Starting /dee2/code/volunteer_pipeline.sh SRR2962700 current disk space = 3058881589248 free memory = 1019326388 SRR2962700 SRAfilesize 2056b0f3e83ade26626f4ec2d68070a6 SRR2962700.sra SRR2962700.sra file validated SRR2962700 is single end SRR2962700 is conventional basespace SRR2962700 read1 length is 46 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR2962700_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 42 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.526 37.0 37.0 37.0 35.0 37.0 2 36.31175 37.0 37.0 37.0 35.0 37.0 3 36.37125 37.0 37.0 37.0 35.0 37.0 4 36.35725 37.0 37.0 37.0 35.0 37.0 5 36.3765 37.0 37.0 37.0 35.0 37.0 6 38.22475 39.0 39.0 39.0 37.0 39.0 7 38.18 39.0 39.0 39.0 37.0 39.0 8 38.15175 39.0 39.0 39.0 37.0 39.0 9 38.2315 39.0 39.0 39.0 37.0 39.0 10 38.15775 39.0 39.0 39.0 37.0 39.0 11 39.73125 41.0 40.0 41.0 37.0 41.0 12 39.641 41.0 40.0 41.0 37.0 41.0 13 39.7045 41.0 40.0 41.0 37.0 41.0 14 39.65125 41.0 40.0 41.0 37.0 41.0 15 39.627 41.0 40.0 41.0 37.0 41.0 16 39.63375 41.0 40.0 41.0 37.0 41.0 17 39.44625 41.0 40.0 41.0 36.0 41.0 18 39.17325 41.0 39.0 41.0 36.0 41.0 19 39.19625 41.0 39.0 41.0 36.0 41.0 20 39.35375 40.0 39.0 41.0 37.0 41.0 21 39.3775 40.0 40.0 41.0 37.0 41.0 22 39.3165 41.0 40.0 41.0 36.0 41.0 23 39.49025 41.0 40.0 41.0 37.0 41.0 24 39.65825 41.0 40.0 41.0 37.0 41.0 25 39.84825 41.0 40.0 41.0 38.0 41.0 26 40.10975 41.0 40.0 41.0 38.0 41.0 27 40.14025 41.0 40.0 41.0 38.0 41.0 28 39.87675 41.0 40.0 41.0 38.0 41.0 29 39.0925 40.0 39.0 40.0 37.0 41.0 30 38.89725 40.0 39.0 40.0 37.0 41.0 31 39.35875 40.0 40.0 41.0 38.0 41.0 32 39.7915 41.0 40.0 41.0 38.0 41.0 33 40.07675 41.0 40.0 41.0 39.0 41.0 34 40.379 41.0 40.0 41.0 39.0 41.0 35 40.1665 41.0 40.0 41.0 39.0 41.0 36 39.21025 40.0 39.0 41.0 37.0 41.0 37 38.94475 40.0 39.0 40.0 37.0 41.0 38 39.68775 40.0 40.0 41.0 38.0 41.0 39 40.3075 41.0 40.0 41.0 39.0 41.0 40 40.15225 41.0 40.0 41.0 39.0 41.0 41 40.03 41.0 40.0 41.0 38.0 41.0 42 39.9765 41.0 40.0 41.0 38.0 41.0 43 39.95975 41.0 40.0 41.0 38.0 41.0 44 39.89075 41.0 40.0 41.0 38.0 41.0 45 40.204 41.0 41.0 41.0 39.0 41.0 46 39.7545 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 11 1.0 12 0.0 13 1.0 14 1.0 15 1.0 16 1.0 17 1.0 18 0.0 19 1.0 20 1.0 21 0.0 22 0.0 23 3.0 24 1.0 25 2.0 26 2.0 27 4.0 28 6.0 29 12.0 30 17.0 31 16.0 32 31.0 33 33.0 34 63.0 35 60.0 36 124.0 37 190.0 38 286.0 39 1183.0 40 1959.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 26.0 20.150000000000002 33.300000000000004 20.549999999999997 2 18.05 34.075 33.175 14.7 3 20.7 30.575000000000003 32.574999999999996 16.150000000000002 4 21.3 28.925 34.225 15.55 5 20.974999999999998 25.825 35.949999999999996 17.25 6 19.950000000000003 27.875 36.35 15.825 7 21.125 27.750000000000004 35.85 15.275 8 24.55 30.325000000000003 29.825000000000003 15.299999999999999 9 18.875 31.974999999999998 32.475 16.675 10 17.525 30.55 37.2 14.725 11 20.25 31.7 32.05 16.0 12 17.299999999999997 32.074999999999996 34.75 15.875 13 17.625 33.875 33.675 14.825 14 18.099999999999998 33.175 33.550000000000004 15.174999999999999 15 17.7 32.175 34.449999999999996 15.675 16 12.975 34.075 35.35 17.599999999999998 17 13.275 27.55 36.375 22.8 18 60.824999999999996 8.725 17.125 13.325000000000001 19 41.65 56.625 0.575 1.15 20 1.275 41.975 0.4 56.35 21 56.474999999999994 1.325 0.625 41.575 22 41.8 56.55 1.375 0.27499999999999997 23 0.2 42.55 56.699999999999996 0.5499999999999999 24 0.3 56.525000000000006 42.8 0.375 25 0.35000000000000003 41.449999999999996 57.9 0.3 26 0.4 0.25 98.075 1.275 27 1.15 0.125 42.05 56.675 28 56.425000000000004 0.25 1.725 41.6 29 41.575 1.15 56.925000000000004 0.35000000000000003 30 0.375 56.325 42.85 0.44999999999999996 31 1.425 41.425 56.65 0.5 32 56.625 0.125 41.75 1.5 33 41.625 0.1 0.5 57.775 34 1.25 0.1 0.775 97.875 35 56.474999999999994 0.125 1.7000000000000002 41.699999999999996 36 41.775 0.22499999999999998 56.625 1.375 37 0.15 0.44999999999999996 42.75 56.65 38 0.17500000000000002 0.475 57.675 41.675000000000004 39 0.1 0.44999999999999996 98.075 1.375 40 0.35000000000000003 0.475 42.775 56.39999999999999 41 1.15 0.6 56.625 41.625 42 56.425000000000004 0.625 41.725 1.225 43 41.425 0.75 1.4749999999999999 56.35 44 0.27499999999999997 0.8 57.49999999999999 41.425 45 1.175 0.975 97.725 0.125 46 56.375 2.075 41.5 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 0.5 28 1.0 29 8.5 30 16.0 31 16.0 32 34.0 33 52.0 34 101.5 35 151.0 36 260.5 37 370.0 38 462.0 39 554.0 40 631.5 41 709.0 42 722.0 43 735.0 44 735.0 45 622.0 46 509.0 47 477.0 48 445.0 49 375.5 50 306.0 51 202.0 52 98.0 53 67.5 54 37.0 55 24.5 56 12.0 57 12.0 58 8.5 59 5.0 60 2.5 61 0.0 62 0.0 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 79.975 #Duplication Level Percentage of deduplicated Percentage of total 1 88.74648327602375 70.975 2 7.533604251328541 12.049999999999999 3 1.6567677399187246 3.975 4 0.6251953735542357 2.0 5 0.5001562988433885 2.0 6 0.15629884338855893 0.75 7 0.12503907471084713 0.7000000000000001 8 0.15629884338855893 1.0 9 0.15629884338855893 1.125 >10 0.34385745545482965 5.425 >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 GTGATTGAATGAAAAATGACGATATTCGTATGCCGTCTTCTGCTTG 50 1.25 Illumina PCR Primer Index 1 (95% over 22bp) CATGGCTGTTAATTTCAGACGATATTCGTATGCCGTCTTCTGCTTG 27 0.675 Illumina Single End Adapter 1 (95% over 22bp) TAATATTGCTATAAGAAGACGATATTCGTATGCCGTCTTCTGCTTG 24 0.6 Illumina Single End Adapter 1 (95% over 22bp) GGCTCCTGATCCAGTTACGACGATATTCGTATGCCGTCTTCTGCTT 21 0.525 Illumina Single End Adapter 2 (95% over 21bp) GCCTCCTCAAATCCTTTGACGATATTCGTATGCCGTCTTCTGCTTG 18 0.44999999999999996 Illumina Single End Adapter 2 (95% over 22bp) TGAAATAAACGTTTCCTGACGATATTCGTATGCCGTCTTCTGCTTG 18 0.44999999999999996 Illumina Single End Adapter 1 (95% over 22bp) GAATTATGTATCTTTAAGACGATATTCGTATGCCGTCTTCTGCTTG 14 0.35000000000000003 Illumina Single End Adapter 1 (95% over 22bp) TATGGTGCTTGGATAATTGACGATATTCGTATGCCGTCTTCTGCTT 14 0.35000000000000003 Illumina Single End Adapter 1 (95% over 21bp) CATGGTTGTTCATATGAAGACGATATTCGTATGCCGTCTTCTGCTT 11 0.27499999999999997 Illumina Single End Adapter 1 (95% over 21bp) AGTGAATAATAAGAAGCGACGATATTCGTATGCCGTCTTCTGCTTG 10 0.25 Illumina Single End Adapter 1 (95% over 22bp) GTTGTTCATATGAAGTAGGACGATATTCGTATGCCGTCTTCTGCTT 10 0.25 Illumina PCR Primer Index 1 (95% over 21bp) GTGATTGAATGAAAAATGGACGATATTCGTATGCCGTCTTCTGCTT 9 0.22499999999999998 Illumina Single End Adapter 1 (95% over 21bp) GGCCACTACTGACCAATCGACGATATTCGTATGCCGTCTTCTGCTT 9 0.22499999999999998 Illumina Single End Adapter 2 (95% over 21bp) CCTGGATGAAAAACTTCGACGATATTCGTATGCCGTCTTCTGCTTG 9 0.22499999999999998 Illumina Single End Adapter 1 (95% over 22bp) CATCTTTTGTTTCTGATGACGATATTCGTATGCCGTCTTCTGCTTG 9 0.22499999999999998 Illumina Single End Adapter 1 (95% over 22bp) GCTATGTACTACATAAGCGACGATATTCGTATGCCGTCTTCTGCTT 9 0.22499999999999998 Illumina Single End Adapter 1 (95% over 21bp) TGTTTTGAAATGATAATGACGATATTCGTATGCCGTCTTCTGCTTG 8 0.2 Illumina PCR Primer Index 2 (95% over 22bp) TTGTCCAAGATAATGTCTGACGATATTCGTATGCCGTCTTCTGCTT 8 0.2 Illumina Single End Adapter 2 (95% over 21bp) GTTGTTCATATGAAGTAGACGATATTCGTATGCCGTCTTCTGCTTG 8 0.2 Illumina Paired End PCR Primer 2 (95% over 22bp) GCAGGTCACCCATCATCTGACGATATTCGTATGCCGTCTTCTGCTT 8 0.2 Illumina Single End Adapter 1 (95% over 21bp) CTGGGATGTAATAAAAATGACGATATTCGTATGCCGTCTTCTGCTT 8 0.2 Illumina Paired End PCR Primer 2 (95% over 21bp) TTGTCCAAGATAATGTCGACGATATTCGTATGCCGTCTTCTGCTTG 7 0.17500000000000002 Illumina Single End Adapter 1 (95% over 22bp) TGCCAACGACGATATTCGTATGCCGTCTTCTGCTTGAAAAAAAAAA 7 0.17500000000000002 Illumina Single End Adapter 1 (95% over 22bp) AGTGAAGGAAGTAATAAAGACGATATTCGTATGCCGTCTTCTGCTT 7 0.17500000000000002 Illumina PCR Primer Index 1 (95% over 21bp) TATGCTTGGAAACTTGAGACGATATTCGTATGCCGTCTTCTGCTTG 7 0.17500000000000002 Illumina Single End Adapter 1 (95% over 22bp) CAATAAGGAAAAGGATATGACGATATTCGTATGCCGTCTTCTGCTT 6 0.15 Illumina Single End Adapter 1 (95% over 21bp) TTCTTTGACAGTGAATTTGACGATATTCGTATGCCGTCTTCTGCTT 6 0.15 Illumina Paired End PCR Primer 2 (95% over 21bp) TTGTCTTGGGTGTTTTATGACGATATTCGTATGCCGTCTTCTGCTT 6 0.15 Illumina Single End Adapter 1 (95% over 21bp) AAATGAAGCACCAGTTCAGACGATATTCGTATGCCGTCTTCTGCTT 6 0.15 Illumina Single End Adapter 1 (95% over 21bp) CGGGCATACATACACACGACGATATTCGTATGCCGTCTTCTGCTTG 6 0.15 Illumina Single End Adapter 2 (95% over 22bp) CTGGGATGTAATAAAAAGACGATATTCGTATGCCGTCTTCTGCTTG 5 0.125 Illumina Paired End PCR Primer 2 (95% over 22bp) CTTGCTTGCTTGCTTTTGACGATATTCGTATGCCGTCTTCTGCTTG 5 0.125 Illumina Single End Adapter 2 (95% over 22bp) TGCTGAAATTGAGCTGCGACGATATTCGTATGCCGTCTTCTGCTTG 5 0.125 Illumina Single End Adapter 2 (95% over 22bp) TTTTCAGGATCATTTCCGACGATATTCGTATGCCGTCTTCTGCTTG 5 0.125 Illumina Single End Adapter 2 (95% over 22bp) CCCTGGCGGGACCAACTGACGATATTCGTATGCCGTCTTCTGCTTG 5 0.125 Illumina Single End Adapter 2 (95% over 22bp) AAGATCCATAAATATGCGACGATATTCGTATGCCGTCTTCTGCTTG 5 0.125 Illumina Single End Adapter 2 (95% over 22bp) CTTCCGATGAGTATAACGACGATATTCGTATGCCGTCTTCTGCTTG 5 0.125 Illumina Single End Adapter 1 (95% over 22bp) TAATATTGCTATAAAAAGACGATATTCGTATGCCGTCTTCTGCTTG 5 0.125 Illumina Paired End PCR Primer 2 (95% over 22bp) TTTAGCGGATCCTGGCTTGACGATATTCGTATGCCGTCTTCTGCTT 5 0.125 Illumina Single End Adapter 1 (95% over 21bp) TAATATTGCTATAAGAAGGACGATATTCGTATGCCGTCTTCTGCTT 5 0.125 Illumina Single End Adapter 1 (95% over 21bp) TTAACTTGCAGTGTGTTCGACGATATTCGTATGCCGTCTTCTGCTT 5 0.125 Illumina Single End Adapter 2 (95% over 21bp) GCTGTTAATTTCATATGGACGATATTCGTATGCCGTCTTCTGCTTG 5 0.125 Illumina Single End Adapter 1 (95% over 22bp) GAATTATGTATCTTTAATGACGATATTCGTATGCCGTCTTCTGCTT 5 0.125 Illumina Single End Adapter 2 (95% over 21bp) CGTGTATTGCAATCTTCGACGATATTCGTATGCCGTCTTCTGCTTG 5 0.125 Illumina Single End Adapter 1 (95% over 22bp) CAATTACAGGTTATTTATGACGATATTCGTATGCCGTCTTCTGCTT 5 0.125 Illumina Single End Adapter 1 (95% over 21bp) AACAAGTAAAATTAAAGCGACGATATTCGTATGCCGTCTTCTGCTT 5 0.125 Illumina Single End Adapter 1 (95% over 21bp) >>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 CTGCTTG 240 0.0 38.333336 40 ATGACGA 55 2.0439438E-7 29.090908 16 TCGACGA 35 4.695968E-4 28.571428 17 AAGACGA 30 0.008119183 26.666668 16 TGACGAT 180 0.0 25.555555 17 AGACGAT 65 8.832085E-7 24.615385 17 TTGACGA 60 1.4609444E-5 23.333334 16 TCTGCTT 395 0.0 23.29114 39 GTATGCC 400 0.0 23.0 28 CGATATT 400 0.0 23.0 20 GATATTC 400 0.0 23.0 21 TTCGTAT 400 0.0 23.0 25 TGCCGTC 400 0.0 23.0 31 TATGCCG 400 0.0 23.0 29 TTCTGCT 400 0.0 23.0 38 CCGTCTT 400 0.0 23.0 33 ATTCGTA 400 0.0 23.0 24 ATGCCGT 400 0.0 23.0 30 GTCTTCT 400 0.0 23.0 35 CGTATGC 400 0.0 23.0 27 >>END_MODULE Read 245333 spots for SRR2962700.sra Written 245333 spots for SRR2962700.sra Read 245333 spots for SRR2962700.sra Written 245333 spots for SRR2962700.sra Read 245333 spots for SRR2962700.sra Written 245333 spots for SRR2962700.sra Read 245333 spots for SRR2962700.sra Written 245333 spots for SRR2962700.sra Read 245333 spots for SRR2962700.sra Written 245333 spots for SRR2962700.sra Read 245333 spots for SRR2962700.sra Written 245333 spots for SRR2962700.sra Read 245333 spots for SRR2962700.sra Written 245333 spots for SRR2962700.sra Read 245333 spots for SRR2962700.sra Written 245333 spots for SRR2962700.sra Read 245333 spots for SRR2962700.sra Written 245333 spots for SRR2962700.sra Read 245333 spots for SRR2962700.sra Written 245333 spots for SRR2962700.sra Read 245333 spots for SRR2962700.sra Written 245333 spots for SRR2962700.sra Read 245333 spots for SRR2962700.sra Written 245333 spots for SRR2962700.sra Read 245333 spots for SRR2962700.sra Written 245333 spots for SRR2962700.sra Read 245333 spots for SRR2962700.sra Written 245333 spots for SRR2962700.sra Read 245333 spots for SRR2962700.sra Written 245333 spots for SRR2962700.sra Read 245333 spots for SRR2962700.sra Written 245333 spots for SRR2962700.sra Read 245333 spots for SRR2962700.sra Written 245333 spots for SRR2962700.sra Read 245333 spots for SRR2962700.sra Written 245333 spots for SRR2962700.sra Read 245341 spots for SRR2962700.sra Written 245341 spots for SRR2962700.sra Read 245333 spots for SRR2962700.sra Written 245333 spots for SRR2962700.sra SRR ids: ['SRR2962700.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_59vhgnvy SRR2962700.sra spots: 4906668 blocks: [[1, 245333], [245334, 490666], [490667, 735999], [736000, 981332], [981333, 1226665], [1226666, 1471998], [1471999, 1717331], [1717332, 1962664], [1962665, 2207997], [2207998, 2453330], [2453331, 2698663], [2698664, 2943996], [2943997, 3189329], [3189330, 3434662], [3434663, 3679995], [3679996, 3925328], [3925329, 4170661], [4170662, 4415994], [4415995, 4661327], [4661328, 4906668]] SRR2962700 file size 748771 SRR2962700 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 SRR2962700 SRR2962700_1.fastq Input file: SRR2962700_1.fastq trimmed: SRR2962700-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 12:04:27 2025 >> started Mon Feb 10 12:04:29 2025 >> done (2.131s) 4906668 reads processed; of these: 4452 ( 0.09%) short reads filtered out after trimming by size control 6 ( 0.00%) empty reads filtered out after trimming by size control 4902210 (99.91%) reads available; of these: 67151 ( 1.37%) trimmed reads available after processing 4835059 (98.63%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 671 0.01% 19 465 0.01% 20 460 0.01% 21 345 0.01% 22 381 0.01% 23 400 0.01% 24 337 0.01% 25 505 0.01% 26 4204 0.09% 27 1426 0.03% 28 683 0.01% 29 542 0.01% 30 455 0.01% 31 385 0.01% 32 273 0.01% 33 347 0.01% 34 2764 0.06% 35 1632 0.03% 36 1363 0.03% 37 610 0.01% 38 940 0.02% 39 9106 0.19% 40 4562 0.09% 41 2923 0.06% 42 2700 0.06% 43 3944 0.08% 44 4593 0.09% 45 20135 0.41% 46 4835059 98.63% 4902210 reads passed initial QC criterion=sequence-density sequence-density=99.73 sequence-density-rank=1 fanout-score=34.68 fanout-score-rank=1 prefix-density=99.72 prefix-fanout=34.7 sequence=GACGATATTCGTATGCCGTCTTCTGCTTGAAAAA criterion=fanout-score sequence-density=99.73 sequence-density-rank=1 fanout-score=34.68 fanout-score-rank=1 prefix-density=99.72 prefix-fanout=34.7 sequence=GACGATATTCGTATGCCGTCTTCTGCTTGAAAAA 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 GACGATATTCGTATGCCGTCTTCTGCTTGAAAAA -o SRR2962700 - Input file: STDIN trimmed: SRR2962700-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): GACGATATTCGTATGCCGTCTTCTGCTTGAAAAA -- 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 12:04:42 2025 >> started Mon Feb 10 12:04:45 2025 >> done (2.987s) 4804166 reads processed; of these: 2830872 (58.93%) short reads filtered out after trimming by size control 368 ( 0.01%) empty reads filtered out after trimming by size control 1972926 (41.07%) reads available; of these: 1971128 (99.91%) trimmed reads available after processing 1798 ( 0.09%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 1963383 99.52% 19 3661 0.19% 20 1460 0.07% 21 1295 0.07% 22 726 0.04% 23 693 0.04% 24 467 0.02% 25 213 0.01% 26 183 0.01% 27 101 0.01% 28 60 0.00% 29 26 0.00% 30 8 0.00% 31 22 0.00% 32 43 0.00% 33 65 0.00% 34 57 0.00% 35 38 0.00% 36 276 0.01% 37 69 0.00% 38 12 0.00% 39 7 0.00% 40 4 0.00% 41 6 0.00% 42 1 0.00% 43 1 0.00% 44 0 0.00% 45 1 0.00% 46 48 0.00% criterion=sequence-density sequence-density=1.35 sequence-density-rank=1 fanout-score=33.68 fanout-score-rank=1 prefix-density=1.33 prefix-fanout=33.7 sequence=GACGATATTCGTATGCCGTCTTCTGCTTGAAAA criterion=fanout-score sequence-density=1.35 sequence-density-rank=1 fanout-score=33.68 fanout-score-rank=1 prefix-density=1.33 prefix-fanout=33.7 sequence=GACGATATTCGTATGCCGTCTTCTGCTTGAAAA Started job on | Feb 10 12:04:56 Started mapping on | Feb 10 12:04:56 Finished on | Feb 10 12:05:32 Mapping speed, Million of reads per hour | 207.10 Number of input reads | 2070970 Average input read length | 19 UNIQUE READS: Uniquely mapped reads number | 1548469 Uniquely mapped reads % | 74.77% Average mapped length | 17.99 Number of splices: Total | 10998 Number of splices: Annotated (sjdb) | 10755 Number of splices: GT/AG | 10863 Number of splices: GC/AG | 90 Number of splices: AT/AC | 34 Number of splices: Non-canonical | 11 Mismatch rate per base, % | 0.01% Deletion rate per base | 0.00% Deletion average length | 0.00 Insertion rate per base | 0.00% Insertion average length | 0.00 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 403444 % of reads mapped to multiple loci | 19.48% Number of reads mapped to too many loci | 14671 % of reads mapped to too many loci | 0.71% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.76% % of reads unmapped: other | 0.28% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 119057 119057 119057 N_multimapping 403444 403444 403444 N_noFeature 146697 309258 1372718 N_ambiguous 18333 3352 1818 UnstrandedReadsAssigned:1383439 PositiveStrandReadsAssigned:1235859 NegativeStrandReadsAssigned:173933 Dataset is classified positive stranded MeadianReadLen=18 20thPercentileLength=18 echo kmer=19 SRR2962700 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: SRR2962700-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 2,070,970 reads, 14,286 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 718 rounds 52401 SRR2962700.ke.tsv 34699 SRR2962700.se.tsv 87100 total ==> SRR2962700.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 0 0 Potri.016G087400.1.v4.1 270 171 0 0 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 0 0 Potri.012G127500.1.v4.1 977 878 0 0 ==> SRR2962700.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 1 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 151 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 2 SRR2962700 completed mapping pipeline successfully