Starting /dee2/code/volunteer_pipeline.sh SRR9668918 current disk space = 3051951763456 free memory = 1495776040 SRR9668918 SRAfilesize 7b77c73f201055f8c7450312c0b9049f SRR9668918.sra SRR9668918.sra file validated SRR9668918 is paired end SRR9668918 is conventional basespace SRR9668918 read1 length is 35-76 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR9668918_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 47 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.476 32.0 32.0 32.0 32.0 32.0 2 31.5525 32.0 32.0 32.0 32.0 32.0 3 31.44425 32.0 32.0 32.0 32.0 32.0 4 31.58775 32.0 32.0 32.0 32.0 32.0 5 31.602 32.0 32.0 32.0 32.0 32.0 6 34.561 36.0 36.0 36.0 32.0 36.0 7 35.16125 36.0 36.0 36.0 36.0 36.0 8 35.21275 36.0 36.0 36.0 36.0 36.0 9 35.2075 36.0 36.0 36.0 36.0 36.0 10-11 35.084500000000006 36.0 36.0 36.0 36.0 36.0 12-13 35.10325 36.0 36.0 36.0 36.0 36.0 14-15 35.129875 36.0 36.0 36.0 36.0 36.0 16-17 35.121 36.0 36.0 36.0 36.0 36.0 18-19 35.064 36.0 36.0 36.0 36.0 36.0 20-21 35.07062500000001 36.0 36.0 36.0 36.0 36.0 22-23 34.958749999999995 36.0 36.0 36.0 36.0 36.0 24-25 35.044 36.0 36.0 36.0 36.0 36.0 26-27 34.907250000000005 36.0 36.0 36.0 34.0 36.0 28-29 35.031875 36.0 36.0 36.0 36.0 36.0 30-31 34.9675 36.0 36.0 36.0 36.0 36.0 32-33 34.9355 36.0 36.0 36.0 34.0 36.0 34-35 34.867125 36.0 36.0 36.0 32.0 36.0 36-37 34.86059014753688 36.0 36.0 36.0 36.0 36.0 38-39 34.835208802200555 36.0 36.0 36.0 32.0 36.0 40-41 34.84021005251313 36.0 36.0 36.0 34.0 36.0 42-43 34.718804701175294 36.0 36.0 36.0 34.0 36.0 44-45 34.75631407851963 36.0 36.0 36.0 34.0 36.0 46-47 34.83470867716929 36.0 36.0 36.0 34.0 36.0 48-49 34.771942985746435 36.0 36.0 36.0 34.0 36.0 50-51 34.704301075268816 36.0 36.0 36.0 32.0 36.0 52-53 34.76215439552735 36.0 36.0 36.0 34.0 36.0 54-55 34.628064032016006 36.0 36.0 36.0 32.0 36.0 56-57 34.588044022011005 36.0 36.0 36.0 32.0 36.0 58-59 34.622637970223536 36.0 36.0 36.0 32.0 36.0 60-61 34.53202401801351 36.0 36.0 36.0 32.0 36.0 62-63 34.37896484174943 36.0 36.0 36.0 32.0 36.0 64-65 34.36903038833577 36.0 36.0 36.0 32.0 36.0 66-67 34.29048811013767 36.0 36.0 36.0 32.0 36.0 68-69 34.280851063829786 36.0 36.0 36.0 32.0 36.0 70-71 34.315480313326795 36.0 36.0 36.0 32.0 36.0 72-73 34.29797504316266 36.0 36.0 36.0 32.0 36.0 74-75 34.2254413834096 36.0 36.0 36.0 32.0 36.0 76 33.288880397401606 36.0 32.0 36.0 27.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 1.0 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 1.0 19 0.0 20 2.0 21 0.0 22 0.0 23 6.0 24 8.0 25 12.0 26 19.0 27 25.0 28 58.0 29 58.0 30 93.0 31 109.0 32 163.0 33 243.0 34 596.0 35 2606.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 38.40960240060015 13.303325831457865 8.577144286071519 39.709927481870466 2 20.605151287821954 15.9039759939985 39.184796199049764 24.306076519129782 3 18.95473868467117 19.954988747186796 26.756689172293076 34.33358339584896 4 24.5311327831958 29.00725181295324 21.10527631907977 25.35633908477119 5 22.05551387846962 33.158289572393095 23.58089522380595 21.205301325331334 6 18.999237998475994 34.391668783337565 25.755651511303025 20.853441706883412 7 15.503875968992247 22.355588897224308 42.5856464116029 19.554888722180543 8 17.879469867466867 21.405351337834457 31.58289572393098 29.132283070767688 9 18.30457614403601 22.255563890972745 32.45811452863216 26.981745436359088 10-11 22.118029507376843 30.945236309077266 22.593148287071767 24.343585896474117 12-13 21.330332583145786 23.69342335583896 28.482120530132534 26.494123530882717 14-15 21.392848212053014 25.04376094023506 27.38184546136534 26.18154538634659 16-17 21.91797949487372 26.294073518379594 27.019254813703427 24.76869217304326 18-19 21.817954488622153 25.70642660665166 26.481620405101275 25.993998499624904 20-21 21.280320080020005 26.994248562140534 26.344086021505376 25.381345336334082 22-23 22.06801700425106 26.469117279319832 26.25656414103526 25.206301575393848 24-25 21.05526381595399 26.206551637909474 27.00675168792198 25.731432858214554 26-27 20.817704426106527 25.893973493373345 27.19429857464366 26.094023505876468 28-29 21.705426356589147 25.693923480870218 26.456614153538382 26.144036009002253 30-31 20.955238809702426 26.006501625406354 27.11927981995499 25.918979744936234 32-33 21.742935733933482 25.30632658164541 27.069267316829208 25.881470367591895 34-35 21.31782945736434 26.86921730432608 26.04401100275069 25.76894223555889 36-37 20.84271067766942 26.981745436359088 26.581645411352838 25.593898474618655 38-39 21.59289822455614 26.106526631657918 25.85646411602901 26.44411102775694 40-41 21.705426356589147 25.818954738684667 26.206551637909474 26.269067266816705 42-43 22.030507626906726 25.868967241810452 26.79419854963741 25.30632658164541 44-45 21.75543885971493 25.543885971492873 27.369342335583895 25.331332833208304 46-47 21.642910727681922 26.18154538634659 25.743935983995996 26.431607901975497 48-49 21.280320080020005 26.506626656664167 26.094023505876468 26.11902975743936 50-51 21.54288572143036 26.106526631657918 26.819204801200303 25.531382845711427 52-53 20.77028885832187 27.210203826434913 26.647492809803673 25.372014505439537 54-55 21.91095547773887 26.825912956478238 25.550275137568786 25.71285642821411 56-57 20.79789894947474 26.125562781390695 26.550775387693847 26.525762881440716 58-59 21.325828642901815 26.71669793621013 26.89180737961226 25.065666041275797 60-61 21.766324743557668 26.332249186890166 26.057042782086565 25.8443832874656 62-63 21.130989615913926 26.360565494807958 26.936069060427876 25.572375828850248 64-65 20.385433612814417 26.204480040045052 26.629958703541483 26.78012764359905 66-67 20.575719649561954 26.670838548185234 26.90863579474343 25.844806007509387 68-69 21.576971214017522 25.65707133917397 27.096370463078852 25.669586983729666 70-71 21.607411116675014 26.064096144216325 26.81522283425138 25.51326990485729 72-73 21.536523929471034 25.4911838790932 26.926952141057935 26.045340050377835 74-75 22.013082365505273 22.760646108663728 27.19263115738887 28.033640368442132 76 23.30913259457394 0.0 39.01413832632786 37.6767290790982 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 1.0 1 0.5 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 0.0 18 0.0 19 1.0 20 2.0 21 3.0 22 3.5 23 5.5 24 7.0 25 6.5 26 7.5 27 11.5 28 16.5 29 18.0 30 26.5 31 33.5 32 30.5 33 31.0 34 48.0 35 72.0 36 91.5 37 105.5 38 127.0 39 146.5 40 161.0 41 196.5 42 219.0 43 222.5 44 224.0 45 248.0 46 274.0 47 294.0 48 274.0 49 243.5 50 244.5 51 238.0 52 234.0 53 215.0 54 194.0 55 163.5 56 137.5 57 131.0 58 122.0 59 111.5 60 99.5 61 64.0 62 35.5 63 30.0 64 20.5 65 14.0 66 13.0 67 13.5 68 7.5 69 4.0 70 5.0 71 5.5 72 10.0 73 10.0 74 4.5 75 1.5 76 0.5 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 0.5 98 0.5 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.025 2 0.025 3 0.025 4 0.025 5 0.025 6 1.575 7 0.025 8 0.025 9 0.025 10-11 0.025 12-13 0.025 14-15 0.025 16-17 0.025 18-19 0.025 20-21 0.025 22-23 0.025 24-25 0.025 26-27 0.025 28-29 0.025 30-31 0.025 32-33 0.025 34-35 0.025 36-37 0.0 38-39 0.0 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0 54-55 0.0 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0 66-67 0.0 68-69 0.0 70-71 0.0 72-73 0.0 74-75 0.0 76 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 35 1.0 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 1.0 53 0.0 54 0.0 55 0.0 56 0.0 57 0.0 58 1.0 59 0.0 60 0.0 61 0.0 62 1.0 63 0.0 64 1.0 65 0.0 66 0.0 67 0.0 68 0.0 69 0.0 70 2.0 71 10.0 72 26.0 73 78.0 74 267.0 75 995.0 76 2617.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 92.10000000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 94.81541802388708 87.325 2 3.5559174809989145 6.550000000000001 3 0.8957654723127036 2.475 4 0.3800217155266015 1.4000000000000001 5 0.16286644951140067 0.75 6 0.02714440825190011 0.15 7 0.05428881650380022 0.35000000000000003 8 0.02714440825190011 0.2 9 0.0 0.0 >10 0.08143322475570033 0.8 >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 GTCAGTATCGCTGCGGGCCTCCACCAGAGTTTCCTCTGGCTTCGCCCCGC 11 0.27499999999999997 No Hit GTTCGATTAGTCTTTCGCCCCTATACCCAAGTCAGACGAACGATTTGCACGTCAGTATCGCTGCGGGCCTCCACC 11 0.27499999999999997 No Hit CGGCAATCGGACGGCGGGCGCACGCGTCGCATCTAGCCCGGATTCTGACT 10 0.25 No Hit CTTTTGTTCCACACGAGATTTCTGTTCTCGTTGAGCTCATCTTAGGACAC 8 0.2 No Hit CCCGACTGTCCCTGTTAATCATTACTCCGATCCCGAAGGCCAACACAATA 7 0.17500000000000002 No Hit CCGACATCGAAGGATCAAAAAGCAACGTCGCTATGAACGCTTGGCTGCCA 7 0.17500000000000002 No Hit GTCGAGTTATCATGAATCATCAGAGCAACGGGCAGAGCCCGCGTCGACCTTTTATCTAATAAATGCGTCCCTTCC 6 0.15 No Hit CCTAGATGTCCAGTCAACTGCTGCGCCTCAACGCATTTCGGGGAGAACCA 5 0.125 No Hit CTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATT 5 0.125 No Hit GCCACGCTTTCACGGTTCGTATTCGTACTGGAAATCAGAATCAAACGAGCTTTTACCCTTTTGTTCCACACG 5 0.125 No Hit GTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCAGAACCCA 5 0.125 No Hit GTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCAT 5 0.125 No Hit CTCATCTTGGGGTGGGCTTACTACTTAGATGCTTTCAGCAGTTATCCGCT 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 0.025 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 pass >>END_MODULE SRR9668918 read2 length is 35-76 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR9668918_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 48 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.2215 32.0 32.0 32.0 32.0 32.0 2 31.06175 32.0 32.0 32.0 32.0 32.0 3 31.05775 32.0 32.0 32.0 32.0 32.0 4 31.013 32.0 32.0 32.0 32.0 32.0 5 30.9755 32.0 32.0 32.0 32.0 32.0 6 34.294 36.0 36.0 36.0 32.0 36.0 7 34.62225 36.0 36.0 36.0 32.0 36.0 8 34.4695 36.0 36.0 36.0 32.0 36.0 9 34.487 36.0 36.0 36.0 32.0 36.0 10-11 34.503375000000005 36.0 36.0 36.0 32.0 36.0 12-13 34.445499999999996 36.0 36.0 36.0 32.0 36.0 14-15 34.361125 36.0 36.0 36.0 32.0 36.0 16-17 34.3895 36.0 36.0 36.0 32.0 36.0 18-19 34.404125 36.0 36.0 36.0 32.0 36.0 20-21 34.268 36.0 36.0 36.0 32.0 36.0 22-23 34.31175 36.0 36.0 36.0 32.0 36.0 24-25 34.344750000000005 36.0 36.0 36.0 32.0 36.0 26-27 34.323499999999996 36.0 36.0 36.0 32.0 36.0 28-29 34.2755 36.0 36.0 36.0 32.0 36.0 30-31 34.12775 36.0 36.0 36.0 32.0 36.0 32-33 34.27175 36.0 36.0 36.0 32.0 36.0 34-35 34.255375 36.0 36.0 36.0 32.0 36.0 36-37 34.17694235588972 36.0 36.0 36.0 32.0 36.0 38-39 34.071189411231764 36.0 36.0 36.0 32.0 36.0 40-41 34.11331471853515 36.0 36.0 36.0 32.0 36.0 42-43 33.95509628962131 36.0 36.0 36.0 32.0 36.0 44-45 33.87162721995079 36.0 36.0 36.0 29.5 36.0 46-47 33.86768767260859 36.0 36.0 36.0 29.5 36.0 48-49 34.09819186338524 36.0 36.0 36.0 32.0 36.0 50-51 34.08779201205727 36.0 36.0 36.0 32.0 36.0 52-53 33.82301718337985 36.0 36.0 36.0 32.0 36.0 54-55 33.912939698492465 36.0 36.0 36.0 32.0 36.0 56-57 33.869723618090454 36.0 36.0 36.0 32.0 36.0 58-59 33.69167321275894 36.0 36.0 36.0 32.0 36.0 60-61 33.788835186590305 36.0 36.0 36.0 27.0 36.0 62-63 33.74236344013288 36.0 36.0 36.0 27.0 36.0 64-65 33.68670519975197 36.0 36.0 36.0 27.0 36.0 66-67 33.674465408805034 36.0 36.0 36.0 27.0 36.0 68-69 33.777965581309964 36.0 36.0 36.0 27.0 36.0 70-71 33.723606999563266 36.0 36.0 36.0 27.0 36.0 72-73 33.53789368783161 36.0 36.0 36.0 27.0 36.0 74-75 33.7390799488042 36.0 36.0 36.0 27.0 36.0 76 32.754731556585554 36.0 32.0 36.0 27.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 10.0 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 1.0 12 0.0 13 1.0 14 1.0 15 5.0 16 6.0 17 5.0 18 12.0 19 3.0 20 5.0 21 9.0 22 18.0 23 7.0 24 19.0 25 36.0 26 49.0 27 63.0 28 96.0 29 83.0 30 99.0 31 119.0 32 186.0 33 280.0 34 611.0 35 2276.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 40.55680963130173 19.964885879107097 10.885377476799599 28.592927012791574 2 29.581348708949612 24.34194033592379 31.937829029832038 14.13888192529456 3 24.185463659147867 26.967418546365913 26.64160401002506 22.205513784461154 4 26.992481203007518 34.48621553884712 19.097744360902254 19.423558897243108 5 28.270676691729324 35.18796992481203 19.674185463659146 16.8671679197995 6 23.007518796992482 35.81453634085213 21.127819548872182 20.050125313283207 7 21.879699248120303 18.847117794486216 36.817042606516296 22.45614035087719 8 23.984962406015036 22.25563909774436 27.04260651629073 26.71679197994987 9 24.260651629072683 23.308270676691727 28.39598997493734 24.035087719298247 10-11 26.015037593984964 30.639097744360903 21.553884711779446 21.791979949874687 12-13 26.954887218045116 23.859649122807017 24.62406015037594 24.561403508771928 14-15 25.13784461152882 26.553884711779446 26.79197994987469 21.51629072681704 16-17 25.329153605015676 26.269592476489027 25.705329153605017 22.695924764890282 18-19 26.478696741854634 26.04010025062657 25.125313283208023 22.355889724310778 20-21 25.933817999498622 26.986713462020557 24.90599147656054 22.17347706192028 22-23 26.320411491657257 26.43332078785598 25.291682348513362 21.954585371973405 24-25 26.836299824517422 27.400350965154175 24.091250940085235 21.67209827024317 26-27 25.451127819548873 27.017543859649123 25.25062656641604 22.280701754385966 28-29 25.971908703285678 27.66491096062202 25.13167795334838 21.231502382743916 30-31 26.711038553309052 26.685922391058646 24.902674871279668 21.70036418435263 32-33 25.11283851554664 28.52306920762287 24.849548645937812 21.51454363089268 34-35 25.2508780732564 27.67185148018063 25.439036628198696 21.638233818364274 36-37 26.69432918395574 27.91399471897397 24.38073682886961 21.01093926820068 38-39 25.283303953664067 26.869806094182824 26.25283303953664 21.59405691261647 40-41 26.26008064516129 27.99899193548387 24.281754032258064 21.459173387096776 42-43 26.200983482536884 27.03316101374354 25.204892195183458 21.560963308536124 44-45 25.454775138959068 27.172814552804446 26.07377463365336 21.29863567458312 46-47 26.151710210778745 27.047835415877824 25.394421305061215 21.406033068282216 48-49 26.173398766830253 26.752233547250537 25.330313325783315 21.7440543601359 50-51 25.70457976849522 26.811776547559134 26.333668847508807 21.14997483643684 52-53 26.205767535574864 26.382067749653697 26.205767535574864 21.206397179196575 54-55 24.80453972257251 27.187894073139972 26.34300126103405 21.664564943253467 56-57 25.630676084762865 26.1226034308779 26.311806256306763 21.93491422805247 58-59 25.782038345105953 24.848637739656912 27.119071644803228 22.250252270433904 60-61 26.90757995467137 26.328380760513724 25.98841601611685 20.77562326869806 62-63 25.970262096774192 25.793850806451612 25.78125 22.454637096774192 64-65 27.385159010600706 26.299848561332663 25.32811711256941 20.986875315497226 66-67 25.73807721423164 26.961897552359325 25.864244259399445 21.43578097400959 68-69 25.34022177419355 27.381552419354836 25.315020161290324 21.963205645161292 70-71 27.204030226700255 25.730478589420652 25.52896725440806 21.536523929471034 72-73 25.80400101291466 26.968852874145355 24.588503418586985 22.638642694353 74-75 26.591458501208702 22.951920494225085 26.69889873757722 23.75772226698899 76 27.35703245749614 0.0 40.1854714064915 32.45749613601237 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 10.0 1 5.0 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 0.5 15 1.0 16 1.5 17 2.5 18 2.0 19 1.0 20 1.0 21 1.0 22 1.5 23 1.0 24 1.0 25 2.0 26 6.0 27 10.0 28 11.5 29 12.0 30 17.0 31 26.0 32 31.5 33 36.0 34 45.0 35 65.0 36 83.5 37 98.0 38 120.5 39 164.0 40 210.0 41 220.5 42 216.5 43 249.5 44 265.5 45 243.5 46 246.0 47 284.5 48 293.5 49 248.0 50 225.0 51 218.0 52 193.5 53 178.0 54 171.5 55 154.0 56 136.0 57 122.0 58 106.0 59 95.0 60 102.0 61 86.0 62 60.0 63 46.0 64 27.0 65 18.0 66 13.5 67 14.5 68 17.0 69 17.0 70 10.5 71 4.5 72 6.5 73 7.0 74 3.0 75 0.0 76 1.0 77 2.0 78 2.0 79 2.0 80 1.0 81 0.0 82 0.5 83 1.0 84 1.0 85 0.5 86 0.5 87 1.5 88 2.0 89 1.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 1.0 98 1.5 99 9.0 100 17.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.325 2 0.27499999999999997 3 0.25 4 0.25 5 0.25 6 0.25 7 0.25 8 0.25 9 0.25 10-11 0.25 12-13 0.25 14-15 0.25 16-17 0.3125 18-19 0.25 20-21 0.27499999999999997 22-23 0.36250000000000004 24-25 0.27499999999999997 26-27 0.25 28-29 0.325 30-31 0.46249999999999997 32-33 0.3 34-35 0.35000000000000003 36-37 0.3383458646616541 38-39 0.46371725780172957 40-41 0.5139776858468096 42-43 0.5517241379310345 44-45 0.6526104417670683 46-47 0.5397941250313834 48-49 0.21346057257659468 50-51 0.17583521728208992 52-53 0.25122472051249845 54-55 0.37688442211055273 56-57 0.4020100502512563 58-59 0.38949616786028396 60-61 0.17596782302664657 62-63 0.21375581541556646 64-65 0.33957992705320084 66-67 0.3018867924528302 68-69 0.16354258397282675 70-71 0.06293266205160479 72-73 0.1769464105156724 74-75 0.02685284640171858 76 0.03862495171881035 >>END_MODULE >>Sequence Length Distribution warn #Length Count 35 10.0 36 0.0 37 0.0 38 1.0 39 0.0 40 1.0 41 0.0 42 1.0 43 2.0 44 2.0 45 0.0 46 0.0 47 1.0 48 0.0 49 1.0 50 0.0 51 0.0 52 1.0 53 0.0 54 0.0 55 0.0 56 0.0 57 0.0 58 1.0 59 0.0 60 2.0 61 0.0 62 1.0 63 0.0 64 1.0 65 0.0 66 0.0 67 0.0 68 1.0 69 1.0 70 1.0 71 6.0 72 20.0 73 80.0 74 284.0 75 993.0 76 2589.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 92.0 #Duplication Level Percentage of deduplicated Percentage of total 1 95.13586956521739 87.52499999999999 2 3.3967391304347823 6.25 3 0.8152173913043478 2.25 4 0.3532608695652174 1.3 5 0.05434782608695652 0.25 6 0.08152173913043478 0.44999999999999996 7 0.02717391304347826 0.17500000000000002 8 0.0 0.0 9 0.0 0.0 >10 0.1358695652173913 1.7999999999999998 >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 GTCTGACATGTGTGCGAGTCAACGGGCGAGTAAACCCGTAAGGCGCAAGGAAGCTGACTGGCGGGATCCCCTCG 20 0.5 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 19 0.475 No Hit GTTAGTTTTACCCTACTGATGACAGTGTCGCAATAGTAATCCAACCTAGTACGAGAGGAACCGTTGATTCGCACA 13 0.325 No Hit GGAGTCTGACATGTGTGCGAGTCAACGGGCGAGTAAACCCGTAAGGCGCA 10 0.25 No Hit NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 10 0.25 No Hit ACCAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTTGAT 7 0.17500000000000002 No Hit CTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAAG 6 0.15 No Hit GTGCGAGTCAACGGGCGAGTAAACCCGTAAGGCGCAAGGAAGCTGACTGG 6 0.15 No Hit AGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAAGTATGAACTAATTCAGACTGTGAAACTGCGA 6 0.15 No Hit CTTACCAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTT 5 0.125 No Hit GCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAAGTA 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 2000742 spots for SRR9668918.sra Written 2000742 spots for SRR9668918.sra Read 2000742 spots for SRR9668918.sra Written 2000742 spots for SRR9668918.sra Read 2000742 spots for SRR9668918.sra Written 2000742 spots for SRR9668918.sra Read 2000742 spots for SRR9668918.sra Written 2000742 spots for SRR9668918.sra Read 2000742 spots for SRR9668918.sra Written 2000742 spots for SRR9668918.sra Read 2000742 spots for SRR9668918.sra Written 2000742 spots for SRR9668918.sra Read 2000742 spots for SRR9668918.sra Written 2000742 spots for SRR9668918.sra Read 2000742 spots for SRR9668918.sra Written 2000742 spots for SRR9668918.sra Read 2000742 spots for SRR9668918.sra Written 2000742 spots for SRR9668918.sra Read 2000746 spots for SRR9668918.sra Written 2000746 spots for SRR9668918.sra Read 2000742 spots for SRR9668918.sra Written 2000742 spots for SRR9668918.sra Read 2000742 spots for SRR9668918.sra Written 2000742 spots for SRR9668918.sra Read 2000742 spots for SRR9668918.sra Written 2000742 spots for SRR9668918.sra Read 2000742 spots for SRR9668918.sra Written 2000742 spots for SRR9668918.sra Read 2000742 spots for SRR9668918.sra Written 2000742 spots for SRR9668918.sra Read 2000742 spots for SRR9668918.sra Written 2000742 spots for SRR9668918.sra Read 2000742 spots for SRR9668918.sra Written 2000742 spots for SRR9668918.sra Read 2000742 spots for SRR9668918.sra Written 2000742 spots for SRR9668918.sra Read 2000742 spots for SRR9668918.sra Written 2000742 spots for SRR9668918.sra Read 2000742 spots for SRR9668918.sra Written 2000742 spots for SRR9668918.sra SRR ids: ['SRR9668918.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_v8etjhi6 SRR9668918.sra spots: 40014844 blocks: [[1, 2000742], [2000743, 4001484], [4001485, 6002226], [6002227, 8002968], [8002969, 10003710], [10003711, 12004452], [12004453, 14005194], [14005195, 16005936], [16005937, 18006678], [18006679, 20007420], [20007421, 22008162], [22008163, 24008904], [24008905, 26009646], [26009647, 28010388], [28010389, 30011130], [30011131, 32011872], [32011873, 34012614], [34012615, 36013356], [36013357, 38014098], [38014099, 40014844]] SRR9668918 file size 7600862 SRR9668918 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 SRR9668918 SRR9668918_1.fastq SRR9668918_2.fastq Input file: SRR9668918_1.fastq Paired file: SRR9668918_2.fastq trimmed: SRR9668918-trimmed-pair1.fastq, SRR9668918-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 16:41:17 2025 >> started Wed Feb 12 16:41:51 2025 >> done (34.159s) 40014844 read pairs processed; of these: 23 ( 0.00%) short read pairs filtered out after trimming by size control 5592 ( 0.01%) empty read pairs filtered out after trimming by size control 40009229 (99.99%) read pairs available; of these: 6396 ( 0.02%) trimmed read pairs available after processing 40002833 (99.98%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 19 5 0.00% 20 4 0.00% 21 6 0.00% 22 13 0.00% 23 20 0.00% 24 21 0.00% 25 24 0.00% 26 33 0.00% 27 26 0.00% 28 50 0.00% 29 41 0.00% 30 36 0.00% 31 33 0.00% 32 38 0.00% 33 40 0.00% 34 55 0.00% 35 183 0.00% 36 217 0.00% 37 209 0.00% 38 241 0.00% 39 208 0.00% 40 259 0.00% 41 266 0.00% 42 283 0.00% 43 257 0.00% 44 347 0.00% 45 370 0.00% 46 274 0.00% 47 391 0.00% 48 430 0.00% 49 478 0.00% 50 558 0.00% 51 677 0.00% 52 689 0.00% 53 664 0.00% 54 808 0.00% 55 1205 0.00% 56 1262 0.00% 57 1139 0.00% 58 1327 0.00% 59 1326 0.00% 60 1489 0.00% 61 1471 0.00% 62 1694 0.00% 63 1992 0.00% 64 1980 0.00% 65 2228 0.01% 66 2399 0.01% 67 2708 0.01% 68 2828 0.01% 69 3208 0.01% 70 4866 0.01% 71 9713 0.02% 72 28026 0.07% 73 305723 0.76% 74 3097314 7.74% 75 18964595 47.40% 76 17562482 43.90% 40009229 reads passed initial QC criterion=sequence-density sequence-density=0.88 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=27 prefix-density=0.82 prefix-fanout=2.0 sequence=CCGTCAATTCCTTT criterion=fanout-score sequence-density=0.12 sequence-density-rank=18 fanout-score=10.83 fanout-score-rank=1 prefix-density=0.65 prefix-fanout=2.0 sequence=CGCATCGCCGGCCCCCATCCACTTCCCTCCCGACAATTTCAAGCACTCTTTGACTCTCTTTTCAAAGTCCTTTTCATCTTTCCCTCGCGGTACTTGTTTGCTATCGGTCTCTCGCCCGTATTTAGCCT criterion=sequence-density sequence-density=0.22 sequence-density-rank=1 fanout-score=7.77 fanout-score-rank=6 prefix-density=1.09 prefix-fanout=1.6 sequence=TGGTGCATGGCTGTCGTCAGCTCGTGCCGTAAGGTGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTCGTGTTTAGTTGCCACCGTTGAGTTTGGAACCCTGAACAGACTGCCGGTGATAAGCCGGAGGAAGGTGAGGATGACGTCAAGTCATCATGCCCCTTATGCCCTGGGCGACACACGTGCTACAATGGCCGGGACAAAGGGTCGCGATCCCGCGAGGGTGAGCTAACTCCAAAAACCCGTCCTCAGTTCGGATTGCAGGCTGCAACTCGCCTGCATGAAGCCGGAATCGCTAGTAATCGCCGGTCAGCCATACGGCGGTGAATTCGTTCCCGGGCCTTGTACACACC criterion=fanout-score sequence-density=0.01 sequence-density-rank=33 fanout-score=19.73 fanout-score-rank=1 prefix-density=0.09 prefix-fanout=2.9 sequence=CAAAACCACATATAGAGGGTGTAATAGCTAAGTAGCCTGTAAGAGATGGCTTCCTCTGTGATTTCATCGGCGGCCGTTGCCACAGTTAACCGCACCCC SRR9668918 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 12 16:42:21 Started mapping on | Feb 12 16:42:23 Finished on | Feb 12 16:48:14 Mapping speed, Million of reads per hour | 410.35 Number of input reads | 40009229 Average input read length | 151 UNIQUE READS: Uniquely mapped reads number | 27998889 Uniquely mapped reads % | 69.98% Average mapped length | 150.28 Number of splices: Total | 11283621 Number of splices: Annotated (sjdb) | 11158389 Number of splices: GT/AG | 11082942 Number of splices: GC/AG | 169968 Number of splices: AT/AC | 7949 Number of splices: Non-canonical | 22762 Mismatch rate per base, % | 0.58% Deletion rate per base | 0.02% Deletion average length | 2.18 Insertion rate per base | 0.02% Insertion average length | 2.41 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1906074 % of reads mapped to multiple loci | 4.76% Number of reads mapped to too many loci | 8091208 % of reads mapped to too many loci | 20.22% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.03% % of reads unmapped: other | 1.00% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 10104324 10104324 10104324 N_multimapping 1906074 1906074 1906074 N_noFeature 2929174 27455876 3055470 N_ambiguous 550475 3373 130704 UnstrandedReadsAssigned:24519240 PositiveStrandReadsAssigned:539640 NegativeStrandReadsAssigned:24812715 Dataset is classified negative stranded MeadianReadLen=76 20thPercentileLength=75 echo kmer=71 SRR9668918 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: SRR9668918-trimmed-pair1.fastq SRR9668918-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 40,009,229 reads, 31,088,048 reads pseudoaligned [quant] estimated average fragment length: 198.885 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,229 rounds 52401 SRR9668918.ke.tsv 34699 SRR9668918.se.tsv 87100 total ==> SRR9668918.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1820.11 469 6.00936 Potri.005G024800.1.v4.1 1035 837.115 127 3.53812 Potri.004G059700.1.v4.1 961 763.115 67 2.04757 Potri.007G009000.2.v4.1 1416 1218.11 0 0 Potri.003G141000.2.v4.1 2943 2745.11 465.823 3.95744 Potri.016G087400.1.v4.1 270 89.6748 1814.44 471.875 Potri.015G069301.1.v4.1 564 366.28 0 0 Potri.010G195200.1.v4.1 1773 1575.11 10 0.148062 Potri.012G127500.1.v4.1 977 779.115 7860 235.275 ==> SRR9668918.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 33 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 347 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 7 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 124 Potri.001G416900.v4.1 4 Potri.001G452600.v4.1 12 SRR9668918 completed mapping pipeline successfully