Starting /dee2/code/volunteer_pipeline.sh SRR1174007 current disk space = 1524307681280 free memory = 1605623012 SRR1174007 SRAfilesize 9dda6647ac49ac9b7be40e39967e5511 SRR1174007.sra SRR1174007.sra file validated SRR1174007 is single end SRR1174007 is conventional basespace SRR1174007 read1 length is 42 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR1174007_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 42 %GC 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 28.022 32.0 26.0 33.0 15.0 33.0 2 30.405 33.0 29.0 34.0 24.0 34.0 3 29.76 32.0 28.0 34.0 21.0 34.0 4 28.5745 31.0 26.0 33.0 18.0 34.0 5 29.168 32.0 27.0 33.0 20.0 34.0 6 28.7515 32.0 27.0 33.0 19.0 34.0 7 28.813 32.0 27.0 33.0 19.0 34.0 8 30.11725 33.0 29.0 34.0 22.0 34.0 9 30.38075 33.0 29.0 34.0 23.0 34.0 10 31.0035 33.0 31.0 34.0 25.0 34.0 11 30.23925 33.0 29.0 34.0 23.0 34.0 12 30.8305 33.0 30.0 34.0 24.0 34.0 13 30.69575 33.0 30.0 34.0 24.0 34.0 14 31.34075 33.0 31.0 34.0 26.0 34.0 15 31.51675 33.0 31.0 34.0 27.0 34.0 16 31.2985 33.0 31.0 34.0 26.0 34.0 17 31.10975 33.0 31.0 34.0 26.0 34.0 18 31.161 33.0 31.0 34.0 26.0 34.0 19 31.34225 33.0 31.0 34.0 26.0 34.0 20 31.305 33.0 31.0 34.0 26.0 34.0 21 31.0505 33.0 31.0 34.0 25.0 34.0 22 30.46125 33.0 30.0 34.0 24.0 34.0 23 31.1825 33.0 31.0 34.0 26.0 34.0 24 31.325 33.0 31.0 34.0 26.0 34.0 25 30.9245 33.0 31.0 34.0 25.0 34.0 26 31.51375 33.0 32.0 34.0 27.0 34.0 27 31.38125 34.0 32.0 34.0 26.0 34.0 28 31.0685 34.0 32.0 34.0 25.0 34.0 29 31.403 33.0 32.0 34.0 27.0 34.0 30 31.28625 34.0 31.0 34.0 27.0 34.0 31 30.84775 33.0 31.0 34.0 25.0 34.0 32 30.1335 33.0 30.0 34.0 22.0 34.0 33 31.2325 33.0 32.0 34.0 26.0 34.0 34 31.31075 34.0 32.0 34.0 26.0 34.0 35 31.32025 34.0 32.0 34.0 26.0 34.0 36 31.097 33.0 32.0 34.0 26.0 34.0 37 30.77925 33.0 31.0 34.0 25.0 34.0 38 30.87625 33.0 31.0 34.0 26.0 34.0 39 30.88325 33.0 31.0 34.0 25.0 34.0 40 30.741 33.0 31.0 34.0 24.0 34.0 41 30.158 33.0 31.0 34.0 23.0 34.0 42 29.80225 33.0 30.0 34.0 22.0 34.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 1 1 0.0 1 2 0.0 1 3 0.0 1 4 0.0 1 5 0.0 1 6 0.0 1 7 0.0 1 8 0.0 1 9 0.0 1 10 0.0 1 11 0.0 1 12 0.0 1 13 0.0 1 14 0.0 1 15 0.0 1 16 0.0 1 17 0.0 1 18 0.0 1 19 0.0 1 20 0.0 1 21 0.0 1 22 0.0 1 23 0.0 1 24 0.0 1 25 0.0 1 26 0.0 1 27 0.0 1 28 0.0 1 29 0.0 1 30 0.0 1 31 0.0 1 32 0.0 1 33 0.0 1 34 0.0 1 35 0.0 1 36 0.0 1 37 0.0 1 38 0.0 1 39 0.0 1 40 0.0 1 41 0.0 1 42 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 4 8.0 5 2.0 6 3.0 7 0.0 8 1.0 9 5.0 10 6.0 11 2.0 12 2.0 13 3.0 14 2.0 15 3.0 16 2.0 17 6.0 18 3.0 19 8.0 20 9.0 21 17.0 22 20.0 23 27.0 24 33.0 25 81.0 26 121.0 27 129.0 28 263.0 29 344.0 30 554.0 31 783.0 32 948.0 33 615.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 19.129782445611404 41.635408852213054 21.205301325331334 18.02950737684421 2 18.388791593695274 52.464348261195894 17.663247435576682 11.48361270953215 3 24.375 23.75 26.85 25.025 4 33.16658329164582 25.68784392196098 19.009504752376188 22.136068034017008 5 32.00800200050013 32.808202050512634 18.554638659664917 16.62915728932233 6 21.349999999999998 38.375 24.525 15.75 7 33.65841460365091 26.30657664416104 26.30657664416104 13.728432108027006 8 19.0 22.425 38.475 20.1 9 21.53576788394197 37.51875937968984 28.939469734867433 12.006003001500751 10 37.025000000000006 25.324999999999996 19.15 18.5 11 20.280070017504375 32.63315828957239 27.881970492623154 19.204801200300075 12 27.150000000000002 21.7 22.7 28.449999999999996 13 26.845133850387793 21.79134350763072 20.41531148361271 30.94821115836878 14 23.28664332166083 36.76838419209605 28.989494747373683 10.955477738869435 15 25.131282820705174 30.03250812703176 29.657414353588397 15.178794698674668 16 28.653653653653656 27.952952952952952 25.925925925925924 17.46746746746747 17 20.83541770885443 28.789394697348676 35.467733866933465 14.907453726863432 18 26.531632908227053 20.530132533133283 34.358589647411854 18.579644911227806 19 23.625 32.775 23.45 20.150000000000002 20 23.825 24.075 35.425000000000004 16.675 21 21.98599299649825 25.812906453226613 29.789894947473737 22.411205602801402 22 32.399299474605954 25.869402051538653 26.444833625218916 15.286464848636477 23 24.2 24.2 36.675000000000004 14.924999999999999 24 25.287643821910955 22.56128064032016 27.71385692846423 24.437218609304654 25 14.05 41.775 25.3 18.875 26 26.038019009504755 10.930465232616308 41.92096048024012 21.11055527763882 27 16.91268451338504 17.888416312234177 18.864148111083313 46.334751063297475 28 13.4783695923981 19.829957489372344 43.135783945986496 23.55588897224306 29 19.82974461692539 12.99449173760641 29.29394091136705 37.88182273410115 30 36.459114778694676 10.652663165791449 35.98399599899975 16.90422605651413 31 14.897346019028543 13.72058087130696 44.99248873309965 26.389584376564844 32 12.537537537537538 33.208208208208205 30.78078078078078 23.473473473473476 33 13.498622589531681 8.0641121963436 53.76909591785625 24.66816929626847 34 36.54135338345865 7.443609022556391 26.11528822055138 29.899749373433583 35 14.593241551939926 6.007509386733417 33.7171464330413 45.68210262828536 36 20.97622027534418 5.657071339173967 25.381727158948685 47.98498122653317 37 36.96468820435763 6.7618332081142 32.98271975957927 23.29075882794891 38 10.31031031031031 9.30930930930931 60.36036036036037 20.02002002002002 39 13.705838135805562 11.525933350037585 34.47757454272112 40.29065397143573 40 19.078617926890335 11.392088132198296 52.60390585878818 16.925388082123185 41 18.637274549098194 18.837675350701403 42.45991983967936 20.06513026052104 42 12.002004510147833 21.297920320721627 22.12478075670258 44.575294412427965 >>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 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 1.5 26 3.0 27 8.0 28 13.0 29 13.0 30 13.5 31 14.0 32 31.0 33 48.0 34 48.0 35 89.5 36 131.0 37 178.0 38 225.0 39 385.0 40 545.0 41 545.0 42 585.5 43 626.0 44 632.0 45 638.0 46 588.0 47 538.0 48 538.0 49 513.5 50 489.0 51 413.5 52 338.0 53 338.0 54 274.0 55 210.0 56 152.0 57 94.0 58 64.0 59 34.0 60 34.0 61 27.5 62 21.0 63 16.0 64 11.0 65 8.5 66 6.0 67 6.0 68 7.5 69 9.0 70 4.5 71 0.0 72 0.0 73 1.5 74 3.0 75 1.5 76 0.0 77 0.0 78 0.0 79 0.0 80 0.5 81 1.0 82 0.5 83 0.0 84 0.0 85 0.5 86 1.0 87 0.5 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 0.5 97 1.0 98 1.0 99 1.0 100 1.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.025 2 0.075 3 0.0 4 0.05 5 0.025 6 0.0 7 0.025 8 0.0 9 0.05 10 0.0 11 0.025 12 0.0 13 0.075 14 0.05 15 0.025 16 0.1 17 0.05 18 0.025 19 0.0 20 0.0 21 0.05 22 0.075 23 0.0 24 0.05 25 0.0 26 0.05 27 0.075 28 0.025 29 0.15 30 0.025 31 0.15 32 0.1 33 0.17500000000000002 34 0.25 35 0.125 36 0.125 37 0.17500000000000002 38 0.1 39 0.22499999999999998 40 0.15 41 0.2 42 0.22499999999999998 >>END_MODULE >>Sequence Length Distribution pass #Length Count 42 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 74.875 #Duplication Level Percentage of deduplicated Percentage of total 1 93.62270450751252 70.1 2 3.0717863105175294 4.6 3 0.9682804674457429 2.175 4 0.3005008347245409 0.8999999999999999 5 0.36727879799666113 1.375 6 0.40066777963272115 1.7999999999999998 7 0.1335559265442404 0.7000000000000001 8 0.10016694490818029 0.6 9 0.20033388981636058 1.35 >10 0.7345575959933223 11.200000000000001 >50 0.0667779632721202 2.675 >100 0.0333889816360601 2.5250000000000004 >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 CATCGAGTAGACCTTGTTATTGTGAGAATTCATCTCGTATGC 101 2.5250000000000004 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTATCTCGTATGCC 56 1.4000000000000001 No Hit TAACGAACGAACGATTTGAACATCTCGTATGCCGTCTTCTGC 51 1.275 Illumina PCR Primer Index 7 (96% over 25bp) AACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTTGAA 49 1.225 RNA PCR Primer, Index 19 (96% over 29bp) TAATTCATGATCTGGATCTCGTATGCCGTCTTCTGCTTGAAA 35 0.8750000000000001 RNA PCR Primer, Index 23 (96% over 28bp) TTTGGATTGAAGGGAGCTCTGATCTCGTATGCCGTCTTCTGC 34 0.8500000000000001 Illumina PCR Primer Index 9 (96% over 25bp) GGGGATGTAGCTCAAAATCTCGTATGCCGTCTTCTGCTTGAA 33 0.8250000000000001 RNA PCR Primer, Index 40 (96% over 30bp) TAGATATTTCAGGTTGTGTGGAATCTCGTATGCCGTCTTCTG 32 0.8 Illumina PCR Primer Index 8 (95% over 24bp) AACGAACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCT 26 0.65 RNA PCR Primer, Index 19 (96% over 27bp) ACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTTGAAA 24 0.6 Illumina PCR Primer Index 7 (96% over 28bp) CTAACGAACGAACGATTTGAACATCTCGTATGCCGTCTTCTG 20 0.5 RNA PCR Primer, Index 19 (96% over 25bp) GGGGATGTAGCTCAGAATCTCGTATGCCGTCTTCTGCTTGAA 19 0.475 RNA PCR Primer, Index 40 (100% over 30bp) AGCGGAGTAGAGCAGTTATCTCGTATGCCGTCTTCTGCTTGA 18 0.44999999999999996 Illumina PCR Primer Index 5 (96% over 29bp) GAACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTTGA 18 0.44999999999999996 Illumina PCR Primer Index 7 (96% over 28bp) GGGATTGTAGTTCAATATCTCGTATGCCGTCTTCTGCTTGAA 17 0.42500000000000004 Illumina PCR Primer Index 6 (96% over 29bp) AGCGGAGTAGAGCAGTATCTCGTATGCCGTCTTCTGCTTGAA 15 0.375 Illumina PCR Primer Index 6 (96% over 28bp) TCCGTCGTAGTCTAGGATCTCGTATGCCGTCTTCTGCTTGAA 15 0.375 RNA PCR Primer, Index 22 (96% over 28bp) CATCGAGTAGACCTTGTTATTGTGAGAATATCTCGTATGCCG 15 0.375 No Hit AAGGAAGCTATAAGATCTCGTATGCCGTCTTCTGCTTGAAAA 13 0.325 RNA PCR Primer, Index 44 (96% over 31bp) AGGGATGTAGCGCAGCATCTCGTATGCCGTCTTCTGCTTGAA 12 0.3 TruSeq Adapter, Index 18 (96% over 28bp) TCCTAACGAACGAACGATTTGAACATCTCGTATGCCGTCTTC 11 0.27499999999999997 Illumina PCR Primer Index 7 (95% over 22bp) ACGAACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTT 11 0.27499999999999997 Illumina PCR Primer Index 7 (96% over 27bp) ACTGGTTGGATCATGCTTCTAATCTCGTATGCCGTCTTCTGC 11 0.27499999999999997 RNA PCR Primer, Index 12 (96% over 27bp) CATCGATTAGACCTTGTTATTGTGAGAATTCATCTCGTATGC 10 0.25 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAAATCTCGT 10 0.25 No Hit CACGACTCTCGGCAACGGATATCTATCTCGTATGCCGTCTTC 9 0.22499999999999998 Illumina PCR Primer Index 2 (95% over 22bp) GACACGACTCTCGGCAACGGATATCTCATCTCGTATGCCGTC 9 0.22499999999999998 No Hit GGGCCTGTAGCTCAGAGGAATCTCGTATGCCGTCTTCTGCTT 9 0.22499999999999998 Illumina PCR Primer Index 12 (96% over 26bp) GGCGGATGTAGCCAAGTGGAATCTCGTATGCCGTCTTCTGCT 9 0.22499999999999998 Illumina PCR Primer Index 8 (96% over 26bp) GGGGGTGTAGCTCATAATCTCGTATGCCGTCTTCTGCTTGAA 9 0.22499999999999998 Illumina PCR Primer Index 12 (96% over 27bp) GACACGACTCTCGGCAACGGATATCATCTCGTATGCCGTCTT 9 0.22499999999999998 TruSeq Adapter, Index 7 (95% over 22bp) AGGGATGTAGCGCAGCTTGGTAGCGCTTTGTTTTATCTCGTA 8 0.2 No Hit CATCCTAACGAACGAACGATTTGAACATCTCGTATGCCGTCT 8 0.2 No Hit GAGGCATCCTAACGAACGAACGATTTGAACATCTCGTATGCC 8 0.2 No Hit CACGACTCTCGGCAACGGATATCATCTCGTATGCCGTCTTCT 7 0.17500000000000002 TruSeq Adapter, Index 7 (95% over 24bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTTATCTCGTAT 7 0.17500000000000002 No Hit AACGATTTGAACATCTCGTATGCCGTCTTCTGCTTGAAAAAA 7 0.17500000000000002 Illumina PCR Primer Index 7 (96% over 28bp) GACACGACTCTCGGCAACGGATATCTATCTCGTATGCCGTCT 7 0.17500000000000002 No Hit TGACAGAAGAGAGTGAGCACATCTCGTATGCCGTCTTCTGCT 6 0.15 Illumina PCR Primer Index 9 (96% over 25bp) GACACGACTCTCGGCAACGGAATCTCGTATGCCGTCTTCTGC 6 0.15 RNA PCR Primer, Index 40 (96% over 25bp) ATATTGGGTAGGTTGTGGTATTTCATTGCATCTCGTATGCCG 6 0.15 No Hit ATCCTAACGAACGAACGATTTGAACATCTCGTATGCCGTCTT 6 0.15 RNA PCR Primer, Index 19 (95% over 22bp) AGCGGAGTAGAGCAATCTCGTATGCCGTCTTCTGCTTGAAAA 6 0.15 Illumina PCR Primer Index 4 (96% over 29bp) GTCAGGATAGCTCAGTATCTCGTATGCCGTCTTCTGCTTGAA 6 0.15 RNA PCR Primer, Index 40 (96% over 30bp) TAGGCATCCTAACGAACGAACGATTTGAACATCTCGTATGCC 6 0.15 No Hit CACGACTCTCGGCAACGGATATATCTCGTATGCCGTCTTCTG 6 0.15 Illumina PCR Primer Index 2 (96% over 25bp) GATCGAGTAGACCTTGTTATTGTGAGAATTCATCTCGTATGC 6 0.15 No Hit AATATTGGGTAGGTTGTGGTATTTCATTGCATCTCGTATGCC 6 0.15 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTATCTCGTAT 6 0.15 No Hit AGCGGAGTAGAGCAGATCTCGTATGCCGTCTTCTGCTTGAAA 6 0.15 Illumina PCR Primer Index 9 (100% over 27bp) TCGGATAACCGTAGTAATTCTAGAGCTAATACGATCTCGTAT 5 0.125 No Hit GTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGTATCTCGT 5 0.125 No Hit CACGACTCTCGGCAACGGATAATCTCGTATGCCGTCTTCTGC 5 0.125 TruSeq Adapter, Index 7 (96% over 25bp) GCACCAGTGGTCTAGTGGTAGAATAGTACCATCTCGTATGCC 5 0.125 No Hit GGGATTGTAGTTCAAATCTCGTATGCCGTCTTCTGCTTGAAA 5 0.125 RNA PCR Primer, Index 13 (96% over 29bp) TAATTCATGATCTGGCATGATCTCGTATGCCGTCTTCTGCTT 5 0.125 Illumina PCR Primer Index 1 (96% over 27bp) GACACGACTCTCGGCAACGGATATCTCGGCATCTCGTATGCC 5 0.125 No Hit CACGACTCTCGGCAACGGATATCTCGATCTCGTATGCCGTCT 5 0.125 Illumina PCR Primer Index 1 (95% over 22bp) AGGCATCCTAACGAACGAACGATTTGAACATCTCGTATGCCG 5 0.125 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGATCTCGTA 5 0.125 No Hit GACACGACTCTCGGCAACGGATAATCTCGTATGCCGTCTTCT 5 0.125 RNA PCR Primer, Index 7 (95% over 23bp) >>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 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTGTTAT 30 7.460676E-6 36.189877 14 TTATTGT 30 7.460676E-6 36.189877 17 CCTTGTT 30 7.460676E-6 36.189877 12 CTTGTTA 30 7.460676E-6 36.189877 13 ACCTTGT 30 7.460676E-6 36.189877 11 GTTATTG 30 7.460676E-6 36.189877 16 TGAGAAT 30 8.1611015E-6 35.737503 23 TGTGAGA 30 8.1611015E-6 35.737503 21 GTAGACC 30 8.1611015E-6 35.737503 7 AGTAGAC 30 8.1611015E-6 35.737503 6 TATTGTG 30 8.1611015E-6 35.737503 18 GTGAGAA 30 8.1611015E-6 35.737503 22 ATTGTGA 30 8.1611015E-6 35.737503 19 TGTAGCT 30 8.1611015E-6 35.737503 6 GGGATGT 30 8.1611015E-6 35.737503 2 CGAGTAG 30 8.1611015E-6 35.737503 4 AGACCTT 30 8.1611015E-6 35.737503 9 GACCTTG 30 8.1611015E-6 35.737503 10 TTGTGAG 30 8.1611015E-6 35.737503 20 ATCGAGT 30 8.1611015E-6 35.737503 2 >>END_MODULE Read 219533 spots for SRR1174007.sra Written 219533 spots for SRR1174007.sra Read 219533 spots for SRR1174007.sra Written 219533 spots for SRR1174007.sra Read 219533 spots for SRR1174007.sra Written 219533 spots for SRR1174007.sra Read 219533 spots for SRR1174007.sra Written 219533 spots for SRR1174007.sra Read 219533 spots for SRR1174007.sra Written 219533 spots for SRR1174007.sra Read 219533 spots for SRR1174007.sra Written 219533 spots for SRR1174007.sra Read 219533 spots for SRR1174007.sra Written 219533 spots for SRR1174007.sra Read 219533 spots for SRR1174007.sra Written 219533 spots for SRR1174007.sra Read 219533 spots for SRR1174007.sra Written 219533 spots for SRR1174007.sra Read 219533 spots for SRR1174007.sra Written 219533 spots for SRR1174007.sra Read 219533 spots for SRR1174007.sra Written 219533 spots for SRR1174007.sra Read 219533 spots for SRR1174007.sra Written 219533 spots for SRR1174007.sra Read 219533 spots for SRR1174007.sra Written 219533 spots for SRR1174007.sra Read 219533 spots for SRR1174007.sra Written 219533 spots for SRR1174007.sra Read 219533 spots for SRR1174007.sra Written 219533 spots for SRR1174007.sra Read 219543 spots for SRR1174007.sra Written 219543 spots for SRR1174007.sra Read 219533 spots for SRR1174007.sra Written 219533 spots for SRR1174007.sra Read 219533 spots for SRR1174007.sra Written 219533 spots for SRR1174007.sra Read 219533 spots for SRR1174007.sra Written 219533 spots for SRR1174007.sra Read 219533 spots for SRR1174007.sra Written 219533 spots for SRR1174007.sra SRR ids: ['SRR1174007.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_c8w5y173 SRR1174007.sra spots: 4390670 blocks: [[1, 219533], [219534, 439066], [439067, 658599], [658600, 878132], [878133, 1097665], [1097666, 1317198], [1317199, 1536731], [1536732, 1756264], [1756265, 1975797], [1975798, 2195330], [2195331, 2414863], [2414864, 2634396], [2634397, 2853929], [2853930, 3073462], [3073463, 3292995], [3292996, 3512528], [3512529, 3732061], [3732062, 3951594], [3951595, 4171127], [4171128, 4390670]] SRR1174007 file size 610737 SRR1174007 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 SRR1174007 SRR1174007_1.fastq Input file: SRR1174007_1.fastq trimmed: SRR1174007-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- 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 -- minimum overlap length for adapter detection (-k): inf -- number of concurrent threads (-t): 20 Mon Dec 9 14:36:56 2024 >> started Mon Dec 9 14:36:59 2024 >> done (3.319s) 4390670 reads processed; of these: 58538 ( 1.33%) short reads filtered out after trimming by size control 8577 ( 0.20%) empty reads filtered out after trimming by size control 4323555 (98.47%) reads available; of these: 1232574 (28.51%) trimmed reads available after processing 3090981 (71.49%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 9212 0.21% 19 10527 0.24% 20 10779 0.25% 21 12701 0.29% 22 14119 0.33% 23 15116 0.35% 24 18136 0.42% 25 17575 0.41% 26 19832 0.46% 27 23129 0.53% 28 20495 0.47% 29 23077 0.53% 30 22041 0.51% 31 21146 0.49% 32 25252 0.58% 33 32292 0.75% 34 27690 0.64% 35 35403 0.82% 36 36740 0.85% 37 56609 1.31% 38 78070 1.81% 39 100765 2.33% 40 214273 4.96% 41 387595 8.96% 42 3090981 71.49% 4323555 reads passed initial QC criterion=sequence-density sequence-density=63.26 sequence-density-rank=1 fanout-score=36.73 fanout-score-rank=1 prefix-density=72.57 prefix-fanout=32.0 sequence=ATCTCGTATGCCGTCTTCTGCTTGAAAAAAA criterion=fanout-score sequence-density=63.26 sequence-density-rank=1 fanout-score=36.73 fanout-score-rank=1 prefix-density=72.57 prefix-fanout=32.0 sequence=ATCTCGTATGCCGTCTTCTGCTTGAAAAAAA Potential 3prime adapter identified. Now checking if in reference sequence Warning: gzbuffer added in zlib v1.2.3.5. Unable to change buffer size from default of 8192. 1 reads; of these: 1 (100.00%) were unpaired; of these: 1 (100.00%) aligned 0 times 0 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate Adapter seq not found in reference. Now shuffling file before clipping skewer v0.2.2 [April 4, 2016] COMMAND LINE: skewer -f sanger -l 18 -t 20 -x ATCTCGTATGCCGTCTTCTGCTTGAAAAAAA -o SRR1174007 - Input file: STDIN trimmed: SRR1174007-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): ATCTCGTATGCCGTCTTCTGCTTGAAAAAAA -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- minimum overlap length for adapter detection (-k): 3 -- number of concurrent threads (-t): 20 Mon Dec 9 14:37:06 2024 >> started Mon Dec 9 14:37:11 2024 >> done (4.211s) 4188444 reads processed; of these: 901194 (21.52%) short reads filtered out after trimming by size control 51784 ( 1.24%) empty reads filtered out after trimming by size control 3235466 (77.25%) reads available; of these: 2960101 (91.49%) trimmed reads available after processing 275365 ( 8.51%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 90217 2.79% 19 144122 4.45% 20 177972 5.50% 21 244031 7.54% 22 143316 4.43% 23 181219 5.60% 24 925208 28.60% 25 112987 3.49% 26 87345 2.70% 27 66195 2.05% 28 61183 1.89% 29 99395 3.07% 30 131224 4.06% 31 156561 4.84% 32 81682 2.52% 33 114490 3.54% 34 96412 2.98% 35 106383 3.29% 36 59211 1.83% 37 35431 1.10% 38 23191 0.72% 39 11144 0.34% 40 8572 0.26% 41 10237 0.32% 42 67738 2.09% criterion=sequence-density sequence-density=6.04 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=16 prefix-density=0.00 prefix-fanout=1.0 sequence=CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATTC criterion=fanout-score sequence-density=0.81 sequence-density-rank=7 fanout-score=41.46 fanout-score-rank=1 prefix-density=1.00 prefix-fanout=33.6 sequence=TCGTATGCCGTCTTCTGCTTGAAAAA Started job on | Dec 09 14:37:27 Started mapping on | Dec 09 14:37:27 Finished on | Dec 09 14:37:59 Mapping speed, Million of reads per hour | 379.19 Number of input reads | 3370577 Average input read length | 26 UNIQUE READS: Uniquely mapped reads number | 1003079 Uniquely mapped reads % | 29.76% Average mapped length | 23.81 Number of splices: Total | 16631 Number of splices: Annotated (sjdb) | 3032 Number of splices: GT/AG | 15840 Number of splices: GC/AG | 528 Number of splices: AT/AC | 2 Number of splices: Non-canonical | 261 Mismatch rate per base, % | 0.54% Deletion rate per base | 0.00% Deletion average length | 1.39 Insertion rate per base | 0.00% Insertion average length | 1.01 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1256629 % of reads mapped to multiple loci | 37.28% Number of reads mapped to too many loci | 849248 % of reads mapped to too many loci | 25.20% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 6.24% % of reads unmapped: other | 1.53% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1110869 1110869 1110869 N_multimapping 1256629 1256629 1256629 N_noFeature 757744 837595 919952 N_ambiguous 5561 2125 416 UnstrandedReadsAssigned:239774 PositiveStrandReadsAssigned:163359 NegativeStrandReadsAssigned:82711 Dataset is classified unstranded MeadianReadLen=24 20thPercentileLength=21 echo kmer=19 SRR1174007 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=19 [quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20 [index] k-mer length: 19 [index] number of targets: 52,972 [index] number of k-mers: 65,492,969 [index] number of equivalence classes: 320,172 [quant] running in single-end mode [quant] will process file 1: SRR1174007-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,370,577 reads, 1,196,039 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 997 rounds 52973 SRR1174007.ke.tsv 35125 SRR1174007.se.tsv 88098 total ==> SRR1174007.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 1.77103 0.425254 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 2.38306 0.762809 PNS24243 293 194 1 2.26378 KQK14069 1603 1504 6.57931 1.92118 KQK14071 474 375 0 0 ==> SRR1174007.se.tsv <== BRADI_1g14170v3 6 BRADI_1g53295v3 8 BRADI_1g59795v3 2 BRADI_1g07683v3 0 BRADI_1g00485v3 1 BRADI_1g20270v3 2 BRADI_1g74790v3 16 BRADI_1g09890v3 0 BRADI_1g77505v3 4 BRADI_1g48960v3 0 SRR1174007 completed mapping pipeline successfully