Starting /dee2/code/volunteer_pipeline.sh SRR1174003 current disk space = 1524669489152 free memory = 1338471992 SRR1174003 SRAfilesize d66d0b2006722825c9c174248756dd50 SRR1174003.sra SRR1174003.sra file validated SRR1174003 is single end SRR1174003 is conventional basespace SRR1174003 read1 length is 42 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR1174003_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 47 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.316 33.0 33.0 33.0 32.0 33.0 2 32.14425 33.0 32.0 34.0 30.0 34.0 3 32.0365 33.0 32.0 34.0 29.0 34.0 4 31.54675 33.0 31.0 33.0 28.0 34.0 5 31.89925 33.0 32.0 33.0 29.0 34.0 6 31.838 33.0 32.0 33.0 29.0 34.0 7 31.46625 33.0 31.0 33.0 28.0 34.0 8 31.5055 33.0 31.0 33.0 28.0 34.0 9 31.5215 33.0 31.0 33.0 28.0 34.0 10 31.69475 33.0 31.0 33.0 28.0 34.0 11 31.4245 33.0 31.0 33.0 28.0 34.0 12 31.66275 33.0 31.0 33.0 28.0 34.0 13 31.30225 33.0 31.0 33.0 27.0 34.0 14 31.3195 33.0 31.0 33.0 27.0 34.0 15 31.053 33.0 31.0 33.0 27.0 34.0 16 31.102 33.0 31.0 33.0 27.0 34.0 17 31.18525 33.0 31.0 33.0 27.0 34.0 18 31.27825 33.0 31.0 33.0 27.0 34.0 19 30.95675 33.0 30.0 33.0 26.0 34.0 20 30.26175 32.0 29.0 33.0 24.0 34.0 21 30.4945 32.0 30.0 33.0 25.0 33.0 22 30.86975 32.0 30.0 33.0 27.0 34.0 23 30.8245 32.0 30.0 33.0 26.0 34.0 24 29.97375 32.0 29.0 33.0 24.0 33.0 25 30.186 32.0 30.0 33.0 25.0 33.0 26 30.336 32.0 30.0 33.0 25.0 34.0 27 29.762 32.0 29.0 33.0 23.0 33.0 28 29.84125 32.0 29.0 33.0 24.0 33.0 29 29.10275 31.0 28.0 33.0 22.0 33.0 30 30.017 32.0 30.0 33.0 24.0 34.0 31 28.453 31.0 27.0 33.0 21.0 33.0 32 28.98675 32.0 29.0 33.0 21.0 33.0 33 28.7505 31.0 28.0 33.0 21.0 33.0 34 28.91275 32.0 28.0 33.0 21.0 33.0 35 27.874 31.0 27.0 32.0 19.0 33.0 36 27.419 30.0 26.0 32.0 19.0 33.0 37 28.448 31.0 28.0 33.0 20.0 33.0 38 27.42875 30.0 26.0 32.0 19.0 33.0 39 27.157 30.0 25.0 32.0 19.0 33.0 40 28.303 31.0 28.0 33.0 19.0 33.0 41 27.71375 31.0 27.0 32.0 18.0 33.0 42 25.7765 29.0 24.0 32.0 4.0 33.0 >>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 4.0 5 3.0 6 1.0 7 0.0 8 1.0 9 3.0 10 0.0 11 0.0 12 2.0 13 3.0 14 2.0 15 2.0 16 7.0 17 5.0 18 12.0 19 14.0 20 20.0 21 27.0 22 39.0 23 68.0 24 73.0 25 91.0 26 117.0 27 153.0 28 244.0 29 374.0 30 623.0 31 971.0 32 924.0 33 217.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 33.58490566037736 31.144654088050316 21.18238993710692 14.08805031446541 2 33.175 21.825 28.9 16.1 3 32.483120780195044 23.755938984746187 19.179794948737182 24.58114528632158 4 30.55763940985246 33.758439609902474 22.330582645661416 13.353338334583645 5 28.28207051762941 25.681420355088775 25.131282820705174 20.905226306576644 6 28.67150362772079 24.843632724543408 29.847385539154363 16.637478108581437 7 30.307576894223555 28.28207051762941 25.906476619154787 15.503875968992247 8 20.665499124343256 24.943707780835627 38.85414060545409 15.536652489367025 9 23.005751437859466 35.45886471617904 27.956989247311824 13.578394598649663 10 41.26031507876969 22.980745186296573 19.42985746436609 16.32908227056764 11 21.98599299649825 22.661330665332667 31.36568284142071 23.986993496748372 12 22.625 23.799999999999997 31.775 21.8 13 27.48435544430538 21.451814768460576 21.176470588235293 29.887359198998748 14 21.825 40.775 24.6 12.8 15 29.28232058014504 33.30832708177044 20.05501375343836 17.35433858464616 16 21.235617808904454 25.18759379689845 37.89394697348674 15.682841420710355 17 23.761880940470235 21.810905452726363 37.543771885942974 16.883441720860432 18 35.525 19.6 23.200000000000003 21.675 19 34.667333666833414 20.710355177588795 26.18809404702351 18.434217108554275 20 27.1703777833375 24.093069802351764 31.848886664998748 16.887665749311985 21 22.705676419104776 27.38184546136534 22.080520130032507 27.831957989497376 22 26.920190142606952 30.297723292469353 24.943707780835627 17.838378784088064 23 30.85 24.125 29.049999999999997 15.975 24 24.981245311327832 25.656414103525883 22.280570142535634 27.081770442610654 25 16.691691691691695 41.791791791791795 22.84784784784785 18.66866866866867 26 11.992989484226339 13.795693540310467 45.96895343014521 28.24236354531798 27 17.375 15.15 20.25 47.225 28 9.82991495747874 15.632816408204103 50.10005002501251 24.437218609304654 29 18.423028785982478 13.316645807259073 17.72215269086358 50.538172715894866 30 50.61265316329082 9.177294323580895 26.056514128532132 14.153538384596148 31 14.078519629907477 17.20430107526882 48.23705926481621 20.4801200300075 32 9.331998999249437 39.77983487615712 22.71703777833375 28.171128346259692 33 13.778444611152787 11.40285071267817 51.26281570392598 23.55588897224306 34 44.24712356178089 14.307153576788394 21.96098049024512 19.484742371185593 35 11.530765382691346 11.78089044522261 26.488244122061033 50.20010005002501 36 14.335751813860394 13.335001250938202 19.914936202151615 52.41431073304979 37 38.73873873873874 11.01101101101101 35.21021021021021 15.04004004004004 38 10.080040020010005 13.331665832916459 54.17708854427213 22.411205602801402 39 12.906453226613307 15.257628814407203 25.662831415707853 46.17308654327164 40 11.258443832874656 18.663997998498875 57.89342006504879 12.184138103577684 41 13.620430645968954 24.887330996494743 47.59639459188783 13.895843765648472 42 7.3219658976930795 24.072216649949848 25.300902708124372 43.3049147442327 >>END_MODULE >>Per sequence GC content warn #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 0.0 20 0.0 21 0.0 22 0.0 23 0.5 24 1.0 25 4.0 26 7.0 27 31.5 28 56.0 29 56.0 30 52.5 31 49.0 32 54.0 33 59.0 34 59.0 35 73.5 36 88.0 37 122.0 38 156.0 39 242.0 40 328.0 41 328.0 42 374.0 43 420.0 44 455.5 45 491.0 46 542.0 47 593.0 48 593.0 49 655.5 50 718.0 51 628.5 52 539.0 53 539.0 54 379.5 55 220.0 56 191.0 57 162.0 58 109.0 59 56.0 60 56.0 61 40.0 62 24.0 63 20.0 64 16.0 65 12.0 66 8.0 67 8.0 68 6.0 69 4.0 70 3.5 71 3.0 72 3.0 73 2.0 74 1.0 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 0.0 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 0.625 2 0.0 3 0.025 4 0.025 5 0.025 6 0.075 7 0.025 8 0.075 9 0.025 10 0.025 11 0.05 12 0.0 13 0.125 14 0.0 15 0.025 16 0.05 17 0.05 18 0.0 19 0.05 20 0.075 21 0.025 22 0.075 23 0.0 24 0.025 25 0.1 26 0.15 27 0.0 28 0.05 29 0.125 30 0.025 31 0.025 32 0.075 33 0.025 34 0.05 35 0.05 36 0.075 37 0.1 38 0.05 39 0.05 40 0.075 41 0.15 42 0.3 >>END_MODULE >>Sequence Length Distribution pass #Length Count 42 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 78.5 #Duplication Level Percentage of deduplicated Percentage of total 1 94.8407643312102 74.45 2 2.229299363057325 3.5000000000000004 3 0.7643312101910829 1.7999999999999998 4 0.5095541401273885 1.6 5 0.4140127388535032 1.625 6 0.15923566878980894 0.75 7 0.12738853503184713 0.7000000000000001 8 0.15923566878980894 1.0 9 0.09554140127388536 0.675 >10 0.5732484076433121 7.199999999999999 >50 0.12738853503184713 6.7 >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 fail #Sequence Count Percentage Possible Source GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCATCTCGTAT 73 1.825 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTATCTCGTAT 73 1.825 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGATCTCGT 66 1.6500000000000001 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCATCTCGTA 56 1.4000000000000001 No Hit TAATTCATGATCTGGATCTCGTATGCCGTCTTCTGCTTGAAA 37 0.9249999999999999 RNA PCR Primer, Index 23 (96% over 28bp) TTTGGATTGAAGGGAGCTCTGATCTCGTATGCCGTCTTCTGC 34 0.8500000000000001 Illumina PCR Primer Index 9 (96% over 25bp) ATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAA 21 0.525 Illumina Single End Adapter 1 (95% over 24bp) GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACCATCTCGTAT 19 0.475 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACATCTCGTATG 17 0.42500000000000004 No Hit CGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTTGAAAA 16 0.4 RNA PCR Primer, Index 19 (96% over 29bp) AGGGCTATAGCTCAGTTCGGATCTCGTATGCCGTCTTCTGCT 16 0.4 TruSeq Adapter, Index 9 (96% over 26bp) TGACAGAAGAGAGTGAGCACATCTCGTATGCCGTCTTCTGCT 14 0.35000000000000003 Illumina PCR Primer Index 9 (96% over 25bp) AACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTTGAA 14 0.35000000000000003 RNA PCR Primer, Index 19 (96% over 29bp) GCACCAGTGGTCTAGTGGTAGAATAGTACCATCTCGTATGCC 13 0.325 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTATCTCGT 13 0.325 No Hit GTCGTTGTAGTATAGTGGTAAGTATTCCCGCATCTCGTATGC 12 0.3 No Hit GAACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTTGA 11 0.27499999999999997 Illumina PCR Primer Index 7 (96% over 28bp) CTAACGAACGAACGATTTGAACATCTCGTATGCCGTCTTCTG 11 0.27499999999999997 RNA PCR Primer, Index 19 (96% over 25bp) TCCGTCGTAGTCTAGGATCTCGTATGCCGTCTTCTGCTTGAA 10 0.25 RNA PCR Primer, Index 22 (96% over 28bp) TCGCTTGGTGCAGATCGGGACATCTCGTATGCCGTCTTCTGC 10 0.25 Illumina PCR Primer Index 3 (95% over 24bp) CGGCGACGGAACCAATCTCGTATGCCGTCTTCTGCTTGAAAA 10 0.25 Illumina PCR Primer Index 4 (96% over 29bp) TAACGAACGAACGATTTGAACATCTCGTATGCCGTCTTCTGC 10 0.25 Illumina PCR Primer Index 7 (96% over 25bp) GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGATCTCGTA 9 0.22499999999999998 No Hit GGGGACGTAGCTCATAATCTCGTATGCCGTCTTCTGCTTGAA 9 0.22499999999999998 RNA PCR Primer, Index 40 (96% over 30bp) GTCGTTGTAGTATAATCTCGTATGCCGTCTTCTGCTTGAAAA 9 0.22499999999999998 Illumina PCR Primer Index 12 (96% over 28bp) AGCGGAGTAGAGCAGTATCTCGTATGCCGTCTTCTGCTTGAA 8 0.2 Illumina PCR Primer Index 6 (96% over 28bp) CACGACTCTCGGCAACGGATATCTATCTCGTATGCCGTCTTC 8 0.2 Illumina PCR Primer Index 2 (95% over 22bp) TCCACAGGCTTTCTTGAACTGATCTCGTATGCCGTCTTCTGC 8 0.2 RNA PCR Primer, Index 29 (96% over 26bp) CGAACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTTG 8 0.2 RNA PCR Primer, Index 19 (96% over 29bp) AACGAACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCT 8 0.2 RNA PCR Primer, Index 19 (96% over 27bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTATCTCGTA 7 0.17500000000000002 No Hit CATCCTAACGAACGAACGATTTGAACATCTCGTATGCCGTCT 7 0.17500000000000002 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTATCTC 7 0.17500000000000002 No Hit TCGTGACCCTGACCATCTCGTATGCCGTCTTCTGCTTGAAAA 7 0.17500000000000002 Illumina PCR Primer Index 1 (96% over 27bp) GGGGATGTAGCTCAGAATCTCGTATGCCGTCTTCTGCTTGAA 6 0.15 RNA PCR Primer, Index 40 (100% over 30bp) GAGGCATCCTAACGAACGAACGATTTGAACATCTCGTATGCC 6 0.15 No Hit ATCCTAACGAACGAACGATTTGAACATCTCGTATGCCGTCTT 6 0.15 RNA PCR Primer, Index 19 (95% over 22bp) GAACGATTTGAACATCTCGTATGCCGTCTTCTGCTTGAAAAA 6 0.15 RNA PCR Primer, Index 19 (96% over 29bp) GGGCCTGTAGCTCAGAGGAATCTCGTATGCCGTCTTCTGCTT 6 0.15 Illumina PCR Primer Index 12 (96% over 26bp) TTGACAGAAGAGAGTGAGCACATCTCGTATGCCGTCTTCTGC 5 0.125 Illumina PCR Primer Index 9 (95% over 24bp) CACGACTCTCGGCAACGGATATCATCTCGTATGCCGTCTTCT 5 0.125 TruSeq Adapter, Index 7 (95% over 24bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCATCTCGTATG 5 0.125 No Hit ATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAACA 5 0.125 Illumina Single End Adapter 1 (95% over 24bp) GTCAGGATAGCTCAGTATCTCGTATGCCGTCTTCTGCTTGAA 5 0.125 RNA PCR Primer, Index 40 (96% over 30bp) GGGGATGTAGCTCAAAATCTCGTATGCCGTCTTCTGCTTGAA 5 0.125 RNA PCR Primer, Index 40 (96% over 30bp) AGCGGAGTAGAGCAGTTATCTCGTATGCCGTCTTCTGCTTGA 5 0.125 Illumina PCR Primer Index 5 (96% over 29bp) CACGACTCTCGGCAACGGATATCTCATCTCGTATGCCGTCTT 5 0.125 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAATCTCGT 5 0.125 No Hit ACGAACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTT 5 0.125 Illumina PCR Primer Index 7 (96% over 27bp) AGGGATATAACTCAGCGGTAGAGTGTCACCTTGACGTGGTGA 5 0.125 No Hit GGGGATGTAGCTCAATCTCGTATGCCGTCTTCTGCTTGAAAA 5 0.125 RNA PCR Primer, Index 32 (96% over 29bp) GCATCCTAACGAACGAACGATTTGAACATCTCGTATGCCGTC 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 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGATTG 40 3.1324817E-8 36.0 1 TTGTAGT 50 5.5079E-9 32.399998 5 TGGTCAG 45 8.843199E-8 32.0 17 TTCAATT 45 8.843199E-8 32.0 11 ATTGGTC 45 8.843199E-8 32.0 15 CACCGCC 45 8.843199E-8 32.0 26 CAATTGG 45 8.843199E-8 32.0 13 TCAATTG 45 8.843199E-8 32.0 12 GGTCAGA 45 8.843199E-8 32.0 18 GTTCAAT 45 8.843199E-8 32.0 10 TAGTTCA 45 8.843199E-8 32.0 8 CAGAGCA 45 8.843199E-8 32.0 21 GAGCACC 45 8.843199E-8 32.0 23 AGAGCAC 45 8.843199E-8 32.0 22 ATTGTAG 45 8.843199E-8 32.0 4 TCAGAGC 45 8.843199E-8 32.0 20 TGTAGTT 45 8.843199E-8 32.0 6 AGCACCG 45 8.843199E-8 32.0 24 TTGGTCA 45 8.843199E-8 32.0 16 GTCAGAG 45 8.843199E-8 32.0 19 >>END_MODULE Read 607061 spots for SRR1174003.sra Written 607061 spots for SRR1174003.sra Read 607061 spots for SRR1174003.sra Written 607061 spots for SRR1174003.sra Read 607061 spots for SRR1174003.sra Written 607061 spots for SRR1174003.sra Read 607061 spots for SRR1174003.sra Written 607061 spots for SRR1174003.sra Read 607061 spots for SRR1174003.sra Written 607061 spots for SRR1174003.sra Read 607061 spots for SRR1174003.sra Written 607061 spots for SRR1174003.sra Read 607061 spots for SRR1174003.sra Written 607061 spots for SRR1174003.sra Read 607061 spots for SRR1174003.sra Written 607061 spots for SRR1174003.sra Read 607061 spots for SRR1174003.sra Written 607061 spots for SRR1174003.sra Read 607061 spots for SRR1174003.sra Written 607061 spots for SRR1174003.sra Read 607061 spots for SRR1174003.sra Written 607061 spots for SRR1174003.sra Read 607061 spots for SRR1174003.sra Written 607061 spots for SRR1174003.sra Read 607061 spots for SRR1174003.sra Written 607061 spots for SRR1174003.sra Read 607068 spots for SRR1174003.sra Written 607068 spots for SRR1174003.sra Read 607061 spots for SRR1174003.sra Written 607061 spots for SRR1174003.sra Read 607061 spots for SRR1174003.sra Written 607061 spots for SRR1174003.sra Read 607061 spots for SRR1174003.sra Written 607061 spots for SRR1174003.sra Read 607061 spots for SRR1174003.sra Written 607061 spots for SRR1174003.sra Read 607061 spots for SRR1174003.sra Written 607061 spots for SRR1174003.sra Read 607061 spots for SRR1174003.sra Written 607061 spots for SRR1174003.sra SRR ids: ['SRR1174003.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_zr3rrv2k SRR1174003.sra spots: 12141227 blocks: [[1, 607061], [607062, 1214122], [1214123, 1821183], [1821184, 2428244], [2428245, 3035305], [3035306, 3642366], [3642367, 4249427], [4249428, 4856488], [4856489, 5463549], [5463550, 6070610], [6070611, 6677671], [6677672, 7284732], [7284733, 7891793], [7891794, 8498854], [8498855, 9105915], [9105916, 9712976], [9712977, 10320037], [10320038, 10927098], [10927099, 11534159], [11534160, 12141227]] SRR1174003 file size 1693770 SRR1174003 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 SRR1174003 SRR1174003_1.fastq Input file: SRR1174003_1.fastq trimmed: SRR1174003-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 14:22:16 2024 >> started Mon Dec 9 14:22:41 2024 >> done (24.795s) 12141227 reads processed; of these: 44779 ( 0.37%) short reads filtered out after trimming by size control 24520 ( 0.20%) empty reads filtered out after trimming by size control 12071928 (99.43%) reads available; of these: 1322728 (10.96%) trimmed reads available after processing 10749200 (89.04%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 6260 0.05% 19 7225 0.06% 20 8659 0.07% 21 10312 0.09% 22 13659 0.11% 23 20877 0.17% 24 23298 0.19% 25 22429 0.19% 26 31361 0.26% 27 52453 0.43% 28 47415 0.39% 29 58663 0.49% 30 61442 0.51% 31 60185 0.50% 32 54828 0.45% 33 51888 0.43% 34 46162 0.38% 35 36267 0.30% 36 39026 0.32% 37 45018 0.37% 38 49591 0.41% 39 65499 0.54% 40 147048 1.22% 41 363163 3.01% 42 10749200 89.04% 12071928 reads passed initial QC criterion=sequence-density sequence-density=76.63 sequence-density-rank=1 fanout-score=39.86 fanout-score-rank=1 prefix-density=77.51 prefix-fanout=39.4 sequence=ATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA criterion=fanout-score sequence-density=76.63 sequence-density-rank=1 fanout-score=39.86 fanout-score-rank=1 prefix-density=77.51 prefix-fanout=39.4 sequence=ATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA 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 ATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA -o SRR1174003 - Input file: STDIN trimmed: SRR1174003-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): ATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA -- 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 14:24:20 2024 >> started Mon Dec 9 14:25:04 2024 >> done (43.040s) 11758372 reads processed; of these: 2224564 (18.92%) short reads filtered out after trimming by size control 413574 ( 3.52%) empty reads filtered out after trimming by size control 9120234 (77.56%) reads available; of these: 8732557 (95.75%) trimmed reads available after processing 387677 ( 4.25%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 231318 2.54% 19 257225 2.82% 20 323244 3.54% 21 714355 7.83% 22 263803 2.89% 23 678306 7.44% 24 3929480 43.09% 25 252677 2.77% 26 136189 1.49% 27 100492 1.10% 28 87210 0.96% 29 107474 1.18% 30 136569 1.50% 31 128306 1.41% 32 173622 1.90% 33 608783 6.68% 34 291078 3.19% 35 294966 3.23% 36 82012 0.90% 37 41613 0.46% 38 25334 0.28% 39 18977 0.21% 40 4875 0.05% 41 7815 0.09% 42 224511 2.46% criterion=sequence-density sequence-density=6.14 sequence-density-rank=1 fanout-score=1.00 fanout-score-rank=17 prefix-density=0.01 prefix-fanout=1.0 sequence=GGGATTGTAGTTCAATTGGTCAGAGCACCGCCC criterion=fanout-score sequence-density=0.84 sequence-density-rank=7 fanout-score=30.39 fanout-score-rank=1 prefix-density=0.81 prefix-fanout=30.4 sequence=TCGTATGCCGTCTTCTGCTTGAAAAA Started job on | Dec 09 14:27:10 Started mapping on | Dec 09 14:27:11 Finished on | Dec 09 14:29:18 Mapping speed, Million of reads per hour | 267.41 Number of input reads | 9433790 Average input read length | 26 UNIQUE READS: Uniquely mapped reads number | 4123933 Uniquely mapped reads % | 43.71% Average mapped length | 23.68 Number of splices: Total | 37006 Number of splices: Annotated (sjdb) | 3705 Number of splices: GT/AG | 35062 Number of splices: GC/AG | 908 Number of splices: AT/AC | 13 Number of splices: Non-canonical | 1023 Mismatch rate per base, % | 0.18% Deletion rate per base | 0.00% Deletion average length | 1.16 Insertion rate per base | 0.00% Insertion average length | 1.02 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 3200342 % of reads mapped to multiple loci | 33.92% Number of reads mapped to too many loci | 1457386 % of reads mapped to too many loci | 15.45% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.75% % of reads unmapped: other | 2.16% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 2109515 2109515 2109515 N_multimapping 3200342 3200342 3200342 N_noFeature 3374080 3634511 3854520 N_ambiguous 21343 11609 1241 UnstrandedReadsAssigned:728510 PositiveStrandReadsAssigned:477813 NegativeStrandReadsAssigned:268172 Dataset is classified unstranded MeadianReadLen=24 20thPercentileLength=23 echo kmer=19 SRR1174003 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: SRR1174003-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 9,433,790 reads, 2,822,101 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,148 rounds 52973 SRR1174003.ke.tsv 35125 SRR1174003.se.tsv 88098 total ==> SRR1174003.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 3.45246 0.423212 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 0 0 PNS24243 293 194 0 0 KQK14069 1603 1504 24 3.57772 KQK14071 474 375 0 0 ==> SRR1174003.se.tsv <== BRADI_1g14170v3 25 BRADI_1g53295v3 3 BRADI_1g59795v3 0 BRADI_1g07683v3 0 BRADI_1g00485v3 1 BRADI_1g20270v3 10 BRADI_1g74790v3 107 BRADI_1g09890v3 0 BRADI_1g77505v3 1 BRADI_1g48960v3 0 SRR1174003 completed mapping pipeline successfully