Starting /dee2/code/volunteer_pipeline.sh SRR1174005 current disk space = 1524478836736 free memory = 1605664936 SRR1174005 SRAfilesize aa20d308224166504b90b4269bbca805 SRR1174005.sra SRR1174005.sra file validated SRR1174005 is single end SRR1174005 is conventional basespace SRR1174005 read1 length is 42 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR1174005_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 31.94825 33.0 33.0 33.0 31.0 33.0 2 31.8925 33.0 32.0 34.0 29.0 34.0 3 31.6765 33.0 32.0 33.0 28.0 34.0 4 31.5975 33.0 31.0 33.0 28.0 34.0 5 31.1425 33.0 31.0 33.0 26.0 34.0 6 31.176 33.0 31.0 33.0 27.0 34.0 7 31.304 33.0 31.0 33.0 27.0 34.0 8 30.73375 32.0 30.0 33.0 26.0 34.0 9 31.06725 33.0 31.0 33.0 27.0 34.0 10 31.2155 33.0 31.0 33.0 27.0 34.0 11 30.861 33.0 30.0 33.0 26.0 34.0 12 30.708 32.0 30.0 33.0 25.0 33.0 13 30.8495 32.0 30.0 33.0 26.0 34.0 14 30.86925 32.0 31.0 33.0 26.0 34.0 15 30.385 32.0 30.0 33.0 25.0 33.0 16 30.1705 32.0 29.0 33.0 24.0 33.0 17 30.6635 32.0 30.0 33.0 25.0 34.0 18 30.07775 32.0 29.0 33.0 24.0 33.0 19 29.836 31.0 29.0 33.0 23.0 33.0 20 30.0375 32.0 29.0 33.0 24.0 33.0 21 30.054 32.0 29.0 33.0 24.0 33.0 22 29.7295 31.0 29.0 33.0 24.0 33.0 23 29.51375 31.0 28.0 33.0 23.0 33.0 24 29.665 31.0 29.0 33.0 23.0 33.0 25 29.1615 31.0 28.0 32.0 23.0 33.0 26 29.762 32.0 29.0 33.0 24.0 33.0 27 28.586 30.0 27.0 32.0 21.0 33.0 28 29.2255 31.0 28.0 33.0 23.0 33.0 29 29.0975 31.0 28.0 33.0 23.0 33.0 30 28.766 31.0 27.0 33.0 22.0 33.0 31 28.08675 30.0 26.0 32.0 21.0 33.0 32 28.61925 31.0 27.0 32.0 21.0 33.0 33 28.5895 31.0 27.0 32.0 22.0 33.0 34 27.89275 30.0 26.0 32.0 20.0 33.0 35 27.52075 30.0 26.0 32.0 20.0 33.0 36 27.57925 30.0 25.0 32.0 20.0 33.0 37 28.1285 31.0 26.0 33.0 20.0 33.0 38 26.929 29.0 24.0 32.0 19.0 33.0 39 27.42325 30.0 25.0 32.0 19.0 33.0 40 27.44725 30.0 26.0 32.0 19.0 33.0 41 26.33775 29.0 24.0 32.0 18.0 33.0 42 25.59125 29.0 23.0 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 6.0 5 1.0 6 2.0 7 2.0 8 2.0 9 2.0 10 4.0 11 3.0 12 3.0 13 4.0 14 3.0 15 9.0 16 7.0 17 9.0 18 12.0 19 6.0 20 26.0 21 40.0 22 70.0 23 71.0 24 84.0 25 100.0 26 153.0 27 202.0 28 314.0 29 476.0 30 713.0 31 879.0 32 675.0 33 122.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 33.095541401273884 30.4968152866242 20.9171974522293 15.490445859872612 2 36.25218914185639 25.619214410808105 19.21441080810608 18.914185639229423 3 40.2 23.1 17.175 19.525000000000002 4 41.220610305152576 26.313156578289142 17.58379189594797 14.882441220610303 5 26.5 36.225 17.5 19.775000000000002 6 25.18759379689845 26.613306653326664 27.888944472236116 20.31015507753877 7 36.725 26.05 22.0 15.225 8 22.95 24.025 36.525 16.5 9 25.437718859429715 35.617808904452225 25.46273136568284 13.48174087043522 10 40.33508377094274 22.780695173793447 19.554888722180543 17.329332333083272 11 22.400000000000002 25.074999999999996 26.375 26.150000000000002 12 23.400000000000002 23.150000000000002 29.75 23.7 13 25.4 22.125 21.675 30.8 14 22.216662496872654 42.15661746309733 21.891418563922944 13.73530147610708 15 30.265132566283143 30.240120060030012 22.71135567783892 16.783391695847925 16 22.886443221610804 34.492246123061534 24.637318659329665 17.983991995998 17 25.594195646735052 32.89967475606705 27.120340255191394 14.385789342006506 18 27.231807951987996 22.05551387846962 30.15753938484621 20.555138784696176 19 24.0 25.8 24.55 25.650000000000002 20 23.95598899724931 25.406351587896975 31.257814453613403 19.379844961240313 21 24.3 25.0 22.775000000000002 27.925 22 30.45 23.724999999999998 26.325 19.5 23 24.64348261195897 22.241681260945708 34.42581936452339 18.689016762571928 24 21.375 26.1 26.950000000000003 25.575 25 15.575 33.375 31.225 19.825 26 21.875 10.525 42.825 24.775 27 16.012009006755065 11.38353765323993 23.892919689767325 48.711533650237676 28 14.653663415853963 11.42785696424106 46.41160290072518 27.506876719179797 29 23.75 11.35 24.474999999999998 40.425 30 36.67750813109832 8.581436077057793 34.2006504878659 20.540405303977984 31 15.178794698674668 11.10277569392348 45.8114528632158 27.906976744186046 32 12.037037037037036 30.73073073073073 34.73473473473474 22.4974974974975 33 14.932466233116559 7.903951975987994 55.70285142571285 21.46073036518259 34 37.378033525143856 7.230422817112834 26.64498373780335 28.74655991993996 35 14.757378689344671 8.504252126063031 32.94147073536769 43.796898449224614 36 21.060530265132567 10.030015007503753 24.68734367183592 44.22211105552776 37 33.991995997999 10.755377688844423 30.940470235117555 24.312156078039017 38 11.805902951475739 13.056528264132067 57.87893946973487 17.258629314657327 39 13.825000000000001 16.625 31.8 37.75 40 19.534767383691847 20.66033016508254 46.59829914957479 13.206603301650826 41 12.48436327245434 30.848136102076555 41.806354766074556 14.861145859394545 42 8.731548661496122 32.9246935201401 21.36602451838879 36.97773329997498 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.5 2 1.0 3 1.0 4 0.5 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 0.5 26 1.0 27 9.5 28 18.0 29 18.0 30 19.5 31 21.0 32 28.0 33 35.0 34 35.0 35 56.5 36 78.0 37 114.5 38 151.0 39 204.0 40 257.0 41 257.0 42 346.5 43 436.0 44 507.0 45 578.0 46 603.0 47 628.0 48 628.0 49 716.5 50 805.0 51 604.0 52 403.0 53 403.0 54 364.0 55 325.0 56 232.0 57 139.0 58 98.5 59 58.0 60 58.0 61 42.5 62 27.0 63 18.0 64 9.0 65 11.5 66 14.0 67 14.0 68 10.0 69 6.0 70 4.0 71 2.0 72 2.0 73 2.0 74 2.0 75 2.0 76 2.0 77 1.0 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 0.5 90 1.0 91 1.0 92 0.5 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 1.5 100 3.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 1.875 2 0.075 3 0.0 4 0.05 5 0.0 6 0.05 7 0.0 8 0.0 9 0.05 10 0.025 11 0.0 12 0.0 13 0.0 14 0.075 15 0.05 16 0.05 17 0.075 18 0.025 19 0.0 20 0.025 21 0.0 22 0.0 23 0.075 24 0.0 25 0.0 26 0.0 27 0.075 28 0.025 29 0.0 30 0.075 31 0.025 32 0.1 33 0.05 34 0.075 35 0.05 36 0.05 37 0.05 38 0.05 39 0.0 40 0.05 41 0.075 42 0.075 >>END_MODULE >>Sequence Length Distribution pass #Length Count 42 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 73.8 #Duplication Level Percentage of deduplicated Percentage of total 1 93.12330623306234 68.72500000000001 2 3.0149051490514904 4.45 3 1.084010840108401 2.4 4 0.6775067750677507 2.0 5 0.5081300813008129 1.875 6 0.27100271002710025 1.2 7 0.13550135501355012 0.7000000000000001 8 0.06775067750677506 0.4 9 0.16937669376693767 1.125 >10 0.8468834688346882 11.85 >50 0.10162601626016261 5.2749999999999995 >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 GGGGATGTAGCTCAGAATCTCGTATGCCGTCTTCTGCTTGAA 91 2.275 RNA PCR Primer, Index 40 (100% over 30bp) GGGGACGTAGCTCATAATCTCGTATGCCGTCTTCTGCTTGAA 69 1.725 RNA PCR Primer, Index 40 (96% over 30bp) TCCGTCGTAGTCTAGGATCTCGTATGCCGTCTTCTGCTTGAA 51 1.275 RNA PCR Primer, Index 22 (96% over 28bp) GGGGATGTAGCTCAAAATCTCGTATGCCGTCTTCTGCTTGAA 46 1.15 RNA PCR Primer, Index 40 (96% over 30bp) GGGCCTGTAGCTCAGAGGAATCTCGTATGCCGTCTTCTGCTT 42 1.05 Illumina PCR Primer Index 12 (96% over 26bp) TGACAGAAGAGAGTGAGCACATCTCGTATGCCGTCTTCTGCT 32 0.8 Illumina PCR Primer Index 9 (96% over 25bp) AACGAACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCT 24 0.6 RNA PCR Primer, Index 19 (96% over 27bp) GGCGGATGTAGCCAAGTGGAATCTCGTATGCCGTCTTCTGCT 21 0.525 Illumina PCR Primer Index 8 (96% over 26bp) GCGTCTGTAGTCCAACGGATCTCGTATGCCGTCTTCTGCTTG 20 0.5 TruSeq Adapter, Index 18 (96% over 27bp) TAACGAACGAACGATTTGAACATCTCGTATGCCGTCTTCTGC 20 0.5 Illumina PCR Primer Index 7 (96% over 25bp) AACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTTGAA 20 0.5 RNA PCR Primer, Index 19 (96% over 29bp) ACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTTGAAA 19 0.475 Illumina PCR Primer Index 7 (96% over 28bp) GGGGATGTAGCTCAGATCTCGTATGCCGTCTTCTGCTTGAAA 19 0.475 Illumina PCR Primer Index 9 (96% over 30bp) TAATTCATGATCTGGATCTCGTATGCCGTCTTCTGCTTGAAA 19 0.475 RNA PCR Primer, Index 23 (96% over 28bp) ACGAACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTT 18 0.44999999999999996 Illumina PCR Primer Index 7 (96% over 27bp) TTGACAGAAGAGAGTGAGCACATCTCGTATGCCGTCTTCTGC 16 0.4 Illumina PCR Primer Index 9 (95% over 24bp) GGGGATGTAGCTCAAATCTCGTATGCCGTCTTCTGCTTGAAA 16 0.4 TruSeq Adapter, Index 13 (96% over 28bp) AGCGGAGTAGAGCAGTATCTCGTATGCCGTCTTCTGCTTGAA 15 0.375 Illumina PCR Primer Index 6 (96% over 28bp) CGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTTGAAAA 15 0.375 RNA PCR Primer, Index 19 (96% over 29bp) TCTGTTGGGCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAA 14 0.35000000000000003 Illumina PCR Primer Index 3 (96% over 30bp) GGGATTGTAGTTCAATATCTCGTATGCCGTCTTCTGCTTGAA 14 0.35000000000000003 Illumina PCR Primer Index 6 (96% over 29bp) CTAACGAACGAACGATTTGAACATCTCGTATGCCGTCTTCTG 14 0.35000000000000003 RNA PCR Primer, Index 19 (96% over 25bp) GAACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTTGA 14 0.35000000000000003 Illumina PCR Primer Index 7 (96% over 28bp) CGAACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTTG 13 0.325 RNA PCR Primer, Index 19 (96% over 29bp) TTTGGATTGAAGGGAGCTCTGATCTCGTATGCCGTCTTCTGC 12 0.3 Illumina PCR Primer Index 9 (96% over 25bp) GACACGACTCTCGGCAACGGATATCTATCTCGTATGCCGTCT 11 0.27499999999999997 No Hit GAGGCATCCTAACGAACGAACGATTTGAACATCTCGTATGCC 10 0.25 No Hit CGGCGACGGAACCAATCTCGTATGCCGTCTTCTGCTTGAAAA 10 0.25 Illumina PCR Primer Index 4 (96% over 29bp) GGGATTGTAGTTCAAATCTCGTATGCCGTCTTCTGCTTGAAA 9 0.22499999999999998 RNA PCR Primer, Index 13 (96% over 29bp) AGCGGAGTAGAGCAGTTATCTCGTATGCCGTCTTCTGCTTGA 9 0.22499999999999998 Illumina PCR Primer Index 5 (96% over 29bp) GGGGGTGTAGCTCATAATCTCGTATGCCGTCTTCTGCTTGAA 9 0.22499999999999998 Illumina PCR Primer Index 12 (96% over 27bp) AGCGGAGTAGAGCAGATCTCGTATGCCGTCTTCTGCTTGAAA 9 0.22499999999999998 Illumina PCR Primer Index 9 (100% over 27bp) TAGATATTTCAGGTTGTGTGGAATCTCGTATGCCGTCTTCTG 9 0.22499999999999998 Illumina PCR Primer Index 8 (95% over 24bp) TCCTAACGAACGAACGATTTGAACATCTCGTATGCCGTCTTC 8 0.2 Illumina PCR Primer Index 7 (95% over 22bp) AGGCATCCTAACGAACGAACGATTTGAACATCTCGTATGCCG 8 0.2 No Hit GCACCAGTGGTCTAGTGGTAGAATAGTACCATCTCGTATGCC 7 0.17500000000000002 No Hit ATCCTAACGAACGAACGATTTGAACATCTCGTATGCCGTCTT 7 0.17500000000000002 RNA PCR Primer, Index 19 (95% over 22bp) GACACGACTCTCGGCATCTCGTATGCCGTCTTCTGCTTGAAA 7 0.17500000000000002 Illumina PCR Primer Index 3 (96% over 29bp) CACGACTCTCGGCAACGGATATCTCATCTCGTATGCCGTCTT 7 0.17500000000000002 No Hit GGGGATGTAGCTCAGATGGTATCTCGTATGCCGTCTTCTGCT 6 0.15 RNA PCR Primer, Index 34 (96% over 27bp) CACGACTCTCGGCAACGGATATCTATCTCGTATGCCGTCTTC 6 0.15 Illumina PCR Primer Index 2 (95% over 22bp) CCTAACGAACGAACGATTTGAACATCTCGTATGCCGTCTTCT 6 0.15 RNA PCR Primer, Index 19 (95% over 24bp) AGGGCTATAGCTCAGTTCGGATCTCGTATGCCGTCTTCTGCT 6 0.15 TruSeq Adapter, Index 9 (96% over 26bp) CACGACTCTCGGCATCTCGTATGCCGTCTTCTGCTTGAAAAA 6 0.15 Illumina PCR Primer Index 3 (96% over 29bp) GCGTCTGTAGTCCAACGGTTAGGATAATTGCATCTCGTATGC 6 0.15 No Hit TGCTTGGACTACATATGGTTGAGGGTTGTATCGTATGCCGTC 6 0.15 No Hit GACACGACTCTCGGCAACGGATAATCTCGTATGCCGTCTTCT 6 0.15 RNA PCR Primer, Index 7 (95% over 23bp) GAACGATTTGAACATCTCGTATGCCGTCTTCTGCTTGAAAAA 5 0.125 RNA PCR Primer, Index 19 (96% over 29bp) CACGACTCTCGGCAACGGATATCATCTCGTATGCCGTCTTCT 5 0.125 TruSeq Adapter, Index 7 (95% over 24bp) GCGTCTGTAGTCCAACGGTTAGGATAATTGCCATCTCGTATG 5 0.125 No Hit ATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAA 5 0.125 Illumina Single End Adapter 1 (95% over 24bp) CATCCTAACGAACGAACGATTTGAACATCTCGTATGCCGTCT 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCATCTCGTATGC 5 0.125 No Hit TCGCTTGGTGCAGATCGGGACATCTCGTATGCCGTCTTCTGC 5 0.125 Illumina PCR Primer Index 3 (95% over 24bp) TGCGGAAGGATCATTGATCTCGTATGCCGTCTTCTGCTTGAA 5 0.125 Illumina PCR Primer Index 5 (96% over 29bp) CACGACTCTCGGCAACGGATATCTCGGCATCTCGTATGCCGT 5 0.125 No Hit GACACGACTCTCGGCAACATCTCGTATGCCGTCTTCTGCTTG 5 0.125 Illumina PCR Primer Index 6 (96% over 28bp) GGGGATGTAGCTCAATCTCGTATGCCGTCTTCTGCTTGAAAA 5 0.125 RNA PCR Primer, Index 32 (96% over 29bp) GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGATCTCGTA 5 0.125 No Hit ACGATTTGAACATCTCGTATGCCGTCTTCTGCTTGAAAAAAA 5 0.125 Illumina PCR Primer Index 7 (96% over 28bp) GACACGACTCTCGGCAACGGATATCATCTCGTATGCCGTCTT 5 0.125 TruSeq Adapter, Index 7 (95% over 22bp) GTCGTTGTAGTATAGTGGTAAGTATTCCCGCATCTCGTATGC 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 AGCTCAG 30 7.779665E-6 35.9875 9 TAGCTCA 45 1.9699655E-9 35.9875 8 TGTAGCT 30 7.779665E-6 35.9875 6 GCTCAGA 30 7.779665E-6 35.9875 10 GTAGCTC 40 3.1421223E-8 35.9875 7 CATCTCG 90 7.431179E-4 13.995138 24 CGTCTTC 320 0.0 13.495313 36 GATCTCG 125 3.780864E-5 12.955501 24 CCGTCTT 335 0.0 12.891045 35 GCCGTCT 340 0.0 12.70147 34 TGCCGTC 345 0.0 12.517391 33 TATGCCG 355 0.0 12.164789 31 ATGCCGT 355 0.0 12.164789 32 GTATGCC 365 0.0 11.831507 30 CGTATGC 380 0.0 11.364473 29 TCGTATG 385 0.0 11.216884 28 CTCGTAT 390 0.0 11.073077 27 TCTCGTA 385 0.0 10.749514 26 ATCTCGT 390 0.0 10.611699 25 >>END_MODULE Read 699737 spots for SRR1174005.sra Written 699737 spots for SRR1174005.sra Read 699737 spots for SRR1174005.sra Written 699737 spots for SRR1174005.sra Read 699737 spots for SRR1174005.sra Written 699737 spots for SRR1174005.sra Read 699737 spots for SRR1174005.sra Written 699737 spots for SRR1174005.sra Read 699737 spots for SRR1174005.sra Written 699737 spots for SRR1174005.sra Read 699737 spots for SRR1174005.sra Written 699737 spots for SRR1174005.sra Read 699737 spots for SRR1174005.sra Written 699737 spots for SRR1174005.sra Read 699737 spots for SRR1174005.sra Written 699737 spots for SRR1174005.sra Read 699737 spots for SRR1174005.sra Written 699737 spots for SRR1174005.sra Read 699737 spots for SRR1174005.sra Written 699737 spots for SRR1174005.sra Read 699737 spots for SRR1174005.sra Written 699737 spots for SRR1174005.sra Read 699737 spots for SRR1174005.sra Written 699737 spots for SRR1174005.sra Read 699737 spots for SRR1174005.sra Written 699737 spots for SRR1174005.sra Read 699737 spots for SRR1174005.sra Written 699737 spots for SRR1174005.sra Read 699737 spots for SRR1174005.sra Written 699737 spots for SRR1174005.sra Read 699737 spots for SRR1174005.sra Written 699737 spots for SRR1174005.sra Read 699737 spots for SRR1174005.sra Written 699737 spots for SRR1174005.sra Read 699737 spots for SRR1174005.sra Written 699737 spots for SRR1174005.sra Read 699742 spots for SRR1174005.sra Written 699742 spots for SRR1174005.sra Read 699737 spots for SRR1174005.sra Written 699737 spots for SRR1174005.sra SRR ids: ['SRR1174005.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_427fl7qr SRR1174005.sra spots: 13994745 blocks: [[1, 699737], [699738, 1399474], [1399475, 2099211], [2099212, 2798948], [2798949, 3498685], [3498686, 4198422], [4198423, 4898159], [4898160, 5597896], [5597897, 6297633], [6297634, 6997370], [6997371, 7697107], [7697108, 8396844], [8396845, 9096581], [9096582, 9796318], [9796319, 10496055], [10496056, 11195792], [11195793, 11895529], [11895530, 12595266], [12595267, 13295003], [13295004, 13994745]] SRR1174005 file size 1953966 SRR1174005 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 SRR1174005 SRR1174005_1.fastq Input file: SRR1174005_1.fastq trimmed: SRR1174005-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 14:32:21 2024 >> started Mon Dec 9 14:32:31 2024 >> done (10.767s) 13994745 reads processed; of these: 38415 ( 0.27%) short reads filtered out after trimming by size control 17814 ( 0.13%) empty reads filtered out after trimming by size control 13938516 (99.60%) reads available; of these: 1205764 ( 8.65%) trimmed reads available after processing 12732752 (91.35%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 5467 0.04% 19 6797 0.05% 20 8050 0.06% 21 9070 0.07% 22 11624 0.08% 23 15160 0.11% 24 17755 0.13% 25 19488 0.14% 26 33244 0.24% 27 58221 0.42% 28 45157 0.32% 29 40886 0.29% 30 33518 0.24% 31 27216 0.20% 32 22822 0.16% 33 23930 0.17% 34 24964 0.18% 35 30288 0.22% 36 37472 0.27% 37 47778 0.34% 38 67133 0.48% 39 99551 0.71% 40 186033 1.33% 41 334140 2.40% 42 12732752 91.35% 13938516 reads passed initial QC criterion=sequence-density sequence-density=86.15 sequence-density-rank=1 fanout-score=34.63 fanout-score-rank=1 prefix-density=89.67 prefix-fanout=33.3 sequence=ATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA criterion=fanout-score sequence-density=86.15 sequence-density-rank=1 fanout-score=34.63 fanout-score-rank=1 prefix-density=89.67 prefix-fanout=33.3 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 SRR1174005 - Input file: STDIN trimmed: SRR1174005-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 14:33:48 2024 >> started Mon Dec 9 14:34:02 2024 >> done (13.468s) 13618090 reads processed; of these: 4180202 (30.70%) short reads filtered out after trimming by size control 219768 ( 1.61%) empty reads filtered out after trimming by size control 9218120 (67.69%) reads available; of these: 8935732 (96.94%) trimmed reads available after processing 282388 ( 3.06%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 379955 4.12% 19 538609 5.84% 20 597421 6.48% 21 697251 7.56% 22 358093 3.88% 23 654346 7.10% 24 3518261 38.17% 25 355209 3.85% 26 224840 2.44% 27 204203 2.22% 28 181822 1.97% 29 218633 2.37% 30 240268 2.61% 31 235340 2.55% 32 202822 2.20% 33 175457 1.90% 34 98183 1.07% 35 66610 0.72% 36 36382 0.39% 37 19675 0.21% 38 12285 0.13% 39 10031 0.11% 40 4050 0.04% 41 5597 0.06% 42 182777 1.98% criterion=sequence-density sequence-density=1.42 sequence-density-rank=1 fanout-score=1.09 fanout-score-rank=8 prefix-density=0.15 prefix-fanout=1.1 sequence=GCGTCTGTAGTCCAACGGTTAGGATAATTGCCTTCCAAGCA criterion=fanout-score sequence-density=0.83 sequence-density-rank=4 fanout-score=28.00 fanout-score-rank=1 prefix-density=1.10 prefix-fanout=21.1 sequence=TCGTATGCCGTCTTCTGCTTGAAAAA Started job on | Dec 09 14:35:00 Started mapping on | Dec 09 14:35:01 Finished on | Dec 09 14:35:34 Mapping speed, Million of reads per hour | 1040.57 Number of input reads | 9538546 Average input read length | 25 UNIQUE READS: Uniquely mapped reads number | 3599999 Uniquely mapped reads % | 37.74% Average mapped length | 23.77 Number of splices: Total | 32277 Number of splices: Annotated (sjdb) | 7315 Number of splices: GT/AG | 29548 Number of splices: GC/AG | 1351 Number of splices: AT/AC | 18 Number of splices: Non-canonical | 1360 Mismatch rate per base, % | 0.16% Deletion rate per base | 0.00% Deletion average length | 1.18 Insertion rate per base | 0.00% Insertion average length | 1.02 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 2868685 % of reads mapped to multiple loci | 30.07% Number of reads mapped to too many loci | 2363671 % of reads mapped to too many loci | 24.78% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 5.76% % of reads unmapped: other | 1.65% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 3069862 3069862 3069862 N_multimapping 2868685 2868685 2868685 N_noFeature 2931359 3169703 3353242 N_ambiguous 15583 6246 1232 UnstrandedReadsAssigned:653057 PositiveStrandReadsAssigned:424050 NegativeStrandReadsAssigned:245525 Dataset is classified unstranded MeadianReadLen=24 20thPercentileLength=21 echo kmer=19 SRR1174005 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: SRR1174005-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 9,538,546 reads, 2,514,463 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,154 rounds 52973 SRR1174005.ke.tsv 35125 SRR1174005.se.tsv 88098 total ==> SRR1174005.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 1.43551 0.291031 PNS24247 1044 945 0 0 PNS24249 1928 1829 0 0 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 2.56449 0.317178 PNS24243 293 194 0 0 KQK14069 1603 1504 31.2893 3.53024 KQK14071 474 375 0 0 ==> SRR1174005.se.tsv <== BRADI_1g14170v3 40 BRADI_1g53295v3 5 BRADI_1g59795v3 2 BRADI_1g07683v3 0 BRADI_1g00485v3 1 BRADI_1g20270v3 2 BRADI_1g74790v3 70 BRADI_1g09890v3 3 BRADI_1g77505v3 1 BRADI_1g48960v3 0 SRR1174005 completed mapping pipeline successfully