Starting /dee2/code/volunteer_pipeline.sh SRR11389783 current disk space = 1545880260608 free memory = 1602972680 SRR11389783 SRAfilesize a62e2acb09ac5def6f8310b1cf430a80 SRR11389783.sra SRR11389783.sra file validated SRR11389783 is paired end SRR11389783 is conventional basespace SRR11389783 read1 length is 35-76 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11389783_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 48 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 28.864 32.0 32.0 32.0 14.0 32.0 2 28.857 32.0 32.0 32.0 14.0 32.0 3 28.85 32.0 32.0 32.0 14.0 32.0 4 29.027 32.0 32.0 32.0 14.0 32.0 5 29.01625 32.0 32.0 32.0 14.0 32.0 6 31.85725 36.0 36.0 36.0 14.0 36.0 7 31.798 36.0 36.0 36.0 14.0 36.0 8 31.6365 36.0 36.0 36.0 14.0 36.0 9 31.82275 36.0 36.0 36.0 14.0 36.0 10-11 31.788249999999998 36.0 36.0 36.0 14.0 36.0 12-13 31.83025 36.0 36.0 36.0 14.0 36.0 14-15 31.725125 36.0 36.0 36.0 14.0 36.0 16-17 31.799 36.0 36.0 36.0 14.0 36.0 18-19 31.8365 36.0 36.0 36.0 14.0 36.0 20-21 31.75025 36.0 36.0 36.0 14.0 36.0 22-23 31.5045 36.0 36.0 36.0 14.0 36.0 24-25 31.345625 36.0 36.0 36.0 14.0 36.0 26-27 31.29625 36.0 36.0 36.0 14.0 36.0 28-29 31.285249999999998 36.0 36.0 36.0 14.0 36.0 30-31 31.15375 36.0 32.0 36.0 14.0 36.0 32-33 31.084625 36.0 32.0 36.0 14.0 36.0 34-35 31.020375 36.0 32.0 36.0 14.0 36.0 36-37 33.44911443375845 36.0 36.0 36.0 24.0 36.0 38-39 33.37239320721379 36.0 36.0 36.0 21.0 36.0 40-41 33.35501664525969 36.0 36.0 36.0 24.0 36.0 42-43 33.37826797385621 36.0 36.0 36.0 24.0 36.0 44-45 33.12976579520697 36.0 36.0 36.0 14.0 36.0 46-47 33.00190631808279 36.0 36.0 36.0 14.0 36.0 48-49 32.84436274509804 36.0 36.0 36.0 14.0 36.0 50-51 32.82230392156863 36.0 36.0 36.0 14.0 36.0 52-53 32.93872549019608 36.0 36.0 36.0 14.0 36.0 54-55 32.5796568627451 36.0 34.0 36.0 14.0 36.0 56-57 32.48576956585473 36.0 34.0 36.0 14.0 36.0 58-59 32.4633514986376 36.0 32.0 36.0 14.0 36.0 60-61 32.224386920980926 36.0 32.0 36.0 14.0 36.0 62-63 32.112125340599455 36.0 32.0 36.0 14.0 36.0 64-65 32.01348773841962 36.0 32.0 36.0 14.0 36.0 66-67 31.79209809264305 36.0 32.0 36.0 14.0 36.0 68-69 31.7681929681112 36.0 32.0 36.0 14.0 36.0 70-71 31.533229374790064 36.0 32.0 36.0 14.0 36.0 72-73 31.426900065357554 36.0 32.0 36.0 14.0 36.0 74-75 31.346143205513776 36.0 32.0 36.0 14.0 36.0 76 30.571951219512194 36.0 32.0 36.0 14.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 315.0 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 2.0 21 4.0 22 4.0 23 17.0 24 20.0 25 26.0 26 45.0 27 58.0 28 93.0 29 157.0 30 202.0 31 299.0 32 425.0 33 665.0 34 1004.0 35 664.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 37.93758480325645 14.599728629579376 11.777476255088196 35.68521031207598 2 25.210312075983715 14.518317503392131 34.626865671641795 25.64450474898236 3 22.686567164179106 21.92672998643148 22.578018995929444 32.808683853459975 4 28.113975576662142 27.516960651289008 19.43012211668928 24.938941655359564 5 24.694708276797826 32.3202170963365 22.116689280868385 20.868385345997286 6 22.997556339940267 31.98479500407277 26.174314417594353 18.843334238392615 7 16.472184531886025 25.80732700135685 38.833107191316145 18.887381275440976 8 17.530529172320218 23.962008141112616 32.83582089552239 25.671641791044774 9 19.755766621438266 22.36092265943012 32.18453188602442 25.698778833107188 10-11 20.814111261872455 32.957937584803254 23.731343283582092 22.496607869742196 12-13 22.347354138398913 24.30122116689281 26.852103120759836 26.499321573948443 14-15 21.940298507462686 27.530529172320218 26.72998643147897 23.79918588873813 16-17 22.795115332428765 26.526458616010856 25.65807327001357 25.020352781546812 18-19 21.329715061058344 26.933514246947084 26.10583446404342 25.63093622795115 20-21 22.645861601085482 26.838534599728632 26.90637720488467 23.609226594301223 22-23 23.05291723202171 25.712347354138398 27.435549525101766 23.79918588873813 24-25 22.564450474898237 26.36363636363636 25.63093622795115 25.440976933514246 26-27 22.293080054274085 26.933514246947084 26.146540027137043 24.62686567164179 28-29 23.351424694708275 26.74355495251018 25.318860244233377 24.586160108548167 30-31 21.967435549525103 27.557666214382632 26.024423337856174 24.45047489823609 32-33 22.645861601085482 26.485753052917232 25.617367706919946 25.25101763907734 34-35 23.039348710990502 27.28629579375848 25.48168249660787 24.192672998643147 36-37 23.499864241107794 26.255769752918816 25.033939723051862 25.21042628292153 38-39 22.923181509177432 26.52617267165194 25.438477226376616 25.112168592794013 40-41 22.937653144568472 25.769126054995915 25.95970596242853 25.333514838007076 42-43 22.766884531590414 25.054466230936818 26.15740740740741 26.02124183006536 44-45 22.80773420479303 24.959150326797385 26.96078431372549 25.272331154684096 46-47 24.27832244008715 24.7140522875817 25.626361655773422 25.381263616557735 48-49 22.07244008714597 25.531045751633986 26.130174291938996 26.266339869281047 50-51 23.311546840958606 24.959150326797385 26.51143790849673 25.217864923747275 52-53 24.29193899782135 24.836601307189543 25.013616557734203 25.857843137254903 54-55 22.113289760348582 26.048474945533766 25.748910675381264 26.08932461873638 56-57 22.02097235462345 25.779654092332834 25.820509328612285 26.37886422443143 58-59 22.79291553133515 26.389645776566756 25.626702997275203 25.190735694822884 60-61 23.37874659400545 25.463215258855588 26.70299727520436 24.455040871934607 62-63 22.602179836512263 25.408719346049047 26.67574931880109 25.313351498637605 64-65 23.487738419618527 24.44141689373297 26.362397820163487 25.708446866485012 66-67 23.35149863760218 24.509536784741144 25.66757493188011 26.471389645776565 68-69 22.581084764240938 24.011992368492777 26.24693376941946 27.159989097846825 70-71 23.25835037491479 24.608043626448534 25.835037491479206 26.298568507157466 72-73 24.11668036154478 24.82881402355519 25.924404272801972 25.130101342098055 74-75 23.40610091079948 22.741072719387017 27.81552696255602 26.037299407257482 76 27.682926829268297 0.0 37.642276422764226 34.67479674796748 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 331.0 1 166.5 2 2.0 3 2.0 4 1.0 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 1.0 17 2.5 18 8.0 19 14.0 20 22.5 21 33.0 22 34.0 23 24.5 24 17.0 25 18.5 26 24.5 27 41.0 28 47.0 29 41.5 30 42.5 31 56.0 32 62.0 33 53.0 34 58.0 35 78.5 36 98.0 37 113.5 38 121.5 39 134.5 40 148.0 41 150.0 42 149.0 43 152.5 44 169.5 45 168.0 46 161.0 47 161.0 48 159.0 49 152.5 50 144.5 51 147.5 52 135.5 53 118.5 54 109.5 55 102.5 56 93.0 57 94.5 58 101.0 59 92.5 60 89.0 61 84.0 62 81.0 63 84.5 64 77.0 65 61.0 66 60.0 67 64.5 68 61.0 69 50.5 70 42.5 71 42.5 72 34.5 73 25.0 74 27.5 75 31.5 76 22.0 77 17.0 78 18.0 79 14.5 80 9.5 81 5.5 82 4.0 83 3.0 84 2.5 85 1.5 86 1.5 87 2.0 88 2.0 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 0.0 100 0.0 >>END_MODULE >>Per base N content warn #Base N-Count 1 7.875 2 7.875 3 7.875 4 7.875 5 7.875 6 7.925 7 7.875 8 7.875 9 7.875 10-11 7.875 12-13 7.875 14-15 7.875 16-17 7.875 18-19 7.875 20-21 7.875 22-23 7.875 24-25 7.875 26-27 7.875 28-29 7.875 30-31 7.875 32-33 7.875 34-35 7.875 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 35 315.0 36 4.0 37 0.0 38 7.0 39 0.0 40 2.0 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 1.0 57 1.0 58 0.0 59 0.0 60 0.0 61 0.0 62 0.0 63 0.0 64 0.0 65 0.0 66 0.0 67 1.0 68 0.0 69 0.0 70 3.0 71 8.0 72 14.0 73 63.0 74 245.0 75 876.0 76 2460.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 87.1 #Duplication Level Percentage of deduplicated Percentage of total 1 96.87141216991964 84.375 2 2.009184845005741 3.5000000000000004 3 0.6027554535017221 1.575 4 0.2583237657864524 0.8999999999999999 5 0.1148105625717566 0.5 6 0.02870264064293915 0.15 7 0.02870264064293915 0.17500000000000002 8 0.0 0.0 9 0.0 0.0 >10 0.0574052812858783 0.95 >50 0.0 0.0 >100 0.02870264064293915 7.875 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences fail #Sequence Count Percentage Possible Source NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 315 7.875 No Hit GCCGAGTTTAATTGCAGTCAATTAGAAGAATAAAGAAGAATTACTGCATT 28 0.7000000000000001 No Hit GTCAATTAGAAGAATAAAGAAGAATTACTGCATTTCGTAACTTATTTTTT 10 0.25 No Hit CCGAGTTTAATTGCAGTCAATTAGAAGAATAAAGAAGAATTACTGCATTT 7 0.17500000000000002 No Hit GTTCAGGACTCCATTTGCAAGCTGCTCGGATAATTTCATTACCTTCACGA 6 0.15 No Hit AGAAGAATTACTGCATTTCGTAACTTATTTTTTCTCTTTTTATTTTGTTT 5 0.125 No Hit GTTTAATTGCAGTCAATTAGAAGAATAAAGAAGAATTACTGCATTTCGTA 5 0.125 No Hit GGCTAGTTCAGGACTCCATTTGCAAGCTGCTCGGATAATTTCATTACCTTCACGAGCAAGATCGCGCCCTTCGTT 5 0.125 No Hit GCGGCTAGTTCAGGACTCCATTTGCAAGCTGCTCGGATAATTTCATTACC 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 0.025 0.0 0.0 0.0 0.0 12 0.025 0.0 0.0 0.0 0.0 13 0.025 0.0 0.0 0.0 0.0 14 0.025 0.0 0.0 0.0 0.0 15 0.025 0.0 0.0 0.0 0.0 16 0.025 0.0 0.0 0.0 0.0 17 0.025 0.0 0.0 0.0 0.0 18 0.025 0.0 0.0 0.0 0.0 19 0.025 0.0 0.0 0.0 0.0 20 0.025 0.0 0.0 0.0 0.0 21 0.025 0.0 0.0 0.0 0.0 22 0.025 0.0 0.0 0.0 0.0 23 0.025 0.0 0.0 0.0 0.0 24 0.025 0.0 0.0 0.0 0.0 25 0.025 0.0 0.0 0.0 0.0 26 0.025 0.0 0.0 0.0 0.0 27 0.1 0.0 0.0 0.0 0.0 28 0.1 0.0 0.0 0.0 0.0 29 0.15 0.0 0.0 0.0 0.0 30 0.175 0.0 0.0 0.0 0.0 31 0.175 0.0 0.0 0.0 0.0 32 0.175 0.0 0.0 0.0 0.0 33 0.175 0.0 0.0 0.0 0.0 34 0.175 0.0 0.0 0.0 0.0 35 0.175 0.0 0.0 0.0 0.0 36 0.175 0.0 0.0 0.0 0.0 37 0.175 0.0 0.0 0.0 0.0 38 0.175 0.0 0.0 0.0 0.0 39 0.2 0.0 0.0 0.0 0.0 40 0.2 0.0 0.0 0.0 0.0 41 0.2 0.0 0.0 0.0 0.0 42 0.2 0.0 0.0 0.0 0.0 43 0.2 0.0 0.0 0.0 0.0 44 0.2 0.0 0.0 0.0 0.0 45 0.2 0.0 0.0 0.0 0.0 46 0.2 0.0 0.0 0.0 0.0 47 0.2 0.0 0.0 0.0 0.0 48 0.2 0.0 0.0 0.0 0.0 49 0.2 0.0 0.0 0.0 0.0 50 0.2 0.0 0.0 0.0 0.0 51 0.2 0.0 0.0 0.0 0.0 52 0.2 0.0 0.0 0.0 0.0 53 0.2 0.0 0.0 0.0 0.0 54 0.2 0.0 0.0 0.0 0.0 55 0.2 0.0 0.0 0.0 0.0 56 0.2 0.0 0.0 0.0 0.0 57 0.2 0.0 0.0 0.0 0.0 58 0.2 0.0 0.0 0.0 0.0 59 0.2 0.0 0.0 0.0 0.0 60 0.2 0.0 0.0 0.0 0.0 61 0.2 0.0 0.0 0.0 0.0 62 0.2 0.0 0.0 0.0 0.0 63 0.2 0.0 0.0 0.0 0.0 64 0.2 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR11389783 read2 length is 35-76 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11389783_2.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 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 28.494 32.0 32.0 32.0 14.0 32.0 2 28.2475 32.0 32.0 32.0 14.0 32.0 3 28.19225 32.0 32.0 32.0 14.0 32.0 4 28.11175 32.0 32.0 32.0 14.0 32.0 5 28.182 32.0 32.0 32.0 14.0 32.0 6 31.20125 36.0 36.0 36.0 14.0 36.0 7 31.20925 36.0 32.0 36.0 14.0 36.0 8 31.0555 36.0 32.0 36.0 14.0 36.0 9 31.0085 36.0 32.0 36.0 14.0 36.0 10-11 31.02175 36.0 34.0 36.0 14.0 36.0 12-13 31.088375 36.0 34.0 36.0 14.0 36.0 14-15 30.89975 36.0 32.0 36.0 14.0 36.0 16-17 31.00875 36.0 32.0 36.0 14.0 36.0 18-19 30.852 36.0 32.0 36.0 14.0 36.0 20-21 30.93475 36.0 32.0 36.0 14.0 36.0 22-23 30.704375 36.0 32.0 36.0 14.0 36.0 24-25 30.61825 36.0 32.0 36.0 14.0 36.0 26-27 30.384999999999998 36.0 32.0 36.0 14.0 36.0 28-29 30.598 36.0 32.0 36.0 14.0 36.0 30-31 30.462375 36.0 32.0 36.0 14.0 36.0 32-33 30.354625 36.0 32.0 36.0 14.0 36.0 34-35 30.3645 36.0 32.0 36.0 14.0 36.0 36-37 32.565652445085036 36.0 36.0 36.0 14.0 36.0 38-39 32.54889901511443 36.0 36.0 36.0 14.0 36.0 40-41 32.50673520169364 36.0 36.0 36.0 14.0 36.0 42-43 32.20969055374593 36.0 34.0 36.0 14.0 36.0 44-45 32.236156351791536 36.0 34.0 36.0 14.0 36.0 46-47 32.16164495114006 36.0 34.0 36.0 14.0 36.0 48-49 32.0971769815418 36.0 32.0 36.0 14.0 36.0 50-51 31.839712269272532 36.0 32.0 36.0 14.0 36.0 52-53 31.818403908794785 36.0 32.0 36.0 14.0 36.0 54-55 31.731813246471226 36.0 32.0 36.0 14.0 36.0 56-57 31.43696184718177 36.0 32.0 36.0 14.0 36.0 58-59 31.402227050516025 36.0 32.0 36.0 14.0 36.0 60-61 31.305540467137426 36.0 32.0 36.0 14.0 36.0 62-63 31.205594785442692 36.0 32.0 36.0 14.0 36.0 64-65 30.987235198261814 36.0 32.0 36.0 14.0 36.0 66-67 31.045084193373167 36.0 32.0 36.0 14.0 36.0 68-69 30.73192934782609 36.0 29.5 36.0 14.0 36.0 70-71 30.703644718638778 36.0 29.5 36.0 14.0 36.0 72-73 30.589694706852555 36.0 27.0 36.0 14.0 36.0 74-75 30.54052231642937 36.0 27.0 36.0 14.0 36.0 76 29.332925336597306 32.0 27.0 36.0 14.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 310.0 3 0.0 4 1.0 5 3.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 1.0 14 2.0 15 10.0 16 14.0 17 11.0 18 7.0 19 13.0 20 12.0 21 17.0 22 25.0 23 30.0 24 41.0 25 86.0 26 71.0 27 91.0 28 134.0 29 164.0 30 224.0 31 299.0 32 413.0 33 557.0 34 861.0 35 603.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 35.9349593495935 21.21951219512195 10.948509485094851 31.8970189701897 2 30.542005420054203 23.089430894308943 28.292682926829265 18.07588075880759 3 24.552845528455283 30.21680216802168 22.086720867208673 23.14363143631436 4 28.292682926829265 31.300813008130078 19.15989159891599 21.246612466124663 5 28.26558265582656 33.360433604336045 19.37669376693767 18.99728997289973 6 21.246612466124663 37.61517615176152 20.16260162601626 20.975609756097562 7 21.761517615176153 18.67208672086721 34.71544715447155 24.850948509485093 8 22.98725941989699 22.52642992680943 25.96909731634589 28.517213336947684 9 24.88479262672811 23.14990512333966 25.698021143941446 26.26728110599078 10-11 26.498508272308108 29.712503390290205 19.134797938703553 24.654190398698127 12-13 27.143244709712427 22.042864894194246 23.846988605534456 26.96690179055887 14-15 25.1900108577633 25.624321389793703 25.06786102062975 24.117806731813246 16-17 26.35795763172189 24.945681694731125 24.22596414991852 24.470396523628462 18-19 25.743380855397145 25.661914460285136 24.263408010862186 24.331296673455533 20-21 26.807065217391308 25.692934782608695 24.03532608695652 23.46467391304348 22-23 27.102295883711452 26.04265724765657 23.434315989675316 23.420730878956665 24-25 26.334374575580604 24.84041830775499 23.794648920277062 25.030558196387343 26-27 26.124779121924696 26.70925649041729 23.188799782520046 23.97716460513796 28-29 26.692902700502103 26.109377120369114 22.662505088885872 24.53521509024291 30-31 26.136517845026464 25.86511059845298 23.59886008956439 24.399511466956167 32-33 25.732899022801302 25.1628664495114 24.82356134636265 24.280673181324648 34-35 27.184993883376375 25.526709256490417 23.773277151012643 23.515019709120565 36-37 26.386623164763456 26.536160957041872 22.892876563349645 24.184339314845023 38-39 26.053848245852596 25.75469132444928 23.45662224639652 24.734838183301605 40-41 26.98736241337138 25.805136567468406 23.12814241065362 24.079358608506592 42-43 26.377363623996736 26.608624676914705 23.302951979322543 23.711059719766016 44-45 25.387755102040817 26.095238095238095 23.523809523809526 24.993197278911563 46-47 26.128330614464385 26.16911364872213 23.015225666122895 24.687330070690592 48-49 26.681187040566297 25.510481894908793 24.135583991287778 23.672747073237137 50-51 26.478988168094652 25.9077927376581 23.21501427988576 24.398204814361485 52-53 26.064481022990073 25.96925588355326 23.520609440892397 24.44565365256428 54-55 26.32938936488508 25.59499524003808 23.419012647898818 24.65660274717802 56-57 25.319553984226275 26.02665216208866 24.354093010606473 24.299700843078597 58-59 26.68390257177847 25.56810450401415 23.581439651653284 24.16655327255409 60-61 25.088483528450855 26.96705690171522 23.441328614211816 24.503130955622108 62-63 26.387377584330796 25.911316648531013 23.000544069640913 24.70076169749728 64-65 27.387755102040817 25.428571428571427 23.496598639455783 23.687074829931973 66-67 25.951604132680806 26.63132137030995 23.423056008700378 23.994018488308864 68-69 26.497005988023954 26.360914534567232 23.584648884050083 23.557430593358735 70-71 26.391724513406835 25.54784265686675 23.478971008574927 24.58146182115149 72-73 24.637681159420293 25.78616352201258 24.336888159693736 25.23926715887339 74-75 25.55539422099608 23.56613910265718 25.439233338173374 25.439233338173374 76 27.217000408663672 0.0 35.63547200653862 37.147527584797714 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 319.0 1 160.5 2 2.5 3 3.0 4 2.5 5 4.0 6 5.5 7 2.5 8 0.0 9 0.5 10 3.5 11 4.5 12 3.0 13 4.5 14 5.5 15 5.0 16 6.0 17 9.0 18 15.5 19 17.5 20 14.5 21 18.0 22 20.0 23 16.0 24 18.0 25 21.0 26 16.0 27 16.5 28 22.0 29 26.5 30 34.5 31 34.5 32 32.5 33 39.0 34 50.5 35 62.5 36 71.0 37 79.0 38 93.5 39 105.5 40 113.5 41 118.0 42 119.0 43 138.5 44 159.5 45 160.5 46 164.5 47 163.0 48 145.5 49 145.0 50 142.0 51 129.5 52 119.5 53 118.0 54 124.5 55 116.5 56 112.0 57 116.0 58 117.5 59 118.5 60 120.0 61 111.0 62 100.5 63 96.5 64 92.0 65 92.5 66 87.5 67 79.5 68 74.0 69 67.5 70 70.5 71 72.5 72 60.5 73 48.0 74 38.0 75 30.0 76 26.0 77 21.0 78 15.0 79 12.5 80 10.0 81 7.5 82 5.0 83 2.0 84 2.5 85 1.5 86 0.5 87 1.0 88 0.5 89 0.5 90 0.5 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 1.0 99 1.5 100 1.0 >>END_MODULE >>Per base N content warn #Base N-Count 1 7.75 2 7.75 3 7.75 4 7.75 5 7.75 6 7.75 7 7.75 8 7.775 9 7.775 10-11 7.825 12-13 7.85 14-15 7.9 16-17 7.95 18-19 7.9375 20-21 8.0 22-23 7.9875 24-25 7.9625 26-27 8.0375 28-29 7.8875 30-31 7.8875 32-33 7.9 34-35 8.0375 36-37 0.3116953516736685 38-39 0.27122321670735017 40-41 0.13570362328674174 42-43 0.23072747014115094 44-45 0.24429967426710095 46-47 0.16286644951140067 48-49 0.2985884907709012 50-51 0.20358306188925082 52-53 0.23072747014115094 54-55 0.20358306188925082 56-57 0.17646260350210397 58-59 0.20369364475828355 60-61 0.24443237370994023 62-63 0.16295491580662683 64-65 0.19011406844106463 66-67 0.10863661053775121 68-69 0.16304347826086957 70-71 0.1359249694168819 72-73 0.15017064846416384 74-75 0.1449905756125852 76 0.1631986944104447 >>END_MODULE >>Sequence Length Distribution warn #Length Count 35 310.0 36 1.0 37 0.0 38 4.0 39 0.0 40 1.0 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 1.0 57 1.0 58 0.0 59 0.0 60 0.0 61 0.0 62 0.0 63 0.0 64 0.0 65 0.0 66 0.0 67 2.0 68 0.0 69 0.0 70 3.0 71 4.0 72 21.0 73 80.0 74 247.0 75 874.0 76 2451.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 88.2 #Duplication Level Percentage of deduplicated Percentage of total 1 97.30725623582767 85.82499999999999 2 1.9557823129251701 3.45 3 0.31179138321995464 0.8250000000000001 4 0.11337868480725624 0.4 5 0.05668934240362812 0.25 6 0.05668934240362812 0.3 7 0.11337868480725624 0.7000000000000001 8 0.02834467120181406 0.2 9 0.0 0.0 >10 0.02834467120181406 0.3 >50 0.0 0.0 >100 0.02834467120181406 7.75 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences fail #Sequence Count Percentage Possible Source NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 310 7.75 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACA 12 0.3 No Hit AAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTCG 8 0.2 No Hit GTTTGGCATATGCCAGCTCTGACCGAAATCTTTGGGGATGATTCTGTATT 7 0.17500000000000002 No Hit CCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTCGAGTT 7 0.17500000000000002 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 7 0.17500000000000002 No Hit AGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGA 7 0.17500000000000002 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 6 0.15 No Hit CAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTAT 6 0.15 No Hit CTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCA 5 0.125 No Hit CTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTG 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 0.025 0.0 0.0 0.0 0.0 12 0.025 0.0 0.0 0.0 0.0 13 0.025 0.0 0.0 0.0 0.0 14 0.025 0.0 0.0 0.0 0.0 15 0.025 0.0 0.0 0.0 0.0 16 0.025 0.0 0.0 0.0 0.0 17 0.025 0.0 0.0 0.0 0.0 18 0.025 0.0 0.0 0.0 0.0 19 0.025 0.0 0.0 0.0 0.0 20 0.025 0.0 0.0 0.0 0.0 21 0.025 0.0 0.0 0.0 0.0 22 0.025 0.0 0.0 0.0 0.0 23 0.075 0.0 0.0 0.0 0.0 24 0.075 0.0 0.0 0.0 0.0 25 0.15 0.0 0.0 0.0 0.0 26 0.15 0.0 0.0 0.0 0.0 27 0.15 0.0 0.0 0.0 0.0 28 0.15 0.0 0.0 0.0 0.0 29 0.15 0.0 0.0 0.0 0.0 30 0.15 0.0 0.0 0.0 0.0 31 0.15 0.0 0.0 0.0 0.0 32 0.15 0.0 0.0 0.0 0.0 33 0.175 0.0 0.0 0.0 0.0 34 0.175 0.0 0.0 0.0 0.0 35 0.2 0.0 0.0 0.0 0.0 36 0.2 0.0 0.0 0.0 0.0 37 0.2 0.0 0.0 0.0 0.0 38 0.2 0.0 0.0 0.0 0.0 39 0.25 0.0 0.0 0.0 0.0 40 0.25 0.0 0.0 0.0 0.0 41 0.25 0.0 0.0 0.0 0.0 42 0.25 0.0 0.0 0.0 0.0 43 0.25 0.0 0.0 0.0 0.0 44 0.25 0.0 0.0 0.0 0.0 45 0.25 0.0 0.0 0.0 0.0 46 0.25 0.0 0.0 0.0 0.0 47 0.25 0.0 0.0 0.0 0.0 48 0.25 0.0 0.0 0.0 0.0 49 0.25 0.0 0.0 0.0 0.0 50 0.25 0.0 0.0 0.0 0.0 51 0.25 0.0 0.0 0.0 0.0 52 0.25 0.0 0.0 0.0 0.0 53 0.25 0.0 0.0 0.0 0.0 54 0.25 0.0 0.0 0.0 0.0 55 0.25 0.0 0.0 0.0 0.0 56 0.25 0.0 0.0 0.0 0.0 57 0.25 0.0 0.0 0.0 0.0 58 0.25 0.0 0.0 0.0 0.0 59 0.25 0.0 0.0 0.0 0.0 60 0.25 0.0 0.0 0.0 0.0 61 0.25 0.0 0.0 0.0 0.0 62 0.25 0.0 0.0 0.0 0.0 63 0.25 0.0 0.0 0.0 0.0 64 0.25 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 414400 spots for SRR11389783.sra Written 414400 spots for SRR11389783.sra Read 414400 spots for SRR11389783.sra Written 414400 spots for SRR11389783.sra Read 414400 spots for SRR11389783.sra Written 414400 spots for SRR11389783.sra Read 414400 spots for SRR11389783.sra Written 414400 spots for SRR11389783.sra Read 414400 spots for SRR11389783.sra Written 414400 spots for SRR11389783.sra Read 414400 spots for SRR11389783.sra Written 414400 spots for SRR11389783.sra Read 414400 spots for SRR11389783.sra Written 414400 spots for SRR11389783.sra Read 414400 spots for SRR11389783.sra Written 414400 spots for SRR11389783.sra Read 414400 spots for SRR11389783.sra Written 414400 spots for SRR11389783.sra Read 414400 spots for SRR11389783.sra Written 414400 spots for SRR11389783.sra Read 414400 spots for SRR11389783.sra Written 414400 spots for SRR11389783.sra Read 414400 spots for SRR11389783.sra Written 414400 spots for SRR11389783.sra Read 414400 spots for SRR11389783.sra Written 414400 spots for SRR11389783.sra Read 414400 spots for SRR11389783.sra Written 414400 spots for SRR11389783.sra Read 414400 spots for SRR11389783.sra Written 414400 spots for SRR11389783.sra Read 414409 spots for SRR11389783.sra Written 414409 spots for SRR11389783.sra Read 414400 spots for SRR11389783.sra Written 414400 spots for SRR11389783.sra Read 414400 spots for SRR11389783.sra Written 414400 spots for SRR11389783.sra Read 414400 spots for SRR11389783.sra Written 414400 spots for SRR11389783.sra Read 414400 spots for SRR11389783.sra Written 414400 spots for SRR11389783.sra SRR ids: ['SRR11389783.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_jyuo439f SRR11389783.sra spots: 8288009 blocks: [[1, 414400], [414401, 828800], [828801, 1243200], [1243201, 1657600], [1657601, 2072000], [2072001, 2486400], [2486401, 2900800], [2900801, 3315200], [3315201, 3729600], [3729601, 4144000], [4144001, 4558400], [4558401, 4972800], [4972801, 5387200], [5387201, 5801600], [5801601, 6216000], [6216001, 6630400], [6630401, 7044800], [7044801, 7459200], [7459201, 7873600], [7873601, 8288009]] SRR11389783 file size 1503500 SRR11389783 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 SRR11389783 SRR11389783_1.fastq SRR11389783_2.fastq Input file: SRR11389783_1.fastq Paired file: SRR11389783_2.fastq trimmed: SRR11389783-trimmed-pair1.fastq, SRR11389783-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 06:17:30 2024 >> started Sat Dec 7 06:17:36 2024 >> done (6.146s) 8288009 read pairs processed; of these: 798 ( 0.01%) short read pairs filtered out after trimming by size control 872239 (10.52%) empty read pairs filtered out after trimming by size control 7414972 (89.47%) read pairs available; of these: 27854 ( 0.38%) trimmed read pairs available after processing 7387118 (99.62%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 776 0.01% 19 4 0.00% 20 1409 0.02% 21 15 0.00% 22 1922 0.03% 23 16 0.00% 24 2362 0.03% 25 18 0.00% 26 2644 0.04% 27 20 0.00% 28 2493 0.03% 29 30 0.00% 30 2083 0.03% 31 22 0.00% 32 1821 0.02% 33 13 0.00% 34 1636 0.02% 35 85 0.00% 36 5758 0.08% 37 70 0.00% 38 3131 0.04% 39 78 0.00% 40 1550 0.02% 41 56 0.00% 42 780 0.01% 43 49 0.00% 44 479 0.01% 45 85 0.00% 46 220 0.00% 47 97 0.00% 48 222 0.00% 49 120 0.00% 50 181 0.00% 51 120 0.00% 52 158 0.00% 53 128 0.00% 54 448 0.01% 55 811 0.01% 56 4807 0.06% 57 2111 0.03% 58 434 0.01% 59 838 0.01% 60 679 0.01% 61 395 0.01% 62 419 0.01% 63 469 0.01% 64 462 0.01% 65 490 0.01% 66 623 0.01% 67 750 0.01% 68 773 0.01% 69 762 0.01% 70 1130 0.02% 71 2004 0.03% 72 10408 0.14% 73 74040 1.00% 74 537956 7.25% 75 3370614 45.46% 76 3372898 45.49% 7414972 reads passed initial QC criterion=sequence-density sequence-density=0.80 sequence-density-rank=1 fanout-score=2.02 fanout-score-rank=31 prefix-density=0.76 prefix-fanout=2.0 sequence=TTCAAATGTACA criterion=fanout-score sequence-density=0.01 sequence-density-rank=36 fanout-score=25.53 fanout-score-rank=1 prefix-density=0.15 prefix-fanout=2.2 sequence=ATTCCATGGACCCGAGAATGCCAATATTAGCACGAATCGTACGGAAATGTAACTCGGTATTCAAACAACTATTCAGAGTTCCTAGAGCTCCTTGTACGGCCTGCTGGAAAACCCGTTGTCGGACCTGATTCATTGCCCTTTGTTTTTCAAAATAAAGGGTTTCGTTTTTAGACTTTTCTAATTGTTCCAAACTAATAGAAGTAGCATTAATCAAATTTTCTTTTTCTCGTTCTATCTCAGAGTATCCATTCATTCGATACTCATCCGCTTCTAGTTCGACTTTCTGTAATCGAATCCGAGCTTTTTCGAGCTGCTCAAAGGTCCCTCTACGCAATTCTTCCGAATTTCGAATAGTACTCAAGATCCTCTGTTTTCGATTATCTAATAAATCTTTTAATGAAAGTAGATTATCTTGCTATTAAGTTTACAACTTTTATGATCTCTTCCCGAACCAAACATGAA criterion=sequence-density sequence-density=0.47 sequence-density-rank=1 fanout-score=2.87 fanout-score-rank=18 prefix-density=0.51 prefix-fanout=2.6 sequence=CAGGTGCTCAAGGAGCTGGAGGAGGTCAAGAAGGAGTACCCGGACGCCTA criterion=fanout-score sequence-density=0.01 sequence-density-rank=38 fanout-score=15.16 fanout-score-rank=1 prefix-density=0.04 prefix-fanout=2.5 sequence=CCTCAAGCCAAAGCCTCTTGCTAAGCGTACCACACTATACAGACGTGCGCGCGCAGCCATGGCACCCACCGTGATGGCTTCCTCCGCCACCTCCGTGGC SRR11389783 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 06:18:24 Started mapping on | Dec 07 06:18:24 Finished on | Dec 07 06:20:02 Mapping speed, Million of reads per hour | 272.39 Number of input reads | 7414972 Average input read length | 150 UNIQUE READS: Uniquely mapped reads number | 5509724 Uniquely mapped reads % | 74.31% Average mapped length | 149.83 Number of splices: Total | 1544692 Number of splices: Annotated (sjdb) | 1461046 Number of splices: GT/AG | 1524728 Number of splices: GC/AG | 16644 Number of splices: AT/AC | 397 Number of splices: Non-canonical | 2923 Mismatch rate per base, % | 1.26% Deletion rate per base | 0.01% Deletion average length | 1.69 Insertion rate per base | 0.01% Insertion average length | 1.64 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1203214 % of reads mapped to multiple loci | 16.23% Number of reads mapped to too many loci | 42193 % of reads mapped to too many loci | 0.57% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 6.19% % of reads unmapped: other | 2.71% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 702039 702039 702039 N_multimapping 1203214 1203214 1203214 N_noFeature 289447 5326498 346451 N_ambiguous 198391 1195 81958 UnstrandedReadsAssigned:5021886 PositiveStrandReadsAssigned:182031 NegativeStrandReadsAssigned:5081315 Dataset is classified negative stranded MeadianReadLen=76 20thPercentileLength=75 echo kmer=71 SRR11389783 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: SRR11389783-trimmed-pair1.fastq SRR11389783-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 7,414,972 reads, 6,151,261 reads pseudoaligned [quant] estimated average fragment length: 202.758 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,083 rounds 52973 SRR11389783.ke.tsv 35125 SRR11389783.se.tsv 88098 total ==> SRR11389783.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 734.437 15.5206 4.24705 PNS24247 1044 842.242 0 0 PNS24249 1928 1726.24 18.8867 2.19881 PNS24246 1044 842.242 0 0 PNS24248 1044 842.242 0 0 PNS24244 1471 1269.24 14.5927 2.3106 PNS24243 293 105.025 0 0 KQK14069 1603 1401.24 278.253 39.908 KQK14071 474 273.895 1.74683 1.28174 ==> SRR11389783.se.tsv <== BRADI_1g14170v3 285 BRADI_1g53295v3 6 BRADI_1g59795v3 158 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 33 BRADI_1g74790v3 98 BRADI_1g09890v3 0 BRADI_1g77505v3 76 BRADI_1g48960v3 0 SRR11389783 completed mapping pipeline successfully