Starting /dee2/code/volunteer_pipeline.sh SRR1033815 current disk space = 1548447850496 free memory = 1598455864 SRR1033815 SRAfilesize b073afaf5655fe9bdff765adb302e622 SRR1033815.sra SRR1033815.sra file validated SRR1033815 is single end SRR1033815 is conventional basespace SRR1033815 read1 length is 46 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR1033815_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 46 %GC 48 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.29075 33.0 33.0 33.0 32.0 33.0 2 31.60775 33.0 31.0 33.0 28.0 34.0 3 30.62275 32.0 30.0 33.0 26.0 33.0 4 29.79025 31.0 29.0 33.0 24.0 33.0 5 30.79025 32.0 30.0 33.0 26.0 33.0 6 30.705 32.0 30.0 33.0 26.0 33.0 7 30.86925 32.0 30.0 33.0 27.0 33.0 8 30.378 32.0 30.0 33.0 25.0 33.0 9 29.42025 31.0 28.0 33.0 23.0 33.0 10 29.68675 32.0 29.0 33.0 23.0 33.0 11 30.30975 32.0 30.0 33.0 25.0 33.0 12 29.55325 31.0 28.0 33.0 24.0 33.0 13 27.86925 30.0 25.0 32.0 20.0 33.0 14 25.98225 28.0 22.0 31.0 17.0 32.0 15 25.59625 28.0 21.0 31.0 16.0 32.0 16 25.787 28.0 22.0 31.0 17.0 33.0 17 25.3635 28.0 21.0 31.0 15.0 33.0 18 29.0975 31.0 28.0 33.0 22.0 33.0 19 27.88075 30.0 26.0 32.0 19.0 33.0 20 27.39425 30.0 25.0 32.0 20.0 33.0 21 28.76725 31.0 28.0 32.0 22.0 33.0 22 28.54075 31.0 27.0 32.0 21.0 33.0 23 28.38725 31.0 27.0 33.0 21.0 33.0 24 27.87775 30.0 26.0 32.0 20.0 33.0 25 27.03675 30.0 24.0 32.0 19.0 33.0 26 27.9145 30.0 26.0 32.0 20.0 33.0 27 27.2945 30.0 26.0 32.0 19.0 33.0 28 26.00625 28.0 23.0 31.0 17.0 33.0 29 25.384 28.0 22.0 31.0 16.0 32.0 30 25.5645 28.0 23.0 31.0 16.0 33.0 31 26.06025 29.0 24.0 32.0 15.0 33.0 32 24.64125 27.0 21.0 31.0 14.0 32.0 33 25.38525 28.0 22.0 31.0 14.0 33.0 34 26.38325 29.0 25.0 32.0 14.0 33.0 35 25.012 28.0 22.0 31.0 12.0 33.0 36 25.1655 28.0 22.0 31.0 10.0 33.0 37 25.25775 28.0 23.0 31.0 10.0 33.0 38 24.1165 27.0 20.0 31.0 7.0 33.0 39 23.23225 26.0 19.0 30.0 4.0 32.0 40 24.58375 28.0 22.0 31.0 4.0 33.0 41 23.31425 27.0 19.0 31.0 4.0 33.0 42 20.5225 23.0 15.0 28.0 4.0 31.0 43 21.18325 24.0 15.0 29.0 4.0 32.0 44 20.9845 25.0 13.0 29.0 4.0 32.0 45 18.53375 23.0 4.0 28.0 4.0 31.0 46 17.27725 21.0 4.0 28.0 4.0 31.0 >>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 1 43 0.0 1 44 0.0 1 45 0.0 1 46 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 4 16.0 5 6.0 6 3.0 7 3.0 8 4.0 9 8.0 10 8.0 11 10.0 12 17.0 13 25.0 14 32.0 15 37.0 16 29.0 17 35.0 18 48.0 19 57.0 20 61.0 21 86.0 22 101.0 23 178.0 24 219.0 25 302.0 26 373.0 27 452.0 28 533.0 29 546.0 30 419.0 31 308.0 32 79.0 33 5.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 18.914185639229423 25.519139354515886 44.283212409306984 11.283462596947711 2 38.72904678508882 22.39179384538404 16.46234676007005 22.416812609457093 3 38.704028021015766 33.12484363272454 13.009757317988491 15.161371028271203 4 23.705926481620406 26.6816704176044 13.253313328332084 36.35908977244311 5 19.204801200300075 37.934483620905226 23.605901475368842 19.254813703425857 6 36.25906476619154 21.330332583145786 27.031757939484873 15.378844711177795 7 35.23380845211303 33.758439609902474 16.129032258064516 14.87871967991998 8 29.2 35.3 16.150000000000002 19.35 9 36.51825912956478 22.411205602801402 28.36418209104552 12.706353176588294 10 36.88688688688689 31.78178178178178 13.313313313313312 18.01801801801802 11 34.733683420855215 22.305576394098527 17.90447611902976 25.056264066016503 12 26.43821910955478 42.94647323661831 16.08304152076038 14.532266133066532 13 49.56217162872154 22.491868901676256 12.43432574430823 15.511633725293972 14 24.661992989484226 34.852278417626444 27.190786179268905 13.294942413620431 15 35.88397099274819 22.43060765191298 27.806951737934483 13.87846961740435 16 25.86293146573287 36.19309654827414 13.006503251625812 24.937468734367183 17 46.4232116058029 25.337668834417208 15.682841420710355 12.556278139069535 18 40.88522130532633 17.854463615903978 11.45286321580395 29.80745186296574 19 35.708927231807955 32.05801450362591 15.053763440860216 17.179294823705927 20 19.23461730865433 32.14107053526764 19.05952976488244 29.5647823911956 21 18.75 20.375 30.95 29.925 22 16.504126031507877 13.12828207051763 38.38459614903726 31.98299574893723 23 30.857714428607153 18.554638659664917 17.479369842460617 33.10827706926732 24 31.41570785392696 13.556778389194598 41.145572786393195 13.881940970485243 25 9.45 22.925 55.50000000000001 12.125 26 12.437437437437438 26.176176176176174 31.23123123123123 30.155155155155157 27 47.85 8.1 35.199999999999996 8.85 28 29.5647823911956 10.25512756378189 34.61730865432716 25.56278139069535 29 11.836836836836836 29.47947947947948 14.364364364364365 44.31931931931932 30 28.760951188986233 5.857321652065081 33.81727158948686 31.564455569461824 31 51.49085442245052 4.234527687296417 26.409421197694815 17.865196692558253 32 10.693713999499122 2.404207362885049 31.02930127723516 55.87277736038067 33 11.4063675106543 2.1057909250438707 29.9824517422913 56.505389822010535 34 28.64661654135338 1.7543859649122806 53.659147869674186 15.939849624060152 35 5.989974937343359 1.7543859649122806 60.576441102756895 31.67919799498747 36 5.870546914199699 1.8815855494229805 39.262418464626194 52.985449071751134 37 20.55722891566265 1.6566265060240966 64.28212851405623 13.50401606425703 38 23.965906242165957 1.7297568312860365 43.77036851341188 30.533968413136126 39 7.64986205166792 2.2322548281916226 39.22748934035616 50.890393779784304 40 11.113898645258406 3.411941796287005 74.91219267436026 10.56196688409433 41 46.94082246740221 6.44433299899699 35.45636910732197 11.158475426278837 42 28.180677540777914 26.3237139272271 17.84190715181932 27.65370138017566 43 8.477552044143465 49.78680712315024 37.32129420617005 4.4143466265362425 44 9.28016052169551 55.50539252570855 31.95385001254076 3.260596940055179 45 27.156469408224677 63.66599799398195 7.647943831494483 1.5295887662988967 46 25.363773206221772 63.37180130456598 9.784244856999498 1.4801806322127444 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 56.0 1 30.0 2 4.0 3 3.0 4 2.0 5 1.0 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 0.5 26 1.0 27 2.5 28 4.0 29 2.5 30 1.0 31 1.0 32 2.0 33 3.0 34 7.0 35 11.0 36 11.0 37 11.0 38 25.0 39 39.0 40 91.5 41 144.0 42 185.5 43 227.0 44 227.0 45 591.0 46 955.0 47 712.5 48 470.0 49 477.0 50 484.0 51 686.5 52 889.0 53 622.5 54 356.0 55 255.5 56 155.0 57 155.0 58 123.5 59 92.0 60 74.0 61 56.0 62 40.0 63 24.0 64 17.0 65 10.0 66 6.0 67 2.0 68 1.0 69 0.0 70 0.0 71 0.5 72 1.0 73 0.5 74 0.0 75 0.0 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 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.5 93 1.0 94 1.0 95 0.5 96 0.0 97 0.0 98 0.0 99 1.0 100 2.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.075 2 0.075 3 0.075 4 0.025 5 0.025 6 0.025 7 0.025 8 0.0 9 0.05 10 0.1 11 0.025 12 0.05 13 0.075 14 0.15 15 0.025 16 0.05 17 0.05 18 0.025 19 0.025 20 0.05 21 0.0 22 0.025 23 0.025 24 0.05 25 0.0 26 0.1 27 0.0 28 0.05 29 0.1 30 0.125 31 0.22499999999999998 32 0.17500000000000002 33 0.27499999999999997 34 0.25 35 0.25 36 0.35000000000000003 37 0.4 38 0.27499999999999997 39 0.325 40 0.35000000000000003 41 0.3 42 0.375 43 0.325 44 0.325 45 0.3 46 0.35000000000000003 >>END_MODULE >>Sequence Length Distribution pass #Length Count 46 4000.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 61.4 #Duplication Level Percentage of deduplicated Percentage of total 1 93.32247557003257 57.3 2 3.3794788273615635 4.15 3 1.0993485342019544 2.025 4 0.7328990228013029 1.7999999999999998 5 0.32573289902280134 1.0 6 0.20358306188925082 0.75 7 0.04071661237785017 0.17500000000000002 8 0.24429967426710095 1.2 9 0.04071661237785017 0.22499999999999998 >10 0.4478827361563518 4.875 >50 0.04071661237785017 1.825 >100 0.08143322475570033 11.75 >500 0.04071661237785017 12.925 >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 TGACAGAAGAGAGTGAGCACTCGTATGCCGTCTTCTGCTTGAAAAA 517 12.925 TruSeq Adapter, Index 19 (95% over 24bp) TCGCTTGGTGCAGATCGGGACTCGTATGCCGTCTTCTGCTTGAAAA 355 8.875 TruSeq Adapter, Index 15 (95% over 24bp) TTGACAGAAGAGAGTGAGCACTCGTATGCCGTCTTCTGCTTGAAAA 115 2.875 TruSeq Adapter, Index 13 (95% over 24bp) TGGAAGGGGCATGCAGAGGAGTCGTATGCCGTCTTCTGCTTGAAAA 73 1.825 Illumina Single End Adapter 2 (95% over 22bp) AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 48 1.2 No Hit CACGACTCTCGGCAACGGATATCTTCGTATGCCGTCTTCTGCTTGG 25 0.625 Illumina Single End Adapter 1 (95% over 22bp) GACACGACTCTCGGCAACGGATATCTTCGTATGCCGTCTTCTGCTT 18 0.44999999999999996 Illumina Single End Adapter 1 (95% over 21bp) AGAATCTTGATGATGCTGCATTCGTATGCCGTCTTCTGCTTGAAAA 17 0.42500000000000004 Illumina Single End Adapter 2 (95% over 22bp) GACACGACTCTCGGCAACGGATATTCGTATGCCGTCTTCTGCTTGG 15 0.375 Illumina Single End Adapter 1 (95% over 22bp) AGTTCTACAGTCCGACGATCTCGTATGCCGTCTTCTGCTTGAAAAA 13 0.325 Illumina PCR Primer Index 1 (96% over 28bp) GGGGATGTAGCTCAGATGGTATCGTATGCCGTCTTCTGCTTGAAAA 13 0.325 TruSeq Adapter, Index 14 (95% over 24bp) GACACGACTCTCGGCAACGGATATCTCGTATGCCGTCTTCTGCTTT 13 0.325 RNA PCR Primer, Index 25 (96% over 29bp) CACGACTCTCGGCAACGGATATCTCGTATGCCGTCTTCTGCTTGAA 12 0.3 Illumina PCR Primer Index 6 (96% over 27bp) AGGTCCCGGCGACGGAACCATCGTATGCCGTCTTCTGCTTGAAAAA 11 0.27499999999999997 Illumina Single End Adapter 1 (95% over 22bp) GGGGATGTAGCTCAGATGGTTCGTATGCCGTCTTCTGCTTGAAAAA 10 0.25 Illumina Single End Adapter 2 (95% over 23bp) TGACAGAAGAGAGTGAGCACTCGTATGCCGTCTTCTGCTTGAAAAC 9 0.22499999999999998 TruSeq Adapter, Index 19 (95% over 24bp) CTGACAGAAGAGAGTGAGCACTCGTATGCCGTCTTCTGCTTGAAAA 8 0.2 TruSeq Adapter, Index 13 (95% over 24bp) AACGAACGAACGATTTGAACTCGTATGCCGTCTTCTGCTTGAAAAA 8 0.2 Illumina Single End Adapter 2 (96% over 25bp) CACGACTCTCGGCAACGGATATCTCTCGTATGCCGTCTTCTGCTTT 8 0.2 Illumina PCR Primer Index 6 (96% over 25bp) GACACGACTCTCGGCAACGGATATCGTATGCCGTCTTCTGCTTGAA 8 0.2 Illumina PCR Primer Index 5 (96% over 25bp) CACGACTCTCGGCAACGGATATCTTCGTATGCCGTCTTCTGCTTGT 8 0.2 Illumina Single End Adapter 1 (95% over 22bp) TCGCTTGGTGCAGATCTGGACTCGTATGCCGTCTTCTGCTTGAAAA 8 0.2 TruSeq Adapter, Index 15 (95% over 24bp) CACGACTCTCGGCAACGGATATCTCGTCGTATGCCGTCTTCTGCTT 7 0.17500000000000002 Illumina Single End Adapter 1 (95% over 21bp) CTAACGAACGAACGATTTGAACTCGTATGCCGTCTTCTGCTTGAAA 6 0.15 Illumina Single End Adapter 2 (96% over 25bp) GACTCTCGGCAACGGATATCTTCGTATGCCGTCTTCTGCTTGAAAA 6 0.15 Illumina Single End Adapter 1 (95% over 22bp) CAGGTCCCGGCGACGGAACCATCGTATGCCGTCTTCTGCTTGAAAA 6 0.15 Illumina Single End Adapter 1 (95% over 22bp) GGGGATGTAGCTCAGATGGTAGTCGTATGCCGTCTTCTGCTTGAAA 6 0.15 Illumina Single End Adapter 2 (95% over 22bp) GACACGACTCTCGGCAACGGATTCGTATGCCGTCTTCTGCTTGAAA 6 0.15 Illumina Single End Adapter 2 (95% over 22bp) TTCTACAGTCCGACGATCTCGTATGCCGTCTTCTGCTTGAAAAAAA 5 0.125 RNA PCR Primer, Index 47 (96% over 29bp) GCGTCTGTAGTCCAACGGTTTCGTATGCCGTCTTCTGCTTGAAAAA 5 0.125 TruSeq Adapter, Index 14 (95% over 24bp) GGTGAACCTGCGGAAGGATCATTGTCGTATGCCGTCTTCTGCTTGG 5 0.125 TruSeq Adapter, Index 20 (95% over 24bp) TGAAGCTGCCAGCATGATCTGATCGTATGCCGTCTTCTGCTTGAAA 5 0.125 Illumina Single End Adapter 1 (95% over 23bp) CACGACTCTCGGCAACGGATATTCGTATGCCGTCTTCTGCTTGAAA 5 0.125 Illumina Single End Adapter 1 (95% over 22bp) GTTCGAGACCTGTATGGGCCACCATCGTATGCCGTCTTCTGCTTGG 5 0.125 Illumina Single End Adapter 2 (95% over 22bp) TCGTGACCTGTATGGGCCACCATCGTATGCCGTCTTCTGCTTGAAA 5 0.125 Illumina Single End Adapter 2 (95% over 22bp) CCACGTCGCACGGATTCGTTCGTATGCCGTCTTCTGCTTGAAAAAA 5 0.125 Illumina Single End Adapter 2 (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 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 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CGCTTGG 55 1.8189894E-12 40.379745 2 TCGCTTG 55 1.8189894E-12 40.379745 1 GCTTGGT 55 1.8189894E-12 40.379745 3 ATCGGGA 50 4.0017767E-11 39.875004 14 CGGGACT 50 4.0017767E-11 39.875004 16 GGGACTC 50 4.0017767E-11 39.875004 17 CAGATCG 50 4.0017767E-11 39.875004 11 TCGGGAC 50 4.0017767E-11 39.875004 15 GTGCAGA 55 1.8189894E-12 39.875 8 CTTGGTG 55 1.8189894E-12 39.875 4 GCAGATC 55 1.8189894E-12 39.875 10 TTGGTGC 55 1.8189894E-12 39.875 5 TGGTGCA 55 1.8189894E-12 39.875 6 TGCAGAT 55 1.8189894E-12 39.875 9 GGTGCAG 55 1.8189894E-12 39.875 7 TGCTTGG 80 0.0 37.382812 40 GGACTCG 60 5.456968E-12 36.552082 18 GACTCGT 60 5.456968E-12 36.552082 19 GATCGGG 55 1.1277734E-10 36.25 13 AGATCGG 55 1.1277734E-10 36.25 12 >>END_MODULE Read 647697 spots for SRR1033815.sra Written 647697 spots for SRR1033815.sra Read 647697 spots for SRR1033815.sra Written 647697 spots for SRR1033815.sra Read 647697 spots for SRR1033815.sra Written 647697 spots for SRR1033815.sra Read 647697 spots for SRR1033815.sra Written 647697 spots for SRR1033815.sra Read 647697 spots for SRR1033815.sra Written 647697 spots for SRR1033815.sra Read 647697 spots for SRR1033815.sra Written 647697 spots for SRR1033815.sra Read 647697 spots for SRR1033815.sra Written 647697 spots for SRR1033815.sra Read 647706 spots for SRR1033815.sra Written 647706 spots for SRR1033815.sra Read 647697 spots for SRR1033815.sra Written 647697 spots for SRR1033815.sra Read 647697 spots for SRR1033815.sra Written 647697 spots for SRR1033815.sra Read 647697 spots for SRR1033815.sra Written 647697 spots for SRR1033815.sra Read 647697 spots for SRR1033815.sra Written 647697 spots for SRR1033815.sra Read 647697 spots for SRR1033815.sra Written 647697 spots for SRR1033815.sra Read 647697 spots for SRR1033815.sra Written 647697 spots for SRR1033815.sra Read 647697 spots for SRR1033815.sra Written 647697 spots for SRR1033815.sra Read 647697 spots for SRR1033815.sra Written 647697 spots for SRR1033815.sra Read 647697 spots for SRR1033815.sra Written 647697 spots for SRR1033815.sra Read 647697 spots for SRR1033815.sra Written 647697 spots for SRR1033815.sra Read 647697 spots for SRR1033815.sra Written 647697 spots for SRR1033815.sra Read 647697 spots for SRR1033815.sra Written 647697 spots for SRR1033815.sra SRR ids: ['SRR1033815.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_a2wwwiq0 SRR1033815.sra spots: 12953949 blocks: [[1, 647697], [647698, 1295394], [1295395, 1943091], [1943092, 2590788], [2590789, 3238485], [3238486, 3886182], [3886183, 4533879], [4533880, 5181576], [5181577, 5829273], [5829274, 6476970], [6476971, 7124667], [7124668, 7772364], [7772365, 8420061], [8420062, 9067758], [9067759, 9715455], [9715456, 10363152], [10363153, 11010849], [11010850, 11658546], [11658547, 12306243], [12306244, 12953949]] SRR1033815 file size 1934521 SRR1033815 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 SRR1033815 SRR1033815_1.fastq Input file: SRR1033815_1.fastq trimmed: SRR1033815-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 Sat Dec 7 01:09:03 2024 >> started Sat Dec 7 01:09:12 2024 >> done (8.397s) 12953949 reads processed; of these: 107649 ( 0.83%) short reads filtered out after trimming by size control 25134 ( 0.19%) empty reads filtered out after trimming by size control 12821166 (98.97%) reads available; of these: 5516798 (43.03%) trimmed reads available after processing 7304368 (56.97%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 27704 0.22% 19 40091 0.31% 20 52052 0.41% 21 52153 0.41% 22 46269 0.36% 23 41657 0.32% 24 54780 0.43% 25 42666 0.33% 26 50834 0.40% 27 49554 0.39% 28 37813 0.29% 29 36433 0.28% 30 46504 0.36% 31 66823 0.52% 32 45640 0.36% 33 59034 0.46% 34 56870 0.44% 35 59931 0.47% 36 93245 0.73% 37 170635 1.33% 38 219150 1.71% 39 202103 1.58% 40 378204 2.95% 41 426026 3.32% 42 452654 3.53% 43 676070 5.27% 44 1264932 9.87% 45 766971 5.98% 46 7304368 56.97% 12821166 reads passed initial QC criterion=sequence-density sequence-density=89.07 sequence-density-rank=1 fanout-score=21.33 fanout-score-rank=4 prefix-density=91.13 prefix-fanout=20.9 sequence=TCGTATGCCGTCTTCTGCTTGAAAAACAA criterion=fanout-score sequence-density=1.53 sequence-density-rank=7 fanout-score=56.94 fanout-score-rank=1 prefix-density=85.88 prefix-fanout=1.0 sequence=TGCCGTCTTCTTCTTGAAAAA 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 TCGTATGCCGTCTTCTGCTTGAAAAACAA -o SRR1033815 - Input file: STDIN trimmed: SRR1033815-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TCGTATGCCGTCTTCTGCTTGAAAAACAA -- 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 Sat Dec 7 01:09:27 2024 >> started Sat Dec 7 01:09:42 2024 >> done (14.998s) 12536251 reads processed; of these: 45208 ( 0.36%) short reads filtered out after trimming by size control 7277 ( 0.06%) empty reads filtered out after trimming by size control 12483766 (99.58%) reads available; of these: 12083210 (96.79%) trimmed reads available after processing 400556 ( 3.21%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 232962 1.87% 19 469753 3.76% 20 2128651 17.05% 21 2830911 22.68% 22 819273 6.56% 23 1176170 9.42% 24 3689067 29.55% 25 630507 5.05% 26 385129 3.09% 27 65593 0.53% 28 7588 0.06% 29 2369 0.02% 30 1017 0.01% 31 1086 0.01% 32 533 0.00% 33 613 0.00% 34 378 0.00% 35 438 0.00% 36 575 0.00% 37 800 0.01% 38 892 0.01% 39 682 0.01% 40 799 0.01% 41 806 0.01% 42 645 0.01% 43 823 0.01% 44 1156 0.01% 45 878 0.01% 46 33672 0.27% criterion=sequence-density sequence-density=9.01 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=9 prefix-density=0.00 prefix-fanout=1.0 sequence=TCGCTTGGTGCAGATCGGGACTCGT criterion=fanout-score sequence-density=0.15 sequence-density-rank=14 fanout-score=6.54 fanout-score-rank=1 prefix-density=0.31 prefix-fanout=3.2 sequence=ATAGCTCAGTTGG Started job on | Dec 07 01:09:58 Started mapping on | Dec 07 01:09:58 Finished on | Dec 07 01:10:40 Mapping speed, Million of reads per hour | 1094.46 Number of input reads | 12768681 Average input read length | 22 UNIQUE READS: Uniquely mapped reads number | 4607784 Uniquely mapped reads % | 36.09% Average mapped length | 22.42 Number of splices: Total | 70024 Number of splices: Annotated (sjdb) | 8500 Number of splices: GT/AG | 69049 Number of splices: GC/AG | 783 Number of splices: AT/AC | 6 Number of splices: Non-canonical | 186 Mismatch rate per base, % | 0.31% Deletion rate per base | 0.00% Deletion average length | 1.08 Insertion rate per base | 0.00% Insertion average length | 1.01 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 4204219 % of reads mapped to multiple loci | 32.93% Number of reads mapped to too many loci | 3420566 % of reads mapped to too many loci | 26.79% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.09% % of reads unmapped: other | 1.11% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 3956678 3956678 3956678 N_multimapping 4204219 4204219 4204219 N_noFeature 2682713 2860030 4420376 N_ambiguous 14869 3889 1343 UnstrandedReadsAssigned:1910202 PositiveStrandReadsAssigned:1743865 NegativeStrandReadsAssigned:186065 Dataset is classified positive stranded MeadianReadLen=22 20thPercentileLength=20 echo kmer=19 SRR1033815 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: SRR1033815-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 12,768,681 reads, 4,163,800 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 989 rounds 52973 SRR1033815.ke.tsv 35125 SRR1033815.se.tsv 88098 total ==> SRR1033815.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 2.22839 0.0428434 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 3.77161 0.096667 PNS24243 293 194 0 0 KQK14069 1603 1504 70.4096 1.64623 KQK14071 474 375 22.1466 2.07674 ==> SRR1033815.se.tsv <== BRADI_1g14170v3 99 BRADI_1g53295v3 1 BRADI_1g59795v3 0 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 7 BRADI_1g74790v3 17 BRADI_1g09890v3 1 BRADI_1g77505v3 0 BRADI_1g48960v3 0 SRR1033815 completed mapping pipeline successfully