Starting /dee2/code/volunteer_pipeline.sh SRR11389812 current disk space = 1544787222528 free memory = 1599938464 SRR11389812 SRAfilesize 31d4afa24d432d6b08e7e83775ce1bbe SRR11389812.sra SRR11389812.sra file validated SRR11389812 is paired end SRR11389812 is conventional basespace SRR11389812 read1 length is 35-76 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11389812_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 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.6005 32.0 32.0 32.0 32.0 32.0 2 30.54475 32.0 32.0 32.0 32.0 32.0 3 30.625 32.0 32.0 32.0 32.0 32.0 4 30.6975 32.0 32.0 32.0 32.0 32.0 5 30.722 32.0 32.0 32.0 32.0 32.0 6 33.78725 36.0 36.0 36.0 32.0 36.0 7 33.929 36.0 36.0 36.0 32.0 36.0 8 33.8755 36.0 36.0 36.0 32.0 36.0 9 33.88925 36.0 36.0 36.0 32.0 36.0 10-11 33.68275 36.0 36.0 36.0 32.0 36.0 12-13 33.797250000000005 36.0 36.0 36.0 32.0 36.0 14-15 33.828625 36.0 36.0 36.0 32.0 36.0 16-17 33.713499999999996 36.0 36.0 36.0 32.0 36.0 18-19 33.7 36.0 36.0 36.0 32.0 36.0 20-21 33.636250000000004 36.0 36.0 36.0 32.0 36.0 22-23 33.52475 36.0 36.0 36.0 32.0 36.0 24-25 33.60124999999999 36.0 36.0 36.0 32.0 36.0 26-27 33.289875 36.0 36.0 36.0 24.0 36.0 28-29 33.296 36.0 36.0 36.0 27.0 36.0 30-31 33.345749999999995 36.0 36.0 36.0 24.0 36.0 32-33 33.326375 36.0 36.0 36.0 27.0 36.0 34-35 33.200874999999996 36.0 36.0 36.0 21.0 36.0 36-37 33.79401528522993 36.0 36.0 36.0 32.0 36.0 38-39 33.73829019317628 36.0 36.0 36.0 29.5 36.0 40-41 33.50447112927951 36.0 36.0 36.0 27.0 36.0 42-43 33.296882984159424 36.0 36.0 36.0 20.5 36.0 44-45 32.38975472662238 36.0 34.0 36.0 14.0 36.0 46-47 32.25855901890649 36.0 34.0 36.0 14.0 36.0 48-49 31.986969557993667 36.0 32.0 36.0 14.0 36.0 50-51 32.34896498849987 36.0 36.0 36.0 14.0 36.0 52-53 32.486455405060056 36.0 36.0 36.0 14.0 36.0 54-55 31.829197503606576 36.0 32.0 36.0 14.0 36.0 56-57 31.572524942440523 36.0 32.0 36.0 14.0 36.0 58-59 31.817809621289662 36.0 34.0 36.0 14.0 36.0 60-61 31.738509911015115 36.0 32.0 36.0 14.0 36.0 62-63 31.22834443874936 36.0 32.0 36.0 14.0 36.0 64-65 31.530761343245324 36.0 32.0 36.0 14.0 36.0 66-67 31.54073791951165 36.0 32.0 36.0 14.0 36.0 68-69 32.06834106913284 36.0 32.0 36.0 14.0 36.0 70-71 32.13299922898997 36.0 32.0 36.0 14.0 36.0 72-73 31.792015280414354 36.0 32.0 36.0 14.0 36.0 74-75 31.415519837520613 36.0 32.0 36.0 14.0 36.0 76 30.58307210031348 36.0 27.0 36.0 14.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 84.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 4.0 22 6.0 23 7.0 24 27.0 25 47.0 26 67.0 27 126.0 28 162.0 29 207.0 30 197.0 31 244.0 32 334.0 33 510.0 34 940.0 35 1038.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 43.48825331971399 10.980592441266598 11.006128702757916 34.52502553626149 2 22.36976506639428 21.195097037793666 33.937691521961185 22.497446373850867 3 20.531154239019408 19.101123595505616 30.0561797752809 30.311542390194074 4 26.86414708886619 24.744637385086822 18.258426966292134 30.132788559754854 5 31.256384065372828 27.65577119509704 22.13993871297242 18.94790602655771 6 29.82321291314374 27.619779656674353 23.46912631309249 19.08788111708942 7 15.67926455566905 30.311542390194074 34.55056179775281 19.458631256384066 8 16.419816138917263 30.4902962206333 29.698672114402452 23.391215526046988 9 26.736465781409603 19.17773237997957 29.67313585291113 24.412665985699693 10-11 26.11082737487232 31.38406537282942 21.424923391215525 21.080183861082737 12-13 21.06741573033708 25.881001021450462 24.527579162410625 28.52400408580184 14-15 21.693054136874363 27.259959141981614 24.744637385086822 26.3023493360572 16-17 24.923391215526046 23.314606741573034 23.82533197139939 27.936670071501535 18-19 21.05464759959142 22.305924412665988 28.664453524004085 27.974974463738512 20-21 25.829928498467826 23.391215526046988 28.179264555669047 22.59959141981614 22-23 21.248882645894522 31.630698505937936 24.837185544630316 22.283233303537223 24-25 22.191011235955056 22.510214504596526 28.447395301327887 26.85137895812053 26-27 20.191570881226053 23.63984674329502 24.597701149425287 31.570881226053636 28-29 25.239494188274364 26.46570443223911 24.830757440286117 23.46404393920041 30-31 21.016343207354442 24.1317671092952 27.617466802860065 27.234422880490293 32-33 21.440429063976506 27.49329587536713 24.40301366364449 26.66326139701188 34-35 21.73135852911134 27.3876404494382 27.208886618998978 23.67211440245148 36-37 21.836291661345932 27.288979696079686 26.95696590473758 23.917762737836803 38-39 25.72486907651041 23.080853237961428 23.591774172946735 27.60250351258143 40-41 25.0 23.556463975472663 23.377618804292283 28.065917220235054 42-43 21.601941747572813 25.67705671946857 28.500255493101683 24.220746039856923 44-45 22.675012774655084 23.645886561062852 26.085845682166582 27.593254982115482 46-47 25.51098620337251 23.837506387327544 22.87940725600409 27.77210015329586 48-49 21.566372812060816 26.881308291810402 27.967292704740004 23.585026191388785 50-51 24.61027344748275 22.8213646818298 28.673651929465883 23.89470994122157 52-53 22.220802453360594 23.40914899054434 23.12803475594173 31.242013800153334 54-55 25.54007414035536 22.855681963441135 27.278537645404576 24.325706250798927 56-57 22.64006139677667 23.369148119723715 27.359938603223334 26.630851880276285 58-59 21.711873080859775 23.59263050153531 27.622824974411465 27.072671443193446 60-61 25.32650448143406 23.188220230473753 27.64404609475032 23.84122919334187 62-63 23.039466940030753 23.641722193746798 26.345463864684778 26.97334700153767 64-65 25.05767751858498 23.04537298128685 27.64675724173289 24.250192258395284 66-67 21.710695050012824 29.687099256219547 24.083098230315468 24.519107463452166 68-69 21.630295250320923 29.69191270860077 24.42875481386393 24.249037227214377 70-71 21.76818298637882 29.69673605756875 23.88846054998715 24.646620406065278 72-73 21.046511627906977 31.356589147286822 23.152454780361754 24.444444444444443 74-75 21.54673283705542 27.019575406672182 25.75130962227736 25.682382133995034 76 26.763322884012542 0.0 38.205329153605014 35.03134796238245 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 89.0 1 44.5 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.5 8 1.0 9 0.5 10 0.0 11 0.5 12 1.0 13 0.5 14 0.0 15 0.5 16 0.5 17 0.0 18 7.0 19 14.0 20 14.0 21 17.5 22 23.5 23 17.5 24 9.0 25 10.0 26 16.0 27 20.5 28 20.5 29 20.5 30 28.0 31 38.5 32 42.5 33 47.0 34 62.5 35 84.0 36 92.0 37 98.0 38 110.5 39 116.5 40 127.0 41 156.0 42 181.0 43 210.5 44 237.5 45 267.5 46 288.5 47 249.0 48 193.5 49 166.5 50 155.0 51 138.0 52 121.0 53 111.0 54 110.0 55 111.5 56 106.5 57 104.0 58 106.0 59 120.0 60 120.0 61 96.5 62 80.5 63 74.0 64 68.5 65 64.0 66 54.5 67 48.0 68 50.5 69 48.5 70 45.5 71 43.5 72 38.0 73 28.0 74 24.0 75 23.5 76 21.0 77 15.0 78 11.5 79 12.0 80 8.5 81 6.5 82 6.0 83 5.0 84 2.5 85 1.5 86 2.5 87 1.0 88 0.0 89 0.5 90 0.5 91 0.5 92 1.0 93 0.5 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 2.1 2 2.1 3 2.1 4 2.1 5 2.1 6 2.4250000000000003 7 2.1 8 2.1 9 2.1 10-11 2.1 12-13 2.1 14-15 2.1 16-17 2.1 18-19 2.1 20-21 2.1 22-23 2.1125000000000003 24-25 2.1 26-27 2.125 28-29 2.1375 30-31 2.1 32-33 2.1125000000000003 34-35 2.1 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 0.012802458071949815 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 84.0 36 1.0 37 0.0 38 1.0 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 1.0 49 0.0 50 0.0 51 0.0 52 0.0 53 1.0 54 1.0 55 2.0 56 0.0 57 1.0 58 0.0 59 1.0 60 3.0 61 2.0 62 0.0 63 1.0 64 0.0 65 1.0 66 2.0 67 2.0 68 2.0 69 3.0 70 0.0 71 12.0 72 18.0 73 68.0 74 332.0 75 909.0 76 2552.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 92.27499999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 97.07396369547548 89.575 2 2.0048767271742074 3.6999999999999997 3 0.46057978867515575 1.275 4 0.1083717149823896 0.4 5 0.0812787862367922 0.375 6 0.1083717149823896 0.6 7 0.0270929287455974 0.17500000000000002 8 0.0270929287455974 0.2 9 0.0 0.0 >10 0.0812787862367922 1.6 >50 0.0270929287455974 2.1 >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 fail #Sequence Count Percentage Possible Source NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 84 2.1 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACTAATGCGCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAA 23 0.575 TruSeq Adapter, Index 3 (97% over 36bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACTAATGCGCATCTCGTAT 21 0.525 TruSeq Adapter, Index 3 (97% over 36bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACTAATGCGCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA 20 0.5 TruSeq Adapter, Index 3 (97% over 36bp) GCCGAGTTTAATTGCAGTCAATTAGAAGAATAAAGAAGAATTACTGCATT 8 0.2 No Hit GTCAATTAGAAGAATAAAGAAGAATTACTGCATTTCGTAACTTATTTTTT 7 0.17500000000000002 No Hit CGTAACTTATTTTTTCTCTTTTTATTTTGTTTCTTTTTATTTAGACCTTC 6 0.15 No Hit CCGAGTTTAATTGCAGTCAATTAGAAGAATAAAGAAGAATTACTGCATTT 6 0.15 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACTAATGCGCATCGCGTATGCCGTCTTCTGCTTGAAAAAAAAAA 6 0.15 TruSeq Adapter, Index 3 (97% over 36bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACTAATGCGCATCGCGTAT 6 0.15 TruSeq Adapter, Index 3 (97% over 36bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACTAATGCGCATCGCGTATGCCGTCTTCTGCTTGAAAAAAAAA 5 0.125 TruSeq Adapter, Index 3 (97% over 36bp) ATTTTTTCTCTTTTTATTTTGTTTCTTTTTATTTAGACCTTCTTCATATT 5 0.125 No Hit GCATTTCGTAACTTATTTTTTCTCTTTTTATTTTGTTTCTTTTTATTTAGACCTTCTTCATATTTAGTTTTATCT 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 0.05 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 0.05 0.0 0.0 0.0 0.0 30 0.05 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 0.075 0.0 0.0 0.0 0.0 36 0.075 0.0 0.0 0.0 0.0 37 0.075 0.0 0.0 0.0 0.0 38 0.075 0.0 0.0 0.0 0.0 39 0.075 0.0 0.0 0.0 0.0 40 0.075 0.0 0.0 0.0 0.0 41 0.075 0.0 0.0 0.0 0.0 42 0.075 0.0 0.0 0.0 0.0 43 0.075 0.0 0.0 0.0 0.0 44 0.075 0.0 0.0 0.0 0.0 45 0.075 0.0 0.0 0.0 0.0 46 0.075 0.0 0.0 0.0 0.0 47 0.075 0.0 0.0 0.0 0.0 48 0.075 0.0 0.0 0.0 0.0 49 0.075 0.0 0.0 0.0 0.0 50 0.075 0.0 0.0 0.0 0.0 51 0.075 0.0 0.0 0.0 0.0 52 0.075 0.0 0.0 0.0 0.0 53 0.075 0.0 0.0 0.0 0.0 54 0.075 0.0 0.0 0.0 0.0 55 0.075 0.0 0.0 0.0 0.0 56 0.075 0.0 0.0 0.0 0.0 57 0.075 0.0 0.0 0.0 0.0 58 0.075 0.0 0.0 0.0 0.0 59 0.075 0.0 0.0 0.0 0.0 60 0.075 0.0 0.0 0.0 0.0 61 0.075 0.0 0.0 0.0 0.0 62 0.075 0.0 0.0 0.0 0.0 63 0.075 0.0 0.0 0.0 0.0 64 0.075 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ACACGTC 45 3.6379788E-12 69.51899 13 ACTAATG 45 3.6379788E-12 69.51899 32 ATCTCGT 25 2.449673E-6 69.51899 42 CACACGT 45 3.6379788E-12 69.51899 12 ACGTCTG 45 3.6379788E-12 69.51899 15 TGCGCAT 30 8.2354745E-8 69.51899 37 CACGTCT 45 3.6379788E-12 69.51899 14 CATCTCG 15 0.002121144 69.51899 41 ATGCGCA 30 8.2354745E-8 69.51899 36 ACTCCAG 45 3.6379788E-12 69.51899 23 GTCTGAA 45 3.6379788E-12 69.51899 17 CTGAACT 45 3.6379788E-12 69.51899 19 TCTCGTA 25 2.449673E-6 69.51899 43 TGCTTGA 15 0.002121144 69.51899 60 TCTGAAC 45 3.6379788E-12 69.51899 18 GCTTGAA 15 0.002121144 69.51899 61 GCGCATC 25 2.449673E-6 69.51899 38 AGCACAC 45 3.6379788E-12 69.51899 10 CACTAAT 45 3.6379788E-12 69.51899 31 TTGAAAA 30 8.2354745E-8 69.51899 63 >>END_MODULE SRR11389812 read2 length is 35-76 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11389812_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 52 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.25525 32.0 32.0 32.0 32.0 32.0 2 29.9265 32.0 32.0 32.0 21.0 32.0 3 29.758 32.0 32.0 32.0 21.0 32.0 4 29.69725 32.0 32.0 32.0 21.0 32.0 5 29.67675 32.0 32.0 32.0 21.0 32.0 6 32.924 36.0 36.0 36.0 21.0 36.0 7 32.7265 36.0 36.0 36.0 14.0 36.0 8 32.16275 36.0 32.0 36.0 14.0 36.0 9 31.90825 36.0 32.0 36.0 14.0 36.0 10-11 31.967 36.0 34.0 36.0 14.0 36.0 12-13 32.000625 36.0 34.0 36.0 14.0 36.0 14-15 31.786375 36.0 32.0 36.0 14.0 36.0 16-17 31.881875 36.0 32.0 36.0 14.0 36.0 18-19 31.752875000000003 36.0 32.0 36.0 14.0 36.0 20-21 31.4125 36.0 32.0 36.0 14.0 36.0 22-23 31.595375 36.0 32.0 36.0 14.0 36.0 24-25 31.316 36.0 32.0 36.0 14.0 36.0 26-27 31.1145 36.0 32.0 36.0 14.0 36.0 28-29 30.883000000000003 36.0 32.0 36.0 14.0 36.0 30-31 31.0485 36.0 32.0 36.0 14.0 36.0 32-33 31.04625 36.0 32.0 36.0 14.0 36.0 34-35 31.094125 36.0 32.0 36.0 14.0 36.0 36-37 31.633631713554987 36.0 34.0 36.0 14.0 36.0 38-39 31.547314578005114 36.0 32.0 36.0 14.0 36.0 40-41 31.630690537084398 36.0 32.0 36.0 14.0 36.0 42-43 31.515984654731458 36.0 32.0 36.0 14.0 36.0 44-45 31.362020460358057 36.0 32.0 36.0 14.0 36.0 46-47 31.272122762148335 36.0 32.0 36.0 14.0 36.0 48-49 31.340328960841234 36.0 32.0 36.0 14.0 36.0 50-51 31.100793041698644 36.0 32.0 36.0 14.0 36.0 52-53 31.002302379125098 36.0 32.0 36.0 14.0 36.0 54-55 31.15406633737991 36.0 32.0 36.0 14.0 36.0 56-57 30.850192061459666 36.0 32.0 36.0 14.0 36.0 58-59 30.86347336065574 36.0 32.0 36.0 14.0 36.0 60-61 30.687294290388067 36.0 32.0 36.0 14.0 36.0 62-63 30.82016418676244 36.0 32.0 36.0 14.0 36.0 64-65 30.661662817551964 36.0 29.5 36.0 14.0 36.0 66-67 30.512714171436286 36.0 27.0 36.0 14.0 36.0 68-69 30.256474555940997 36.0 27.0 36.0 14.0 36.0 70-71 30.33454619576833 36.0 27.0 36.0 14.0 36.0 72-73 30.343161824457916 36.0 27.0 36.0 14.0 36.0 74-75 30.302838617138487 36.0 27.0 36.0 14.0 36.0 76 29.576987447698745 36.0 27.0 36.0 14.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 90.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 2.0 11 0.0 12 1.0 13 0.0 14 3.0 15 37.0 16 96.0 17 117.0 18 62.0 19 28.0 20 14.0 21 16.0 22 15.0 23 18.0 24 27.0 25 54.0 26 58.0 27 93.0 28 103.0 29 140.0 30 192.0 31 240.0 32 365.0 33 543.0 34 925.0 35 761.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 44.62090163934426 17.802254098360656 9.170081967213115 28.40676229508197 2 35.11782786885246 21.746926229508194 26.793032786885245 16.3422131147541 3 30.877462266564336 25.63315425940138 20.0818623688923 23.407521105141978 4 36.08695652173913 27.340153452685424 17.263427109974426 19.30946291560102 5 34.50127877237852 28.874680306905372 17.51918158567775 19.104859335038363 6 28.61892583120205 31.713554987212277 20.076726342710998 19.59079283887468 7 28.61892583120205 15.396419437340153 33.42710997442455 22.55754475703325 8 29.00997697620875 20.158608339728833 23.919160910718855 26.912253773343565 9 31.422722620266118 21.084953940634595 23.490276356192428 24.00204708290686 10-11 33.99538698103537 26.37109174782163 18.528959507944645 21.104561763198358 12-13 33.260813923726644 19.810596365497823 21.947786025083186 24.980803685692347 14-15 31.903967133136472 23.31493131339068 22.506098343818202 22.275003209654642 16-17 32.050295098793946 22.73543751603798 22.389017192712345 22.825250192455734 18-19 32.575173477255206 22.950398355178617 21.498329478283217 22.97609868928296 20-21 32.03346203346204 23.17889317889318 22.586872586872587 22.2007722007722 22-23 32.31856133590237 23.622350674373795 21.811175337186896 22.24791265253693 24-25 31.803573724129063 24.0262244504435 21.51947551099113 22.650726314436305 26-27 30.63086213542336 24.592059617114224 22.896055505589104 21.881022741873313 28-29 27.001287001287 27.812097812097814 21.866151866151867 23.32046332046332 30-31 27.841273918068577 26.64697572877873 22.280724284063183 23.23102606908951 32-33 26.01646937725167 25.19300051466804 26.8013381369017 21.98919197117859 34-35 28.516328104911288 23.977886346104395 24.11931087683209 23.386474672152225 36-37 30.34571062740077 24.263764404609475 21.754161331626122 23.636363636363637 38-39 28.042056673932553 27.208616489293497 22.47724067188101 22.272086164892933 40-41 27.105803800719052 26.322547508988187 23.677452491011813 22.894196199280945 42-43 28.838759292489108 25.19866700845937 23.506793129966674 22.455780569084848 44-45 28.315182575272264 24.90711082639334 24.317745035233823 22.459961563100578 46-47 27.54905732974221 25.650891368475055 24.84288829036809 21.957163011414647 48-49 26.054081763424325 25.080097398436497 26.75893886966551 22.10688196847366 50-51 25.028790786948175 27.61356365962892 25.054382597568782 22.303262955854127 52-53 28.207099833397407 26.823016788414712 22.45290272971934 22.516980648468536 54-55 29.47880650531438 25.278524779101037 23.53694455115892 21.705724164425664 56-57 30.599692465402356 25.20502306509482 22.437211686314708 21.75807278318811 58-59 31.804202972834446 23.295745771399282 23.141978472578163 21.75807278318811 60-61 31.436626938357044 23.72164552095348 22.3119313084711 22.529796232218377 62-63 32.17447081462476 23.681847338037205 22.19371391917896 21.949967928159076 64-65 31.60056475420357 23.3217815428058 22.30779104094468 22.769862662045952 66-67 29.831770900218313 24.96468473096186 21.61294465134198 23.590599717477847 68-69 25.854536108969416 29.388332048316627 22.56489334361347 22.19223849910049 70-71 26.049987116722495 28.0468951301211 23.473331615562998 22.429786137593403 72-73 24.552296911497535 29.47054243446665 23.410329613288347 22.56683104074747 74-75 24.46428571428571 27.692307692307693 24.07967032967033 23.763736263736263 76 29.623430962343093 0.0 32.67782426778243 37.69874476987447 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 90.0 1 45.0 2 0.0 3 0.5 4 1.0 5 0.5 6 0.5 7 1.0 8 1.0 9 0.5 10 0.0 11 1.0 12 2.0 13 1.0 14 1.0 15 1.0 16 1.0 17 3.0 18 6.0 19 10.5 20 13.5 21 14.5 22 12.0 23 7.5 24 8.0 25 10.0 26 11.5 27 14.0 28 16.0 29 19.0 30 25.0 31 29.5 32 31.5 33 30.5 34 47.5 35 74.0 36 79.5 37 85.0 38 96.5 39 107.5 40 124.0 41 151.0 42 170.5 43 169.5 44 153.0 45 156.5 46 173.0 47 154.0 48 135.5 49 149.0 50 157.5 51 141.5 52 130.5 53 136.5 54 134.5 55 128.5 56 132.5 57 126.0 58 120.0 59 133.5 60 139.0 61 130.5 62 119.5 63 104.0 64 93.5 65 95.0 66 98.5 67 93.5 68 79.0 69 78.5 70 76.0 71 65.0 72 63.5 73 51.0 74 44.5 75 46.0 76 40.0 77 28.5 78 22.5 79 22.5 80 15.0 81 7.5 82 6.0 83 8.0 84 8.5 85 6.0 86 4.5 87 2.5 88 1.0 89 1.5 90 2.5 91 2.5 92 2.0 93 1.0 94 0.5 95 0.5 96 0.0 97 0.0 98 0.5 99 2.0 100 3.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 2.4 2 2.4 3 2.275 4 2.25 5 2.25 6 2.25 7 2.25 8 2.275 9 2.3 10-11 2.45 12-13 2.325 14-15 2.6374999999999997 16-17 2.5749999999999997 18-19 2.725 20-21 2.875 22-23 2.6875 24-25 2.7625 26-27 2.7125 28-29 2.875 30-31 2.6625 32-33 2.85 34-35 2.775 36-37 0.1278772378516624 38-39 0.26854219948849106 40-41 0.40920716112531963 42-43 0.23017902813299232 44-45 0.1918158567774936 46-47 0.29411764705882354 48-49 0.20462974804962272 50-51 0.03837298541826554 52-53 0.19186492709132769 54-55 0.07677543186180423 56-57 0.07682458386683738 58-59 0.05122950819672131 60-61 0.0 62-63 0.012827090815802975 64-65 0.03849114703618168 66-67 0.038510911424903725 68-69 0.0 70-71 0.01288161793121216 72-73 0.1166558651976669 74-75 0.09606147934678194 76 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 35 90.0 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 1.0 49 0.0 50 0.0 51 0.0 52 0.0 53 1.0 54 1.0 55 2.0 56 0.0 57 1.0 58 0.0 59 1.0 60 3.0 61 2.0 62 0.0 63 1.0 64 0.0 65 1.0 66 2.0 67 2.0 68 2.0 69 3.0 70 11.0 71 5.0 72 27.0 73 79.0 74 243.0 75 1132.0 76 2390.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 94.22500000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 97.02838949323429 91.425 2 2.5205624834173523 4.75 3 0.26532236667551073 0.75 4 0.10612894667020428 0.4 5 0.0 0.0 6 0.02653223666755107 0.15 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.02653223666755107 0.27499999999999997 >50 0.02653223666755107 2.25 >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 fail #Sequence Count Percentage Possible Source NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 90 2.25 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACA 11 0.27499999999999997 No Hit GTAAGTTAGAAGGGGAACGCGAAATCACTTTAGGTTTTGTTGATTTATTGCGCGACGATTTTATTGAAAA 6 0.15 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 0.05 0.0 0.0 0.0 0.0 32 0.05 0.0 0.0 0.0 0.0 33 0.05 0.0 0.0 0.0 0.0 34 0.05 0.0 0.0 0.0 0.0 35 0.05 0.0 0.0 0.0 0.0 36 0.05 0.0 0.0 0.0 0.0 37 0.075 0.0 0.0 0.0 0.0 38 0.075 0.0 0.0 0.0 0.0 39 0.075 0.0 0.0 0.0 0.0 40 0.075 0.0 0.0 0.0 0.0 41 0.075 0.0 0.0 0.0 0.0 42 0.075 0.0 0.0 0.0 0.0 43 0.075 0.0 0.0 0.0 0.0 44 0.075 0.0 0.0 0.0 0.0 45 0.075 0.0 0.0 0.0 0.0 46 0.075 0.0 0.0 0.0 0.0 47 0.075 0.0 0.0 0.0 0.0 48 0.075 0.0 0.0 0.0 0.0 49 0.075 0.0 0.0 0.0 0.0 50 0.075 0.0 0.0 0.0 0.0 51 0.075 0.0 0.0 0.0 0.0 52 0.075 0.0 0.0 0.0 0.0 53 0.075 0.0 0.0 0.0 0.0 54 0.075 0.0 0.0 0.0 0.0 55 0.075 0.0 0.0 0.0 0.0 56 0.075 0.0 0.0 0.0 0.0 57 0.075 0.0 0.0 0.0 0.0 58 0.075 0.0 0.0 0.0 0.0 59 0.075 0.0 0.0 0.0 0.0 60 0.075 0.0 0.0 0.0 0.0 61 0.075 0.0 0.0 0.0 0.0 62 0.075 0.0 0.0 0.0 0.0 63 0.075 0.0 0.0 0.0 0.0 64 0.075 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1284657 spots for SRR11389812.sra Written 1284657 spots for SRR11389812.sra Read 1284657 spots for SRR11389812.sra Written 1284657 spots for SRR11389812.sra Read 1284657 spots for SRR11389812.sra Written 1284657 spots for SRR11389812.sra Read 1284666 spots for SRR11389812.sra Written 1284666 spots for SRR11389812.sra Read 1284657 spots for SRR11389812.sra Written 1284657 spots for SRR11389812.sra Read 1284657 spots for SRR11389812.sra Written 1284657 spots for SRR11389812.sra Read 1284657 spots for SRR11389812.sra Written 1284657 spots for SRR11389812.sra Read 1284657 spots for SRR11389812.sra Written 1284657 spots for SRR11389812.sra Read 1284657 spots for SRR11389812.sra Written 1284657 spots for SRR11389812.sra Read 1284657 spots for SRR11389812.sra Written 1284657 spots for SRR11389812.sra Read 1284657 spots for SRR11389812.sra Written 1284657 spots for SRR11389812.sra Read 1284657 spots for SRR11389812.sra Written 1284657 spots for SRR11389812.sra Read 1284657 spots for SRR11389812.sra Written 1284657 spots for SRR11389812.sra Read 1284657 spots for SRR11389812.sra Written 1284657 spots for SRR11389812.sra Read 1284657 spots for SRR11389812.sra Written 1284657 spots for SRR11389812.sra Read 1284657 spots for SRR11389812.sra Written 1284657 spots for SRR11389812.sra Read 1284657 spots for SRR11389812.sra Written 1284657 spots for SRR11389812.sra Read 1284657 spots for SRR11389812.sra Written 1284657 spots for SRR11389812.sra Read 1284657 spots for SRR11389812.sra Written 1284657 spots for SRR11389812.sra Read 1284657 spots for SRR11389812.sra Written 1284657 spots for SRR11389812.sra SRR ids: ['SRR11389812.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_kf646otj SRR11389812.sra spots: 25693149 blocks: [[1, 1284657], [1284658, 2569314], [2569315, 3853971], [3853972, 5138628], [5138629, 6423285], [6423286, 7707942], [7707943, 8992599], [8992600, 10277256], [10277257, 11561913], [11561914, 12846570], [12846571, 14131227], [14131228, 15415884], [15415885, 16700541], [16700542, 17985198], [17985199, 19269855], [19269856, 20554512], [20554513, 21839169], [21839170, 23123826], [23123827, 24408483], [24408484, 25693149]] SRR11389812 file size 4836757 SRR11389812 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 SRR11389812 SRR11389812_1.fastq SRR11389812_2.fastq Input file: SRR11389812_1.fastq Paired file: SRR11389812_2.fastq trimmed: SRR11389812-trimmed-pair1.fastq, SRR11389812-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 07:07:35 2024 >> started Sat Dec 7 07:07:54 2024 >> done (19.288s) 25693149 read pairs processed; of these: 813 ( 0.00%) short read pairs filtered out after trimming by size control 3070684 (11.95%) empty read pairs filtered out after trimming by size control 22621652 (88.05%) read pairs available; of these: 35273 ( 0.16%) trimmed read pairs available after processing 22586379 (99.84%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 567 0.00% 19 38 0.00% 20 879 0.00% 21 13 0.00% 22 1147 0.01% 23 16 0.00% 24 1294 0.01% 25 22 0.00% 26 1503 0.01% 27 21 0.00% 28 1364 0.01% 29 16 0.00% 30 941 0.00% 31 9 0.00% 32 672 0.00% 33 11 0.00% 34 531 0.00% 35 368 0.00% 36 2576 0.01% 37 470 0.00% 38 1409 0.01% 39 517 0.00% 40 945 0.00% 41 781 0.00% 42 1085 0.00% 43 1070 0.00% 44 1351 0.01% 45 1347 0.01% 46 1515 0.01% 47 1823 0.01% 48 1912 0.01% 49 2135 0.01% 50 2420 0.01% 51 2706 0.01% 52 3241 0.01% 53 3507 0.02% 54 3841 0.02% 55 4854 0.02% 56 5802 0.03% 57 5729 0.03% 58 6409 0.03% 59 6736 0.03% 60 7498 0.03% 61 7824 0.03% 62 8658 0.04% 63 9722 0.04% 64 10552 0.05% 65 11646 0.05% 66 12633 0.06% 67 14387 0.06% 68 14161 0.06% 69 15497 0.07% 70 17452 0.08% 71 21660 0.10% 72 43560 0.19% 73 223345 0.99% 74 1616383 7.15% 75 10135674 44.81% 76 10377407 45.87% 22621652 reads passed initial QC criterion=sequence-density sequence-density=0.94 sequence-density-rank=1 fanout-score=2.03 fanout-score-rank=19 prefix-density=0.89 prefix-fanout=2.0 sequence=TTCAAATGTACA criterion=fanout-score sequence-density=0.02 sequence-density-rank=28 fanout-score=23.03 fanout-score-rank=1 prefix-density=0.31 prefix-fanout=1.1 sequence=CAAAAACAGCTAATTGGAAAGCAATAGTCATATTTCTAATCCTCCAAGCTATCATCAAATAAAGTTGACTACATATTTGATCCCTCACTTAACCTAAATTGTAAAAAATACAAGAAGTAGGAGGGGTTTAATCATGAATCCATTGATTCTTCTCTTTAATTAATAATTAAAACTTATTACTTACCGCTTTTATTTGGATATGGGGATTAGGGTAGGGGATTTAGTCTTTATTTCAAAAGCGGGTATAGCGGATCTTCTATCCGTGTATACAGTATACAGAAATATATCGAAAAAGGATTTGCATCTGAGATGTTTCTAGAGGTTAGTAGATCCTTTTATTTTTATATGGCTGTGTTCTATTTCTAGGAGTAAAATAGGGATTAAGCTGTGGAGAGATGGCTGAGTGGTT criterion=sequence-density sequence-density=0.77 sequence-density-rank=1 fanout-score=2.20 fanout-score-rank=17 prefix-density=0.77 prefix-fanout=2.2 sequence=CAGGTGCTCAAGGAGCTGGAGGAGGTCAAGAAGGAGTACCCGGACGCCTA criterion=fanout-score sequence-density=0.01 sequence-density-rank=28 fanout-score=7.46 fanout-score-rank=1 prefix-density=0.05 prefix-fanout=2.2 sequence=CCTCAAGCCAAAGCCTCTTGCTAAGCGTACCACACTATACAGACGTGCGCGCGCAGCCATGGCACCCACCGTGATGGCTTCCTCCGCCACCTCCGTGGC SRR11389812 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 07:08:20 Started mapping on | Dec 07 07:08:21 Finished on | Dec 07 07:09:57 Mapping speed, Million of reads per hour | 848.31 Number of input reads | 22621652 Average input read length | 150 UNIQUE READS: Uniquely mapped reads number | 18419613 Uniquely mapped reads % | 81.42% Average mapped length | 150.16 Number of splices: Total | 7257771 Number of splices: Annotated (sjdb) | 6910428 Number of splices: GT/AG | 7160770 Number of splices: GC/AG | 84224 Number of splices: AT/AC | 1879 Number of splices: Non-canonical | 10898 Mismatch rate per base, % | 0.64% Deletion rate per base | 0.01% Deletion average length | 1.67 Insertion rate per base | 0.01% Insertion average length | 1.61 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 2907343 % of reads mapped to multiple loci | 12.85% Number of reads mapped to too many loci | 104776 % of reads mapped to too many loci | 0.46% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.41% % of reads unmapped: other | 1.85% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1294696 1294696 1294696 N_multimapping 2907343 2907343 2907343 N_noFeature 694566 17848475 881226 N_ambiguous 622512 4271 272237 UnstrandedReadsAssigned:17102535 PositiveStrandReadsAssigned:566867 NegativeStrandReadsAssigned:17266150 Dataset is classified negative stranded MeadianReadLen=76 20thPercentileLength=75 echo kmer=71 SRR11389812 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: SRR11389812-trimmed-pair1.fastq SRR11389812-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 22,621,652 reads, 20,042,863 reads pseudoaligned [quant] estimated average fragment length: 184.843 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,521 rounds 52973 SRR11389812.ke.tsv 35125 SRR11389812.se.tsv 88098 total ==> SRR11389812.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 752.173 8.24603 0.732016 PNS24247 1044 860.157 10.6207 0.824461 PNS24249 1928 1744.16 90.1485 3.45117 PNS24246 1044 860.157 10.6207 0.824461 PNS24248 1044 860.157 10.6207 0.824461 PNS24244 1471 1287.16 78.7432 4.08484 PNS24243 293 123.07 0 0 KQK14069 1603 1419.16 1488.1 70.0156 KQK14071 474 291.857 108.463 24.8144 ==> SRR11389812.se.tsv <== BRADI_1g14170v3 1741 BRADI_1g53295v3 23 BRADI_1g59795v3 225 BRADI_1g07683v3 0 BRADI_1g00485v3 5 BRADI_1g20270v3 337 BRADI_1g74790v3 316 BRADI_1g09890v3 0 BRADI_1g77505v3 154 BRADI_1g48960v3 0 SRR11389812 completed mapping pipeline successfully