Starting /dee2/code/volunteer_pipeline.sh SRR9321779 current disk space = 3051766812672 free memory = 1581080368 SRR9321779 SRAfilesize fd3378666f78ac3fd29cfad7fa5e9cbe SRR9321779.sra SRR9321779.sra file validated SRR9321779 is paired end SRR9321779 is conventional basespace SRR9321779 read1 length is 38-76 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR9321779_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 38-76 %GC 47 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.58275 32.0 32.0 32.0 32.0 32.0 2 31.52225 32.0 32.0 32.0 32.0 32.0 3 31.60325 32.0 32.0 32.0 32.0 32.0 4 31.68225 32.0 32.0 32.0 32.0 32.0 5 31.66625 32.0 32.0 32.0 32.0 32.0 6 35.02275 36.0 36.0 36.0 36.0 36.0 7 35.355 36.0 36.0 36.0 36.0 36.0 8 35.31625 36.0 36.0 36.0 36.0 36.0 9 35.30925 36.0 36.0 36.0 36.0 36.0 10-11 35.333749999999995 36.0 36.0 36.0 36.0 36.0 12-13 35.28375 36.0 36.0 36.0 36.0 36.0 14-15 35.293875 36.0 36.0 36.0 36.0 36.0 16-17 35.249875 36.0 36.0 36.0 36.0 36.0 18-19 35.307249999999996 36.0 36.0 36.0 36.0 36.0 20-21 35.2125 36.0 36.0 36.0 36.0 36.0 22-23 35.260374999999996 36.0 36.0 36.0 36.0 36.0 24-25 35.255375 36.0 36.0 36.0 36.0 36.0 26-27 35.177625 36.0 36.0 36.0 36.0 36.0 28-29 35.164625 36.0 36.0 36.0 36.0 36.0 30-31 35.174625000000006 36.0 36.0 36.0 36.0 36.0 32-33 35.170249999999996 36.0 36.0 36.0 36.0 36.0 34-35 35.094125000000005 36.0 36.0 36.0 36.0 36.0 36-37 35.117000000000004 36.0 36.0 36.0 36.0 36.0 38-39 35.17739137909477 36.0 36.0 36.0 36.0 36.0 40-41 35.121405351337835 36.0 36.0 36.0 36.0 36.0 42-43 35.050262565641404 36.0 36.0 36.0 36.0 36.0 44-45 35.047261815453865 36.0 36.0 36.0 36.0 36.0 46-47 35.10027506876719 36.0 36.0 36.0 36.0 36.0 48-49 34.97624406101525 36.0 36.0 36.0 36.0 36.0 50-51 35.04476119029758 36.0 36.0 36.0 36.0 36.0 52-53 35.051012753188296 36.0 36.0 36.0 36.0 36.0 54-55 34.91235308827207 36.0 36.0 36.0 36.0 36.0 56-57 34.90860215053763 36.0 36.0 36.0 36.0 36.0 58-59 34.91085271317829 36.0 36.0 36.0 34.0 36.0 60-61 34.80895223805952 36.0 36.0 36.0 36.0 36.0 62-63 34.865091272818205 36.0 36.0 36.0 34.0 36.0 64-65 34.86244910402188 36.0 36.0 36.0 36.0 36.0 66-67 34.825912956478234 36.0 36.0 36.0 36.0 36.0 68-69 34.77023225147725 36.0 36.0 36.0 34.0 36.0 70-71 34.70863579474343 36.0 36.0 36.0 32.0 36.0 72-73 34.65493982742057 36.0 36.0 36.0 32.0 36.0 74-75 34.64612349982637 36.0 36.0 36.0 32.0 36.0 76 34.22103250478011 36.0 36.0 36.0 32.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 22 2.0 23 0.0 24 2.0 25 13.0 26 16.0 27 15.0 28 29.0 29 61.0 30 88.0 31 97.0 32 101.0 33 200.0 34 417.0 35 2959.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 35.325 11.475 9.175 44.025 2 22.075 15.5 37.325 25.1 3 19.6 18.224999999999998 24.65 37.525 4 22.975 28.125 21.2 27.700000000000003 5 23.025000000000002 33.300000000000004 22.8 20.875 6 20.166793025018954 32.92898660601466 25.878190548395246 21.02602982057114 7 15.299999999999999 21.875 42.0 20.825 8 19.0 22.2 31.4 27.400000000000002 9 18.575 22.375 33.175 25.874999999999996 10-11 22.275 29.9375 22.4875 25.3 12-13 21.775 23.4125 28.549999999999997 26.2625 14-15 21.762500000000003 25.25 26.787499999999998 26.200000000000003 16-17 22.7 25.9875 25.912499999999998 25.4 18-19 21.375 27.125 26.375 25.124999999999996 20-21 21.337500000000002 26.224999999999998 27.625 24.8125 22-23 22.3375 26.325 26.700000000000003 24.637500000000003 24-25 22.075 25.637500000000003 26.4625 25.825 26-27 21.325 25.724999999999998 27.0875 25.8625 28-29 21.95 26.437500000000004 26.4625 25.15 30-31 21.4375 26.275 25.974999999999998 26.3125 32-33 21.9 24.2875 27.0 26.8125 34-35 21.575 25.837500000000002 27.400000000000002 25.1875 36-37 21.6625 27.150000000000002 25.7125 25.474999999999998 38-39 22.877859732466558 25.653206650831358 25.66570821352669 25.803225403175396 40-41 21.59289822455614 26.406601650412604 25.918979744936234 26.081520380095025 42-43 21.930482620655166 26.006501625406354 27.25681420355089 24.8062015503876 44-45 21.680420105026258 25.731432858214554 27.031757939484873 25.55638909727432 46-47 22.643160790197552 25.85646411602901 26.494123530882717 25.006251562890725 48-49 22.143035758939735 25.256314078519633 25.881470367591895 26.71917979494874 50-51 20.86771692923231 26.331582895723933 27.04426106526632 25.756439109777446 52-53 21.517879469867466 25.993998499624904 28.14453613403351 24.343585896474117 54-55 22.06801700425106 27.144286071517882 25.893973493373345 24.893723430857715 56-57 21.742935733933482 25.618904726181547 26.831707926981746 25.806451612903224 58-59 21.24281070267567 25.681420355088775 27.00675168792198 26.069017254313575 60-61 22.73068267066767 26.081520380095025 26.331582895723933 24.85621405351338 62-63 22.05551387846962 25.431357839459867 26.744186046511626 25.76894223555889 64-65 21.370513942728522 25.734650493935224 26.597474052769787 26.297361510566464 66-67 22.061030515257627 26.150575287643825 26.600800400200097 25.18759379689845 68-69 21.713570981863665 27.267041901188243 25.56597873671044 25.453408380237647 70-71 20.963704630788484 26.245306633291616 26.821026282853566 25.96996245306633 72-73 21.553349252230742 26.4169913283901 26.555234384818398 25.474425034560767 74-75 22.095035272194863 22.387861040862507 28.17782510315453 27.3392785837881 76 25.812619502868067 0.0 37.32313575525812 36.864244741873804 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.0 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 0.5 18 0.5 19 0.5 20 1.0 21 1.0 22 1.5 23 4.0 24 6.5 25 7.0 26 6.5 27 9.5 28 11.0 29 10.5 30 18.5 31 29.5 32 34.5 33 37.0 34 54.0 35 71.5 36 87.5 37 110.0 38 124.0 39 134.5 40 157.5 41 192.0 42 211.5 43 231.0 44 244.0 45 256.0 46 272.5 47 278.0 48 268.5 49 253.5 50 245.5 51 231.0 52 208.5 53 179.5 54 170.5 55 175.5 56 174.5 57 145.5 58 114.5 59 125.5 60 124.5 61 74.0 62 36.5 63 35.0 64 32.0 65 22.0 66 16.0 67 16.0 68 10.5 69 4.0 70 2.0 71 2.0 72 6.5 73 7.0 74 3.0 75 2.0 76 1.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 1.075 7 0.0 8 0.0 9 0.0 10-11 0.0 12-13 0.0 14-15 0.0 16-17 0.0 18-19 0.0 20-21 0.0 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.0 30-31 0.0 32-33 0.0 34-35 0.0 36-37 0.0 38-39 0.0 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0 54-55 0.0 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0 66-67 0.0 68-69 0.0 70-71 0.0 72-73 0.0 74-75 0.0 76 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 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 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 1.0 65 0.0 66 0.0 67 0.0 68 1.0 69 2.0 70 0.0 71 4.0 72 25.0 73 75.0 74 269.0 75 1007.0 76 2615.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 92.15 #Duplication Level Percentage of deduplicated Percentage of total 1 94.46554530656537 87.05000000000001 2 3.798155181768855 7.000000000000001 3 1.0580575149213238 2.9250000000000003 4 0.3798155181768855 1.4000000000000001 5 0.16277807921866522 0.75 6 0.02712967986977754 0.15 7 0.08138903960933261 0.525 8 0.02712967986977754 0.2 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source CGGCAATCGGACGGCGGGCGCACGCGTCGCATCTAGCCCGGATTCTGACT 8 0.2 No Hit CCTATACCCAAGTCAGACGAACGATTTGCACGTCAGTATCGCTGCGGGCC 7 0.17500000000000002 No Hit ATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAG 7 0.17500000000000002 No Hit GCCACGCTTTCACGGTTCGTATTCGTACTGGAAATCAGAATCAAACGAGCTTTTACCCTTTTGTTCCACACG 7 0.17500000000000002 No Hit CTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGCAGTTGTTCGTCTT 6 0.15 No Hit CTTTTATCTAATAAATGCGTCCCTTCCAGAAGTCGGGGTTTGTTGCACGT 5 0.125 No Hit GTTCGATTAGTCTTTCGCCCCTATACCCAAGTCAGACGAACGATTTGCACGTCAGTATCGCTGCGGGCCTCCACC 5 0.125 No Hit CCCGACTGTCCCTGTTAATCATTACTCCGATCCCGAAGGCCAACACAATA 5 0.125 No Hit CTTTGACTCTCTTTTCAAAGTCCTTTTCATCTTTCCCTCGCGGTACTTGT 5 0.125 No Hit CTCGTACTAGGTTGGATTACTATTGCGACACTGTCATCAGTAGGGTAAAA 5 0.125 No Hit GTCGAGTTATCATGAATCATCAGAGCAACGGGCAGAGCCCGCGTCGACCTTTTATCTAATAAATGCGTCCCTTCC 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 SRR9321779 read2 length is 38-76 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR9321779_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 38-76 %GC 48 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.3725 32.0 32.0 32.0 32.0 32.0 2 31.2505 32.0 32.0 32.0 32.0 32.0 3 31.2625 32.0 32.0 32.0 32.0 32.0 4 31.135 32.0 32.0 32.0 32.0 32.0 5 31.08675 32.0 32.0 32.0 32.0 32.0 6 34.63625 36.0 36.0 36.0 32.0 36.0 7 34.665 36.0 36.0 36.0 32.0 36.0 8 34.796 36.0 36.0 36.0 32.0 36.0 9 34.784 36.0 36.0 36.0 32.0 36.0 10-11 34.727875 36.0 36.0 36.0 32.0 36.0 12-13 34.845124999999996 36.0 36.0 36.0 32.0 36.0 14-15 34.61275 36.0 36.0 36.0 32.0 36.0 16-17 34.639624999999995 36.0 36.0 36.0 34.0 36.0 18-19 34.68375 36.0 36.0 36.0 32.0 36.0 20-21 34.676375 36.0 36.0 36.0 32.0 36.0 22-23 34.61325 36.0 36.0 36.0 32.0 36.0 24-25 34.562250000000006 36.0 36.0 36.0 32.0 36.0 26-27 34.539874999999995 36.0 36.0 36.0 32.0 36.0 28-29 34.515 36.0 36.0 36.0 32.0 36.0 30-31 34.516 36.0 36.0 36.0 32.0 36.0 32-33 34.586125 36.0 36.0 36.0 32.0 36.0 34-35 34.42825 36.0 36.0 36.0 32.0 36.0 36-37 34.512875 36.0 36.0 36.0 32.0 36.0 38-39 34.3691689172293 36.0 36.0 36.0 32.0 36.0 40-41 34.43260815203801 36.0 36.0 36.0 32.0 36.0 42-43 34.41372843210803 36.0 36.0 36.0 32.0 36.0 44-45 34.17881530787899 36.0 36.0 36.0 32.0 36.0 46-47 34.164207103551774 36.0 36.0 36.0 32.0 36.0 48-49 34.242121060530266 36.0 36.0 36.0 32.0 36.0 50-51 34.13519259629815 36.0 36.0 36.0 32.0 36.0 52-53 34.2343671835918 36.0 36.0 36.0 32.0 36.0 54-55 34.10592796398199 36.0 36.0 36.0 32.0 36.0 56-57 34.160205102551274 36.0 36.0 36.0 32.0 36.0 58-59 33.95710355177589 36.0 36.0 36.0 32.0 36.0 60-61 33.9672336168084 36.0 36.0 36.0 29.5 36.0 62-63 33.89394697348675 36.0 36.0 36.0 29.5 36.0 64-65 33.89380442034878 36.0 36.0 36.0 32.0 36.0 66-67 33.75856892669502 36.0 36.0 36.0 27.0 36.0 68-69 33.751527140099824 36.0 36.0 36.0 27.0 36.0 70-71 33.87130696044066 36.0 36.0 36.0 29.5 36.0 72-73 33.71077696955624 36.0 36.0 36.0 27.0 36.0 74-75 33.8055597680944 36.0 36.0 36.0 27.0 36.0 76 32.82350718065004 36.0 32.0 36.0 27.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 9 1.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 7.0 16 5.0 17 7.0 18 3.0 19 4.0 20 9.0 21 6.0 22 7.0 23 16.0 24 27.0 25 35.0 26 45.0 27 43.0 28 52.0 29 66.0 30 89.0 31 130.0 32 160.0 33 275.0 34 557.0 35 2456.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 36.0 19.375 11.975 32.65 2 29.799999999999997 25.4 30.475 14.325 3 23.925 25.025 27.825 23.225 4 25.2 34.699999999999996 20.25 19.85 5 28.449999999999996 35.15 19.400000000000002 17.0 6 23.200000000000003 35.975 21.425 19.400000000000002 7 22.6 19.7 36.5 21.2 8 24.275 23.1 25.95 26.674999999999997 9 24.25 23.3 28.449999999999996 24.0 10-11 26.55 29.1375 21.762500000000003 22.55 12-13 25.868967241810452 24.281070267566893 25.593898474618655 24.256064016004 14-15 24.934350381393024 27.085156933850197 25.859697386519947 22.12079529823684 16-17 26.331582895723933 26.25656414103526 25.406351587896975 22.005501375343837 18-19 25.71892973243311 27.169292323080768 25.03125781445361 22.080520130032507 20-21 25.240655081885237 26.615826978372297 25.728216027003377 22.415301912739093 22-23 25.46273136568284 26.713356678339167 25.18759379689845 22.63631815907954 24-25 25.403175396924617 26.553319164895612 25.790723840480062 22.252781597699713 26-27 25.86293146573287 27.07603801900951 25.062531265632813 21.99849924962481 28-29 25.95648912228057 28.569642410602654 24.63115778944736 20.84271067766942 30-31 26.184819307240215 26.522445917218956 24.65924721770664 22.633487557834187 32-33 25.209453545079402 27.5728398149306 24.90934100287608 22.308365637113916 34-35 24.2875 26.8625 25.650000000000002 23.200000000000003 36-37 25.478184773096636 26.715839479934996 25.340667583447928 22.46530816352044 38-39 26.263131565782892 27.176088044022013 24.69984992496248 21.860930465232617 40-41 26.53239929947461 26.432324243182386 25.356517388041034 21.678759069301975 42-43 26.088044022011005 26.688344172086044 25.162581290645324 22.061030515257627 44-45 24.987493746873437 26.600800400200097 25.65032516258129 22.761380690345174 46-47 25.869402051538653 26.444833625218916 25.494120590442833 22.191643732799598 48-49 25.65674255691769 27.020265198899175 25.519139354515886 21.80385288966725 50-51 25.94445834375782 27.257943457593193 25.04378283712785 21.75381536152114 52-53 25.785061929188043 26.685850118854 25.59739772300763 21.93169022895033 54-55 25.622419617165022 27.01113474290004 25.697485299637187 21.66896034029776 56-57 25.168876657493122 28.3087315486615 24.580935701776333 21.94145609206905 58-59 26.04779181784061 26.735893907168773 25.59739772300763 21.618916551982988 60-61 27.627627627627625 25.713213213213216 24.924924924924923 21.734234234234233 62-63 26.063563563563562 25.875875875875877 25.33783783783784 22.722722722722725 64-65 26.48310387984981 26.29536921151439 25.344180225281605 21.877346683354194 66-67 26.189283925888834 26.877816725087634 24.749624436654983 22.183274912368553 68-69 25.597696833145577 27.062210539491797 26.010764801602203 21.329327825760423 70-71 25.961658939982456 27.114396692143846 24.92168901140208 22.00225535647162 72-73 25.326797385620914 27.161890397184514 25.150829562594268 22.360482654600304 74-75 26.4905962384954 22.515672935841003 27.09083633453381 23.902894491129786 76 26.66414523449319 0.0 37.67019667170953 35.665658093797276 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 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 1.0 15 1.5 16 0.5 17 0.0 18 0.0 19 0.0 20 0.5 21 1.5 22 1.0 23 1.0 24 3.5 25 5.5 26 7.0 27 8.0 28 8.0 29 8.0 30 13.0 31 21.5 32 30.0 33 36.5 34 44.5 35 62.0 36 82.0 37 98.5 38 124.5 39 164.5 40 183.5 41 200.5 42 226.5 43 230.5 44 248.5 45 266.0 46 274.0 47 292.5 48 291.5 49 268.0 50 240.5 51 214.5 52 200.0 53 182.0 54 160.0 55 154.5 56 149.0 57 130.5 58 114.0 59 104.0 60 104.0 61 92.0 62 74.5 63 47.0 64 14.5 65 15.0 66 18.0 67 16.5 68 15.0 69 11.0 70 6.5 71 4.5 72 8.5 73 12.0 74 6.0 75 0.5 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.5 85 0.5 86 0.0 87 0.0 88 0.0 89 0.5 90 1.0 91 1.0 92 1.0 93 0.5 94 0.0 95 0.0 96 0.0 97 0.5 98 0.5 99 9.0 100 18.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-11 0.0 12-13 0.025 14-15 0.0375 16-17 0.025 18-19 0.025 20-21 0.0125 22-23 0.05 24-25 0.0125 26-27 0.05 28-29 0.025 30-31 0.0375 32-33 0.0375 34-35 0.0 36-37 0.0125 38-39 0.037504688086010755 40-41 0.05001250312578145 42-43 0.025006251562890724 44-45 0.012504689258471927 46-47 0.02501250625312656 48-49 0.02501250625312656 50-51 0.02501250625312656 52-53 0.03751875937968985 54-55 0.03751875937968985 56-57 0.02501250625312656 58-59 0.03751875937968985 60-61 0.05002501250625312 62-63 0.05002501250625312 64-65 0.06253908692933083 66-67 0.07505629221916438 68-69 0.050043788314775434 70-71 0.08763144717075613 72-73 0.07535795026375283 74-75 0.053326223170243964 76 0.07558578987150416 >>END_MODULE >>Sequence Length Distribution warn #Length Count 38 1.0 39 0.0 40 0.0 41 0.0 42 0.0 43 0.0 44 1.0 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 1.0 65 0.0 66 0.0 67 0.0 68 1.0 69 2.0 70 0.0 71 2.0 72 22.0 73 75.0 74 289.0 75 960.0 76 2646.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 92.825 #Duplication Level Percentage of deduplicated Percentage of total 1 95.39455965526528 88.55 2 3.258820360894156 6.05 3 0.8618367896579585 2.4 4 0.21545919741448963 0.8 5 0.0 0.0 6 0.13466199838405601 0.75 7 0.026932399676811204 0.17500000000000002 8 0.026932399676811204 0.2 9 0.0 0.0 >10 0.08079719903043361 1.075 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 18 0.44999999999999996 No Hit GTCTGACATGTGTGCGAGTCAACGGGCGAGTAAACCCGTAAGGCGCAAGGAAGCTGACTGGCGGGATCCCCTCG 15 0.375 No Hit GTTAGTTTTACCCTACTGATGACAGTGTCGCAATAGTAATCCAACCTAGTACGAGAGGAACCGTTGATTCGCACA 10 0.25 No Hit CTGACATGTGTGCGAGTCAACGGGCGAGTAAACCCGTAAGGCGCAAGGAA 8 0.2 No Hit CTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAAG 7 0.17500000000000002 No Hit GGAGTCTGACATGTGTGCGAGTCAACGGGCGAGTAAACCCGTAAGGCGCA 6 0.15 No Hit CCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAA 6 0.15 No Hit GGCGGGACTACCCGCTGAGTTTAAGCATATCAATAAGCGGAGGAAAAGAA 6 0.15 No Hit ACCAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTTGAT 6 0.15 No Hit GCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAAGTA 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 0.0 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 1409715 spots for SRR9321779.sra Written 1409715 spots for SRR9321779.sra Read 1409715 spots for SRR9321779.sra Written 1409715 spots for SRR9321779.sra Read 1409715 spots for SRR9321779.sra Written 1409715 spots for SRR9321779.sra Read 1409715 spots for SRR9321779.sra Written 1409715 spots for SRR9321779.sra Read 1409715 spots for SRR9321779.sra Written 1409715 spots for SRR9321779.sra Read 1409715 spots for SRR9321779.sra Written 1409715 spots for SRR9321779.sra Read 1409715 spots for SRR9321779.sra Written 1409715 spots for SRR9321779.sra Read 1409715 spots for SRR9321779.sra Written 1409715 spots for SRR9321779.sra Read 1409715 spots for SRR9321779.sra Written 1409715 spots for SRR9321779.sra Read 1409715 spots for SRR9321779.sra Written 1409715 spots for SRR9321779.sra Read 1409715 spots for SRR9321779.sra Written 1409715 spots for SRR9321779.sra Read 1409715 spots for SRR9321779.sra Written 1409715 spots for SRR9321779.sra Read 1409715 spots for SRR9321779.sra Written 1409715 spots for SRR9321779.sra Read 1409715 spots for SRR9321779.sra Written 1409715 spots for SRR9321779.sra Read 1409715 spots for SRR9321779.sra Written 1409715 spots for SRR9321779.sra Read 1409715 spots for SRR9321779.sra Written 1409715 spots for SRR9321779.sra Read 1409715 spots for SRR9321779.sra Written 1409715 spots for SRR9321779.sra Read 1409715 spots for SRR9321779.sra Written 1409715 spots for SRR9321779.sra Read 1409715 spots for SRR9321779.sra Written 1409715 spots for SRR9321779.sra Read 1409715 spots for SRR9321779.sra Written 1409715 spots for SRR9321779.sra SRR ids: ['SRR9321779.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_xg6wosey SRR9321779.sra spots: 28194300 blocks: [[1, 1409715], [1409716, 2819430], [2819431, 4229145], [4229146, 5638860], [5638861, 7048575], [7048576, 8458290], [8458291, 9868005], [9868006, 11277720], [11277721, 12687435], [12687436, 14097150], [14097151, 15506865], [15506866, 16916580], [16916581, 18326295], [18326296, 19736010], [19736011, 21145725], [21145726, 22555440], [22555441, 23965155], [23965156, 25374870], [25374871, 26784585], [26784586, 28194300]] SRR9321779 file size 5348994 SRR9321779 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 SRR9321779 SRR9321779_1.fastq SRR9321779_2.fastq Input file: SRR9321779_1.fastq Paired file: SRR9321779_2.fastq trimmed: SRR9321779-trimmed-pair1.fastq, SRR9321779-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 Wed Feb 12 14:58:16 2025 >> started Wed Feb 12 14:58:51 2025 >> done (34.750s) 28194300 read pairs processed; of these: 4105 ( 0.01%) short read pairs filtered out after trimming by size control 8186 ( 0.03%) empty read pairs filtered out after trimming by size control 28182009 (99.96%) read pairs available; of these: 14078 ( 0.05%) trimmed read pairs available after processing 28167931 (99.95%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 3 0.00% 19 1 0.00% 20 4 0.00% 21 1 0.00% 22 12 0.00% 23 15 0.00% 24 14 0.00% 25 15 0.00% 26 15 0.00% 27 15 0.00% 28 20 0.00% 29 24 0.00% 30 21 0.00% 31 25 0.00% 32 31 0.00% 33 36 0.00% 34 36 0.00% 35 148 0.00% 36 161 0.00% 37 186 0.00% 38 215 0.00% 39 183 0.00% 40 230 0.00% 41 205 0.00% 42 230 0.00% 43 256 0.00% 44 306 0.00% 45 270 0.00% 46 251 0.00% 47 307 0.00% 48 375 0.00% 49 441 0.00% 50 492 0.00% 51 478 0.00% 52 575 0.00% 53 651 0.00% 54 622 0.00% 55 904 0.00% 56 942 0.00% 57 1027 0.00% 58 1275 0.00% 59 1512 0.01% 60 1937 0.01% 61 2058 0.01% 62 2094 0.01% 63 2237 0.01% 64 2473 0.01% 65 2832 0.01% 66 2955 0.01% 67 3348 0.01% 68 3214 0.01% 69 3270 0.01% 70 4236 0.02% 71 7220 0.03% 72 19932 0.07% 73 215459 0.76% 74 2179203 7.73% 75 13348417 47.37% 76 12368594 43.89% 28182009 reads passed initial QC criterion=sequence-density sequence-density=0.81 sequence-density-rank=1 fanout-score=1.96 fanout-score-rank=30 prefix-density=0.75 prefix-fanout=2.0 sequence=CCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCAGAACCCAAAAACTTTGATTTCTCATAAGGTGCTGGCGGAGTCCTAAAAGCAACATCCGCCAATCCCTGGTCGGCATCGTTTATGGTTGAGACTAGGACGGTATCTGATCGTCTTCGAGCCCCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGCAGTTGTTCGTCTTTCATAAATCCAAGAATTTCACCTCTGACTATGAAATACGAATGCCCCCGACTGTCCCTGTTAATCATTACTCCGATCCCGAAGGCCAACACAATAGGATCGAAATCCTATGATGTTATCCCATGCTAATGTATCCAGAGCGTAGGCTTGCTTTGAGCACTCTAATTTCTTCAAAGTAACAGCACCGGAGGCACGACCCGGCCAGTTAAGGCCAGGAGCGCATCGCCG criterion=fanout-score sequence-density=0.06 sequence-density-rank=30 fanout-score=10.55 fanout-score-rank=1 prefix-density=0.10 prefix-fanout=5.9 sequence=GCTCCAAGCATGGCCCACCTGGAATGGATGACTTCAAGCTCACGGTTCTTGGCAAAGGTCTCTGGGTCAGCAGAGAGGCCAGCAGTGTCCCAGCCGTAGTCACCAGGGAACTCACCAGTCAAGTAGGATGGGGGCTCACCAGAGAACGGGCCCAAGTATTTAACACGGTCTGGTCCGTACCATGGGCTCCCGGAGGGAACAGGCTTGGTGGTTTTCCTCATGGAGACACGGCCATTGCCCATGATCTCAGAGGAGGAGGGGTTGAGCTTCACC criterion=sequence-density sequence-density=0.36 sequence-density-rank=1 fanout-score=2.17 fanout-score-rank=27 prefix-density=0.39 prefix-fanout=2.1 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.02 sequence-density-rank=29 fanout-score=14.67 fanout-score-rank=1 prefix-density=0.12 prefix-fanout=2.6 sequence=CAAAACCACATATAGAGGGTGTAATAGCTAAGTAGCCTGTAAGAGATGGCTTCCTCTGTGATTTCATCGGCGGCCGTTGCCACAGTTAACCGCACCCC SRR9321779 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 12 14:59:32 Started mapping on | Feb 12 14:59:32 Finished on | Feb 12 15:02:04 Mapping speed, Million of reads per hour | 667.47 Number of input reads | 28182009 Average input read length | 151 UNIQUE READS: Uniquely mapped reads number | 20409406 Uniquely mapped reads % | 72.42% Average mapped length | 150.35 Number of splices: Total | 8121562 Number of splices: Annotated (sjdb) | 8031182 Number of splices: GT/AG | 7965533 Number of splices: GC/AG | 133439 Number of splices: AT/AC | 5973 Number of splices: Non-canonical | 16617 Mismatch rate per base, % | 0.52% Deletion rate per base | 0.02% Deletion average length | 2.21 Insertion rate per base | 0.02% Insertion average length | 2.26 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1469912 % of reads mapped to multiple loci | 5.22% Number of reads mapped to too many loci | 5274940 % of reads mapped to too many loci | 18.72% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.04% % of reads unmapped: other | 0.60% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 6302991 6302991 6302991 N_multimapping 1469912 1469912 1469912 N_noFeature 2051651 19994033 2144882 N_ambiguous 442669 2988 117849 UnstrandedReadsAssigned:17915086 PositiveStrandReadsAssigned:412385 NegativeStrandReadsAssigned:18146675 Dataset is classified negative stranded MeadianReadLen=76 20thPercentileLength=75 echo kmer=71 SRR9321779 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: 52,400 [index] number of k-mers: 62,057,036 [index] number of equivalence classes: 130,681 [quant] running in paired-end mode [quant] will process pair 1: SRR9321779-trimmed-pair1.fastq SRR9321779-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 28,182,009 reads, 22,141,537 reads pseudoaligned [quant] estimated average fragment length: 200.574 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,070 rounds 52401 SRR9321779.ke.tsv 34699 SRR9321779.se.tsv 87100 total ==> SRR9321779.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1818.43 254 4.35474 Potri.005G024800.1.v4.1 1035 835.426 97 3.61983 Potri.004G059700.1.v4.1 961 761.426 48 1.96534 Potri.007G009000.2.v4.1 1416 1216.43 0 0 Potri.003G141000.2.v4.1 2943 2743.43 262.102 2.97852 Potri.016G087400.1.v4.1 270 88.5983 1280.59 450.618 Potri.015G069301.1.v4.1 564 364.607 0 0 Potri.010G195200.1.v4.1 1773 1573.43 2 0.0396285 Potri.012G127500.1.v4.1 977 777.426 3408 136.667 ==> SRR9321779.se.tsv <== Potri.001G166300.v4.1 1 Potri.001G448400.v4.1 20 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 285 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 2 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 57 Potri.001G416900.v4.1 1 Potri.001G452600.v4.1 8 SRR9321779 completed mapping pipeline successfully