Starting /dee2/code/volunteer_pipeline.sh SRR19784172 current disk space = 1551034531840 free memory = 1590724024 SRR19784172 SRAfilesize 9335be8401df6aaab8c93a76442a1a21 SRR19784172.sra SRR19784172.sra file validated SRR19784172 is paired end SRR19784172 is conventional basespace SRR19784172 read1 length is 35-76 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR19784172_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 35-76 %GC 53 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.29825 32.0 32.0 32.0 32.0 32.0 2 31.4525 32.0 32.0 32.0 32.0 32.0 3 31.47475 32.0 32.0 32.0 32.0 32.0 4 31.5165 32.0 32.0 32.0 32.0 32.0 5 31.4895 32.0 32.0 32.0 32.0 32.0 6 34.7735 36.0 36.0 36.0 36.0 36.0 7 34.823 36.0 36.0 36.0 32.0 36.0 8 34.7815 36.0 36.0 36.0 32.0 36.0 9 34.91275 36.0 36.0 36.0 32.0 36.0 10-11 34.674375 36.0 36.0 36.0 32.0 36.0 12-13 34.86625 36.0 36.0 36.0 32.0 36.0 14-15 34.811375 36.0 36.0 36.0 32.0 36.0 16-17 34.82225 36.0 36.0 36.0 32.0 36.0 18-19 34.7355 36.0 36.0 36.0 32.0 36.0 20-21 34.859125 36.0 36.0 36.0 32.0 36.0 22-23 34.72825 36.0 36.0 36.0 32.0 36.0 24-25 34.74075 36.0 36.0 36.0 32.0 36.0 26-27 34.652 36.0 36.0 36.0 32.0 36.0 28-29 34.691874999999996 36.0 36.0 36.0 32.0 36.0 30-31 34.622625 36.0 36.0 36.0 32.0 36.0 32-33 34.5985 36.0 36.0 36.0 32.0 36.0 34-35 34.602374999999995 36.0 36.0 36.0 32.0 36.0 36-37 34.48711855927964 36.0 36.0 36.0 32.0 36.0 38-39 34.65107553776889 36.0 36.0 36.0 32.0 36.0 40-41 34.461230615307656 36.0 36.0 36.0 32.0 36.0 42-43 34.50937968984492 36.0 36.0 36.0 32.0 36.0 44-45 34.55340170085043 36.0 36.0 36.0 32.0 36.0 46-47 34.381315657828914 36.0 36.0 36.0 32.0 36.0 48-49 34.35192596298149 36.0 36.0 36.0 32.0 36.0 50-51 34.558904452226116 36.0 36.0 36.0 32.0 36.0 52-53 34.464482241120564 36.0 36.0 36.0 32.0 36.0 54-55 34.500250125062536 36.0 36.0 36.0 32.0 36.0 56-57 34.40045022511256 36.0 36.0 36.0 32.0 36.0 58-59 34.39607303651826 36.0 36.0 36.0 32.0 36.0 60-61 34.243259227900275 36.0 36.0 36.0 32.0 36.0 62-63 34.29632830544818 36.0 36.0 36.0 32.0 36.0 64-65 34.39856003056502 36.0 36.0 36.0 32.0 36.0 66-67 34.25200226129758 36.0 36.0 36.0 32.0 36.0 68-69 34.2154788121606 36.0 36.0 36.0 32.0 36.0 70-71 34.27096171905001 36.0 36.0 36.0 32.0 36.0 72-73 34.194168439095165 36.0 36.0 36.0 32.0 36.0 74-75 34.11562816818068 36.0 36.0 36.0 32.0 36.0 76 33.72498173849525 36.0 36.0 36.0 27.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 2.0 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 1.0 20 1.0 21 6.0 22 6.0 23 10.0 24 19.0 25 16.0 26 29.0 27 26.0 28 52.0 29 66.0 30 93.0 31 141.0 32 223.0 33 277.0 34 617.0 35 2415.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 38.71935967983992 8.404202101050526 10.755377688844423 42.12106053026513 2 21.846846846846844 11.636636636636636 30.98098098098098 35.53553553553554 3 21.935967983991997 14.732366183091546 19.93496748374187 43.39669834917459 4 29.71485742871436 20.01000500250125 17.808904452226113 32.46623311655828 5 28.4392196098049 24.662331165582792 21.53576788394197 25.362681340670335 6 26.95302687766893 28.585782466716907 21.50213514192414 22.95905551369003 7 21.98599299649825 21.935967983991997 34.61730865432716 21.46073036518259 8 23.261630815407706 22.486243121560783 28.61430715357679 25.63781890945473 9 23.58679339669835 21.5607803901951 29.864932466233117 24.987493746873437 10-11 25.237618809404704 29.214607303651825 21.710855427713856 23.836918459229615 12-13 25.437718859429715 21.99849924962481 24.987493746873437 27.576288144072038 14-15 24.19959979989995 23.82441220610305 25.50025012506253 26.475737868934466 16-17 25.26263131565783 22.911455727863935 25.65032516258129 26.17558779389695 18-19 25.72536268134067 24.77488744372186 23.774387193596798 25.72536268134067 20-21 25.437718859429715 24.224612306153077 24.674837418709355 25.662831415707853 22-23 25.475237618809405 24.562281140570285 24.437218609304654 25.52526263131566 24-25 25.50025012506253 23.12406203101551 24.137068534267133 27.238619309654826 26-27 24.956217162872154 24.055541656242184 24.030522892169127 26.957718288716535 28-29 24.54033771106942 24.315196998123827 24.953095684803 26.19136960600375 30-31 26.43821910955478 22.936468234117058 24.174587293646823 26.450725362681343 32-33 24.574787393696848 24.537268634317158 23.736868434217108 27.151075537768882 34-35 26.40070035017509 23.036518259129565 24.462231115557778 26.100550275137568 36-37 25.153220762976858 23.364602876798 23.652282676672918 27.82989368355222 38-39 25.30015007503752 24.249624812406203 23.74937468734367 26.700850425212607 40-41 25.275137568784395 24.062031015507753 23.06153076538269 27.60130065032516 42-43 25.925462731365684 24.212106053026513 23.32416208104052 26.538269134567283 44-45 25.137568784392194 23.761880940470235 22.973986993496748 28.12656328164082 46-47 25.200100050025014 23.974487243621812 23.6368184092046 27.188594297148573 48-49 25.619524405506883 23.69211514392991 22.340425531914892 28.34793491864831 50-51 24.712356178089045 23.986993496748372 23.024012006003 28.27663831915958 52-53 26.23811905952976 25.175087543771884 21.698349174587296 26.88844422211106 54-55 24.974987493746873 23.874437218609305 22.973986993496748 28.176588294147077 56-57 24.987493746873437 24.674837418709355 22.461230615307652 27.876438219109556 58-59 26.40070035017509 24.712356178089045 22.71135567783892 26.17558779389695 60-61 25.513013013013015 23.86136136136136 24.11161161161161 26.514014014014016 62-63 24.840365594090397 24.37711280831351 23.71353449355202 27.068987104044073 64-65 26.36261120160381 23.94436787370004 22.553564716200977 27.139456208495176 66-67 25.73971915747242 23.28234704112337 22.85606820461384 28.121865596790368 68-69 25.272795685438354 24.256866925874828 23.17822651448639 27.292110874200425 70-71 25.514558232931726 24.17168674698795 22.602911646586346 27.710843373493976 72-73 26.34293621839225 23.67593407975846 23.298528116744244 26.682601585105044 74-75 26.56002115282919 20.967741935483872 23.677948175568485 28.794288736118457 76 29.03579254930606 0.0 34.00292184075968 36.96128560993426 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 24.0 1 13.0 2 1.0 3 0.5 4 1.0 5 1.0 6 1.0 7 1.5 8 2.0 9 4.0 10 8.0 11 11.0 12 12.0 13 7.5 14 4.5 15 3.0 16 0.5 17 1.5 18 2.5 19 3.0 20 4.0 21 6.0 22 4.5 23 1.5 24 2.0 25 2.5 26 3.5 27 4.5 28 5.0 29 6.0 30 8.0 31 13.0 32 18.5 33 21.0 34 27.0 35 43.0 36 53.5 37 62.5 38 86.5 39 112.0 40 124.5 41 136.0 42 148.5 43 171.5 44 199.5 45 187.5 46 174.0 47 179.5 48 185.0 49 172.5 50 152.0 51 140.5 52 135.5 53 138.0 54 134.5 55 128.5 56 126.0 57 123.5 58 121.0 59 132.5 60 133.0 61 124.0 62 121.5 63 111.0 64 102.0 65 112.5 66 112.5 67 101.5 68 95.0 69 90.5 70 85.0 71 71.5 72 70.0 73 66.0 74 59.0 75 58.0 76 47.0 77 33.5 78 22.5 79 15.5 80 13.0 81 9.5 82 12.0 83 14.5 84 8.0 85 3.0 86 2.5 87 3.5 88 3.0 89 1.0 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 0.5 100 1.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.05 2 0.1 3 0.05 4 0.05 5 0.05 6 0.475 7 0.05 8 0.05 9 0.05 10-11 0.05 12-13 0.05 14-15 0.05 16-17 0.05 18-19 0.05 20-21 0.05 22-23 0.05 24-25 0.05 26-27 0.075 28-29 0.0625 30-31 0.05 32-33 0.05 34-35 0.05 36-37 0.01250625312656328 38-39 0.0 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0750375187593797 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 0.012518778167250874 64-65 0.0 66-67 0.0 68-69 0.0 70-71 0.0 72-73 0.0 74-75 0.013218770654329148 76 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 35 2.0 36 0.0 37 0.0 38 0.0 39 0.0 40 0.0 41 0.0 42 0.0 43 0.0 44 0.0 45 0.0 46 0.0 47 0.0 48 0.0 49 0.0 50 0.0 51 0.0 52 0.0 53 0.0 54 0.0 55 0.0 56 0.0 57 0.0 58 0.0 59 1.0 60 2.0 61 0.0 62 2.0 63 1.0 64 3.0 65 0.0 66 2.0 67 0.0 68 1.0 69 1.0 70 2.0 71 1.0 72 15.0 73 55.0 74 259.0 75 915.0 76 2738.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 94.025 #Duplication Level Percentage of deduplicated Percentage of total 1 95.82557830364264 90.10000000000001 2 2.977931401223079 5.6000000000000005 3 0.7976601967561818 2.25 4 0.2658867322520606 1.0 5 0.05317734645041213 0.25 6 0.05317734645041213 0.3 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.026588673225206066 0.5 >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 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 20 0.5 No Hit CCCTTCGTTACGAGCTTGTACACAGGCTTCTAAAGCCACTCGATTAGCTGCTGCACCAGGTGCATTTCCCCAAGG 6 0.15 No Hit CTTCGTTACGAGCTTGTACACAGGCTTCTAAAGCCACTCGATTAGCTGCT 6 0.15 No Hit CCTCGATCGGCCACACCTGCATGCACCTGATCCTTCCACCGTTGCTGACG 5 0.125 No Hit CCCAAGGATGTCCTAAAGTTCCTCCACCAAATTGTAATACAGAATCATCC 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 SRR19784172 read2 length is 59-76 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR19784172_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 59-76 %GC 53 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.56925 32.0 32.0 32.0 32.0 32.0 2 30.47525 32.0 32.0 32.0 32.0 32.0 3 30.377 32.0 32.0 32.0 21.0 32.0 4 30.44825 32.0 32.0 32.0 32.0 32.0 5 30.35775 32.0 32.0 32.0 21.0 32.0 6 33.69875 36.0 36.0 36.0 21.0 36.0 7 33.74275 36.0 36.0 36.0 21.0 36.0 8 33.3585 36.0 36.0 36.0 21.0 36.0 9 33.72825 36.0 36.0 36.0 32.0 36.0 10-11 33.650499999999994 36.0 36.0 36.0 27.0 36.0 12-13 33.64175 36.0 36.0 36.0 27.0 36.0 14-15 33.586749999999995 36.0 36.0 36.0 29.5 36.0 16-17 33.502750000000006 36.0 36.0 36.0 29.5 36.0 18-19 33.332125000000005 36.0 36.0 36.0 21.0 36.0 20-21 33.57875 36.0 36.0 36.0 27.0 36.0 22-23 33.8005 36.0 36.0 36.0 32.0 36.0 24-25 33.564750000000004 36.0 36.0 36.0 32.0 36.0 26-27 33.45425 36.0 36.0 36.0 21.0 36.0 28-29 33.273375 36.0 36.0 36.0 21.0 36.0 30-31 33.525375 36.0 36.0 36.0 27.0 36.0 32-33 33.552625 36.0 36.0 36.0 27.0 36.0 34-35 33.54925 36.0 36.0 36.0 24.0 36.0 36-37 33.5095 36.0 36.0 36.0 24.0 36.0 38-39 33.600375 36.0 36.0 36.0 27.0 36.0 40-41 33.456875 36.0 36.0 36.0 24.0 36.0 42-43 33.261875 36.0 36.0 36.0 17.5 36.0 44-45 33.507000000000005 36.0 36.0 36.0 24.0 36.0 46-47 33.43675 36.0 36.0 36.0 21.0 36.0 48-49 33.38175 36.0 36.0 36.0 21.0 36.0 50-51 33.392250000000004 36.0 36.0 36.0 21.0 36.0 52-53 33.4645 36.0 36.0 36.0 21.0 36.0 54-55 33.36024999999999 36.0 36.0 36.0 17.5 36.0 56-57 33.38175 36.0 36.0 36.0 21.0 36.0 58-59 33.331 36.0 36.0 36.0 21.0 36.0 60-61 33.16812609457093 36.0 36.0 36.0 17.5 36.0 62-63 33.24009661400204 36.0 36.0 36.0 17.5 36.0 64-65 33.269605203698305 36.0 36.0 36.0 21.0 36.0 66-67 33.18856295712973 36.0 36.0 36.0 14.0 36.0 68-69 33.185482319486354 36.0 36.0 36.0 17.5 36.0 70-71 33.09801955377287 36.0 36.0 36.0 17.5 36.0 72-73 33.10933235351207 36.0 36.0 36.0 17.5 36.0 74-75 33.16891346068718 36.0 36.0 36.0 14.0 36.0 76 32.97683823529412 36.0 36.0 36.0 21.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 14 12.0 15 14.0 16 8.0 17 18.0 18 22.0 19 21.0 20 24.0 21 26.0 22 21.0 23 28.0 24 29.0 25 44.0 26 53.0 27 75.0 28 75.0 29 89.0 30 128.0 31 171.0 32 213.0 33 329.0 34 617.0 35 1983.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 33.70110330992979 15.697091273821465 13.11434302908726 37.487462387161486 2 26.3 23.425 24.4 25.874999999999996 3 25.025 25.15 22.475 27.35 4 28.725 27.400000000000002 17.1 26.775 5 30.175 26.55 19.55 23.724999999999998 6 24.675 32.475 18.6 24.25 7 23.175 20.125 30.525000000000002 26.174999999999997 8 26.36977733299975 21.19089316987741 22.016512384288216 30.422817112834625 9 24.525 20.925 25.525 29.025000000000002 10-11 26.840855106888363 27.140892611576444 19.302412801600198 26.715839479934996 12-13 28.4 21.65 22.175 27.775 14-15 26.3 24.6 23.674999999999997 25.424999999999997 16-17 27.70058830892477 23.745149580673424 22.19301539616973 26.361246714232067 18-19 26.5114532482163 23.895356114657655 22.65615220928777 26.937038427838278 20-21 27.306826706676667 23.118279569892472 23.680920230057513 25.893973493373345 22-23 27.0125 23.575 22.537499999999998 26.875 24-25 26.740842605325664 24.190523815476936 22.877859732466558 26.190773846730842 26-27 27.007755816862648 24.405804353264948 22.10407805854391 26.482361771328495 28-29 26.657475874169695 23.950369720516356 22.68454693570623 26.70760746960772 30-31 26.819204801200303 25.11877969492373 22.305576394098527 25.756439109777446 32-33 27.3 23.5875 22.3625 26.75 34-35 27.737499999999997 23.724999999999998 22.2625 26.275 36-37 27.581895473868467 24.20605151287822 22.36809202300575 25.84396099024756 38-39 26.989489489489486 24.84984984984985 21.634134134134133 26.526526526526528 40-41 28.24427480916031 24.0020022525341 22.462770616944063 25.29095232136153 42-43 25.85818090704084 24.417439238286143 22.688549235780506 27.035830618892508 44-45 27.4990616789691 23.533091455023143 22.106843488052043 26.86100337795571 46-47 27.55344418052256 24.915614451806476 20.702587823477934 26.828353544193025 48-49 27.298922575795544 23.703332498120773 21.849160611375595 27.148584314708092 50-51 27.102102102102105 24.36186186186186 22.15965965965966 26.376376376376378 52-53 28.028503562945367 24.090511313914238 21.152644080510065 26.728341042630326 54-55 27.2625 24.2625 22.400000000000002 26.075 56-57 27.169292323080768 25.756439109777446 21.380345086271568 25.693923480870218 58-59 27.987972939113003 23.903783512904035 22.62590829366074 25.482335254322226 60-61 26.84883429430935 25.3823013286538 21.809977437954377 25.958886939082475 62-63 27.96143250688705 24.129727022289003 21.550212872526924 26.35862759829702 64-65 28.32811521603006 23.318722604884158 21.878522229179712 26.474639949906077 66-67 27.502819195589524 24.057135697281044 22.340558827214636 26.099486279914796 68-69 26.598144898470792 24.868388067184757 22.474304336926547 26.059162697417896 70-71 26.544450025113008 24.39728779507785 22.13711702661979 26.92114515318935 72-73 26.649842271293377 23.43217665615142 22.410094637223974 27.50788643533123 74-75 27.183953549749273 22.565320665083135 22.76326207442597 27.487463710741622 76 29.852941176470587 0.0 31.25 38.89705882352941 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 17.0 1 15.5 2 8.0 3 2.0 4 2.0 5 1.5 6 2.5 7 3.5 8 3.0 9 5.5 10 5.5 11 6.5 12 10.0 13 6.5 14 4.5 15 4.5 16 2.0 17 1.0 18 2.0 19 2.0 20 0.5 21 0.5 22 2.5 23 3.5 24 3.0 25 4.5 26 5.0 27 4.0 28 5.0 29 6.5 30 7.0 31 14.0 32 25.0 33 27.0 34 26.5 35 42.0 36 65.0 37 80.0 38 95.0 39 103.0 40 104.0 41 122.0 42 134.5 43 153.5 44 173.5 45 162.0 46 155.5 47 165.0 48 149.0 49 129.5 50 132.5 51 136.5 52 133.5 53 133.5 54 138.0 55 128.5 56 134.5 57 141.5 58 132.5 59 131.0 60 133.0 61 135.0 62 138.0 63 127.5 64 110.5 65 110.0 66 108.5 67 102.5 68 113.5 69 106.5 70 90.5 71 90.0 72 88.5 73 78.0 74 60.5 75 52.5 76 47.0 77 42.0 78 32.0 79 21.5 80 18.0 81 12.0 82 8.5 83 8.0 84 6.0 85 6.5 86 5.0 87 1.5 88 1.0 89 1.5 90 1.5 91 2.0 92 3.0 93 2.0 94 0.5 95 0.0 96 0.0 97 0.5 98 1.5 99 2.5 100 3.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.3 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.075 9 0.0 10-11 0.0125 12-13 0.0 14-15 0.0 16-17 0.13749999999999998 18-19 0.13749999999999998 20-21 0.025 22-23 0.0 24-25 0.0125 26-27 0.075 28-29 0.2625 30-31 0.025 32-33 0.0 34-35 0.0 36-37 0.025 38-39 0.1 40-41 0.11249999999999999 42-43 0.22499999999999998 44-45 0.08750000000000001 46-47 0.0125 48-49 0.22499999999999998 50-51 0.1 52-53 0.0125 54-55 0.0 56-57 0.025 58-59 0.22499999999999998 60-61 0.22511255627813906 62-63 0.087576629550857 64-65 0.012521913348359628 66-67 0.0 68-69 0.012532898859506203 70-71 0.17548257708698922 72-73 0.20148595894723584 74-75 0.013194352816994326 76 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 59 1.0 60 2.0 61 0.0 62 1.0 63 1.0 64 4.0 65 0.0 66 1.0 67 0.0 68 1.0 69 0.0 70 0.0 71 9.0 72 19.0 73 47.0 74 249.0 75 945.0 76 2720.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 95.125 #Duplication Level Percentage of deduplicated Percentage of total 1 96.1892247043364 91.5 2 2.864651773981603 5.45 3 0.683311432325887 1.95 4 0.18396846254927726 0.7000000000000001 5 0.052562417871222074 0.25 6 0.026281208935611037 0.15 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 CCTCAACCTGGGGTTCCGCCCGAAGAAGCAGGGGCTGCAGTAGCTGCCGA 6 0.15 No Hit CCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGCAA 5 0.125 No Hit CTTACCAGGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTT 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 1412494 spots for SRR19784172.sra Written 1412494 spots for SRR19784172.sra Read 1412494 spots for SRR19784172.sra Written 1412494 spots for SRR19784172.sra Read 1412494 spots for SRR19784172.sra Written 1412494 spots for SRR19784172.sra Read 1412494 spots for SRR19784172.sra Written 1412494 spots for SRR19784172.sra Read 1412494 spots for SRR19784172.sra Written 1412494 spots for SRR19784172.sra Read 1412494 spots for SRR19784172.sra Written 1412494 spots for SRR19784172.sra Read 1412494 spots for SRR19784172.sra Written 1412494 spots for SRR19784172.sra Read 1412494 spots for SRR19784172.sra Written 1412494 spots for SRR19784172.sra Read 1412494 spots for SRR19784172.sra Written 1412494 spots for SRR19784172.sra Read 1412494 spots for SRR19784172.sra Written 1412494 spots for SRR19784172.sra Read 1412511 spots for SRR19784172.sra Written 1412511 spots for SRR19784172.sra Read 1412494 spots for SRR19784172.sra Written 1412494 spots for SRR19784172.sra Read 1412494 spots for SRR19784172.sra Written 1412494 spots for SRR19784172.sra Read 1412494 spots for SRR19784172.sra Written 1412494 spots for SRR19784172.sra Read 1412494 spots for SRR19784172.sra Written 1412494 spots for SRR19784172.sra Read 1412494 spots for SRR19784172.sra Written 1412494 spots for SRR19784172.sra Read 1412494 spots for SRR19784172.sra Written 1412494 spots for SRR19784172.sra Read 1412494 spots for SRR19784172.sra Written 1412494 spots for SRR19784172.sra Read 1412494 spots for SRR19784172.sra Written 1412494 spots for SRR19784172.sra Read 1412494 spots for SRR19784172.sra Written 1412494 spots for SRR19784172.sra SRR ids: ['SRR19784172.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_tuavdmmj SRR19784172.sra spots: 28249897 blocks: [[1, 1412494], [1412495, 2824988], [2824989, 4237482], [4237483, 5649976], [5649977, 7062470], [7062471, 8474964], [8474965, 9887458], [9887459, 11299952], [11299953, 12712446], [12712447, 14124940], [14124941, 15537434], [15537435, 16949928], [16949929, 18362422], [18362423, 19774916], [19774917, 21187410], [21187411, 22599904], [22599905, 24012398], [24012399, 25424892], [25424893, 26837386], [26837387, 28249897]] SRR19784172 file size 5382088 SRR19784172 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 SRR19784172 SRR19784172_1.fastq SRR19784172_2.fastq Input file: SRR19784172_1.fastq Paired file: SRR19784172_2.fastq trimmed: SRR19784172-trimmed-pair1.fastq, SRR19784172-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- number of concurrent threads (-t): 20 Fri Dec 6 13:16:34 2024 >> started Fri Dec 6 13:17:19 2024 >> done (44.530s) 28249897 read pairs processed; of these: 5 ( 0.00%) short read pairs filtered out after trimming by size control 44624 ( 0.16%) empty read pairs filtered out after trimming by size control 28205268 (99.84%) read pairs available; of these: 40736 ( 0.14%) trimmed read pairs available after processing 28164532 (99.86%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 19 1 0.00% 20 6 0.00% 21 6 0.00% 22 30 0.00% 23 43 0.00% 24 57 0.00% 25 88 0.00% 26 108 0.00% 27 135 0.00% 28 143 0.00% 29 189 0.00% 30 234 0.00% 31 708 0.00% 32 813 0.00% 33 357 0.00% 34 1102 0.00% 35 664 0.00% 36 665 0.00% 37 781 0.00% 38 861 0.00% 39 939 0.00% 40 1061 0.00% 41 1189 0.00% 42 1261 0.00% 43 1334 0.00% 44 1463 0.01% 45 1464 0.01% 46 1629 0.01% 47 1734 0.01% 48 1870 0.01% 49 2020 0.01% 50 2182 0.01% 51 2533 0.01% 52 2771 0.01% 53 2918 0.01% 54 3276 0.01% 55 3575 0.01% 56 3655 0.01% 57 3904 0.01% 58 4370 0.02% 59 4577 0.02% 60 5081 0.02% 61 5596 0.02% 62 6137 0.02% 63 6962 0.02% 64 7552 0.03% 65 8159 0.03% 66 8733 0.03% 67 9590 0.03% 68 10206 0.04% 69 11441 0.04% 70 15867 0.06% 71 18104 0.06% 72 35934 0.13% 73 220417 0.78% 74 1774008 6.29% 75 12383735 43.91% 76 13621030 48.29% 28205268 reads passed initial QC criterion=sequence-density sequence-density=0.45 sequence-density-rank=1 fanout-score=1.98 fanout-score-rank=33 prefix-density=0.43 prefix-fanout=2.0 sequence=TTCAAATGTACA criterion=fanout-score sequence-density=0.11 sequence-density-rank=28 fanout-score=91.53 fanout-score-rank=1 prefix-density=0.90 prefix-fanout=11.6 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.44 sequence-density-rank=1 fanout-score=3.52 fanout-score-rank=18 prefix-density=0.59 prefix-fanout=2.6 sequence=CTCGCCATGTTCTCCATGTTCGGG criterion=fanout-score sequence-density=0.18 sequence-density-rank=14 fanout-score=119.16 fanout-score-rank=1 prefix-density=1.21 prefix-fanout=17.6 sequence=GCCGCCGCCGCC SRR19784172 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 06 13:17:49 Started mapping on | Dec 06 13:17:50 Finished on | Dec 06 13:20:04 Mapping speed, Million of reads per hour | 757.75 Number of input reads | 28205268 Average input read length | 150 UNIQUE READS: Uniquely mapped reads number | 20979295 Uniquely mapped reads % | 74.38% Average mapped length | 150.47 Number of splices: Total | 7540202 Number of splices: Annotated (sjdb) | 7206826 Number of splices: GT/AG | 7429965 Number of splices: GC/AG | 98809 Number of splices: AT/AC | 1869 Number of splices: Non-canonical | 9559 Mismatch rate per base, % | 0.40% Deletion rate per base | 0.01% Deletion average length | 1.86 Insertion rate per base | 0.00% Insertion average length | 1.87 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 4213829 % of reads mapped to multiple loci | 14.94% Number of reads mapped to too many loci | 595813 % of reads mapped to too many loci | 2.11% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.79% % of reads unmapped: other | 4.78% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 3012148 3012148 3012148 N_multimapping 4213829 4213829 4213829 N_noFeature 735428 20071424 1299852 N_ambiguous 452347 2956 115676 UnstrandedReadsAssigned:19791520 PositiveStrandReadsAssigned:904915 NegativeStrandReadsAssigned:19563767 Dataset is classified negative stranded MeadianReadLen=76 20thPercentileLength=75 echo kmer=71 SRR19784172 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: SRR19784172-trimmed-pair1.fastq SRR19784172-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 28,205,268 reads, 23,217,012 reads pseudoaligned [quant] estimated average fragment length: 159.318 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,129 rounds 52973 SRR19784172.ke.tsv 35125 SRR19784172.se.tsv 88098 total ==> SRR19784172.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 777.75 0 0 PNS24247 1044 885.682 31.3434 2.00551 PNS24249 1928 1769.68 171.576 5.49435 PNS24246 1044 885.682 31.3434 2.00551 PNS24248 1044 885.682 31.3434 2.00551 PNS24244 1471 1312.68 21.3941 0.923613 PNS24243 293 139.99 0 0 KQK14069 1603 1444.68 5154.63 202.2 KQK14071 474 316.485 803.908 143.949 ==> SRR19784172.se.tsv <== BRADI_1g14170v3 6209 BRADI_1g53295v3 9 BRADI_1g59795v3 653 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 154 BRADI_1g74790v3 135 BRADI_1g09890v3 0 BRADI_1g77505v3 244 BRADI_1g48960v3 0 SRR19784172 completed mapping pipeline successfully