Starting /dee2/code/volunteer_pipeline.sh SRR11389806 current disk space = 1544880173056 free memory = 1599902012 SRR11389806 SRAfilesize c7e1cea7fc21a48960a58007ae9fccb7 SRR11389806.sra SRR11389806.sra file validated SRR11389806 is paired end SRR11389806 is conventional basespace SRR11389806 read1 length is 35-76 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11389806_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 46 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.103 32.0 32.0 32.0 32.0 32.0 2 30.15575 32.0 32.0 32.0 32.0 32.0 3 30.02275 32.0 32.0 32.0 32.0 32.0 4 30.184 32.0 32.0 32.0 32.0 32.0 5 30.093 32.0 32.0 32.0 32.0 32.0 6 33.20025 36.0 36.0 36.0 32.0 36.0 7 33.16475 36.0 36.0 36.0 21.0 36.0 8 33.16725 36.0 36.0 36.0 21.0 36.0 9 33.108 36.0 36.0 36.0 21.0 36.0 10-11 33.121624999999995 36.0 36.0 36.0 26.5 36.0 12-13 33.14575 36.0 36.0 36.0 21.0 36.0 14-15 33.165625 36.0 36.0 36.0 26.5 36.0 16-17 33.0645 36.0 36.0 36.0 24.0 36.0 18-19 33.096625 36.0 36.0 36.0 24.0 36.0 20-21 33.10525 36.0 36.0 36.0 24.0 36.0 22-23 32.929125 36.0 36.0 36.0 21.0 36.0 24-25 32.90075 36.0 36.0 36.0 21.0 36.0 26-27 32.84125 36.0 36.0 36.0 14.0 36.0 28-29 32.624624999999995 36.0 36.0 36.0 14.0 36.0 30-31 32.67975 36.0 36.0 36.0 17.5 36.0 32-33 32.598875 36.0 36.0 36.0 14.0 36.0 34-35 32.661125 36.0 36.0 36.0 14.0 36.0 36-37 33.77274359328854 36.0 36.0 36.0 32.0 36.0 38-39 33.65344603381014 36.0 36.0 36.0 29.5 36.0 40-41 33.751235370611184 36.0 36.0 36.0 27.0 36.0 42-43 33.47424557752341 36.0 36.0 36.0 24.0 36.0 44-45 33.07637262555295 36.0 36.0 36.0 14.0 36.0 46-47 32.9367681498829 36.0 36.0 36.0 14.0 36.0 48-49 32.91423490427168 36.0 36.0 36.0 14.0 36.0 50-51 32.89042165538782 36.0 36.0 36.0 14.0 36.0 52-53 32.90577946088523 36.0 36.0 36.0 14.0 36.0 54-55 32.563508706740805 36.0 32.0 36.0 14.0 36.0 56-57 32.350183287861434 36.0 32.0 36.0 14.0 36.0 58-59 32.462159604950116 36.0 34.0 36.0 14.0 36.0 60-61 32.45385620915033 36.0 32.0 36.0 14.0 36.0 62-63 32.0142738612567 36.0 32.0 36.0 14.0 36.0 64-65 32.20647671460459 36.0 32.0 36.0 14.0 36.0 66-67 32.01078124112067 36.0 32.0 36.0 14.0 36.0 68-69 32.20143049417128 36.0 32.0 36.0 14.0 36.0 70-71 32.26593973765246 36.0 32.0 36.0 14.0 36.0 72-73 31.860498505765634 36.0 32.0 36.0 14.0 36.0 74-75 31.70132258508005 36.0 32.0 36.0 14.0 36.0 76 30.795677799607073 36.0 27.0 36.0 14.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 153.0 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 0.0 21 5.0 22 10.0 23 16.0 24 27.0 25 34.0 26 56.0 27 71.0 28 119.0 29 167.0 30 193.0 31 238.0 32 369.0 33 509.0 34 939.0 35 1093.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 39.45931894983104 13.750974785547179 13.153106316610346 33.63659994801144 2 22.58903041330907 17.96204834936314 34.806342604626984 24.642578632700808 3 21.237327787886663 21.081362100337923 27.423966727319986 30.25734338445542 4 26.59214972706005 27.216012477255003 20.665453600207954 25.526384195476997 5 27.6579152586431 31.401091759812843 22.848973225890305 18.09201975565376 6 24.23689016436212 30.159144273415077 26.689277328463344 18.914688233759456 7 15.674551598648298 26.72212113335066 38.34156485573174 19.261762412269302 8 16.246425786327006 27.527943852352482 31.73901741616844 24.486612945152068 9 23.342864569794646 21.861190538081622 32.648817260202755 22.147127631920977 10-11 21.887184819339744 33.10371718221991 23.1219131791006 21.887184819339744 12-13 21.978164803743176 25.435404211073564 27.77488952430465 24.811541460878605 14-15 20.639459318949832 26.51416688328568 27.51494671172342 25.33142708604107 16-17 22.913958929035612 25.604367039251365 26.241226930075385 25.240447101637642 18-19 21.419287756693528 26.098258383155702 27.90486093059527 24.577592929555497 20-21 22.004159085001298 26.436184039511307 28.74967507148427 22.80998180400312 22-23 21.747042766151043 28.753412192902637 26.465618094371507 23.03392694657481 24-25 21.445282037951653 26.462178320769432 26.69612685209254 25.39641278918638 26-27 20.865834633385337 25.676027041081646 27.262090483619346 26.19604784191368 28-29 23.950071512157066 27.538681575867898 25.952411910024704 22.55883500195033 30-31 21.929026387625115 25.997660210581046 27.700506954374106 24.37280644741973 32-33 21.086843473738952 28.042121684867393 26.768070722828913 24.102964118564742 34-35 21.957878315132607 27.89911596463859 27.119084763390532 23.023920956838275 36-37 21.64868027564686 27.99375893901963 27.01859316083734 23.338967624496163 38-39 23.615084525357606 26.202860858257477 25.44863459037711 24.733420026007803 40-41 22.470741222366712 25.643693107932382 26.527958387516254 25.35760728218466 42-43 21.83922996878252 26.560874089490117 27.900624349635795 23.699271592091574 44-45 22.02706219099662 24.74629195940671 27.20530835284934 26.021337496747332 46-47 22.9247983346344 25.657038771792873 25.46187874056727 25.956284153005466 48-49 20.611581001951855 25.855562784645414 29.66818477553676 23.864671437865972 50-51 22.462259239979176 24.86985944820406 27.62883914627798 25.03904216553878 52-53 22.080458273662284 24.54107538080979 25.777893503450073 27.600572842077852 54-55 22.371335504885995 24.89902280130293 27.80456026058632 24.925081433224754 56-57 21.544079290558162 25.965049556598853 27.464788732394368 25.02608242044862 58-59 21.29798903107861 26.077304779315746 27.579002350483155 25.045703839122485 60-61 23.140279775134005 25.297424499934635 27.755262125768077 23.807033599163287 62-63 22.34724584587204 24.780845217846394 28.31348946748659 24.558419468794977 64-65 24.695561084195365 24.2503600890402 28.07385098860809 22.980227838156345 66-67 21.206557377049183 28.18360655737705 25.56065573770492 25.049180327868854 68-69 22.019432773109244 26.15546218487395 25.630252100840334 26.19485294117647 70-71 21.927172341264626 28.000525831471013 26.041803601945578 24.030498225318787 72-73 21.940259053661116 28.09939201691779 26.367961934972246 23.592386994448848 74-75 22.97788972851945 24.811083123425693 27.273999440246293 24.937027707808564 76 25.776031434184677 0.0 38.46758349705304 35.75638506876228 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 157.0 1 79.0 2 0.5 3 0.0 4 0.0 5 0.5 6 0.5 7 0.5 8 1.0 9 0.5 10 0.0 11 1.0 12 2.0 13 1.5 14 0.5 15 1.5 16 3.0 17 3.0 18 14.0 19 25.5 20 28.0 21 32.0 22 37.5 23 35.5 24 28.5 25 25.0 26 32.0 27 51.0 28 51.5 29 43.0 30 49.5 31 56.5 32 69.5 33 79.5 34 82.0 35 87.5 36 105.0 37 130.0 38 143.5 39 150.5 40 152.0 41 159.5 42 169.5 43 182.0 44 198.0 45 208.5 46 222.0 47 198.5 48 175.5 49 160.0 50 138.5 51 138.5 52 124.0 53 101.0 54 90.5 55 91.5 56 91.5 57 91.5 58 93.5 59 98.5 60 90.0 61 75.5 62 76.0 63 72.0 64 56.5 65 51.0 66 55.5 67 55.0 68 49.0 69 42.5 70 36.0 71 33.5 72 31.0 73 23.0 74 19.0 75 17.0 76 17.0 77 16.5 78 9.0 79 5.0 80 7.5 81 7.5 82 6.0 83 6.0 84 4.5 85 3.0 86 1.5 87 0.0 88 0.5 89 0.5 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 3.8249999999999997 2 3.8249999999999997 3 3.8249999999999997 4 3.8249999999999997 5 3.8249999999999997 6 4.175 7 3.8249999999999997 8 3.8249999999999997 9 3.8249999999999997 10-11 3.8249999999999997 12-13 3.8249999999999997 14-15 3.8249999999999997 16-17 3.8249999999999997 18-19 3.8249999999999997 20-21 3.8249999999999997 22-23 3.8375 24-25 3.8249999999999997 26-27 3.85 28-29 3.8625 30-31 3.8375 32-33 3.85 34-35 3.85 36-37 0.013000520020800833 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 0.013071895424836603 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 35 153.0 36 2.0 37 0.0 38 0.0 39 0.0 40 0.0 41 1.0 42 0.0 43 1.0 44 0.0 45 0.0 46 0.0 47 0.0 48 1.0 49 0.0 50 0.0 51 0.0 52 3.0 53 1.0 54 1.0 55 2.0 56 2.0 57 2.0 58 4.0 59 2.0 60 0.0 61 3.0 62 1.0 63 2.0 64 1.0 65 4.0 66 3.0 67 2.0 68 2.0 69 3.0 70 1.0 71 11.0 72 18.0 73 50.0 74 302.0 75 877.0 76 2545.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 88.35 #Duplication Level Percentage of deduplicated Percentage of total 1 95.89700056593095 84.725 2 2.77306168647425 4.9 3 0.6508205998868138 1.725 4 0.1414827391058291 0.5 5 0.08488964346349745 0.375 6 0.08488964346349745 0.44999999999999996 7 0.1414827391058291 0.8750000000000001 8 0.056593095642331635 0.4 9 0.0 0.0 >10 0.1414827391058291 2.225 >50 0.0 0.0 >100 0.028296547821165818 3.8249999999999997 >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 153 3.8249999999999997 No Hit GCCGAGTTTAATTGCAGTCAATTAGAAGAATAAAGAAGAATTACTGCATT 37 0.9249999999999999 No Hit GTCAATTAGAAGAATAAAGAAGAATTACTGCATTTCGTAACTTATTTTTT 20 0.5 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACTAATGCGCATCTCGTAT 12 0.3 TruSeq Adapter, Index 3 (97% over 36bp) GTTTAATTGCAGTCAATTAGAAGAATAAAGAAGAATTACTGCATTTCGTA 10 0.25 No Hit ATTTTTTCTCTTTTTATTTTGTTTCTTTTTATTTAGACCTTCTTCATATT 10 0.25 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACTAATGCGCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA 8 0.2 TruSeq Adapter, Index 3 (97% over 36bp) GAAGAATTACTGCATTTCGTAACTTATTTTTTCTCTTTTTATTTTGTTTC 8 0.2 No Hit AGAAGAATTACTGCATTTCGTAACTTATTTTTTCTCTTTTTATTTTGTTT 7 0.17500000000000002 No Hit CGAGTTTAATTGCAGTCAATTAGAAGAATAAAGAAGAATTACTGCATTTC 7 0.17500000000000002 No Hit CCGAGTTTAATTGCAGTCAATTAGAAGAATAAAGAAGAATTACTGCATTT 7 0.17500000000000002 No Hit GCGGCTAGTTCAGGACTCCATTTGCAAGCTGCTCGGATAATTTCATTACC 7 0.17500000000000002 No Hit GAAAAATAGAAAACTCAAAGCAATGTCAGAGTTGACAAAACTGAGCTGAC 7 0.17500000000000002 No Hit CGTAACTTATTTTTTCTCTTTTTATTTTGTTTCTTTTTATTTAGACCTTC 6 0.15 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACTAATGCGCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAA 6 0.15 TruSeq Adapter, Index 3 (97% over 36bp) GTCAGGGTTCAAATGTACATATGCTCCTCGAGCCCATGTCGGTACATTCA 6 0.15 No Hit GTCGAAGCCGATGATGCGGACATAGGCGTCAGGGTACTCCTTCTTCACCT 5 0.125 No Hit CTTATTTTTTCTCTTTTTATTTTGTTTCTTTTTATTTAGACCTTCTTCATATTTAGTTTTATCTATTAATCGAT 5 0.125 No Hit CTGCATTTCGTAACTTATTTTTTCTCTTTTTATTTTGTTTCTTTTTATTT 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 0.025 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 0.025 0.0 0.0 0.0 0.0 28 0.025 0.0 0.0 0.0 0.0 29 0.025 0.0 0.0 0.0 0.0 30 0.025 0.0 0.0 0.0 0.0 31 0.025 0.0 0.0 0.0 0.0 32 0.025 0.0 0.0 0.0 0.0 33 0.025 0.0 0.0 0.0 0.0 34 0.025 0.0 0.0 0.0 0.0 35 0.025 0.0 0.0 0.0 0.0 36 0.025 0.0 0.0 0.0 0.0 37 0.025 0.0 0.0 0.0 0.0 38 0.025 0.0 0.0 0.0 0.0 39 0.025 0.0 0.0 0.0 0.0 40 0.025 0.0 0.0 0.0 0.0 41 0.025 0.0 0.0 0.0 0.0 42 0.025 0.0 0.0 0.0 0.0 43 0.025 0.0 0.0 0.0 0.0 44 0.025 0.0 0.0 0.0 0.0 45 0.025 0.0 0.0 0.0 0.0 46 0.025 0.0 0.0 0.0 0.0 47 0.025 0.0 0.0 0.0 0.0 48 0.025 0.0 0.0 0.0 0.0 49 0.025 0.0 0.0 0.0 0.0 50 0.025 0.0 0.0 0.0 0.0 51 0.025 0.0 0.0 0.0 0.0 52 0.025 0.0 0.0 0.0 0.0 53 0.025 0.0 0.0 0.0 0.0 54 0.025 0.0 0.0 0.0 0.0 55 0.025 0.0 0.0 0.0 0.0 56 0.025 0.0 0.0 0.0 0.0 57 0.025 0.0 0.0 0.0 0.0 58 0.025 0.0 0.0 0.0 0.0 59 0.025 0.0 0.0 0.0 0.0 60 0.025 0.0 0.0 0.0 0.0 61 0.025 0.0 0.0 0.0 0.0 62 0.025 0.0 0.0 0.0 0.0 63 0.025 0.0 0.0 0.0 0.0 64 0.025 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTTTTAT 15 3.0927194E-4 111.43749 70 ACACGTC 20 7.237958E-5 69.46754 13 ACTAATG 20 7.237958E-5 69.46754 32 GTCACTA 20 7.237958E-5 69.46754 29 CAGTCAC 20 7.237958E-5 69.46754 27 ACGTCTG 20 7.237958E-5 69.46754 15 TGCGCAT 20 7.237958E-5 69.46754 37 CCAGTCA 20 7.237958E-5 69.46754 26 CACGTCT 20 7.237958E-5 69.46754 14 AAGAGCA 20 7.237958E-5 69.46754 7 CTCCAGT 20 7.237958E-5 69.46754 24 GATCGGA 20 7.237958E-5 69.46754 1 ATGCGCA 20 7.237958E-5 69.46754 36 ACTCCAG 20 7.237958E-5 69.46754 23 TAATGCG 20 7.237958E-5 69.46754 34 TCCAGTC 20 7.237958E-5 69.46754 25 TCGGAAG 20 7.237958E-5 69.46754 3 AACTCCA 20 7.237958E-5 69.46754 22 GAGCACA 20 7.237958E-5 69.46754 9 CGGAAGA 20 7.237958E-5 69.46754 4 >>END_MODULE SRR11389806 read2 length is 35-76 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11389806_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 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 29.8705 32.0 32.0 32.0 21.0 32.0 2 29.58375 32.0 32.0 32.0 14.0 32.0 3 29.42825 32.0 32.0 32.0 14.0 32.0 4 29.36275 32.0 32.0 32.0 14.0 32.0 5 29.3815 32.0 32.0 32.0 14.0 32.0 6 32.631 36.0 36.0 36.0 21.0 36.0 7 32.46725 36.0 36.0 36.0 14.0 36.0 8 32.04025 36.0 36.0 36.0 14.0 36.0 9 31.87175 36.0 32.0 36.0 14.0 36.0 10-11 31.9265 36.0 34.0 36.0 14.0 36.0 12-13 32.062875 36.0 36.0 36.0 14.0 36.0 14-15 31.820375 36.0 34.0 36.0 14.0 36.0 16-17 31.953375 36.0 36.0 36.0 14.0 36.0 18-19 31.732625 36.0 36.0 36.0 14.0 36.0 20-21 31.70975 36.0 34.0 36.0 14.0 36.0 22-23 31.716 36.0 34.0 36.0 14.0 36.0 24-25 31.627625000000002 36.0 34.0 36.0 14.0 36.0 26-27 31.312 36.0 32.0 36.0 14.0 36.0 28-29 31.156 36.0 32.0 36.0 14.0 36.0 30-31 31.30675 36.0 34.0 36.0 14.0 36.0 32-33 31.29475 36.0 32.0 36.0 14.0 36.0 34-35 31.340625 36.0 36.0 36.0 14.0 36.0 36-37 32.43736668736669 36.0 36.0 36.0 14.0 36.0 38-39 32.16709979209979 36.0 36.0 36.0 14.0 36.0 40-41 32.25441787941788 36.0 36.0 36.0 14.0 36.0 42-43 32.25305432804783 36.0 36.0 36.0 14.0 36.0 44-45 32.06721268850754 36.0 34.0 36.0 14.0 36.0 46-47 31.863624544981796 36.0 32.0 36.0 14.0 36.0 48-49 31.994272975080253 36.0 34.0 36.0 14.0 36.0 50-51 31.814304291287385 36.0 32.0 36.0 14.0 36.0 52-53 31.71762859328785 36.0 32.0 36.0 14.0 36.0 54-55 31.72081073802873 36.0 32.0 36.0 14.0 36.0 56-57 31.583248592708212 36.0 32.0 36.0 14.0 36.0 58-59 31.431224243859788 36.0 32.0 36.0 14.0 36.0 60-61 31.33690258553147 36.0 32.0 36.0 14.0 36.0 62-63 31.340823625126482 36.0 32.0 36.0 14.0 36.0 64-65 31.27200116654074 36.0 32.0 36.0 14.0 36.0 66-67 31.1380468302116 36.0 32.0 36.0 14.0 36.0 68-69 30.69122241488622 36.0 32.0 36.0 14.0 36.0 70-71 31.019728514434163 36.0 32.0 36.0 14.0 36.0 72-73 30.740517672440433 36.0 32.0 36.0 14.0 36.0 74-75 30.75990643588381 36.0 32.0 36.0 14.0 36.0 76 29.583126550868485 36.0 27.0 36.0 14.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 150.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 1.0 10 1.0 11 0.0 12 1.0 13 0.0 14 7.0 15 17.0 16 42.0 17 59.0 18 45.0 19 17.0 20 18.0 21 17.0 22 23.0 23 24.0 24 31.0 25 49.0 26 59.0 27 92.0 28 91.0 29 159.0 30 199.0 31 262.0 32 381.0 33 520.0 34 944.0 35 791.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 39.16883116883117 21.194805194805195 11.220779220779221 28.415584415584416 2 31.558441558441558 23.2987012987013 27.4025974025974 17.740259740259738 3 27.974025974025974 28.285714285714285 22.207792207792206 21.532467532467532 4 31.272727272727273 29.974025974025974 18.49350649350649 20.259740259740262 5 30.987012987012985 31.818181818181817 19.454545454545453 17.740259740259738 6 26.5974025974026 34.23376623376623 20.7012987012987 18.467532467532468 7 25.272727272727273 17.71428571428571 33.01298701298701 24.0 8 27.74746687451286 22.96700441673162 23.408677578591842 25.87685113016368 9 26.287051482059283 23.11492459698388 25.559022360894435 25.039001560062403 10-11 29.37117562817341 28.0562426767348 20.114568415570886 22.458013279520898 12-13 28.183118741058657 21.927428794381584 23.969306801924827 25.92014566263493 14-15 27.426931106471812 25.247912317327764 23.825678496868477 23.499478079331944 16-17 28.51740774546877 24.318685617420783 23.86230277741557 23.301603859694875 18-19 28.10704960835509 24.68668407310705 23.85117493472585 23.35509138381201 20-21 28.41651424091978 25.359289260517375 24.209563626861772 22.01463287170107 22-23 27.682067345340645 24.74549725920125 24.17123466457844 23.401200730879665 24-25 28.44647519582245 24.843342036553526 22.87206266318538 23.838120104438644 26-27 27.890890107021665 26.533542156095013 23.30984077264422 22.265726964239104 28-29 26.24771361379671 28.59942513718317 22.22367389600209 22.92918735301803 30-31 26.552713987473904 26.500521920668056 24.269311064718163 22.677453027139872 32-33 25.57471264367816 26.01880877742947 26.162486938349005 22.243991640543364 34-35 26.394149144573593 25.89787122894084 25.166514300639935 22.541465325845632 36-37 27.75680249967452 26.064314542377293 23.798984507225622 22.379898450722564 38-39 26.20195439739414 27.322475570032573 24.039087947882738 22.436482084690553 40-41 25.930278104191146 27.000913957435696 24.363493928711318 22.705314009661837 42-43 26.264337851929092 26.629301355578725 25.078206465067783 22.028154327424403 44-45 25.45928338762215 26.449511400651467 25.276872964169385 22.814332247557005 46-47 26.05403994256624 27.09829004046469 24.461558543271114 22.38611147369795 48-49 25.247653806047964 26.016684045881128 25.7429614181439 22.99270072992701 50-51 25.026014568158168 28.225806451612907 23.998439125910508 22.749739854318417 52-53 25.51832051114878 27.930629808319207 23.210327291693833 23.34072238883818 54-55 25.850606179116152 27.766914352757137 23.960370225524706 22.422109242602005 56-57 28.079331941544883 26.239561586638832 24.0866388308977 21.59446764091858 58-59 28.088273700705145 26.96526508226691 23.648472185949334 21.29798903107861 60-61 28.31396108136346 26.32884941883244 23.2597623089983 22.0974271908058 62-63 27.762521250163463 26.716359356610436 23.290179155224273 22.230940238001832 64-65 28.453581249181614 25.847846012832264 22.783815634411418 22.9147571035747 66-67 26.931654204381477 27.377672832218288 22.95684113865932 22.733831824740918 68-69 25.432843651626442 28.73819517313746 24.475341028331584 21.35362014690451 70-71 25.085413929040733 27.16162943495401 24.796320630749015 22.956636005256243 72-73 24.120536306916236 28.129563255011288 24.757732643037304 22.99216779503518 74-75 23.72047244094488 27.432508436445445 24.732845894263217 24.114173228346456 76 27.33664185277089 0.0 35.9387923904053 36.72456575682382 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 154.0 1 77.5 2 0.5 3 0.5 4 1.0 5 0.5 6 0.0 7 1.0 8 2.0 9 2.0 10 2.0 11 1.0 12 0.0 13 3.0 14 5.0 15 4.5 16 5.5 17 7.0 18 21.0 19 24.5 20 16.5 21 21.0 22 22.0 23 20.0 24 22.5 25 23.5 26 27.0 27 28.0 28 28.0 29 38.0 30 42.5 31 50.0 32 55.0 33 50.5 34 56.0 35 72.0 36 79.5 37 82.0 38 96.5 39 112.5 40 118.5 41 145.5 42 165.0 43 150.0 44 144.5 45 147.0 46 151.5 47 170.5 48 172.0 49 170.5 50 173.0 51 150.5 52 121.5 53 104.0 54 109.0 55 115.0 56 115.5 57 117.5 58 118.5 59 114.0 60 118.0 61 123.5 62 120.5 63 105.0 64 84.0 65 76.5 66 73.5 67 63.5 68 57.0 69 59.0 70 53.5 71 46.0 72 39.5 73 37.0 74 33.0 75 24.0 76 23.5 77 22.0 78 16.5 79 15.0 80 13.0 81 9.0 82 6.0 83 3.5 84 3.5 85 3.5 86 1.5 87 1.0 88 1.0 89 0.5 90 0.0 91 1.0 92 2.0 93 1.0 94 0.0 95 0.5 96 1.0 97 1.0 98 0.5 99 1.5 100 3.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 3.75 2 3.75 3 3.75 4 3.75 5 3.75 6 3.75 7 3.75 8 3.775 9 3.85 10-11 3.9875000000000003 12-13 3.8875 14-15 4.2 16-17 4.1375 18-19 4.25 20-21 4.324999999999999 22-23 4.2250000000000005 24-25 4.25 26-27 4.2250000000000005 28-29 4.324999999999999 30-31 4.2 32-33 4.3 34-35 4.2875000000000005 36-37 0.22083658093011174 38-39 0.27286902286902287 40-41 0.4807692307692308 42-43 0.28593709383935534 44-45 0.22100884035361415 46-47 0.4030161206448258 48-49 0.24704199713951372 50-51 0.02600780234070221 52-53 0.24713839750260144 54-55 0.15618898867629832 56-57 0.1563314226159458 58-59 0.10435690060005218 60-61 0.013058239749281797 62-63 0.026147208785462152 64-65 0.07850320554755985 66-67 0.104835539247805 68-69 0.0 70-71 0.02627430373095113 72-73 0.1855041738439115 74-75 0.1544293134915064 76 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 35 150.0 36 2.0 37 0.0 38 0.0 39 0.0 40 0.0 41 1.0 42 0.0 43 1.0 44 0.0 45 0.0 46 0.0 47 0.0 48 1.0 49 0.0 50 0.0 51 0.0 52 2.0 53 1.0 54 1.0 55 2.0 56 2.0 57 2.0 58 4.0 59 2.0 60 0.0 61 4.0 62 1.0 63 2.0 64 1.0 65 4.0 66 3.0 67 1.0 68 2.0 69 3.0 70 4.0 71 17.0 72 27.0 73 73.0 74 251.0 75 1018.0 76 2418.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 90.725 #Duplication Level Percentage of deduplicated Percentage of total 1 96.50041333700744 87.55 2 2.1769082391843484 3.95 3 0.6337834114081015 1.725 4 0.3031138054560485 1.0999999999999999 5 0.19289060347203085 0.8750000000000001 6 0.055111600992008826 0.3 7 0.08266740148801323 0.525 8 0.0 0.0 9 0.027555800496004413 0.22499999999999998 >10 0.0 0.0 >50 0.0 0.0 >100 0.027555800496004413 3.75 >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 150 3.75 No Hit GTTTGGCATATGCCAGCTCTGACCGAAATCTTTGGGGATGATTCTGTATT 9 0.22499999999999998 No Hit CCGGTAGATACTATCGATTAATAGATAAAACTAAATATGAAGAAGGTCTAAATAAAAAGAAACAAAATAAAAAG 7 0.17500000000000002 No Hit ATTAATAGATAAAACTAAATATGAAGAAGGTCTAAATAAAAAGAAACAAAATAAAAAGAGAAAAAATAAGTTACG 7 0.17500000000000002 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 7 0.17500000000000002 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACA 6 0.15 No Hit ATCGATTAATAGATAAAACTAAATATGAAGAAGGTCTAAATAAAAAGAAA 6 0.15 No Hit GCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATC 5 0.125 No Hit TGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGAT 5 0.125 No Hit AAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTCG 5 0.125 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 5 0.125 No Hit AATAGATAAAACTAAATATGAAGAAGGTCTAAATAAAAAGAAACAAAATA 5 0.125 No Hit GATTAATAGATAAAACTAAATATGAAGAAGGTCTAAATAAAAAGAAACAA 5 0.125 No Hit AGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGA 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 0.025 0.0 0.0 0.0 0.0 18 0.025 0.0 0.0 0.0 0.0 19 0.05 0.0 0.0 0.0 0.0 20 0.05 0.0 0.0 0.0 0.0 21 0.05 0.0 0.0 0.0 0.0 22 0.05 0.0 0.0 0.0 0.0 23 0.05 0.0 0.0 0.0 0.0 24 0.05 0.0 0.0 0.0 0.0 25 0.05 0.0 0.0 0.0 0.0 26 0.05 0.0 0.0 0.0 0.0 27 0.05 0.0 0.0 0.0 0.0 28 0.05 0.0 0.0 0.0 0.0 29 0.075 0.0 0.0 0.0 0.0 30 0.075 0.0 0.0 0.0 0.0 31 0.075 0.0 0.0 0.0 0.0 32 0.075 0.0 0.0 0.0 0.0 33 0.075 0.0 0.0 0.0 0.0 34 0.075 0.0 0.0 0.0 0.0 35 0.1 0.0 0.0 0.0 0.0 36 0.1 0.0 0.0 0.0 0.0 37 0.1 0.0 0.0 0.0 0.0 38 0.1 0.0 0.0 0.0 0.0 39 0.1 0.0 0.0 0.0 0.0 40 0.1 0.0 0.0 0.0 0.0 41 0.1 0.0 0.0 0.0 0.0 42 0.1 0.0 0.0 0.0 0.0 43 0.1 0.0 0.0 0.0 0.0 44 0.1 0.0 0.0 0.0 0.0 45 0.1 0.0 0.0 0.0 0.0 46 0.1 0.0 0.0 0.0 0.0 47 0.1 0.0 0.0 0.0 0.0 48 0.1 0.0 0.0 0.0 0.0 49 0.1 0.0 0.0 0.0 0.0 50 0.1 0.0 0.0 0.0 0.0 51 0.1 0.0 0.0 0.0 0.0 52 0.1 0.0 0.0 0.0 0.0 53 0.1 0.0 0.0 0.0 0.0 54 0.1 0.0 0.0 0.0 0.0 55 0.1 0.0 0.0 0.0 0.0 56 0.1 0.0 0.0 0.0 0.0 57 0.1 0.0 0.0 0.0 0.0 58 0.1 0.0 0.0 0.0 0.0 59 0.1 0.0 0.0 0.0 0.0 60 0.1 0.0 0.0 0.0 0.0 61 0.1 0.0 0.0 0.0 0.0 62 0.1 0.0 0.0 0.0 0.0 63 0.1 0.0 0.0 0.0 0.0 64 0.1 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1310017 spots for SRR11389806.sra Written 1310017 spots for SRR11389806.sra Read 1310017 spots for SRR11389806.sra Written 1310017 spots for SRR11389806.sra Read 1310017 spots for SRR11389806.sra Written 1310017 spots for SRR11389806.sra Read 1310017 spots for SRR11389806.sra Written 1310017 spots for SRR11389806.sra Read 1310017 spots for SRR11389806.sra Written 1310017 spots for SRR11389806.sra Read 1310017 spots for SRR11389806.sra Written 1310017 spots for SRR11389806.sra Read 1310017 spots for SRR11389806.sra Written 1310017 spots for SRR11389806.sra Read 1310017 spots for SRR11389806.sra Written 1310017 spots for SRR11389806.sra Read 1310017 spots for SRR11389806.sra Written 1310017 spots for SRR11389806.sra Read 1310017 spots for SRR11389806.sra Written 1310017 spots for SRR11389806.sra Read 1310017 spots for SRR11389806.sra Written 1310017 spots for SRR11389806.sra Read 1310017 spots for SRR11389806.sra Written 1310017 spots for SRR11389806.sra Read 1310017 spots for SRR11389806.sra Written 1310017 spots for SRR11389806.sra Read 1310017 spots for SRR11389806.sra Written 1310017 spots for SRR11389806.sra Read 1310017 spots for SRR11389806.sra Written 1310017 spots for SRR11389806.sra Read 1310017 spots for SRR11389806.sra Written 1310017 spots for SRR11389806.sra Read 1310017 spots for SRR11389806.sra Written 1310017 spots for SRR11389806.sra Read 1310020 spots for SRR11389806.sra Written 1310020 spots for SRR11389806.sra Read 1310017 spots for SRR11389806.sra Written 1310017 spots for SRR11389806.sra Read 1310017 spots for SRR11389806.sra Written 1310017 spots for SRR11389806.sra SRR ids: ['SRR11389806.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_dw1fbth9 SRR11389806.sra spots: 26200343 blocks: [[1, 1310017], [1310018, 2620034], [2620035, 3930051], [3930052, 5240068], [5240069, 6550085], [6550086, 7860102], [7860103, 9170119], [9170120, 10480136], [10480137, 11790153], [11790154, 13100170], [13100171, 14410187], [14410188, 15720204], [15720205, 17030221], [17030222, 18340238], [18340239, 19650255], [19650256, 20960272], [20960273, 22270289], [22270290, 23580306], [23580307, 24890323], [24890324, 26200343]] SRR11389806 file size 4886200 SRR11389806 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 SRR11389806 SRR11389806_1.fastq SRR11389806_2.fastq Input file: SRR11389806_1.fastq Paired file: SRR11389806_2.fastq trimmed: SRR11389806-trimmed-pair1.fastq, SRR11389806-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 06:59:45 2024 >> started Sat Dec 7 07:00:09 2024 >> done (24.330s) 26200343 read pairs processed; of these: 1731 ( 0.01%) short read pairs filtered out after trimming by size control 2125575 ( 8.11%) empty read pairs filtered out after trimming by size control 24073037 (91.88%) read pairs available; of these: 88477 ( 0.37%) trimmed read pairs available after processing 23984560 (99.63%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 4358 0.02% 19 136 0.00% 20 6315 0.03% 21 138 0.00% 22 7289 0.03% 23 159 0.00% 24 7420 0.03% 25 109 0.00% 26 8133 0.03% 27 118 0.00% 28 7328 0.03% 29 85 0.00% 30 4757 0.02% 31 70 0.00% 32 3335 0.01% 33 55 0.00% 34 2517 0.01% 35 557 0.00% 36 5873 0.02% 37 637 0.00% 38 2761 0.01% 39 805 0.00% 40 1589 0.01% 41 1189 0.00% 42 1587 0.01% 43 1571 0.01% 44 1987 0.01% 45 2045 0.01% 46 2483 0.01% 47 2687 0.01% 48 2859 0.01% 49 3309 0.01% 50 3560 0.01% 51 3964 0.02% 52 4780 0.02% 53 5244 0.02% 54 5970 0.02% 55 6806 0.03% 56 9376 0.04% 57 9243 0.04% 58 9397 0.04% 59 10154 0.04% 60 10982 0.05% 61 11765 0.05% 62 13227 0.05% 63 14900 0.06% 64 16601 0.07% 65 17665 0.07% 66 19067 0.08% 67 21428 0.09% 68 21710 0.09% 69 23232 0.10% 70 25736 0.11% 71 32158 0.13% 72 55653 0.23% 73 254718 1.06% 74 1780222 7.40% 75 11138993 46.27% 76 10462225 43.46% 24073037 reads passed initial QC criterion=sequence-density sequence-density=1.43 sequence-density-rank=1 fanout-score=1.99 fanout-score-rank=27 prefix-density=1.35 prefix-fanout=2.0 sequence=TTCAAATGTACA criterion=fanout-score sequence-density=0.01 sequence-density-rank=34 fanout-score=23.27 fanout-score-rank=1 prefix-density=0.12 prefix-fanout=1.0 sequence=TTTTAGAGGCACATCACACATGCTGATTCATGGGGGGATCAATACCAGTTGGTGAGGAAGAAATTACAAAGGCTAAAAATTACAACCAACAGCAGGGGCCAGGTTCGCATTACTACATACACACATGGCGCATTGCCTTTCTCTCTCCACCGATCAACCCACGTACACGCATATGCACGGAGGAAGTGTTCTTCTCCGATGATCGACCGATCCTTTTTCTAGTTAGACTCGAGCTGCGCGTACCAGACGCCCTGGATCTTGACGTCCTTGGGCGCCTTGGCGCCGAGGTCGGTGTCGGACGGCTGCACGCTCTCGAAGACGCCGATGACCTCCCCGGTCTCCGGCTTGCTCTTGGTGACGCTGAGCGTGATGTTCCCCTGCGACGACGACGCGTTCTTCACGTTCTCCTTGGCCAGCTCCTCCTCATCCCCTCTGCCTCCGGCGGGGAGCGCCACCGCGTTGTCATACCCGGTCGACCCACCACGGCCCTTGGGGTCAAGGAACGAGGACC criterion=sequence-density sequence-density=0.77 sequence-density-rank=1 fanout-score=2.35 fanout-score-rank=18 prefix-density=0.80 prefix-fanout=2.3 sequence=CAGGTGCTCAAGGAGCTGGAGGAGGTCAAGAAGGAGTACCCGGACGCCTA criterion=fanout-score sequence-density=0.01 sequence-density-rank=31 fanout-score=10.94 fanout-score-rank=1 prefix-density=0.04 prefix-fanout=2.0 sequence=CCTCAAGCCAAAGCCTCTTGCTAAGCGTACCACACTATACAGACGTGCGCGCGCAGCCATGGCACCCACCGTGATGGCTTCCTCCGCCACCTCCGTGGC SRR11389806 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 07:00:40 Started mapping on | Dec 07 07:00:41 Finished on | Dec 07 07:02:30 Mapping speed, Million of reads per hour | 795.07 Number of input reads | 24073037 Average input read length | 150 UNIQUE READS: Uniquely mapped reads number | 18008465 Uniquely mapped reads % | 74.81% Average mapped length | 150.02 Number of splices: Total | 4992636 Number of splices: Annotated (sjdb) | 4702630 Number of splices: GT/AG | 4925869 Number of splices: GC/AG | 55699 Number of splices: AT/AC | 962 Number of splices: Non-canonical | 10106 Mismatch rate per base, % | 0.59% Deletion rate per base | 0.01% Deletion average length | 1.66 Insertion rate per base | 0.01% Insertion average length | 1.53 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 4097567 % of reads mapped to multiple loci | 17.02% Number of reads mapped to too many loci | 171942 % of reads mapped to too many loci | 0.71% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.61% % of reads unmapped: other | 2.85% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1967005 1967005 1967005 N_multimapping 4097567 4097567 4097567 N_noFeature 774302 17384001 958290 N_ambiguous 756735 5003 379197 UnstrandedReadsAssigned:16477428 PositiveStrandReadsAssigned:619461 NegativeStrandReadsAssigned:16670978 Dataset is classified negative stranded MeadianReadLen=76 20thPercentileLength=75 echo kmer=71 SRR11389806 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: SRR11389806-trimmed-pair1.fastq SRR11389806-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 24,073,037 reads, 20,629,154 reads pseudoaligned [quant] estimated average fragment length: 171.57 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,173 rounds 52973 SRR11389806.ke.tsv 35125 SRR11389806.se.tsv 88098 total ==> SRR11389806.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 765.496 0 0 PNS24247 1044 873.43 0 0 PNS24249 1928 1757.43 57.6837 2.06948 PNS24246 1044 873.43 0 0 PNS24248 1044 873.43 0 0 PNS24244 1471 1300.43 56.3163 2.73045 PNS24243 293 132.077 0 0 KQK14069 1603 1432.43 330 14.5254 KQK14071 474 304.526 0 0 ==> SRR11389806.se.tsv <== BRADI_1g14170v3 327 BRADI_1g53295v3 11 BRADI_1g59795v3 154 BRADI_1g07683v3 0 BRADI_1g00485v3 5 BRADI_1g20270v3 138 BRADI_1g74790v3 266 BRADI_1g09890v3 1 BRADI_1g77505v3 180 BRADI_1g48960v3 0 SRR11389806 completed mapping pipeline successfully