Starting /dee2/code/volunteer_pipeline.sh SRR1174004 current disk space = 1524599484416 free memory = 1605652636 SRR1174004 SRAfilesize b4f44ded9889f87f94c862f32add3f29 SRR1174004.sra SRR1174004.sra file validated SRR1174004 is single end SRR1174004 is conventional basespace SRR1174004 read1 length is 42 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR1174004_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 32.2485 33.0 33.0 33.0 32.0 33.0 2 32.15975 33.0 32.0 34.0 30.0 34.0 3 32.22625 33.0 32.0 34.0 30.0 34.0 4 31.897 33.0 32.0 33.0 29.0 34.0 5 31.33025 33.0 31.0 33.0 27.0 34.0 6 31.517 33.0 31.0 33.0 28.0 34.0 7 31.69825 33.0 31.0 33.0 29.0 34.0 8 30.84225 32.0 30.0 33.0 26.0 34.0 9 30.7925 32.0 30.0 33.0 26.0 34.0 10 31.3745 33.0 31.0 33.0 28.0 34.0 11 30.89775 32.0 30.0 33.0 26.0 34.0 12 31.011 32.0 31.0 33.0 27.0 34.0 13 30.528 32.0 30.0 33.0 26.0 33.0 14 30.76125 32.0 30.0 33.0 26.0 34.0 15 30.7795 32.0 30.0 33.0 26.0 34.0 16 30.45175 32.0 30.0 33.0 25.0 34.0 17 30.397 32.0 30.0 33.0 25.0 33.0 18 30.89325 32.0 30.0 33.0 27.0 34.0 19 30.5145 32.0 30.0 33.0 25.0 33.0 20 30.574 32.0 30.0 33.0 25.0 34.0 21 30.438 32.0 30.0 33.0 25.0 33.0 22 30.23775 32.0 30.0 33.0 25.0 33.0 23 30.06475 32.0 29.0 33.0 24.0 33.0 24 29.687 31.0 29.0 33.0 24.0 33.0 25 29.5455 31.0 28.0 33.0 23.0 33.0 26 29.9995 32.0 29.0 33.0 25.0 33.0 27 28.7455 31.0 27.0 33.0 22.0 33.0 28 29.049 31.0 28.0 33.0 22.0 33.0 29 29.14925 31.0 28.0 33.0 22.0 33.0 30 29.17875 31.0 28.0 33.0 22.0 33.0 31 28.29925 30.0 26.0 32.0 21.0 33.0 32 29.24425 31.0 28.0 33.0 22.0 33.0 33 28.95525 31.0 28.0 33.0 22.0 33.0 34 28.57025 31.0 27.0 33.0 21.0 33.0 35 28.0795 30.0 26.0 32.0 21.0 33.0 36 28.161 30.0 27.0 32.0 21.0 33.0 37 28.2075 31.0 26.0 33.0 20.0 33.0 38 27.491 30.0 25.0 32.0 20.0 33.0 39 27.37825 30.0 25.0 32.0 19.0 33.0 40 27.917 31.0 26.0 32.0 19.0 33.0 41 26.65925 29.0 25.0 32.0 18.0 33.0 42 26.1235 29.0 24.0 32.0 17.0 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 6.0 5 1.0 6 3.0 7 2.0 8 1.0 9 0.0 10 2.0 11 3.0 12 4.0 13 2.0 14 4.0 15 6.0 16 8.0 17 4.0 18 11.0 19 10.0 20 17.0 21 29.0 22 44.0 23 44.0 24 74.0 25 89.0 26 120.0 27 230.0 28 306.0 29 516.0 30 662.0 31 896.0 32 752.0 33 154.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 36.514731805590536 29.539158902039787 17.149332661798038 16.796776630571646 2 38.66366366366366 25.0 19.96996996996997 16.366366366366368 3 38.288288288288285 20.895895895895897 17.29229229229229 23.523523523523522 4 40.78519629907477 24.981245311327832 16.029007251812956 18.204551137784446 5 29.532383095773945 32.83320830207552 18.72968242060515 18.904726181545385 6 23.025000000000002 28.199999999999996 31.5 17.275 7 41.225 23.0 22.575 13.200000000000001 8 21.305326331582897 20.855213803450862 42.460615153788446 15.378844711177795 9 21.349999999999998 40.825 25.55 12.275 10 46.5 22.275 16.325 14.899999999999999 11 21.510755377688845 24.937468734367183 25.56278139069535 27.988994497248626 12 22.436218109054526 21.285642821410704 32.94147073536769 23.336668334167083 13 22.57257257257257 19.994994994994993 20.82082082082082 36.61161161161161 14 18.10905452726363 45.84792396198099 23.011505752876438 13.031515757878939 15 30.597948461346007 29.422066549912433 24.218163622717036 15.761821366024517 16 23.549999999999997 31.724999999999998 28.775000000000002 15.950000000000001 17 24.675 28.549999999999997 32.5 14.274999999999999 18 30.08252063015754 19.929982495623904 31.882970742685675 18.104526131532882 19 26.18809404702351 24.512256128064035 25.56278139069535 23.736868434217108 20 21.691268451338505 25.69427070302727 34.07555666750062 18.5389041781336 21 20.775 25.324999999999996 27.500000000000004 26.400000000000002 22 32.9 21.525 24.4 21.175 23 23.775 20.175 37.375 18.675 24 22.514400200350615 26.771850738792885 25.820185324317556 24.893563736538944 25 17.90447611902976 31.43285821455364 30.632658164541137 20.030007501875467 26 25.75 10.6 40.875 22.775000000000002 27 15.403850962740684 15.25381345336334 23.50587646911728 45.83645911477869 28 13.928482120530134 15.303825956489122 40.960240060015 29.80745186296574 29 26.38159539884971 9.577394348587147 26.881720430107524 37.15928982245561 30 34.70867716929232 8.727181795448862 34.958739684921234 21.605401350337583 31 13.4783695923981 11.902975743935984 41.46036509127281 33.158289572393095 32 15.103775943985998 25.6064016004001 34.93373343335834 24.356089022255563 33 15.024999999999999 8.825 55.025 21.125 34 30.775000000000002 8.525 29.525000000000002 31.175000000000004 35 14.36077057793345 8.656492369276958 36.00200150112585 40.98073555166375 36 23.23080770192548 9.552388097024256 28.732183045761438 38.48462115528882 37 29.175 11.875 32.074999999999996 26.875 38 11.836836836836836 14.614614614614615 54.27927927927928 19.26926926926927 39 16.204051012753187 17.5293823455864 35.35883970992748 30.90772693173293 40 21.61080540270135 21.785892946473236 41.695847923961985 14.907453726863432 41 12.327737409170634 32.92407917815084 38.01052367827612 16.737659734402406 42 10.32064128256513 35.045090180360724 23.74749498997996 30.886773547094187 >>END_MODULE >>Per sequence GC content fail #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 0.5 24 1.0 25 1.5 26 2.0 27 12.5 28 23.0 29 23.0 30 23.5 31 24.0 32 24.0 33 24.0 34 24.0 35 58.5 36 93.0 37 131.5 38 170.0 39 251.0 40 332.0 41 332.0 42 395.5 43 459.0 44 504.0 45 549.0 46 574.5 47 600.0 48 600.0 49 670.5 50 741.0 51 551.5 52 362.0 53 362.0 54 362.0 55 362.0 56 240.5 57 119.0 58 82.5 59 46.0 60 46.0 61 41.5 62 37.0 63 28.0 64 19.0 65 16.0 66 13.0 67 13.0 68 12.5 69 12.0 70 8.0 71 4.0 72 4.0 73 3.0 74 2.0 75 1.5 76 1.0 77 1.0 78 1.0 79 1.0 80 1.5 81 2.0 82 1.0 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 1.0 100 2.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.7250000000000001 2 0.1 3 0.1 4 0.025 5 0.025 6 0.0 7 0.0 8 0.025 9 0.0 10 0.0 11 0.05 12 0.05 13 0.1 14 0.05 15 0.075 16 0.0 17 0.0 18 0.025 19 0.05 20 0.075 21 0.0 22 0.0 23 0.0 24 0.17500000000000002 25 0.025 26 0.0 27 0.025 28 0.025 29 0.025 30 0.025 31 0.025 32 0.025 33 0.0 34 0.0 35 0.075 36 0.025 37 0.0 38 0.1 39 0.025 40 0.05 41 0.22499999999999998 42 0.2 >>END_MODULE >>Sequence Length Distribution pass #Length Count 42 4000.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 68.625 #Duplication Level Percentage of deduplicated Percentage of total 1 91.47540983606557 62.775000000000006 2 4.335154826958106 5.949999999999999 3 1.3479052823315119 2.775 4 0.546448087431694 1.5 5 0.4007285974499089 1.375 6 0.2185792349726776 0.8999999999999999 7 0.32786885245901637 1.575 8 0.29143897996357016 1.6 9 0.0 0.0 >10 0.8743169398907104 12.5 >50 0.18214936247723132 9.049999999999999 >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 GGGCCTGTAGCTCAGAGGAATCTCGTATGCCGTCTTCTGCTT 89 2.225 Illumina PCR Primer Index 12 (96% over 26bp) GGGGATGTAGCTCAGAATCTCGTATGCCGTCTTCTGCTTGAA 85 2.125 RNA PCR Primer, Index 40 (100% over 30bp) GGGGACGTAGCTCATAATCTCGTATGCCGTCTTCTGCTTGAA 66 1.6500000000000001 RNA PCR Primer, Index 40 (96% over 30bp) GGGGATGTAGCTCAAAATCTCGTATGCCGTCTTCTGCTTGAA 66 1.6500000000000001 RNA PCR Primer, Index 40 (96% over 30bp) GGCGGATGTAGCCAAGTGGAATCTCGTATGCCGTCTTCTGCT 56 1.4000000000000001 Illumina PCR Primer Index 8 (96% over 26bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCATCTCGTATGC 38 0.95 No Hit GGGATTGTAGTTCAATATCTCGTATGCCGTCTTCTGCTTGAA 34 0.8500000000000001 Illumina PCR Primer Index 6 (96% over 29bp) TAACGAACGAACGATTTGAACATCTCGTATGCCGTCTTCTGC 32 0.8 Illumina PCR Primer Index 7 (96% over 25bp) CATCGAGTAGACCTTGTTATTGTGAGAATTATCTCGTATGCC 30 0.75 No Hit AGCGGAGTAGAGCAGTTATCTCGTATGCCGTCTTCTGCTTGA 29 0.7250000000000001 Illumina PCR Primer Index 5 (96% over 29bp) AGCGGAGTAGAGCAGTATCTCGTATGCCGTCTTCTGCTTGAA 28 0.7000000000000001 Illumina PCR Primer Index 6 (96% over 28bp) GTCGTTGTAGTATAGTGGTAAGTATTCCCGCCATCTCGTATG 25 0.625 No Hit AACGAACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCT 24 0.6 RNA PCR Primer, Index 19 (96% over 27bp) ACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTTGAAA 23 0.575 Illumina PCR Primer Index 7 (96% over 28bp) CGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTTGAAAA 22 0.5499999999999999 RNA PCR Primer, Index 19 (96% over 29bp) TCCGTCGTAGTCTAGGATCTCGTATGCCGTCTTCTGCTTGAA 21 0.525 RNA PCR Primer, Index 22 (96% over 28bp) GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTATCTCGTAT 21 0.525 No Hit GGGGGTGTAGCTCATAATCTCGTATGCCGTCTTCTGCTTGAA 20 0.5 Illumina PCR Primer Index 12 (96% over 27bp) AACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTTGAA 20 0.5 RNA PCR Primer, Index 19 (96% over 29bp) ACGAACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTT 18 0.44999999999999996 Illumina PCR Primer Index 7 (96% over 27bp) CTAACGAACGAACGATTTGAACATCTCGTATGCCGTCTTCTG 18 0.44999999999999996 RNA PCR Primer, Index 19 (96% over 25bp) GGGGATGTAGCTCAAATCTCGTATGCCGTCTTCTGCTTGAAA 16 0.4 TruSeq Adapter, Index 13 (96% over 28bp) CGAACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTTG 14 0.35000000000000003 RNA PCR Primer, Index 19 (96% over 29bp) GGGGATGTAGCTCAGATCTCGTATGCCGTCTTCTGCTTGAAA 14 0.35000000000000003 Illumina PCR Primer Index 9 (96% over 30bp) GGGATTGTAGTTCAAATCTCGTATGCCGTCTTCTGCTTGAAA 13 0.325 RNA PCR Primer, Index 13 (96% over 29bp) GGGGATGTAGCTCAGATGGTATCTCGTATGCCGTCTTCTGCT 10 0.25 RNA PCR Primer, Index 34 (96% over 27bp) ATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAA 10 0.25 Illumina Single End Adapter 1 (95% over 24bp) GCACCAGTGGTCTAGTGGTAGAATAGTACCATCTCGTATGCC 10 0.25 No Hit AGCGGAGTAGAGCAGATCTCGTATGCCGTCTTCTGCTTGAAA 10 0.25 Illumina PCR Primer Index 9 (100% over 27bp) TGACAGAAGAGAGTGAGCACATCTCGTATGCCGTCTTCTGCT 8 0.2 Illumina PCR Primer Index 9 (96% over 25bp) AGCGGAGTAGAGCAATCTCGTATGCCGTCTTCTGCTTGAAAA 8 0.2 Illumina PCR Primer Index 4 (96% over 29bp) GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACATCTCGTATG 8 0.2 No Hit GAACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTTGA 8 0.2 Illumina PCR Primer Index 7 (96% over 28bp) GACACGACTCTCGGCAACGGATATCTATCTCGTATGCCGTCT 8 0.2 No Hit GCGTCTGTAGTCCAACGGTTAGGATAATTGCATCTCGTATGC 8 0.2 No Hit GGGGATGTAGCTCAGATGGATCTCGTATGCCGTCTTCTGCTT 8 0.2 RNA PCR Primer, Index 23 (96% over 27bp) GTCGTTGTAGTATAGTGGTAAGTATTCCCGCATCTCGTATGC 8 0.2 No Hit CCTAACGAACGAACGATTTGAACATCTCGTATGCCGTCTTCT 7 0.17500000000000002 RNA PCR Primer, Index 19 (95% over 24bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGATCTCG 7 0.17500000000000002 No Hit CACGACTCTCGGCAACGGATATCTCATCTCGTATGCCGTCTT 7 0.17500000000000002 No Hit GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTATCTCGTA 7 0.17500000000000002 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCATCTCGTAT 7 0.17500000000000002 No Hit AACGATTTGAACATCTCGTATGCCGTCTTCTGCTTGAAAAAA 7 0.17500000000000002 Illumina PCR Primer Index 7 (96% over 28bp) GGGGATGTAGCTCAATCTCGTATGCCGTCTTCTGCTTGAAAA 7 0.17500000000000002 RNA PCR Primer, Index 32 (96% over 29bp) TAGATATTTCAGGTTGTGTGGAATCTCGTATGCCGTCTTCTG 7 0.17500000000000002 Illumina PCR Primer Index 8 (95% over 24bp) TAATTCATGATCTGGATCTCGTATGCCGTCTTCTGCTTGAAA 7 0.17500000000000002 RNA PCR Primer, Index 23 (96% over 28bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTATCTCGT 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATATCTCGTATGCCG 6 0.15 No Hit GTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTATCTCGTAT 6 0.15 No Hit AGGGATGTAGCGCAGCTATCTCGTATGCCGTCTTCTGCTTGA 6 0.15 RNA PCR Primer, Index 38 (96% over 29bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAATCTCGT 6 0.15 No Hit ACGATTTGAACATCTCGTATGCCGTCTTCTGCTTGAAAAAAA 6 0.15 Illumina PCR Primer Index 7 (96% over 28bp) GACACGACTCTCGGCAACGATCTCGTATGCCGTCTTCTGCTT 5 0.125 RNA PCR Primer, Index 36 (96% over 28bp) GAACGATTTGAACATCTCGTATGCCGTCTTCTGCTTGAAAAA 5 0.125 RNA PCR Primer, Index 19 (96% over 29bp) TCCGTCGTAGTCTAGGTGGTTAGGATACTCGGCATCTCGTAT 5 0.125 No Hit CACGACTCTCGGCAACGGATATCATCTCGTATGCCGTCTTCT 5 0.125 TruSeq Adapter, Index 7 (95% over 24bp) CACGACTCTCGGCATCTCGTATGCCGTCTTCTGCTTGAAAAA 5 0.125 Illumina PCR Primer Index 3 (96% over 29bp) GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTATCTCGTAT 5 0.125 No Hit GGCGGATGTAGCCAAGTGGATCTCGTATGCCGTCTTCTGCTT 5 0.125 RNA PCR Primer, Index 23 (100% over 28bp) GCGTCTGTAGTCCAACGGATCTCGTATGCCGTCTTCTGCTTG 5 0.125 TruSeq Adapter, Index 18 (96% over 27bp) CCGTCGTAGTCTAGGATCTCGTATGCCGTCTTCTGCTTGAAA 5 0.125 Illumina PCR Primer Index 1 (96% over 27bp) GTCGTTGTAGTATAATCTCGTATGCCGTCTTCTGCTTGAAAA 5 0.125 Illumina PCR Primer Index 12 (96% over 28bp) ACTGGTTGGATCATGCTTCTAATCTCGTATGCCGTCTTCTGC 5 0.125 RNA PCR Primer, Index 12 (96% over 27bp) >>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 warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTGTAGT 20 0.0017759365 36.35443 5 TGTAGCT 20 0.0017759365 36.35443 6 TAGCTCA 25 1.137179E-4 36.354427 8 GTAGCTC 25 1.137179E-4 36.354427 7 GAGTAGA 30 3.322481E-4 30.295357 5 TTGAAAA 70 1.00180565E-4 18.177216 36 GCATCTC 50 0.007035939 17.949999 23 CTTGAAA 90 7.5699267E-4 13.961112 35 GCTTGAA 145 5.0392737E-7 13.789612 36 CATCTCG 85 0.009080758 12.6705885 24 TGCTTGA 160 1.7917791E-6 12.340626 35 CTGCTTG 160 1.7917791E-6 12.340626 34 TCTGCTT 175 4.91641E-6 11.282857 33 TTCTGCT 195 1.6496011E-5 10.125642 32 CTTCTGC 215 4.874952E-5 9.183722 31 CCGTCTT 330 5.8202204E-8 8.70303 35 TCTTCTG 230 1.0250244E-4 8.584783 30 CGTCTTC 320 3.44824E-7 8.52057 36 TGCCGTC 350 1.4545185E-7 8.205714 33 ATGCCGT 350 1.4545185E-7 8.205714 32 >>END_MODULE Read 632810 spots for SRR1174004.sra Written 632810 spots for SRR1174004.sra Read 632810 spots for SRR1174004.sra Written 632810 spots for SRR1174004.sra Read 632810 spots for SRR1174004.sra Written 632810 spots for SRR1174004.sra Read 632810 spots for SRR1174004.sra Written 632810 spots for SRR1174004.sra Read 632810 spots for SRR1174004.sra Written 632810 spots for SRR1174004.sra Read 632810 spots for SRR1174004.sra Written 632810 spots for SRR1174004.sra Read 632810 spots for SRR1174004.sra Written 632810 spots for SRR1174004.sra Read 632810 spots for SRR1174004.sra Written 632810 spots for SRR1174004.sra Read 632810 spots for SRR1174004.sra Written 632810 spots for SRR1174004.sra Read 632810 spots for SRR1174004.sra Written 632810 spots for SRR1174004.sra Read 632810 spots for SRR1174004.sra Written 632810 spots for SRR1174004.sra Read 632810 spots for SRR1174004.sra Written 632810 spots for SRR1174004.sra Read 632810 spots for SRR1174004.sra Written 632810 spots for SRR1174004.sra Read 632810 spots for SRR1174004.sra Written 632810 spots for SRR1174004.sra Read 632810 spots for SRR1174004.sra Written 632810 spots for SRR1174004.sra Read 632810 spots for SRR1174004.sra Written 632810 spots for SRR1174004.sra Read 632810 spots for SRR1174004.sra Written 632810 spots for SRR1174004.sra Read 632810 spots for SRR1174004.sra Written 632810 spots for SRR1174004.sra Read 632810 spots for SRR1174004.sra Written 632810 spots for SRR1174004.sra Read 632810 spots for SRR1174004.sra Written 632810 spots for SRR1174004.sra SRR ids: ['SRR1174004.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_e1pru7ro SRR1174004.sra spots: 12656200 blocks: [[1, 632810], [632811, 1265620], [1265621, 1898430], [1898431, 2531240], [2531241, 3164050], [3164051, 3796860], [3796861, 4429670], [4429671, 5062480], [5062481, 5695290], [5695291, 6328100], [6328101, 6960910], [6960911, 7593720], [7593721, 8226530], [8226531, 8859340], [8859341, 9492150], [9492151, 10124960], [10124961, 10757770], [10757771, 11390580], [11390581, 12023390], [12023391, 12656200]] SRR1174004 file size 1766111 SRR1174004 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 SRR1174004 SRR1174004_1.fastq Input file: SRR1174004_1.fastq trimmed: SRR1174004-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 14:26:56 2024 >> started Mon Dec 9 14:27:06 2024 >> done (9.677s) 12656200 reads processed; of these: 42874 ( 0.34%) short reads filtered out after trimming by size control 23230 ( 0.18%) empty reads filtered out after trimming by size control 12590096 (99.48%) reads available; of these: 1280224 (10.17%) trimmed reads available after processing 11309872 (89.83%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 4839 0.04% 19 5702 0.05% 20 6564 0.05% 21 7579 0.06% 22 9822 0.08% 23 13595 0.11% 24 15348 0.12% 25 16095 0.13% 26 21992 0.17% 27 35245 0.28% 28 31441 0.25% 29 37978 0.30% 30 38966 0.31% 31 37895 0.30% 32 38562 0.31% 33 45701 0.36% 34 59383 0.47% 35 69457 0.55% 36 60441 0.48% 37 46064 0.37% 38 62537 0.50% 39 96986 0.77% 40 196091 1.56% 41 321941 2.56% 42 11309872 89.83% 12590096 reads passed initial QC criterion=sequence-density sequence-density=80.40 sequence-density-rank=1 fanout-score=36.87 fanout-score-rank=1 prefix-density=85.94 prefix-fanout=34.5 sequence=ATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA criterion=fanout-score sequence-density=80.40 sequence-density-rank=1 fanout-score=36.87 fanout-score-rank=1 prefix-density=85.94 prefix-fanout=34.5 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 SRR1174004 - Input file: STDIN trimmed: SRR1174004-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 14:29:30 2024 >> started Mon Dec 9 14:29:44 2024 >> done (13.902s) 12279230 reads processed; of these: 4069500 (33.14%) short reads filtered out after trimming by size control 209495 ( 1.71%) empty reads filtered out after trimming by size control 8000235 (65.15%) reads available; of these: 7704817 (96.31%) trimmed reads available after processing 295418 ( 3.69%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 309314 3.87% 19 549162 6.86% 20 532300 6.65% 21 527874 6.60% 22 308687 3.86% 23 531542 6.64% 24 2364815 29.56% 25 263299 3.29% 26 196736 2.46% 27 158499 1.98% 28 141878 1.77% 29 186938 2.34% 30 273789 3.42% 31 341363 4.27% 32 269873 3.37% 33 305578 3.82% 34 211596 2.64% 35 171965 2.15% 36 90411 1.13% 37 47076 0.59% 38 29797 0.37% 39 13249 0.17% 40 4498 0.06% 41 6124 0.08% 42 163872 2.05% criterion=sequence-density sequence-density=3.63 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=17 prefix-density=0.00 prefix-fanout=1.0 sequence=CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATTC criterion=fanout-score sequence-density=0.01 sequence-density-rank=33 fanout-score=227.59 fanout-score-rank=1 prefix-density=0.99 prefix-fanout=1.5 sequence=GGTCTAGTGGTTAGGACATTGGACTCTGAATCCAGTAACCCGAG Started job on | Dec 09 14:30:12 Started mapping on | Dec 09 14:30:12 Finished on | Dec 09 14:30:45 Mapping speed, Million of reads per hour | 906.67 Number of input reads | 8311101 Average input read length | 26 UNIQUE READS: Uniquely mapped reads number | 2472844 Uniquely mapped reads % | 29.75% Average mapped length | 23.90 Number of splices: Total | 30415 Number of splices: Annotated (sjdb) | 5537 Number of splices: GT/AG | 28643 Number of splices: GC/AG | 995 Number of splices: AT/AC | 9 Number of splices: Non-canonical | 768 Mismatch rate per base, % | 0.18% Deletion rate per base | 0.00% Deletion average length | 1.26 Insertion rate per base | 0.00% Insertion average length | 1.04 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 2932207 % of reads mapped to multiple loci | 35.28% Number of reads mapped to too many loci | 2386582 % of reads mapped to too many loci | 28.72% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.74% % of reads unmapped: other | 1.51% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 2906050 2906050 2906050 N_multimapping 2932207 2932207 2932207 N_noFeature 1992948 2159369 2297639 N_ambiguous 14174 5334 734 UnstrandedReadsAssigned:465722 PositiveStrandReadsAssigned:308141 NegativeStrandReadsAssigned:174471 Dataset is classified unstranded MeadianReadLen=24 20thPercentileLength=21 echo kmer=19 SRR1174004 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: SRR1174004-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 8,311,101 reads, 2,698,469 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,118 rounds 52973 SRR1174004.ke.tsv 35125 SRR1174004.se.tsv 88098 total ==> SRR1174004.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0.666667 0.122052 PNS24249 1928 1829 0 0 PNS24246 1044 945 0.666667 0.122052 PNS24248 1044 945 0.666667 0.122052 PNS24244 1471 1372 0 0 PNS24243 293 194 0 0 KQK14069 1603 1504 18.8031 2.16298 KQK14071 474 375 0 0 ==> SRR1174004.se.tsv <== BRADI_1g14170v3 20 BRADI_1g53295v3 6 BRADI_1g59795v3 2 BRADI_1g07683v3 0 BRADI_1g00485v3 1 BRADI_1g20270v3 4 BRADI_1g74790v3 44 BRADI_1g09890v3 0 BRADI_1g77505v3 1 BRADI_1g48960v3 0 SRR1174004 completed mapping pipeline successfully