Starting /dee2/code/volunteer_pipeline.sh SRR1174001 current disk space = 1524710309888 free memory = 1605737432 SRR1174001 SRAfilesize c41b11d0377dad017d5bd7bfc2e3762b SRR1174001.sra SRR1174001.sra file validated SRR1174001 is single end SRR1174001 is conventional basespace SRR1174001 read1 length is 42 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR1174001_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 fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.87475 33.0 31.0 33.0 26.0 33.0 2 29.94925 32.0 29.0 33.0 23.0 34.0 3 28.971 31.0 27.0 33.0 21.0 34.0 4 27.54425 30.0 25.0 33.0 17.0 33.0 5 28.19725 31.0 26.0 33.0 19.0 33.0 6 28.2795 31.0 26.0 33.0 19.0 33.0 7 28.29575 31.0 26.0 33.0 19.0 33.0 8 28.62575 31.0 27.0 33.0 20.0 33.0 9 29.2135 32.0 28.0 33.0 21.0 34.0 10 29.6425 32.0 28.0 33.0 22.0 34.0 11 27.74925 30.0 25.0 33.0 18.0 33.0 12 28.3565 31.0 26.0 33.0 19.0 33.0 13 28.91275 31.0 27.0 33.0 21.0 34.0 14 28.84325 31.0 27.0 33.0 20.0 34.0 15 28.29275 31.0 26.0 33.0 19.0 33.0 16 26.574 29.0 23.0 32.0 16.0 33.0 17 27.1775 30.0 24.0 32.0 18.0 33.0 18 27.20175 30.0 24.0 33.0 17.0 33.0 19 26.5565 29.0 24.0 32.0 16.0 33.0 20 26.2545 29.0 23.0 32.0 14.0 33.0 21 25.2145 28.0 21.0 31.0 13.0 33.0 22 25.0685 28.0 21.0 31.0 13.0 33.0 23 26.55375 30.0 24.0 32.0 16.0 33.0 24 25.47675 29.0 22.0 31.0 12.0 33.0 25 26.11025 29.0 23.0 32.0 14.0 33.0 26 26.32525 30.0 24.0 32.0 12.0 33.0 27 22.5185 25.0 17.0 30.0 7.0 32.0 28 23.36725 26.0 19.0 31.0 8.0 32.0 29 23.42025 26.0 19.0 31.0 7.0 32.0 30 23.418 26.0 19.0 31.0 7.0 33.0 31 23.3 26.0 19.0 30.0 7.0 32.0 32 24.447 28.0 21.0 31.0 5.0 33.0 33 24.26875 28.0 21.0 31.0 4.0 33.0 34 23.94175 27.0 20.0 31.0 4.0 33.0 35 21.28875 23.0 15.0 30.0 4.0 32.0 36 22.75175 26.0 18.0 31.0 4.0 33.0 37 22.80025 26.0 18.0 31.0 4.0 33.0 38 22.54225 26.0 18.0 30.0 4.0 32.0 39 22.51775 26.0 18.0 30.0 4.0 32.0 40 22.35675 26.0 17.0 31.0 4.0 32.0 41 21.93125 26.0 15.0 31.0 4.0 32.0 42 19.216 23.0 4.0 29.0 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 >>END_MODULE >>Per sequence quality scores warn #Quality Count 4 12.0 5 3.0 6 6.0 7 11.0 8 6.0 9 13.0 10 14.0 11 37.0 12 33.0 13 29.0 14 34.0 15 34.0 16 36.0 17 39.0 18 32.0 19 53.0 20 70.0 21 107.0 22 142.0 23 228.0 24 306.0 25 367.0 26 426.0 27 492.0 28 483.0 29 433.0 30 320.0 31 188.0 32 44.0 33 2.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 27.595696772579437 38.17863397548161 20.94070552914686 13.284963722792096 2 27.370527895921942 33.65023767825869 23.667750813109834 15.31148361270953 3 30.172629472104077 26.945208906680012 19.664748561421067 23.217413059794847 4 32.89144572286143 30.040020010005 21.585792896448226 15.482741370685343 5 24.025 34.225 22.2 19.55 6 23.1807951987997 29.332333083270818 29.307326831707925 18.179544886221557 7 29.549999999999997 29.049999999999997 25.924999999999997 15.475 8 20.130032508127034 24.58114528632158 36.809202300575144 18.479619904976243 9 23.43671835917959 33.56678339169585 29.139569784892444 13.856928464232116 10 35.83395848962241 26.70667666916729 21.205301325331334 16.25406351587897 11 21.9 24.675 31.8 21.625 12 24.787393696848426 25.212606303151574 27.913956978489246 22.086043021510758 13 25.775 25.424999999999997 25.525 23.275000000000002 14 22.05551387846962 42.26056514128532 22.980745186296573 12.703175793948487 15 28.371278458844134 33.074806104578435 23.042281711283465 15.511633725293972 16 19.854963740935233 30.38259564891223 32.0830207551888 17.67941985496374 17 25.874999999999996 26.950000000000003 31.95 15.225 18 30.83270817704426 22.655663915978995 25.93148287071768 20.580145036259065 19 27.250000000000004 25.7 27.950000000000003 19.1 20 23.705926481620406 28.382095523880967 30.932733183295824 16.9792448112028 21 23.15578894723681 29.857464366091524 24.33108277069267 22.655663915978995 22 27.525 28.599999999999998 26.5 17.375 23 24.88744372186093 27.5887943971986 29.289644822411205 18.234117058529264 24 22.05 23.799999999999997 28.525 25.624999999999996 25 18.543543543543546 36.73673673673674 25.375375375375377 19.344344344344343 26 19.42985746436609 13.328332083020754 43.91097774443611 23.330832708177045 27 17.471839799749684 16.345431789737173 25.00625782227785 41.17647058823529 28 14.997496244366552 16.800200300450676 44.99248873309965 23.209814722083124 29 20.28514257128564 14.232116058029016 25.237618809404704 40.24512256128064 30 38.61930965482742 11.78089044522261 28.414207103551774 21.1855927963982 31 16.50801603206413 14.453907815631261 45.41583166332666 23.622244488977955 32 14.568706118355065 31.59478435305918 30.06519558676028 23.771313941825476 33 14.486215538847116 10.200501253132831 51.00250626566416 24.31077694235589 34 37.01754385964912 8.897243107769423 29.19799498746867 24.887218045112782 35 16.194534971170718 9.827024316871396 32.61469039859614 41.36375031336175 36 17.790027562014533 7.767476822851416 28.890002505637685 45.55249310949637 37 35.02257902659308 8.404415454089314 33.492222779729055 23.08078273958856 38 13.752505010020041 11.54809619238477 54.934869739478955 19.76452905811623 39 16.02306920762287 12.311935807422266 32.221664994984955 39.44332998996991 40 17.088449010273116 15.985968428965172 49.536457028313706 17.38912553244801 41 13.952905811623245 21.693386773547093 46.943887775551104 17.409819639278556 42 12.581617277749874 24.711200401808135 26.695128076343543 36.012054244098444 >>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 1.0 19 2.0 20 3.0 21 4.0 22 4.0 23 6.5 24 9.0 25 8.5 26 8.0 27 18.5 28 29.0 29 29.0 30 31.5 31 34.0 32 45.0 33 56.0 34 56.0 35 107.5 36 159.0 37 214.5 38 270.0 39 354.0 40 438.0 41 438.0 42 506.0 43 574.0 44 594.0 45 614.0 46 580.5 47 547.0 48 547.0 49 541.5 50 536.0 51 444.5 52 353.0 53 353.0 54 274.5 55 196.0 56 147.0 57 98.0 58 65.0 59 32.0 60 32.0 61 27.5 62 23.0 63 15.0 64 7.0 65 5.5 66 4.0 67 4.0 68 3.0 69 2.0 70 1.5 71 1.0 72 1.0 73 1.5 74 2.0 75 1.0 76 0.0 77 0.5 78 1.0 79 1.0 80 0.5 81 0.0 82 0.5 83 1.0 84 1.0 85 0.5 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 0.075 2 0.075 3 0.075 4 0.05 5 0.0 6 0.025 7 0.0 8 0.025 9 0.05 10 0.025 11 0.0 12 0.05 13 0.0 14 0.025 15 0.075 16 0.025 17 0.0 18 0.025 19 0.0 20 0.025 21 0.025 22 0.0 23 0.05 24 0.0 25 0.1 26 0.025 27 0.125 28 0.15 29 0.05 30 0.05 31 0.2 32 0.3 33 0.25 34 0.25 35 0.27499999999999997 36 0.22499999999999998 37 0.35000000000000003 38 0.2 39 0.3 40 0.22499999999999998 41 0.2 42 0.44999999999999996 >>END_MODULE >>Sequence Length Distribution pass #Length Count 42 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 83.72500000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 94.35652433562257 79.0 2 2.7769483427888924 4.65 3 1.1048074051955807 2.775 4 0.2985965959988056 1.0 5 0.4478948939982084 1.875 6 0.20901761719916392 1.05 7 0.17915795759928338 1.05 8 0.0 0.0 9 0.11943863839952225 0.8999999999999999 >10 0.5076142131979695 7.7 >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 fail #Sequence Count Percentage Possible Source TAATTCATGATCTGGATCTCGTATGCCGTCTTCTGCTTGAAA 41 1.0250000000000001 RNA PCR Primer, Index 23 (96% over 28bp) AACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTTGAA 35 0.8750000000000001 RNA PCR Primer, Index 19 (96% over 29bp) GCACCAGTGGTCTAGTGGTAGAATAGTACCATCTCGTATGCC 32 0.8 No Hit TAACGAACGAACGATTTGAACATCTCGTATGCCGTCTTCTGC 25 0.625 Illumina PCR Primer Index 7 (96% over 25bp) TTTGGATTGAAGGGAGCTCTGATCTCGTATGCCGTCTTCTGC 24 0.6 Illumina PCR Primer Index 9 (96% over 25bp) ACGAACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTT 20 0.5 Illumina PCR Primer Index 7 (96% over 27bp) GGGCCTGTAGCTCAGAGGAATCTCGTATGCCGTCTTCTGCTT 15 0.375 Illumina PCR Primer Index 12 (96% over 26bp) ACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTTGAAA 14 0.35000000000000003 Illumina PCR Primer Index 7 (96% over 28bp) AACGAACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCT 14 0.35000000000000003 RNA PCR Primer, Index 19 (96% over 27bp) TAGATATTTCAGGTTGTGTGGAATCTCGTATGCCGTCTTCTG 14 0.35000000000000003 Illumina PCR Primer Index 8 (95% over 24bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCATCTCGTAT 12 0.3 No Hit GGGGATGTAGCTCAAAATCTCGTATGCCGTCTTCTGCTTGAA 11 0.27499999999999997 RNA PCR Primer, Index 40 (96% over 30bp) GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTATCTCGTAT 11 0.27499999999999997 No Hit CACGACTCTCGGCAACGGATATCATCTCGTATGCCGTCTTCT 10 0.25 TruSeq Adapter, Index 7 (95% over 24bp) GGGATTGTAGTTCAATATCTCGTATGCCGTCTTCTGCTTGAA 10 0.25 Illumina PCR Primer Index 6 (96% over 29bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCATCTCGTA 10 0.25 No Hit CTAACGAACGAACGATTTGAACATCTCGTATGCCGTCTTCTG 10 0.25 RNA PCR Primer, Index 19 (96% over 25bp) CGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTTGAAAA 9 0.22499999999999998 RNA PCR Primer, Index 19 (96% over 29bp) GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGATCTCGTA 9 0.22499999999999998 No Hit GAACGATTTGAACATCTCGTATGCCGTCTTCTGCTTGAAAAA 9 0.22499999999999998 RNA PCR Primer, Index 19 (96% over 29bp) TCCGTCGTAGTCTAGGATCTCGTATGCCGTCTTCTGCTTGAA 9 0.22499999999999998 RNA PCR Primer, Index 22 (96% over 28bp) GGGGATGTAGCTCAGAATCTCGTATGCCGTCTTCTGCTTGAA 7 0.17500000000000002 RNA PCR Primer, Index 40 (100% over 30bp) CGGATAACCGTAGTAATTCTAGAGCTAATACGTATCTCGTAT 7 0.17500000000000002 No Hit TGCAAGTATGAACTAATTTGAACTGTGAAACATCTCGTATGC 7 0.17500000000000002 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGATCTCGT 7 0.17500000000000002 No Hit GACACGACTCTCGGCAACGGATATCTATCTCGTATGCCGTCT 7 0.17500000000000002 No Hit GGGGACGTAGCTCATAATCTCGTATGCCGTCTTCTGCTTGAA 7 0.17500000000000002 RNA PCR Primer, Index 40 (96% over 30bp) AGCGGAGTAGAGCAGTATCTCGTATGCCGTCTTCTGCTTGAA 6 0.15 Illumina PCR Primer Index 6 (96% over 28bp) TGACAGAAGAGAGTGAGCACATCTCGTATGCCGTCTTCTGCT 6 0.15 Illumina PCR Primer Index 9 (96% over 25bp) GACACGACTCTCGGCAACGGATATCATCTCGTATGCCGTCTT 6 0.15 TruSeq Adapter, Index 7 (95% over 22bp) GTCGTTGTAGTATAGTGGTAAGTATTCCCGCATCTCGTATGC 6 0.15 No Hit TGCAAGTATGAACTAATTTGAACTGTGAAACTGCATCTCGTA 6 0.15 No Hit AGGGCTATAGCTCAGTTCGGATCTCGTATGCCGTCTTCTGCT 6 0.15 TruSeq Adapter, Index 9 (96% over 26bp) GGCGGATGTAGCCAAGTGGAATCTCGTATGCCGTCTTCTGCT 6 0.15 Illumina PCR Primer Index 8 (96% over 26bp) CACGACTCTCGGCAACGGATATCTATCTCGTATGCCGTCTTC 5 0.125 Illumina PCR Primer Index 2 (95% over 22bp) GGGGATGTAGCTCAGATGGTAGAGCATCTCGTATGCCGTCTT 5 0.125 RNA PCR Primer, Index 43 (95% over 23bp) GCACCAGTGGTCTAGTGGTAGAATAGTACCCATCTCGTATGC 5 0.125 No Hit CATCCTAACGAACGAACGATTTGAACATCTCGTATGCCGTCT 5 0.125 No Hit ATCCTAACGAACGAACGATTTGAACATCTCGTATGCCGTCTT 5 0.125 RNA PCR Primer, Index 19 (95% over 22bp) GGGGATGTAGCTCAAATGGTATCTCGTATGCCGTCTTCTGCT 5 0.125 RNA PCR Primer, Index 34 (96% over 27bp) GGGGGTGTAGCTCATAATCTCGTATGCCGTCTTCTGCTTGAA 5 0.125 Illumina PCR Primer Index 12 (96% over 27bp) GGGTGTTTGGTCTAGTGGTATGATTCTCGCATCTCGTATGCC 5 0.125 No Hit GAACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTTGA 5 0.125 Illumina PCR Primer Index 7 (96% over 28bp) GATAACCGTAGTAATTCTAGAGCTATCTCGTATGCCGTCTTC 5 0.125 RNA PCR Primer, Index 38 (95% over 23bp) GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACCATCTCGTAT 5 0.125 No Hit GACACGACTCTCGGCAACGGATATCTCATCTCGTATGCCGTC 5 0.125 No Hit CGAACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTTG 5 0.125 RNA PCR Primer, Index 19 (96% over 29bp) ACTGAGATCCAGCCCCACGTCGCACGGATTCGTATCTCGTAT 5 0.125 No Hit GTCGTTGTAGTATAATCTCGTATGCCGTCTTCTGCTTGAAAA 5 0.125 Illumina PCR Primer Index 12 (96% over 28bp) >>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 CGTCTTC 245 1.8189894E-12 13.336089 36 CCGTCTT 275 1.4551915E-11 11.732727 35 GCCGTCT 280 2.0008883E-11 11.523214 34 TGCCGTC 300 6.91216E-11 10.755 33 ATGCCGT 310 1.2369128E-10 10.408065 32 TATGCCG 320 2.3119355E-9 9.643196 31 GTATGCC 325 2.9940566E-9 9.49484 30 TCGTATG 330 3.8617145E-9 9.350978 28 ATCTCGT 315 2.3106622E-8 9.220013 25 CGTATGC 315 2.7935857E-7 8.643762 29 TCTCGTA 320 3.519399E-7 8.508702 26 CTCGTAT 325 4.416488E-7 8.3778 27 >>END_MODULE Read 299109 spots for SRR1174001.sra Written 299109 spots for SRR1174001.sra Read 299109 spots for SRR1174001.sra Written 299109 spots for SRR1174001.sra Read 299109 spots for SRR1174001.sra Written 299109 spots for SRR1174001.sra Read 299109 spots for SRR1174001.sra Written 299109 spots for SRR1174001.sra Read 299109 spots for SRR1174001.sra Written 299109 spots for SRR1174001.sra Read 299109 spots for SRR1174001.sra Written 299109 spots for SRR1174001.sra Read 299109 spots for SRR1174001.sra Written 299109 spots for SRR1174001.sra Read 299109 spots for SRR1174001.sra Written 299109 spots for SRR1174001.sra Read 299109 spots for SRR1174001.sra Written 299109 spots for SRR1174001.sra Read 299109 spots for SRR1174001.sra Written 299109 spots for SRR1174001.sra Read 299109 spots for SRR1174001.sra Written 299109 spots for SRR1174001.sra Read 299109 spots for SRR1174001.sra Written 299109 spots for SRR1174001.sra Read 299109 spots for SRR1174001.sra Written 299109 spots for SRR1174001.sra Read 299109 spots for SRR1174001.sra Written 299109 spots for SRR1174001.sra Read 299109 spots for SRR1174001.sra Written 299109 spots for SRR1174001.sra Read 299109 spots for SRR1174001.sra Written 299109 spots for SRR1174001.sra Read 299109 spots for SRR1174001.sra Written 299109 spots for SRR1174001.sra Read 299109 spots for SRR1174001.sra Written 299109 spots for SRR1174001.sra Read 299109 spots for SRR1174001.sra Written 299109 spots for SRR1174001.sra Read 299125 spots for SRR1174001.sra Written 299125 spots for SRR1174001.sra SRR ids: ['SRR1174001.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_wezvbm4z SRR1174001.sra spots: 5982196 blocks: [[1, 299109], [299110, 598218], [598219, 897327], [897328, 1196436], [1196437, 1495545], [1495546, 1794654], [1794655, 2093763], [2093764, 2392872], [2392873, 2691981], [2691982, 2991090], [2991091, 3290199], [3290200, 3589308], [3589309, 3888417], [3888418, 4187526], [4187527, 4486635], [4486636, 4785744], [4785745, 5084853], [5084854, 5383962], [5383963, 5683071], [5683072, 5982196]] SRR1174001 file size 833272 SRR1174001 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 SRR1174001 SRR1174001_1.fastq Input file: SRR1174001_1.fastq trimmed: SRR1174001-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 14:21:46 2024 >> started Mon Dec 9 14:21:49 2024 >> done (3.121s) 5982196 reads processed; of these: 66763 ( 1.12%) short reads filtered out after trimming by size control 9339 ( 0.16%) empty reads filtered out after trimming by size control 5906094 (98.73%) reads available; of these: 1610291 (27.26%) trimmed reads available after processing 4295803 (72.74%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 11002 0.19% 19 12903 0.22% 20 14235 0.24% 21 16426 0.28% 22 18818 0.32% 23 20866 0.35% 24 25547 0.43% 25 24633 0.42% 26 25675 0.43% 27 30218 0.51% 28 28135 0.48% 29 31401 0.53% 30 31393 0.53% 31 29856 0.51% 32 35157 0.60% 33 46851 0.79% 34 43764 0.74% 35 44901 0.76% 36 45949 0.78% 37 71666 1.21% 38 106108 1.80% 39 119374 2.02% 40 259569 4.39% 41 515844 8.73% 42 4295803 72.74% 5906094 reads passed initial QC criterion=sequence-density sequence-density=65.64 sequence-density-rank=1 fanout-score=38.03 fanout-score-rank=1 prefix-density=74.15 prefix-fanout=33.7 sequence=ATCTCGTATGCCGTCTTCTGCTTGAAAAAAA criterion=fanout-score sequence-density=65.64 sequence-density-rank=1 fanout-score=38.03 fanout-score-rank=1 prefix-density=74.15 prefix-fanout=33.7 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 SRR1174001 - Input file: STDIN trimmed: SRR1174001-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 14:22:01 2024 >> started Mon Dec 9 14:22:09 2024 >> done (7.495s) 5727122 reads processed; of these: 1129512 (19.72%) short reads filtered out after trimming by size control 81841 ( 1.43%) empty reads filtered out after trimming by size control 4515769 (78.85%) reads available; of these: 4158186 (92.08%) trimmed reads available after processing 357583 ( 7.92%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 145504 3.22% 19 205697 4.56% 20 227648 5.04% 21 347063 7.69% 22 208712 4.62% 23 256485 5.68% 24 1313424 29.09% 25 186683 4.13% 26 133463 2.96% 27 108620 2.41% 28 106338 2.35% 29 119259 2.64% 30 190577 4.22% 31 139627 3.09% 32 134149 2.97% 33 185730 4.11% 34 154638 3.42% 35 114332 2.53% 36 56784 1.26% 37 30288 0.67% 38 18933 0.42% 39 11117 0.25% 40 10054 0.22% 41 15028 0.33% 42 95616 2.12% criterion=sequence-density sequence-density=1.89 sequence-density-rank=1 fanout-score=1.00 fanout-score-rank=13 prefix-density=0.01 prefix-fanout=1.0 sequence=GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGAT criterion=fanout-score sequence-density=0.01 sequence-density-rank=27 fanout-score=236.62 fanout-score-rank=1 prefix-density=2.02 prefix-fanout=1.3 sequence=GGTCTAGTGGTTAGGACATTGGACTCTGAATCCAGTAACCCGAGT Started job on | Dec 09 14:24:45 Started mapping on | Dec 09 14:24:45 Finished on | Dec 09 14:25:02 Mapping speed, Million of reads per hour | 994.18 Number of input reads | 4694741 Average input read length | 26 UNIQUE READS: Uniquely mapped reads number | 1430976 Uniquely mapped reads % | 30.48% Average mapped length | 23.87 Number of splices: Total | 25419 Number of splices: Annotated (sjdb) | 6143 Number of splices: GT/AG | 24268 Number of splices: GC/AG | 665 Number of splices: AT/AC | 5 Number of splices: Non-canonical | 481 Mismatch rate per base, % | 0.42% Deletion rate per base | 0.00% Deletion average length | 1.30 Insertion rate per base | 0.00% Insertion average length | 1.01 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1339647 % of reads mapped to multiple loci | 28.54% Number of reads mapped to too many loci | 1555428 % of reads mapped to too many loci | 33.13% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 6.55% % of reads unmapped: other | 1.31% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1924118 1924118 1924118 N_multimapping 1339647 1339647 1339647 N_noFeature 1083654 1189451 1319852 N_ambiguous 10702 5247 527 UnstrandedReadsAssigned:336620 PositiveStrandReadsAssigned:236278 NegativeStrandReadsAssigned:110597 Dataset is classified unstranded MeadianReadLen=24 20thPercentileLength=21 echo kmer=19 SRR1174001 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: SRR1174001-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 4,694,741 reads, 1,480,433 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,035 rounds 52973 SRR1174001.ke.tsv 35125 SRR1174001.se.tsv 88098 total ==> SRR1174001.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 0 0 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 4 1.28819 PNS24243 293 194 0 0 KQK14069 1603 1504 7 2.05648 KQK14071 474 375 0 0 ==> SRR1174001.se.tsv <== BRADI_1g14170v3 7 BRADI_1g53295v3 0 BRADI_1g59795v3 0 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 7 BRADI_1g74790v3 26 BRADI_1g09890v3 1 BRADI_1g77505v3 0 BRADI_1g48960v3 0 SRR1174001 completed mapping pipeline successfully