Starting /dee2/code/volunteer_pipeline.sh SRR11389810 current disk space = 1544760197120 free memory = 1599989912 SRR11389810 SRAfilesize 66242e6a8ee5245efa87a7b3db75855b SRR11389810.sra SRR11389810.sra file validated SRR11389810 is paired end SRR11389810 is conventional basespace SRR11389810 read1 length is 35-76 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11389810_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 30.6115 32.0 32.0 32.0 32.0 32.0 2 30.461 32.0 32.0 32.0 32.0 32.0 3 30.54225 32.0 32.0 32.0 32.0 32.0 4 30.47825 32.0 32.0 32.0 32.0 32.0 5 30.58675 32.0 32.0 32.0 32.0 32.0 6 33.57675 36.0 36.0 36.0 32.0 36.0 7 33.58775 36.0 36.0 36.0 32.0 36.0 8 33.57225 36.0 36.0 36.0 32.0 36.0 9 33.5575 36.0 36.0 36.0 32.0 36.0 10-11 33.608875 36.0 36.0 36.0 29.5 36.0 12-13 33.602875 36.0 36.0 36.0 32.0 36.0 14-15 33.61024999999999 36.0 36.0 36.0 32.0 36.0 16-17 33.647999999999996 36.0 36.0 36.0 32.0 36.0 18-19 33.579625 36.0 36.0 36.0 32.0 36.0 20-21 33.498999999999995 36.0 36.0 36.0 32.0 36.0 22-23 33.39375 36.0 36.0 36.0 29.5 36.0 24-25 33.387 36.0 36.0 36.0 29.5 36.0 26-27 33.204 36.0 36.0 36.0 24.0 36.0 28-29 33.093875 36.0 36.0 36.0 24.0 36.0 30-31 33.055499999999995 36.0 36.0 36.0 21.0 36.0 32-33 33.01275 36.0 36.0 36.0 17.5 36.0 34-35 33.052875 36.0 36.0 36.0 21.0 36.0 36-37 33.89430477167778 36.0 36.0 36.0 32.0 36.0 38-39 33.86377629553617 36.0 36.0 36.0 32.0 36.0 40-41 33.722934838378656 36.0 36.0 36.0 27.0 36.0 42-43 33.79476654694715 36.0 36.0 36.0 29.5 36.0 44-45 33.57503848127244 36.0 36.0 36.0 27.0 36.0 46-47 33.56682914315033 36.0 36.0 36.0 24.0 36.0 48-49 33.42085684966649 36.0 36.0 36.0 21.0 36.0 50-51 33.51885582349923 36.0 36.0 36.0 27.0 36.0 52-53 33.238968701898415 36.0 36.0 36.0 21.0 36.0 54-55 32.925346331452026 36.0 32.0 36.0 17.5 36.0 56-57 33.0758081067214 36.0 34.0 36.0 21.0 36.0 58-59 32.90584915341201 36.0 34.0 36.0 14.0 36.0 60-61 32.8074653668548 36.0 34.0 36.0 14.0 36.0 62-63 32.568496664956385 36.0 32.0 36.0 14.0 36.0 64-65 32.68381221139046 36.0 32.0 36.0 14.0 36.0 66-67 32.484094407388405 36.0 32.0 36.0 14.0 36.0 68-69 32.3297845048743 36.0 32.0 36.0 14.0 36.0 70-71 32.17600779723862 36.0 32.0 36.0 14.0 36.0 72-73 32.283964046209974 36.0 32.0 36.0 14.0 36.0 74-75 32.141551419356986 36.0 32.0 36.0 14.0 36.0 76 30.69670905011219 36.0 27.0 36.0 14.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 102.0 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 1.0 21 2.0 22 5.0 23 12.0 24 15.0 25 24.0 26 48.0 27 58.0 28 89.0 29 139.0 30 191.0 31 255.0 32 381.0 33 545.0 34 982.0 35 1151.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 36.58286300667009 13.237557721908672 12.314007183170856 37.86557208825038 2 24.243201641867625 13.981528989225245 36.53155464340688 25.243714725500254 3 22.24217547460236 21.062083119548486 22.011287839917905 34.68445356593124 4 27.270395074397126 28.937916880451514 19.984607491021038 23.807080554130323 5 25.808106721395585 31.78553104155977 23.293996921498202 19.112365315546434 6 23.063063063063062 31.45431145431146 26.023166023166024 19.45945945945946 7 16.957414058491533 24.91021036428938 38.71216008209338 19.420215495125706 8 19.343252950230887 23.601847101077475 30.041046690610568 27.013853258081067 9 19.8306824012314 20.369420215495126 34.50487429451001 25.295023088763468 10-11 22.53719856336583 31.33658286300667 22.614161108260646 23.512057465366855 12-13 23.499230374551054 24.525397639815292 26.46228835300154 25.513083632632117 14-15 22.55002565418163 25.25654181631606 27.052334530528476 25.141097998973834 16-17 23.063109286813752 25.79527963057979 26.385325808106717 24.756285274499742 18-19 22.255002565418163 25.384812724474088 26.449461262185736 25.910723447922013 20-21 23.935351462288352 25.73114417650077 25.590046177526936 24.74345818368394 22-23 22.434581836839403 27.001026167265263 26.82144689584402 23.74294510005131 24-25 23.640328373524884 25.94920472036942 25.307850179579273 25.10261672652642 26-27 21.735781229939658 26.871228655796635 26.06239568622416 25.330594428039543 28-29 23.469780572308483 25.625561401257542 25.073784165276532 25.83087386115745 30-31 22.761098280728767 26.712856043110083 25.352835514498334 25.17321016166282 32-33 22.524371472550026 26.385325808106717 26.000513083632633 25.08978963571062 34-35 22.229348383786558 26.051821446895847 25.8594150846588 25.8594150846588 36-37 22.504490633820886 26.17397998460354 25.968693867077242 25.352835514498334 38-39 22.92201128783992 26.398152898922522 25.98768599281683 24.692149820420727 40-41 22.88353001539251 26.269881990764492 25.21806054386865 25.62852744997435 42-43 22.63981528989225 24.576706003078503 26.66752180605439 26.115956900974858 44-45 22.58850692662904 25.359158542842486 25.93637762955362 26.115956900974858 46-47 23.37095946639302 24.858902001026166 26.269881990764492 25.50025654181632 48-49 22.58850692662904 25.397639815289892 26.2955361723961 25.718317085684966 50-51 22.473063109286816 25.346331452026682 26.42380708055413 25.756798358132375 52-53 23.717290918419703 24.076449461262186 25.52591072344792 26.680348896870186 54-55 22.370446382760388 25.448948178553106 26.000513083632633 26.180092355053873 56-57 22.524371472550026 25.295023088763468 26.770138532580813 25.410466906105693 58-59 22.72960492560287 25.333504361210878 26.064648537711648 25.872242175474604 60-61 23.444116514820994 23.995893750802004 26.08751443603234 26.472475298344666 62-63 22.8450487429451 24.409953822473064 27.347357619291945 25.397639815289892 64-65 23.781426372498718 24.114930733709596 26.50076962544895 25.60287326834274 66-67 22.58850692662904 24.884556182657775 25.808106721395585 26.7188301693176 68-69 23.46074910210364 22.691123653155465 26.244227809132887 27.603899435608003 70-71 23.450930083386787 24.297626683771647 26.029506093649772 26.22193713919179 72-73 23.598401855909266 24.73256862997809 25.22232246423508 26.44670704987756 74-75 23.90922598946373 22.761042820478185 26.678373632311224 26.651357557746856 76 26.58937920718025 0.0 35.228122662677634 38.182498130142115 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 102.0 1 51.5 2 0.5 3 0.0 4 0.0 5 0.0 6 0.5 7 0.5 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.5 15 1.0 16 1.0 17 1.0 18 7.5 19 15.5 20 22.0 21 28.5 22 30.0 23 24.5 24 15.0 25 9.5 26 13.5 27 33.0 28 42.5 29 37.0 30 36.5 31 44.0 32 56.5 33 63.5 34 71.0 35 78.0 36 86.5 37 102.5 38 123.5 39 134.5 40 149.5 41 179.5 42 194.5 43 181.0 44 177.5 45 194.5 46 204.0 47 194.5 48 174.5 49 167.0 50 166.0 51 148.0 52 128.5 53 109.5 54 95.0 55 109.5 56 111.5 57 115.5 58 123.0 59 112.0 60 94.5 61 95.0 62 106.5 63 85.5 64 61.0 65 62.0 66 65.5 67 63.5 68 62.0 69 54.5 70 48.0 71 48.0 72 41.5 73 33.0 74 28.0 75 22.5 76 18.5 77 13.5 78 9.0 79 7.0 80 6.5 81 7.5 82 6.5 83 4.0 84 4.5 85 2.5 86 1.0 87 2.0 88 1.5 89 1.0 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 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 2.55 2 2.55 3 2.55 4 2.55 5 2.55 6 2.875 7 2.55 8 2.55 9 2.55 10-11 2.55 12-13 2.55 14-15 2.55 16-17 2.55 18-19 2.55 20-21 2.55 22-23 2.55 24-25 2.55 26-27 2.6374999999999997 28-29 2.5875 30-31 2.5749999999999997 32-33 2.55 34-35 2.55 36-37 0.02565418163160595 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 0.038481272447408926 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 35 102.0 36 0.0 37 0.0 38 0.0 39 0.0 40 0.0 41 0.0 42 0.0 43 0.0 44 0.0 45 0.0 46 0.0 47 0.0 48 0.0 49 0.0 50 0.0 51 0.0 52 0.0 53 0.0 54 0.0 55 0.0 56 0.0 57 0.0 58 0.0 59 0.0 60 0.0 61 0.0 62 0.0 63 0.0 64 0.0 65 0.0 66 0.0 67 0.0 68 0.0 69 0.0 70 1.0 71 8.0 72 19.0 73 43.0 74 251.0 75 902.0 76 2674.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 91.55 #Duplication Level Percentage of deduplicated Percentage of total 1 96.47733478973238 88.325 2 2.2665210267613327 4.15 3 0.6553795740032768 1.7999999999999998 4 0.2730748225013654 1.0 5 0.1365374112506827 0.625 6 0.05461496450027307 0.3 7 0.027307482250136534 0.17500000000000002 8 0.0 0.0 9 0.027307482250136534 0.22499999999999998 >10 0.05461496450027307 0.8500000000000001 >50 0.0 0.0 >100 0.027307482250136534 2.55 >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 102 2.55 No Hit GCCGAGTTTAATTGCAGTCAATTAGAAGAATAAAGAAGAATTACTGCATT 23 0.575 No Hit GTCAATTAGAAGAATAAAGAAGAATTACTGCATTTCGTAACTTATTTTTT 11 0.27499999999999997 No Hit GTCAGGGTTCAAATGTACATATGCTCCTCGAGCCCATGTCGGTACATTCA 9 0.22499999999999998 No Hit GTTTAATTGCAGTCAATTAGAAGAATAAAGAAGAATTACTGCATTTCGTA 7 0.17500000000000002 No Hit GGCTAGTTCAGGACTCCATTTGCAAGCTGCTCGGATAATTTCATTACCTTCACGAGCAAGATCGCGCCCTTCGTT 6 0.15 No Hit CTTCGTTACGAGCTTGTACACAGGCTTCTAAAGCCACTCGATTAGCTGCT 6 0.15 No Hit GAAAAATAGAAAACTCAAAGCAATGTCAGAGTTGACAAAACTGAGCTGAC 5 0.125 No Hit CCGGCGCGAACTCGAATTTGATCGCCTTCCATACTTCACAAGCTGCGGCT 5 0.125 No Hit GAAAAAGGTACATAAAATCGGTGTGACCCGTTCTTGTATTATAAGAAATC 5 0.125 No Hit CTTCACAAGCTGCGGCTAGTTCAGGACTCCATTTGCAAGCTGCTCGGATAATTTCATTACCTTCACGAGCA 5 0.125 No Hit GAAGAATTACTGCATTTCGTAACTTATTTTTTCTCTTTTTATTTTGTTTC 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10 0.0 0.0 0.0 0.0 0.0 11 0.0 0.0 0.0 0.0 0.0 12 0.0 0.0 0.0 0.0 0.0 13 0.0 0.0 0.0 0.0 0.0 14 0.0 0.0 0.0 0.0 0.0 15 0.0 0.0 0.0 0.0 0.0 16 0.0 0.0 0.0 0.0 0.0 17 0.0 0.0 0.0 0.0 0.0 18 0.0 0.0 0.0 0.0 0.0 19 0.0 0.0 0.0 0.0 0.0 20 0.0 0.0 0.0 0.0 0.0 21 0.025 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 0.05 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 0.05 0.0 0.0 0.0 0.0 38 0.05 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 SRR11389810 read2 length is 35-76 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11389810_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 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.20175 32.0 32.0 32.0 32.0 32.0 2 29.85525 32.0 32.0 32.0 21.0 32.0 3 29.80975 32.0 32.0 32.0 21.0 32.0 4 29.75325 32.0 32.0 32.0 21.0 32.0 5 29.90875 32.0 32.0 32.0 21.0 32.0 6 33.1475 36.0 36.0 36.0 21.0 36.0 7 33.2175 36.0 36.0 36.0 21.0 36.0 8 32.76825 36.0 36.0 36.0 14.0 36.0 9 32.89675 36.0 36.0 36.0 21.0 36.0 10-11 32.814125000000004 36.0 36.0 36.0 17.5 36.0 12-13 32.941874999999996 36.0 36.0 36.0 21.0 36.0 14-15 32.694125 36.0 36.0 36.0 14.0 36.0 16-17 32.7555 36.0 36.0 36.0 14.0 36.0 18-19 32.531875 36.0 36.0 36.0 14.0 36.0 20-21 32.426874999999995 36.0 36.0 36.0 14.0 36.0 22-23 32.60125 36.0 36.0 36.0 14.0 36.0 24-25 32.485125 36.0 36.0 36.0 14.0 36.0 26-27 32.4705 36.0 36.0 36.0 14.0 36.0 28-29 32.263125 36.0 36.0 36.0 14.0 36.0 30-31 32.370125 36.0 36.0 36.0 14.0 36.0 32-33 32.421625 36.0 36.0 36.0 14.0 36.0 34-35 32.410624999999996 36.0 36.0 36.0 14.0 36.0 36-37 33.2216944801027 36.0 36.0 36.0 17.5 36.0 38-39 33.01258023106547 36.0 36.0 36.0 14.0 36.0 40-41 32.933376123234915 36.0 36.0 36.0 14.0 36.0 42-43 32.964698331193844 36.0 36.0 36.0 14.0 36.0 44-45 32.83350449293967 36.0 36.0 36.0 14.0 36.0 46-47 32.787804878048775 36.0 34.0 36.0 14.0 36.0 48-49 32.66598202824133 36.0 34.0 36.0 14.0 36.0 50-51 32.603209242618746 36.0 34.0 36.0 14.0 36.0 52-53 32.42002567394095 36.0 32.0 36.0 14.0 36.0 54-55 32.518998716302946 36.0 32.0 36.0 14.0 36.0 56-57 32.30192554557125 36.0 32.0 36.0 14.0 36.0 58-59 32.062387676508344 36.0 32.0 36.0 14.0 36.0 60-61 32.03414634146341 36.0 32.0 36.0 14.0 36.0 62-63 31.985879332477538 36.0 32.0 36.0 14.0 36.0 64-65 32.01412066752246 36.0 32.0 36.0 14.0 36.0 66-67 31.73735558408216 36.0 32.0 36.0 14.0 36.0 68-69 31.58125802310655 36.0 32.0 36.0 14.0 36.0 70-71 31.493207199398192 36.0 32.0 36.0 14.0 36.0 72-73 31.553156714940698 36.0 32.0 36.0 14.0 36.0 74-75 31.452065598939882 36.0 32.0 36.0 14.0 36.0 76 30.125291828793774 36.0 27.0 36.0 14.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 105.0 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 2.0 13 2.0 14 2.0 15 3.0 16 8.0 17 11.0 18 10.0 19 8.0 20 9.0 21 19.0 22 18.0 23 30.0 24 36.0 25 47.0 26 68.0 27 82.0 28 101.0 29 166.0 30 194.0 31 280.0 32 421.0 33 553.0 34 989.0 35 836.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 36.517719568567024 19.82537236774525 10.503338469440164 33.153569594247564 2 30.482794042116073 23.189522342064713 28.50539291217257 17.822290703646637 3 25.622593068035943 27.77920410783055 21.28369704749679 25.314505776636715 4 27.75353016688062 33.27342747111682 18.921694480102698 20.051347881899872 5 28.985879332477538 32.041078305519896 19.897304236200256 19.07573812580231 6 23.72272143774069 34.68549422336329 20.56482670089859 21.02695763799743 7 23.414634146341466 17.252888318356867 35.8408215661104 23.49165596919127 8 24.9743062692703 22.07091469681398 23.6896197327852 29.265159301130524 9 24.49241840143922 21.022873297352866 26.471344127473657 28.013364173734256 10-11 27.864214992927867 28.89288928892889 19.686254339719685 23.556641378423556 12-13 27.238853912373123 22.125144545804957 23.641269433380444 26.994732108441475 14-15 25.663488791548573 24.980675083741303 25.083741303787683 24.272094820922444 16-17 28.3507145616068 23.818720226599716 23.818720226599716 24.01184498519377 18-19 27.269210933470863 24.8968540484786 23.904074265085097 23.929860752965446 20-21 27.25748194014448 24.935500515995873 23.284313725490197 24.522703818369454 22-23 27.12868736313281 24.835759371377044 23.6248872858431 24.410665979647046 24-25 26.68901495616297 25.077359463641052 23.53017019082001 24.703455389375968 26-27 26.975125660523265 25.38986982858616 22.799329810542595 24.835674700347983 28-29 27.073390945440472 25.332129498258737 23.81013801109248 23.784341545208306 30-31 27.090042509339174 23.81811155481128 23.869638026536133 25.22220790931341 32-33 26.028634077131436 24.60982845350187 24.95808074293822 24.40345672642848 34-35 26.666666666666668 25.918762088974855 23.27530625402966 24.139264990328822 36-37 26.899832840426903 24.34100552912434 23.196605374823196 25.562556255625562 38-39 25.858741798533387 26.32188344268622 23.195677344654573 24.623697414125818 40-41 26.494845360824744 25.347938144329895 22.809278350515463 25.347938144329895 42-43 26.212842619997428 25.646634924720114 23.4718826405868 24.668639814695663 44-45 26.922087940344564 26.25353561326819 22.65363846747236 24.17073797891489 46-47 26.921591348010814 26.07184241019699 23.02047122441097 23.986095017381228 48-49 27.18034473887317 24.183174684846925 24.32467198353486 24.31180859274505 50-51 26.817364500385306 25.378885178525557 22.989982019008476 24.813768302080657 52-53 26.254180602006688 25.868278878312324 23.604322099305378 24.27321842037561 54-55 26.696658097686377 25.552699228791774 23.431876606683804 24.318766066838045 56-57 26.557882564563794 25.838365668765256 24.232301169214956 23.371450597455993 58-59 27.393036104329948 24.88757548503148 23.4228446614416 24.296543749196967 60-61 27.48395378690629 25.41720154043646 23.016688061617458 24.082156611039796 62-63 26.161745827984596 26.93196405648267 23.388960205391527 23.517329910141207 64-65 26.888489208633093 25.719424460431657 23.021582733812952 24.370503597122305 66-67 26.20760534429599 25.79650565262076 24.07502569373073 23.92086330935252 68-69 26.17458279845956 26.456996148908857 23.478818998716303 23.889602053915276 70-71 27.081192189105856 24.807297019527237 24.126413155190132 23.98509763617677 72-73 25.851132686084142 25.72168284789644 23.624595469255663 24.802588996763756 74-75 26.894563426688634 23.215266337177376 25.31576057111477 24.57440966501922 76 27.39299610894942 0.0 35.83657587548638 36.77042801556421 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 105.0 1 52.5 2 0.5 3 0.5 4 0.0 5 0.0 6 1.0 7 1.0 8 0.0 9 0.0 10 1.0 11 2.0 12 1.5 13 2.5 14 3.0 15 3.0 16 4.0 17 5.0 18 7.0 19 11.0 20 13.0 21 11.5 22 14.0 23 15.5 24 15.5 25 16.0 26 17.0 27 17.0 28 18.0 29 22.0 30 23.0 31 26.0 32 34.0 33 38.5 34 43.0 35 69.0 36 86.5 37 81.5 38 85.5 39 102.5 40 120.0 41 133.5 42 145.5 43 171.0 44 186.5 45 175.5 46 181.5 47 178.0 48 170.0 49 175.0 50 168.5 51 143.0 52 131.5 53 136.5 54 135.5 55 132.0 56 123.0 57 118.5 58 119.5 59 131.5 60 132.0 61 116.5 62 98.5 63 103.0 64 105.5 65 85.0 66 75.5 67 74.0 68 72.0 69 77.5 70 65.0 71 44.5 72 40.0 73 39.5 74 39.0 75 34.5 76 30.0 77 23.5 78 15.5 79 9.0 80 8.0 81 7.0 82 7.0 83 9.0 84 7.0 85 2.5 86 0.5 87 0.0 88 0.5 89 1.0 90 2.0 91 1.5 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.5 99 2.5 100 4.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 2.65 2 2.65 3 2.625 4 2.625 5 2.625 6 2.625 7 2.625 8 2.7 9 2.725 10-11 2.7875 12-13 2.7125 14-15 2.9749999999999996 16-17 2.9125 18-19 3.05 20-21 3.1 22-23 2.9625 24-25 3.05 26-27 3.0124999999999997 28-29 3.0875 30-31 2.9625 32-33 3.0875 34-35 3.0625 36-37 0.1668806161745828 38-39 0.21822849807445444 40-41 0.38510911424903727 42-43 0.24390243902439024 44-45 0.1540436456996149 46-47 0.2952503209242619 48-49 0.20539152759948653 50-51 0.051347881899871634 52-53 0.20539152759948653 54-55 0.12836970474967907 56-57 0.08985879332477535 58-59 0.08985879332477535 60-61 0.0 62-63 0.0 64-65 0.07702182284980745 66-67 0.07702182284980745 68-69 0.0 70-71 0.0 72-73 0.11636927851047324 74-75 0.10970927043335163 76 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 35 105.0 36 0.0 37 0.0 38 0.0 39 0.0 40 0.0 41 0.0 42 0.0 43 0.0 44 0.0 45 0.0 46 0.0 47 0.0 48 0.0 49 0.0 50 0.0 51 0.0 52 0.0 53 0.0 54 0.0 55 0.0 56 0.0 57 0.0 58 0.0 59 0.0 60 0.0 61 0.0 62 0.0 63 0.0 64 0.0 65 0.0 66 0.0 67 0.0 68 0.0 69 0.0 70 6.0 71 9.0 72 26.0 73 69.0 74 278.0 75 937.0 76 2570.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 92.475 #Duplication Level Percentage of deduplicated Percentage of total 1 96.59367396593674 89.325 2 2.51419302514193 4.65 3 0.48661800486618007 1.35 4 0.21627466882941337 0.8 5 0.054068667207353344 0.25 6 0.027034333603676672 0.15 7 0.0 0.0 8 0.0 0.0 9 0.027034333603676672 0.22499999999999998 >10 0.054068667207353344 0.625 >50 0.0 0.0 >100 0.027034333603676672 2.625 >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 105 2.625 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACA 13 0.325 No Hit CTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTG 12 0.3 No Hit AAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTCG 9 0.22499999999999998 No Hit GCCAGGTGTTATACCAGTAGCTTCAGGTGGTATTCATGTTTGGCATATGC 6 0.15 No Hit TGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGAT 5 0.125 No Hit GTTTGGCATATGCCAGCTCTGACCGAAATCTTTGGGGATGATTCTGTATT 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10 0.0 0.0 0.0 0.0 0.0 11 0.0 0.0 0.0 0.0 0.0 12 0.0 0.0 0.0 0.0 0.0 13 0.0 0.0 0.0 0.0 0.0 14 0.0 0.0 0.0 0.0 0.0 15 0.0 0.0 0.0 0.0 0.0 16 0.0 0.0 0.0 0.0 0.0 17 0.0 0.0 0.0 0.0 0.0 18 0.0 0.0 0.0 0.0 0.0 19 0.0 0.0 0.0 0.0 0.0 20 0.0 0.0 0.0 0.0 0.0 21 0.0 0.0 0.0 0.0 0.0 22 0.0 0.0 0.0 0.0 0.0 23 0.0 0.0 0.0 0.0 0.0 24 0.0 0.0 0.0 0.0 0.0 25 0.0 0.0 0.0 0.0 0.0 26 0.0 0.0 0.0 0.0 0.0 27 0.0 0.0 0.0 0.0 0.0 28 0.0 0.0 0.0 0.0 0.0 29 0.0 0.0 0.0 0.0 0.0 30 0.0 0.0 0.0 0.0 0.0 31 0.0 0.0 0.0 0.0 0.0 32 0.0 0.0 0.0 0.0 0.0 33 0.0 0.0 0.0 0.0 0.0 34 0.0 0.0 0.0 0.0 0.0 35 0.0 0.0 0.0 0.0 0.0 36 0.0 0.0 0.0 0.0 0.0 37 0.0 0.0 0.0 0.0 0.0 38 0.0 0.0 0.0 0.0 0.0 39 0.0 0.0 0.0 0.0 0.0 40 0.0 0.0 0.0 0.0 0.0 41 0.0 0.0 0.0 0.0 0.0 42 0.0 0.0 0.0 0.0 0.0 43 0.0 0.0 0.0 0.0 0.0 44 0.0 0.0 0.0 0.0 0.0 45 0.0 0.0 0.0 0.0 0.0 46 0.0 0.0 0.0 0.0 0.0 47 0.0 0.0 0.0 0.0 0.0 48 0.0 0.0 0.0 0.0 0.0 49 0.0 0.0 0.0 0.0 0.0 50 0.0 0.0 0.0 0.0 0.0 51 0.0 0.0 0.0 0.0 0.0 52 0.0 0.0 0.0 0.0 0.0 53 0.0 0.0 0.0 0.0 0.0 54 0.0 0.0 0.0 0.0 0.0 55 0.0 0.0 0.0 0.0 0.0 56 0.0 0.0 0.0 0.0 0.0 57 0.0 0.0 0.0 0.0 0.0 58 0.0 0.0 0.0 0.0 0.0 59 0.0 0.0 0.0 0.0 0.0 60 0.0 0.0 0.0 0.0 0.0 61 0.0 0.0 0.0 0.0 0.0 62 0.0 0.0 0.0 0.0 0.0 63 0.0 0.0 0.0 0.0 0.0 64 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1189293 spots for SRR11389810.sra Written 1189293 spots for SRR11389810.sra Read 1189293 spots for SRR11389810.sra Written 1189293 spots for SRR11389810.sra Read 1189293 spots for SRR11389810.sra Written 1189293 spots for SRR11389810.sra Read 1189293 spots for SRR11389810.sra Written 1189293 spots for SRR11389810.sra Read 1189293 spots for SRR11389810.sra Written 1189293 spots for SRR11389810.sra Read 1189293 spots for SRR11389810.sra Written 1189293 spots for SRR11389810.sra Read 1189293 spots for SRR11389810.sra Written 1189293 spots for SRR11389810.sra Read 1189293 spots for SRR11389810.sra Written 1189293 spots for SRR11389810.sra Read 1189293 spots for SRR11389810.sra Written 1189293 spots for SRR11389810.sra Read 1189293 spots for SRR11389810.sra Written 1189293 spots for SRR11389810.sra Read 1189293 spots for SRR11389810.sra Written 1189293 spots for SRR11389810.sra Read 1189293 spots for SRR11389810.sra Written 1189293 spots for SRR11389810.sra Read 1189293 spots for SRR11389810.sra Written 1189293 spots for SRR11389810.sra Read 1189293 spots for SRR11389810.sra Written 1189293 spots for SRR11389810.sra Read 1189293 spots for SRR11389810.sra Written 1189293 spots for SRR11389810.sra Read 1189293 spots for SRR11389810.sra Written 1189293 spots for SRR11389810.sra Read 1189293 spots for SRR11389810.sra Written 1189293 spots for SRR11389810.sra Read 1189293 spots for SRR11389810.sra Written 1189293 spots for SRR11389810.sra Read 1189293 spots for SRR11389810.sra Written 1189293 spots for SRR11389810.sra Read 1189306 spots for SRR11389810.sra Written 1189306 spots for SRR11389810.sra SRR ids: ['SRR11389810.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_08zk31ep SRR11389810.sra spots: 23785873 blocks: [[1, 1189293], [1189294, 2378586], [2378587, 3567879], [3567880, 4757172], [4757173, 5946465], [5946466, 7135758], [7135759, 8325051], [8325052, 9514344], [9514345, 10703637], [10703638, 11892930], [11892931, 13082223], [13082224, 14271516], [14271517, 15460809], [15460810, 16650102], [16650103, 17839395], [17839396, 19028688], [19028689, 20217981], [20217982, 21407274], [21407275, 22596567], [22596568, 23785873]] SRR11389810 file size 4469447 SRR11389810 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 SRR11389810 SRR11389810_1.fastq SRR11389810_2.fastq Input file: SRR11389810_1.fastq Paired file: SRR11389810_2.fastq trimmed: SRR11389810-trimmed-pair1.fastq, SRR11389810-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 07:06:44 2024 >> started Sat Dec 7 07:07:08 2024 >> done (23.701s) 23785873 read pairs processed; of these: 1156 ( 0.00%) short read pairs filtered out after trimming by size control 827655 ( 3.48%) empty read pairs filtered out after trimming by size control 22957062 (96.52%) read pairs available; of these: 59950 ( 0.26%) trimmed read pairs available after processing 22897112 (99.74%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 2501 0.01% 19 27 0.00% 20 4122 0.02% 21 31 0.00% 22 4842 0.02% 23 26 0.00% 24 5243 0.02% 25 33 0.00% 26 5854 0.03% 27 40 0.00% 28 5586 0.02% 29 29 0.00% 30 4011 0.02% 31 39 0.00% 32 3315 0.01% 33 38 0.00% 34 2682 0.01% 35 119 0.00% 36 7826 0.03% 37 108 0.00% 38 4201 0.02% 39 121 0.00% 40 1877 0.01% 41 150 0.00% 42 898 0.00% 43 118 0.00% 44 557 0.00% 45 182 0.00% 46 322 0.00% 47 219 0.00% 48 369 0.00% 49 231 0.00% 50 345 0.00% 51 325 0.00% 52 383 0.00% 53 415 0.00% 54 717 0.00% 55 979 0.00% 56 2568 0.01% 57 2076 0.01% 58 1681 0.01% 59 1061 0.00% 60 1199 0.01% 61 1177 0.01% 62 1220 0.01% 63 1236 0.01% 64 1562 0.01% 65 1664 0.01% 66 1689 0.01% 67 2193 0.01% 68 2138 0.01% 69 2631 0.01% 70 3435 0.01% 71 5251 0.02% 72 30882 0.13% 73 214482 0.93% 74 1628247 7.09% 75 10422328 45.40% 76 10569461 46.04% 22957062 reads passed initial QC criterion=sequence-density sequence-density=1.09 sequence-density-rank=1 fanout-score=2.01 fanout-score-rank=23 prefix-density=1.03 prefix-fanout=2.0 sequence=TTCAAATGTACA criterion=fanout-score sequence-density=0.01 sequence-density-rank=30 fanout-score=46.31 fanout-score-rank=1 prefix-density=0.26 prefix-fanout=1.0 sequence=TACGGAGCTGAATCGATGGCCACAGTTGAATCTCGAAATACATACATGAGCAAGCATATGACTCACAGAGATGGAGAAATATATAGTATCAGCTGGCTCATCAATGATCCTGCATGTATATAGTTTGCAGGCGCGTACATTATAACAACACATCATCATATATTGACACCCTTGAAACGGAGAAATTAAGGCGGGCCGGGCGATGCATCAATCAGTTGACGGTGACCTTGCCGACCATGCCGGCCCCGGCATGTGGCTCGCAGTAGAAGCCGTAGGTGCCAGGGACAGTGAGCGTGACGGAGAAAGTCTCGCCGGGGGCGTTGAGGTACTCCTCCTGGGAGATCTTGGAGACGTCGACGCCGCTGGGCACGGCGTCCTCGTCG criterion=sequence-density sequence-density=0.77 sequence-density-rank=1 fanout-score=2.24 fanout-score-rank=19 prefix-density=0.77 prefix-fanout=2.2 sequence=CAGGTGCTCAAGGAGCTGGAGGAGGTCAAGAAGGAGTACCCGGACGCCTA criterion=fanout-score sequence-density=0.01 sequence-density-rank=30 fanout-score=8.51 fanout-score-rank=1 prefix-density=0.04 prefix-fanout=2.5 sequence=CCTCAAGCCAAAGCCTCTTGCTAAGCGTACCACACTATACAGACGTGCGCGCGCAGCCATGGCACCCACCGTGATGGCTTCCTCCGCCACCTCCGTGGC SRR11389810 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 07:07:33 Started mapping on | Dec 07 07:07:33 Finished on | Dec 07 07:09:34 Mapping speed, Million of reads per hour | 683.02 Number of input reads | 22957062 Average input read length | 150 UNIQUE READS: Uniquely mapped reads number | 18536112 Uniquely mapped reads % | 80.74% Average mapped length | 150.35 Number of splices: Total | 7095106 Number of splices: Annotated (sjdb) | 6729153 Number of splices: GT/AG | 6997759 Number of splices: GC/AG | 84713 Number of splices: AT/AC | 1936 Number of splices: Non-canonical | 10698 Mismatch rate per base, % | 0.63% Deletion rate per base | 0.01% Deletion average length | 1.67 Insertion rate per base | 0.01% Insertion average length | 1.60 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 3162277 % of reads mapped to multiple loci | 13.77% Number of reads mapped to too many loci | 102257 % of reads mapped to too many loci | 0.45% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.44% % of reads unmapped: other | 1.60% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1258673 1258673 1258673 N_multimapping 3162277 3162277 3162277 N_noFeature 669602 17975332 832459 N_ambiguous 678837 3960 314560 UnstrandedReadsAssigned:17187673 PositiveStrandReadsAssigned:556820 NegativeStrandReadsAssigned:17389093 Dataset is classified negative stranded MeadianReadLen=76 20thPercentileLength=75 echo kmer=71 SRR11389810 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: SRR11389810-trimmed-pair1.fastq SRR11389810-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 22,957,062 reads, 20,561,905 reads pseudoaligned [quant] estimated average fragment length: 211.174 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,389 rounds 52973 SRR11389810.ke.tsv 35125 SRR11389810.se.tsv 88098 total ==> SRR11389810.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 725.929 0 0 PNS24247 1044 833.826 30.9481 2.39946 PNS24249 1928 1717.83 60.2055 2.26575 PNS24246 1044 833.826 30.9481 2.39946 PNS24248 1044 833.826 30.9481 2.39946 PNS24244 1471 1260.83 56.9502 2.92008 PNS24243 293 102.582 0 0 KQK14069 1603 1392.83 453.454 21.047 KQK14071 474 266.335 2.27089 0.551217 ==> SRR11389810.se.tsv <== BRADI_1g14170v3 468 BRADI_1g53295v3 20 BRADI_1g59795v3 208 BRADI_1g07683v3 0 BRADI_1g00485v3 11 BRADI_1g20270v3 272 BRADI_1g74790v3 358 BRADI_1g09890v3 0 BRADI_1g77505v3 235 BRADI_1g48960v3 0 SRR11389810 completed mapping pipeline successfully