATTGTCTCGTACGGTTAAGAGCCTCCGCCCGTCTCTGGGACTATGGACGGGCACGCTCATATCAGGCTATATTTGGTCCGGGTTATTATCGTCGCGGTTACCGTAATACTTCAGATCAGTTAAGTAGGGCCATATGCCTCGGGAATAAGCTGACGGTGACAAGGTTTCCCCCTAATCGAGACGCTGCAATAACACAGGGGCATACAGTAACCAGGCAAGAGTTCAATCGCTTAGTTTCGTGGCGGGATTTGAGGAAAACTGCGACTGTTCTTTAACCAAACATCCGTGCGATTCGTGCCACTCGTAGACGGCATCTCACAGTCACTGAAGGCTATTAAAGAGTTAGCACCCACCATTGGATGAAGCCCAGGATAAGTGACCCCCCCGGACCTTGGAGTTTCATGCTAATCAAAGAAGAGCTAATCCGACGTAAAGTTGCG SRR5487670 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 12 06:09:55 Started mapping on | Feb 12 06:09:55 Finished on | Feb 12 06:15:53 Mapping speed, Million of reads per hour | 190.95 Number of input reads | 18989336 Average input read length | 294 UNIQUE READS: Uniquely mapped reads number | 14324326 Uniquely mapped reads % | 75.43% Average mapped length | 294.30 Number of splices: Total | 12631232 Number of splices: Annotated (sjdb) | 12417293 Number of splices: GT/AG | 12388819 Number of splices: GC/AG | 204156 Number of splices: AT/AC | 9627 Number of splices: Non-canonical | 28630 Mismatch rate per base, % | 0.21% Deletion rate per base | 0.02% Deletion average length | 2.24 Insertion rate per base | 0.02% Insertion average length | 1.95 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 473987 % of reads mapped to multiple loci | 2.50% Number of reads mapped to too many loci | 2021036 % of reads mapped to too many loci | 10.64% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 10.18% % of reads unmapped: other | 1.25% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 4202877 4202877 4202877 N_multimapping 473987 473987 473987 N_noFeature 651094 14079024 745100 N_ambiguous 232380 1312 80206 UnstrandedReadsAssigned:13440852 PositiveStrandReadsAssigned:243990 NegativeStrandReadsAssigned:13499020 Dataset is classified negative stranded MeadianReadLen=150 20thPercentileLength=150 echo kmer=145 SRR5487670 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: SRR5487670-trimmed-pair1.fastq SRR5487670-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 18,989,336 reads, 15,129,641 reads pseudoaligned [quant] estimated average fragment length: 235.236 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,083 rounds 52401 SRR5487670.ke.tsv 34699 SRR5487670.se.tsv 87100 total ==> SRR5487670.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1783.76 740 24.0614 Potri.005G024800.1.v4.1 1035 800.764 567 41.0682 Potri.004G059700.1.v4.1 961 726.791 16 1.27684 Potri.007G009000.2.v4.1 1416 1181.76 0 0 Potri.003G141000.2.v4.1 2943 2708.76 368 7.87959 Potri.016G087400.1.v4.1 270 78.3577 586 433.753 Potri.015G069301.1.v4.1 564 332.921 0 0 Potri.010G195200.1.v4.1 1773 1538.76 39 1.47001 Potri.012G127500.1.v4.1 977 742.775 2392 186.78 ==> SRR5487670.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 125 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 247 Potri.001G212900.v4.1 50 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 133 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 2 SRR5487670 completed mapping pipeline successfully