Starting /dee2/code/volunteer_pipeline.sh SRR2962701 current disk space = 3058805170176 free memory = 1347023060 SRR2962701 SRAfilesize 8313aeb7790b1a635561eb8ed11e3a5e SRR2962701.sra SRR2962701.sra file validated SRR2962701 is single end SRR2962701 is conventional basespace SRR2962701 read1 length is 46 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR2962701_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.53125 37.0 37.0 37.0 35.0 37.0 2 36.23875 37.0 37.0 37.0 35.0 37.0 3 36.29125 37.0 37.0 37.0 35.0 37.0 4 36.29375 37.0 37.0 37.0 35.0 37.0 5 36.3545 37.0 37.0 37.0 35.0 37.0 6 38.19075 39.0 39.0 39.0 37.0 39.0 7 38.1565 39.0 39.0 39.0 37.0 39.0 8 38.1175 39.0 39.0 39.0 35.0 39.0 9 38.14925 39.0 39.0 39.0 37.0 39.0 10 38.0645 39.0 39.0 39.0 37.0 39.0 11 39.6055 41.0 40.0 41.0 37.0 41.0 12 39.53175 41.0 40.0 41.0 37.0 41.0 13 39.4995 41.0 40.0 41.0 37.0 41.0 14 39.51875 41.0 39.0 41.0 37.0 41.0 15 39.484 41.0 39.0 41.0 36.0 41.0 16 39.483 41.0 40.0 41.0 36.0 41.0 17 39.547 41.0 40.0 41.0 37.0 41.0 18 39.65575 41.0 40.0 41.0 37.0 41.0 19 39.634 41.0 39.0 41.0 37.0 41.0 20 39.949 41.0 40.0 41.0 38.0 41.0 21 39.74775 41.0 40.0 41.0 38.0 41.0 22 39.80125 41.0 40.0 41.0 38.0 41.0 23 39.6905 41.0 40.0 41.0 37.0 41.0 24 38.73175 40.0 38.0 41.0 36.0 41.0 25 38.72975 40.0 38.0 41.0 36.0 41.0 26 39.42175 40.0 39.0 41.0 37.0 41.0 27 39.08675 40.0 39.0 41.0 37.0 41.0 28 39.31075 40.0 39.0 41.0 37.0 41.0 29 39.01025 40.0 39.0 40.0 37.0 41.0 30 38.95475 40.0 39.0 40.0 37.0 41.0 31 39.36575 40.0 40.0 41.0 38.0 41.0 32 39.66675 41.0 40.0 41.0 38.0 41.0 33 39.93525 41.0 40.0 41.0 38.0 41.0 34 40.35775 41.0 40.0 41.0 39.0 41.0 35 40.09675 41.0 40.0 41.0 38.0 41.0 36 38.99875 40.0 39.0 41.0 37.0 41.0 37 38.6645 40.0 39.0 40.0 37.0 41.0 38 39.492 40.0 40.0 41.0 38.0 41.0 39 40.2255 41.0 40.0 41.0 39.0 41.0 40 40.0135 41.0 40.0 41.0 38.0 41.0 41 39.9485 41.0 40.0 41.0 38.0 41.0 42 39.79375 41.0 40.0 41.0 38.0 41.0 43 39.76675 41.0 40.0 41.0 38.0 41.0 44 39.71125 41.0 40.0 41.0 38.0 41.0 45 40.10775 41.0 40.0 41.0 39.0 41.0 46 39.519 41.0 40.0 41.0 38.0 41.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 1101 1 0.0 1101 2 0.0 1101 3 0.0 1101 4 0.0 1101 5 0.0 1101 6 0.0 1101 7 0.0 1101 8 0.0 1101 9 0.0 1101 10 0.0 1101 11 0.0 1101 12 0.0 1101 13 0.0 1101 14 0.0 1101 15 0.0 1101 16 0.0 1101 17 0.0 1101 18 0.0 1101 19 0.0 1101 20 0.0 1101 21 0.0 1101 22 0.0 1101 23 0.0 1101 24 0.0 1101 25 0.0 1101 26 0.0 1101 27 0.0 1101 28 0.0 1101 29 0.0 1101 30 0.0 1101 31 0.0 1101 32 0.0 1101 33 0.0 1101 34 0.0 1101 35 0.0 1101 36 0.0 1101 37 0.0 1101 38 0.0 1101 39 0.0 1101 40 0.0 1101 41 0.0 1101 42 0.0 1101 43 0.0 1101 44 0.0 1101 45 0.0 1101 46 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 0.0 14 0.0 15 1.0 16 2.0 17 1.0 18 0.0 19 1.0 20 0.0 21 2.0 22 1.0 23 1.0 24 3.0 25 3.0 26 4.0 27 5.0 28 8.0 29 7.0 30 18.0 31 24.0 32 32.0 33 36.0 34 59.0 35 88.0 36 128.0 37 198.0 38 306.0 39 1425.0 40 1646.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 29.225 18.675 30.95 21.15 2 17.825 32.550000000000004 32.85 16.775000000000002 3 21.85 30.4 30.15 17.599999999999998 4 20.225 28.199999999999996 35.025 16.55 5 19.45 25.424999999999997 36.475 18.65 6 20.025000000000002 28.025 34.449999999999996 17.5 7 23.575 26.325 33.925 16.175 8 21.625 32.15 30.0 16.225 9 20.9 31.924999999999997 30.7 16.475 10 20.75 30.775000000000002 32.375 16.1 11 21.099999999999998 28.825 33.074999999999996 17.0 12 19.15 31.075000000000003 33.15 16.625 13 20.150000000000002 30.425 32.75 16.675 14 19.15 29.7 34.525 16.625 15 18.224999999999998 30.45 33.4 17.925 16 13.55 31.1 37.375 17.974999999999998 17 10.975 23.0 41.9 24.125 18 5.975 6.8500000000000005 74.275 12.9 19 0.2 57.074999999999996 41.9 0.8250000000000001 20 0.25 97.475 0.5499999999999999 1.725 21 0.65 42.85 0.475 56.025000000000006 22 0.525 55.425000000000004 0.5 43.55 23 0.675 41.575 0.42500000000000004 57.325 24 1.7500000000000002 0.2 0.7250000000000001 97.32499999999999 25 55.825 0.17500000000000002 1.7999999999999998 42.199999999999996 26 42.05 0.325 55.925000000000004 1.7000000000000002 27 1.4000000000000001 0.35000000000000003 42.6 55.65 28 55.574999999999996 0.475 2.0 41.949999999999996 29 41.825 1.25 56.125 0.8 30 0.625 55.400000000000006 43.2 0.775 31 1.725 41.6 55.800000000000004 0.8750000000000001 32 55.800000000000004 0.125 41.975 2.1 33 42.05 0.1 0.8500000000000001 56.99999999999999 34 1.375 0.1 1.3 97.225 35 55.65 0.17500000000000002 2.0500000000000003 42.125 36 41.975 0.42500000000000004 56.074999999999996 1.525 37 0.325 0.625 43.45 55.60000000000001 38 0.3 0.7250000000000001 56.89999999999999 42.075 39 0.35000000000000003 0.775 97.35000000000001 1.525 40 0.5 0.8 43.125 55.574999999999996 41 1.325 0.8500000000000001 55.85 41.975 42 55.55 0.95 42.175000000000004 1.325 43 41.775 1.15 1.7000000000000002 55.375 44 0.44999999999999996 1.375 56.599999999999994 41.575 45 1.2 1.725 96.925 0.15 46 55.35 2.9250000000000003 41.675000000000004 0.05 >>END_MODULE >>Per sequence GC content pass #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 0.0 26 0.0 27 0.0 28 0.0 29 0.5 30 1.0 31 1.0 32 3.5 33 6.0 34 19.0 35 32.0 36 81.5 37 131.0 38 210.5 39 290.0 40 403.5 41 517.0 42 579.0 43 641.0 44 641.0 45 680.0 46 719.0 47 652.0 48 585.0 49 549.5 50 514.0 51 422.0 52 330.0 53 238.0 54 146.0 55 104.0 56 62.0 57 62.0 58 39.5 59 17.0 60 13.0 61 9.0 62 4.5 63 0.0 64 0.0 65 0.0 66 0.0 67 0.0 68 0.0 69 0.0 70 0.0 71 0.0 72 0.0 73 0.0 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 0.0 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 0.0 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 0.0 26 0.0 27 0.0 28 0.0 29 0.0 30 0.0 31 0.0 32 0.0 33 0.0 34 0.0 35 0.0 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 >>END_MODULE >>Sequence Length Distribution pass #Length Count 46 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 80.675 #Duplication Level Percentage of deduplicated Percentage of total 1 88.44127672761078 71.35000000000001 2 7.9330647660365665 12.8 3 1.4874496436318563 3.5999999999999996 4 0.8986674930275798 2.9000000000000004 5 0.43383947939262474 1.7500000000000002 6 0.27889680818097307 1.35 7 0.09296560272699102 0.525 8 0.12395413696932135 0.8 9 0.030988534242330338 0.22499999999999998 >10 0.27889680818097307 4.7 >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 GTGATTGAATGAAAAATTAACACCGTCGTATGCCGTCTTCTGCTTG 48 1.2 Illumina Paired End PCR Primer 2 (95% over 22bp) GCCTCCTCAAATCCTTTTAACACCGTCGTATGCCGTCTTCTGCTTG 30 0.75 Illumina Single End Adapter 2 (95% over 22bp) TGAAATAAACGTTTCCTTAACACCGTCGTATGCCGTCTTCTGCTTG 24 0.6 Illumina Single End Adapter 1 (95% over 22bp) GGCTCCTGATCCAGTTACTAACACCGTCGTATGCCGTCTTCTGCTT 20 0.5 Illumina Single End Adapter 2 (95% over 21bp) GTGATTGAATGAAAAATGTAACACCGTCGTATGCCGTCTTCTGCTT 19 0.475 Illumina Single End Adapter 1 (95% over 21bp) TTGTCCAAGATAATGTCTAACACCGTCGTATGCCGTCTTCTGCTTG 14 0.35000000000000003 Illumina Single End Adapter 1 (95% over 22bp) GGTAGCAGATATCACCTCTAACACCGTCGTATGCCGTCTTCTGCTT 12 0.3 Illumina Single End Adapter 1 (95% over 21bp) GAATTATGTATCTTTAATTAACACCGTCGTATGCCGTCTTCTGCTT 11 0.27499999999999997 Illumina Single End Adapter 2 (95% over 21bp) CCTGGATGAAAAACTTCTAACACCGTCGTATGCCGTCTTCTGCTTG 10 0.25 Illumina Single End Adapter 1 (95% over 22bp) TTGTCCAAGATAATGTCTTAACACCGTCGTATGCCGTCTTCTGCTT 9 0.22499999999999998 Illumina Single End Adapter 2 (95% over 21bp) CGTGTATTGCAATCTTCTAACACCGTCGTATGCCGTCTTCTGCTTG 8 0.2 Illumina Single End Adapter 1 (95% over 22bp) GCTGTTAATTTCATATGTAACACCGTCGTATGCCGTCTTCTGCTTG 8 0.2 Illumina Single End Adapter 1 (95% over 22bp) GTGTTAATGGAAGGAAATTAACACCGTCGTATGCCGTCTTCTGCTT 8 0.2 Illumina Single End Adapter 2 (95% over 21bp) TGTTTTGAAATGATAATTAACACCGTCGTATGCCGTCTTCTGCTTG 8 0.2 Illumina Paired End PCR Primer 2 (95% over 22bp) TAATATTGCTATAAGAATAACACCGTCGTATGCCGTCTTCTGCTTG 7 0.17500000000000002 Illumina Single End Adapter 1 (95% over 22bp) AGTGAATAATAAGAAGCTAACACCGTCGTATGCCGTCTTCTGCTTG 7 0.17500000000000002 Illumina Single End Adapter 1 (95% over 22bp) TGCCAACTAACACCGTCGTATGCCGTCTTCTGCTTGAAAAAAAAAA 7 0.17500000000000002 Illumina Single End Adapter 1 (95% over 22bp) GTTTGAAAATTTGAAGCTAACACCGTCGTATGCCGTCTTCTGCTTG 6 0.15 Illumina Single End Adapter 1 (95% over 22bp) TTGTCTTGGGTGTTTTATTAACACCGTCGTATGCCGTCTTCTGCTT 6 0.15 Illumina Single End Adapter 1 (95% over 21bp) GCCTCCTCAAATCCTTTCTAACACCGTCGTATGCCGTCTTCTGCTT 6 0.15 Illumina Single End Adapter 1 (95% over 21bp) CAATAAGGAAAAGGATATTAACACCGTCGTATGCCGTCTTCTGCTT 6 0.15 Illumina Single End Adapter 1 (95% over 21bp) GAATTATGTATCTTTAATAACACCGTCGTATGCCGTCTTCTGCTTG 6 0.15 Illumina Single End Adapter 1 (95% over 22bp) GCTGTTAATTTCATATGGTAACACCGTCGTATGCCGTCTTCTGCTT 6 0.15 Illumina Single End Adapter 1 (95% over 21bp) AGGTTTTAATTTCTGTCTAACACCGTCGTATGCCGTCTTCTGCTTG 6 0.15 Illumina Single End Adapter 1 (95% over 22bp) CTGGGATGTAATAAAAATTAACACCGTCGTATGCCGTCTTCTGCTT 6 0.15 Illumina PCR Primer Index 1 (95% over 21bp) GTTGTTCATATGAAGTAGTAACACCGTCGTATGCCGTCTTCTGCTT 6 0.15 Illumina Paired End PCR Primer 2 (95% over 21bp) TGAAATAAACGTTTCCTTTAACACCGTCGTATGCCGTCTTCTGCTT 5 0.125 Illumina Single End Adapter 2 (95% over 21bp) TGTTTCCGTTACTGCTGCTAACACCGTCGTATGCCGTCTTCTGCTT 5 0.125 Illumina Single End Adapter 2 (95% over 21bp) GATGCAGATAGTATTGCTAACACCGTCGTATGCCGTCTTCTGCTTG 5 0.125 Illumina PCR Primer Index 1 (95% over 22bp) AACAAGTAAAATTAAAGCTAACACCGTCGTATGCCGTCTTCTGCTT 5 0.125 Illumina Single End Adapter 1 (95% over 21bp) GTCATTATATAAGGATTTTAACACCGTCGTATGCCGTCTTCTGCTT 5 0.125 Illumina Single End Adapter 2 (95% over 21bp) GTGTGAAGTACTTTGATTAACACCGTCGTATGCCGTCTTCTGCTTG 5 0.125 Illumina Single End Adapter 1 (95% over 22bp) TTTTCAGGATCATTTCCTAACACCGTCGTATGCCGTCTTCTGCTTG 5 0.125 Illumina Single End Adapter 2 (95% over 22bp) GTCTCTATCCTTTTCCTTAACACCGTCGTATGCCGTCTTCTGCTTG 5 0.125 Illumina Single End Adapter 1 (95% over 22bp) CGTCAGACCGTGGCGGTTTAACACCGTCGTATGCCGTCTTCTGCTT 5 0.125 Illumina Single End Adapter 1 (95% over 21bp) TGCTGAAATTGAGCTGCTAACACCGTCGTATGCCGTCTTCTGCTTG 5 0.125 Illumina Single End Adapter 2 (95% over 22bp) TCAACTGGATTTAGTCTTAACACCGTCGTATGCCGTCTTCTGCTTG 5 0.125 Illumina Paired End PCR Primer 2 (95% over 22bp) GAAAAACAATAACTTTTTAACACCGTCGTATGCCGTCTTCTGCTTG 5 0.125 Illumina Single End Adapter 2 (95% over 22bp) GGCTCCTGATCCAGTTATAACACCGTCGTATGCCGTCTTCTGCTTG 5 0.125 Illumina Single End Adapter 1 (95% over 22bp) CATGGCTGTTAATTTCATAACACCGTCGTATGCCGTCTTCTGCTTG 5 0.125 Illumina Single End Adapter 1 (95% over 22bp) >>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 ACTAACA 30 3.7618393E-6 40.000004 16 TGCTAAC 20 0.00111172 40.000004 15 CTGCTTG 250 0.0 38.4 40 CCTAACA 25 0.0033271667 32.0 17 AATTAAC 25 0.0033271667 32.0 15 GCTAACA 40 2.707939E-5 30.000002 16 ATTAACA 70 1.4624675E-9 28.571428 16 CTAACAC 100 0.0 28.0 17 TTTTAAC 30 0.008119183 26.666668 15 GTATGCC 400 0.0 24.0 28 TGCCGTC 400 0.0 24.0 31 GTCGTAT 400 0.0 24.0 25 CACCGTC 400 0.0 24.0 21 TATGCCG 400 0.0 24.0 29 TTCTGCT 400 0.0 24.0 38 ACACCGT 400 0.0 24.0 20 ACCGTCG 400 0.0 24.0 22 CCGTCTT 400 0.0 24.0 33 CCGTCGT 400 0.0 24.0 23 TCTGCTT 400 0.0 24.0 39 >>END_MODULE Read 240263 spots for SRR2962701.sra Written 240263 spots for SRR2962701.sra Read 240263 spots for SRR2962701.sra Written 240263 spots for SRR2962701.sra Read 240263 spots for SRR2962701.sra Written 240263 spots for SRR2962701.sra Read 240263 spots for SRR2962701.sra Written 240263 spots for SRR2962701.sra Read 240263 spots for SRR2962701.sra Written 240263 spots for SRR2962701.sra Read 240263 spots for SRR2962701.sra Written 240263 spots for SRR2962701.sra Read 240263 spots for SRR2962701.sra Written 240263 spots for SRR2962701.sra Read 240263 spots for SRR2962701.sra Written 240263 spots for SRR2962701.sra Read 240263 spots for SRR2962701.sra Written 240263 spots for SRR2962701.sra Read 240263 spots for SRR2962701.sra Written 240263 spots for SRR2962701.sra Read 240263 spots for SRR2962701.sra Written 240263 spots for SRR2962701.sra Read 240263 spots for SRR2962701.sra Written 240263 spots for SRR2962701.sra Read 240263 spots for SRR2962701.sra Written 240263 spots for SRR2962701.sra Read 240263 spots for SRR2962701.sra Written 240263 spots for SRR2962701.sra Read 240268 spots for SRR2962701.sra Written 240268 spots for SRR2962701.sra Read 240263 spots for SRR2962701.sra Written 240263 spots for SRR2962701.sra Read 240263 spots for SRR2962701.sra Written 240263 spots for SRR2962701.sra Read 240263 spots for SRR2962701.sra Written 240263 spots for SRR2962701.sra Read 240263 spots for SRR2962701.sra Written 240263 spots for SRR2962701.sra Read 240263 spots for SRR2962701.sra Written 240263 spots for SRR2962701.sra SRR ids: ['SRR2962701.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd__lqi1ez7 SRR2962701.sra spots: 4805265 blocks: [[1, 240263], [240264, 480526], [480527, 720789], [720790, 961052], [961053, 1201315], [1201316, 1441578], [1441579, 1681841], [1681842, 1922104], [1922105, 2162367], [2162368, 2402630], [2402631, 2642893], [2642894, 2883156], [2883157, 3123419], [3123420, 3363682], [3363683, 3603945], [3603946, 3844208], [3844209, 4084471], [4084472, 4324734], [4324735, 4564997], [4564998, 4805265]] SRR2962701 file size 733267 SRR2962701 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 SRR2962701 SRR2962701_1.fastq Input file: SRR2962701_1.fastq trimmed: SRR2962701-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 Feb 10 12:08:34 2025 >> started Mon Feb 10 12:08:36 2025 >> done (2.136s) 4805265 reads processed; of these: 327 ( 0.01%) short reads filtered out after trimming by size control 5 ( 0.00%) empty reads filtered out after trimming by size control 4804933 (99.99%) reads available; of these: 80773 ( 1.68%) trimmed reads available after processing 4724160 (98.32%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 108 0.00% 19 218 0.00% 20 668 0.01% 21 528 0.01% 22 907 0.02% 23 1693 0.04% 24 1712 0.04% 25 2157 0.04% 26 1109 0.02% 27 540 0.01% 28 906 0.02% 29 569 0.01% 30 461 0.01% 31 436 0.01% 32 331 0.01% 33 423 0.01% 34 3351 0.07% 35 1690 0.04% 36 1461 0.03% 37 696 0.01% 38 1031 0.02% 39 13001 0.27% 40 6651 0.14% 41 3842 0.08% 42 3402 0.07% 43 5079 0.11% 44 4953 0.10% 45 22850 0.48% 46 4724160 98.32% 4804933 reads passed initial QC criterion=sequence-density sequence-density=99.79 sequence-density-rank=1 fanout-score=34.80 fanout-score-rank=1 prefix-density=99.78 prefix-fanout=34.8 sequence=TAACACCGTCGTATGCCGTCTTCTGCTTGAAAAA criterion=fanout-score sequence-density=99.79 sequence-density-rank=1 fanout-score=34.80 fanout-score-rank=1 prefix-density=99.78 prefix-fanout=34.8 sequence=TAACACCGTCGTATGCCGTCTTCTGCTTGAAAAA 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 TAACACCGTCGTATGCCGTCTTCTGCTTGAAAAA -o SRR2962701 - Input file: STDIN trimmed: SRR2962701-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TAACACCGTCGTATGCCGTCTTCTGCTTGAAAAA -- 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 Feb 10 12:08:43 2025 >> started Mon Feb 10 12:08:46 2025 >> done (3.083s) 4708834 reads processed; of these: 2712537 (57.61%) short reads filtered out after trimming by size control 457 ( 0.01%) empty reads filtered out after trimming by size control 1995840 (42.39%) reads available; of these: 1994455 (99.93%) trimmed reads available after processing 1385 ( 0.07%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 1979103 99.16% 19 3348 0.17% 20 1951 0.10% 21 1694 0.08% 22 1231 0.06% 23 1460 0.07% 24 1236 0.06% 25 785 0.04% 26 893 0.04% 27 1108 0.06% 28 987 0.05% 29 665 0.03% 30 215 0.01% 31 151 0.01% 32 153 0.01% 33 161 0.01% 34 108 0.01% 35 97 0.00% 36 380 0.02% 37 45 0.00% 38 3 0.00% 39 0 0.00% 40 0 0.00% 41 2 0.00% 42 3 0.00% 43 2 0.00% 44 1 0.00% 45 1 0.00% 46 57 0.00% criterion=sequence-density sequence-density=1.23 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=12 prefix-density=0.00 prefix-fanout=1.0 sequence=GGCTCCTGATCCAGTTAC criterion=fanout-score sequence-density=0.21 sequence-density-rank=19 fanout-score=11.39 fanout-score-rank=1 prefix-density=0.10 prefix-fanout=11.4 sequence=TAACACCGTCGTATGCCGTCTTCTGCTTGAAAAA Started job on | Feb 10 12:08:55 Started mapping on | Feb 10 12:08:56 Finished on | Feb 10 12:09:32 Mapping speed, Million of reads per hour | 209.19 Number of input reads | 2091939 Average input read length | 19 UNIQUE READS: Uniquely mapped reads number | 1580398 Uniquely mapped reads % | 75.55% Average mapped length | 18.02 Number of splices: Total | 15984 Number of splices: Annotated (sjdb) | 15725 Number of splices: GT/AG | 15797 Number of splices: GC/AG | 138 Number of splices: AT/AC | 45 Number of splices: Non-canonical | 4 Mismatch rate per base, % | 0.01% Deletion rate per base | 0.00% Deletion average length | 1.00 Insertion rate per base | 0.00% Insertion average length | 0.00 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 397309 % of reads mapped to multiple loci | 18.99% Number of reads mapped to too many loci | 13097 % of reads mapped to too many loci | 0.63% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.64% % of reads unmapped: other | 0.19% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 114232 114232 114232 N_multimapping 397309 397309 397309 N_noFeature 132763 315584 1385108 N_ambiguous 17616 3330 1854 UnstrandedReadsAssigned:1430019 PositiveStrandReadsAssigned:1261484 NegativeStrandReadsAssigned:193436 Dataset is classified positive stranded MeadianReadLen=18 20thPercentileLength=18 echo kmer=19 SRR2962701 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: 52,400 [index] number of k-mers: 59,590,899 [index] number of equivalence classes: 293,668 [quant] running in single-end mode [quant] will process file 1: SRR2962701-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 2,091,939 reads, 20,980 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 628 rounds 52401 SRR2962701.ke.tsv 34699 SRR2962701.se.tsv 87100 total ==> SRR2962701.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 0 0 Potri.005G024800.1.v4.1 1035 936 0 0 Potri.004G059700.1.v4.1 961 862 0 0 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 1 20.2214 Potri.016G087400.1.v4.1 270 171 2 672.626 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 1 34.3546 Potri.012G127500.1.v4.1 977 878 0 0 ==> SRR2962701.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 4 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 105 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 3 SRR2962701 completed mapping pipeline successfully