Starting /dee2/code/volunteer_pipeline.sh SRR1033814 current disk space = 1548438093824 free memory = 1599704616 SRR1033814 SRAfilesize 35fc26a946454a2889e014c554709804 SRR1033814.sra SRR1033814.sra file validated SRR1033814 is single end SRR1033814 is conventional basespace SRR1033814 read1 length is 46 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR1033814_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 49 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.82625 33.0 33.0 33.0 31.0 33.0 2 31.37875 33.0 31.0 33.0 28.0 34.0 3 29.839 32.0 29.0 33.0 23.0 33.0 4 29.66425 31.0 28.0 33.0 23.0 33.0 5 29.437 31.0 28.0 33.0 23.0 33.0 6 29.6645 31.0 28.0 33.0 24.0 33.0 7 28.09725 30.0 26.0 32.0 20.0 33.0 8 28.33775 30.0 26.0 32.0 20.0 33.0 9 28.89275 31.0 27.0 32.0 22.0 33.0 10 28.17825 30.0 26.0 32.0 21.0 33.0 11 29.8145 31.0 29.0 33.0 24.0 33.0 12 26.4385 29.0 23.0 31.0 17.0 33.0 13 23.24125 25.0 18.0 30.0 11.0 32.0 14 24.47525 26.0 20.0 30.0 14.0 32.0 15 25.50525 27.0 21.0 31.0 16.0 33.0 16 25.7125 27.0 22.0 31.0 17.0 32.0 17 25.017 27.0 21.0 30.0 16.0 32.0 18 24.91825 27.0 21.0 30.0 16.0 32.0 19 28.357 30.0 26.0 32.0 22.0 33.0 20 28.1515 30.0 27.0 32.0 21.0 33.0 21 27.77875 30.0 26.0 32.0 20.0 33.0 22 27.4725 30.0 25.0 32.0 20.0 33.0 23 26.80925 29.0 24.0 31.0 19.0 33.0 24 26.719 29.0 24.0 32.0 19.0 33.0 25 27.178 30.0 25.0 32.0 19.0 33.0 26 27.2095 29.0 25.0 32.0 19.0 33.0 27 25.635 28.0 22.0 31.0 17.0 32.0 28 24.50375 26.0 21.0 30.0 15.0 32.0 29 25.08925 27.0 22.0 30.0 15.0 32.0 30 26.0835 28.0 24.0 31.0 17.0 32.0 31 25.05425 27.0 22.0 31.0 15.0 32.0 32 24.33275 26.0 21.0 30.0 15.0 32.0 33 25.13 27.0 22.0 31.0 15.0 32.0 34 24.694 27.0 22.0 30.0 14.0 32.0 35 24.09375 26.0 21.0 30.0 12.0 32.0 36 24.782 28.0 22.0 31.0 11.0 32.0 37 24.71675 28.0 22.0 31.0 8.0 32.0 38 23.93725 27.0 20.0 31.0 4.0 33.0 39 22.668 25.0 19.0 29.0 4.0 31.0 40 22.82425 26.0 20.0 30.0 4.0 32.0 41 20.55175 23.0 12.0 29.0 4.0 32.0 42 18.6515 20.0 11.0 26.0 4.0 30.0 43 19.07075 22.0 12.0 27.0 4.0 30.0 44 20.281 24.0 4.0 30.0 4.0 32.0 45 16.40225 21.0 4.0 28.0 4.0 31.0 46 12.9855 4.0 4.0 22.0 4.0 27.0 >>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 1 43 0.0 1 44 0.0 1 45 0.0 1 46 0.0 >>END_MODULE >>Per sequence quality scores warn #Quality Count 4 16.0 5 3.0 6 3.0 7 6.0 8 8.0 9 6.0 10 15.0 11 11.0 12 19.0 13 34.0 14 40.0 15 44.0 16 45.0 17 37.0 18 58.0 19 73.0 20 120.0 21 133.0 22 201.0 23 252.0 24 327.0 25 395.0 26 428.0 27 446.0 28 439.0 29 370.0 30 256.0 31 162.0 32 52.0 33 1.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 21.286876907426247 25.661241098677518 39.6998982706002 13.351983723296032 2 38.284571142785694 23.40585146286572 17.22930732683171 21.080270067516878 3 36.8 31.05 13.725000000000001 18.425 4 27.63881940970485 26.113056528264135 13.081540770385192 33.16658329164582 5 21.61621215911934 36.50237678258694 21.66624968726545 20.21516137102827 6 33.26663331665833 20.96048024012006 26.43821910955478 19.334667333666832 7 32.7663831915958 32.816408204102046 18.05902951475738 16.358179089544773 8 26.375 32.9 19.55 21.175 9 34.583645911477866 21.955488872218055 28.057014253563388 15.403850962740684 10 36.36818409204602 28.83941970985493 14.057028514257128 20.735367683841922 11 35.608902225556385 22.680670167541887 18.829707426856714 22.88072018004501 12 28.1351689612015 37.64705882352941 16.670838548185234 17.546933667083856 13 43.824999999999996 22.525000000000002 15.825 17.825 14 26.275 34.125 26.35 13.25 15 36.25906476619154 23.43085771442861 25.481370342585645 14.828707176794198 16 27.077077077077078 35.26026026026026 14.014014014014014 23.64864864864865 17 43.75781836377283 24.31823867900926 18.01351013259945 13.910432824618463 18 39.06406406406406 16.616616616616618 14.13913913913914 30.180180180180184 19 34.058514628657164 31.08277069267317 15.803950987746937 19.05476369092273 20 21.224999999999998 29.225 22.175 27.375 21 19.179794948737182 22.18054513628407 29.882470617654416 28.75718929732433 22 20.255063765941486 13.42835708927232 35.13378344586147 31.182795698924732 23 29.057264316079017 20.4801200300075 18.97974493623406 31.48287071767942 24 28.907226806701676 14.128532133033259 40.685171292823206 16.27906976744186 25 9.857393044783588 18.8141105829372 57.46810107580686 13.860395296472355 26 14.135601701275958 21.441080810607957 30.24768576432324 34.17563172379284 27 49.48711533650238 7.180385288966725 33.55016262196647 9.782336752564422 28 26.088044022011005 9.37968984492246 40.04502251125563 24.487243621810904 29 13.75687843921961 32.191095547773884 15.35767883941971 38.6943471735868 30 27.591387080620933 5.032548823234852 39.65948923385078 27.71657486229344 31 52.51816587321473 3.9589075419694315 24.154347281383114 19.368579303432725 32 11.773547094188377 1.3276553106212425 28.45691382765531 58.441883767535074 33 13.219829744616925 0.17526289434151227 28.542814221331998 58.06209313970957 34 33.734335839599 0.12531328320802004 47.24310776942356 18.897243107769423 35 6.019563581640331 0.17557060446450964 62.25232004013043 31.552545773764734 36 7.373965387509405 0.1254075746175069 38.55028843742162 53.95033860045147 37 18.478533768516193 0.07532011046949535 66.25659050966608 15.18955561134823 38 19.87452948557089 0.0752823086574655 50.012547051442915 30.037641154328732 39 7.7830780818478535 0.2761737383881496 39.24177755460708 52.69897062515692 40 12.484300427028385 1.1303692539562924 74.6043707611153 11.780959557900026 41 46.87735139202408 4.464509656383245 35.51542513167795 13.142713819914723 42 24.140526976160604 21.530740276035132 21.25470514429109 33.07402760351317 43 10.737581535373808 41.344706472654295 42.6743602609132 5.243351731058706 44 9.06813627254509 48.07114228456914 38.80260521042084 4.05811623246493 45 32.16432865731463 57.08917835671342 9.268537074148297 1.4779559118236472 46 14.43997990959317 57.207433450527375 27.096936212958312 1.255650426921145 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 1.0 1 0.5 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 2.0 30 4.0 31 4.0 32 2.5 33 1.0 34 2.5 35 4.0 36 10.5 37 17.0 38 34.0 39 51.0 40 106.0 41 161.0 42 230.5 43 300.0 44 300.0 45 608.0 46 916.0 47 710.0 48 504.0 49 529.0 50 554.0 51 677.0 52 800.0 53 551.5 54 303.0 55 249.5 56 196.0 57 196.0 58 144.0 59 92.0 60 75.5 61 59.0 62 42.0 63 25.0 64 16.0 65 7.0 66 5.0 67 3.0 68 2.0 69 1.0 70 1.0 71 1.0 72 1.0 73 0.5 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 1.7000000000000002 2 0.025 3 0.0 4 0.05 5 0.075 6 0.05 7 0.05 8 0.0 9 0.025 10 0.05 11 0.025 12 0.125 13 0.0 14 0.0 15 0.025 16 0.1 17 0.075 18 0.1 19 0.025 20 0.0 21 0.025 22 0.025 23 0.025 24 0.025 25 0.075 26 0.075 27 0.075 28 0.05 29 0.05 30 0.15 31 0.22499999999999998 32 0.2 33 0.15 34 0.25 35 0.325 36 0.325 37 0.42500000000000004 38 0.375 39 0.42500000000000004 40 0.475 41 0.325 42 0.375 43 0.35000000000000003 44 0.2 45 0.2 46 0.44999999999999996 >>END_MODULE >>Sequence Length Distribution pass #Length Count 46 4000.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 67.35 #Duplication Level Percentage of deduplicated Percentage of total 1 93.61544172234595 63.05 2 2.858203414996288 3.85 3 1.1135857461024499 2.25 4 0.6681514476614699 1.7999999999999998 5 0.33407572383073497 1.125 6 0.4083147735708983 1.6500000000000001 7 0.22271714922048996 1.05 8 0.22271714922048996 1.2 9 0.07423904974016332 0.44999999999999996 >10 0.3711952487008166 4.375 >50 0.0 0.0 >100 0.11135857461024498 19.2 >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 TGACAGAAGAGAGTGAGCACTCGTATGCCGTCTTCTGCTTGAAAAA 420 10.5 TruSeq Adapter, Index 19 (95% over 24bp) TCGCTTGGTGCAGATCGGGACTCGTATGCCGTCTTCTGCTTGAAAA 240 6.0 TruSeq Adapter, Index 15 (95% over 24bp) TTGACAGAAGAGAGTGAGCACTCGTATGCCGTCTTCTGCTTGAAAA 108 2.7 TruSeq Adapter, Index 13 (95% over 24bp) TGGAAGGGGCATGCAGAGGAGTCGTATGCCGTCTTCTGCTTGAAAA 33 0.8250000000000001 Illumina Single End Adapter 2 (95% over 22bp) GACACGACTCTCGGCAACGGATATCTTCGTATGCCGTCTTCTGCTT 25 0.625 Illumina Single End Adapter 1 (95% over 21bp) CACGACTCTCGGCAACGGATATCTTCGTATGCCGTCTTCTGCTTGT 24 0.6 Illumina Single End Adapter 1 (95% over 22bp) CACGACTCTCGGCAACGGATATCTCTCGTATGCCGTCTTCTGCTTT 22 0.5499999999999999 Illumina PCR Primer Index 6 (96% over 25bp) AGAATCTTGATGATGCTGCATTCGTATGCCGTCTTCTGCTTGAAAA 14 0.35000000000000003 Illumina Single End Adapter 2 (95% over 22bp) GGGGATGTAGCTCAGATGGTATCGTATGCCGTCTTCTGCTTGAAAA 14 0.35000000000000003 TruSeq Adapter, Index 14 (95% over 24bp) CACGACTCTCGGCAACGGATATCTTCGTATGCCGTCTTCTGCTTGG 12 0.3 Illumina Single End Adapter 1 (95% over 22bp) NGACAGAAGAGAGTGAGCACTCGTATGCCGTCTTCTGCTTGAAAAA 11 0.27499999999999997 TruSeq Adapter, Index 19 (95% over 24bp) TGAAGCTGCCAGCATGATCTGATCGTATGCCGTCTTCTGCTTGAAA 10 0.25 Illumina Single End Adapter 1 (95% over 23bp) TGACAGAAGAGATTGAGCACTCGTATGCCGTCTTCTGCTTGAAAAA 10 0.25 TruSeq Adapter, Index 13 (95% over 24bp) GGGGATGTAGCTCAGATGGTTCGTATGCCGTCTTCTGCTTGAAAAA 9 0.22499999999999998 Illumina Single End Adapter 2 (95% over 23bp) GGGGATGTAGCTCAGATGGTAGTCGTATGCCGTCTTCTGCTTGAAA 9 0.22499999999999998 Illumina Single End Adapter 2 (95% over 22bp) GCGTCTGTAGTCCAACGGTTTCGTATGCCGTCTTCTGCTTGAAAAA 8 0.2 TruSeq Adapter, Index 14 (95% over 24bp) CTGACAGAAGAGAGTGAGCACTCGTATGCCGTCTTCTGCTTGAAAA 8 0.2 TruSeq Adapter, Index 13 (95% over 24bp) GGGGATGTAGCTCAGATGGTAGATCGTATGCCGTCTTCTGCTTGAA 8 0.2 Illumina Single End Adapter 2 (95% over 24bp) TGACAGAAGAGCGTGAGCACTCGTATGCCGTCTTCTGCTTGAAAAA 8 0.2 TruSeq Adapter, Index 13 (95% over 24bp) GACACGACTCTCGGCAACGGATTCGTATGCCGTCTTCTGCTTGAAA 8 0.2 Illumina Single End Adapter 2 (95% over 22bp) CCACGTCGCACGGATTCGTTCGTATGCCGTCTTCTGCTTGAAAAAA 8 0.2 Illumina Single End Adapter 2 (95% over 23bp) GACACGACTCTCGGCAACGGATATCTCGTATGCCGTCTTCTGCTTT 7 0.17500000000000002 RNA PCR Primer, Index 25 (96% over 29bp) TCGCTTGGTGCATATCGGGACTCGTATGCCGTCTTCTGCTTGAAAA 7 0.17500000000000002 TruSeq Adapter, Index 21 (96% over 25bp) TCGTGACCTGTATGGGCCACCATCGTATGCCGTCTTCTGCTTGAAA 7 0.17500000000000002 Illumina Single End Adapter 2 (95% over 22bp) GACACGACTCTCGGCAACGGATATTCGTATGCCGTCTTCTGCTTGT 7 0.17500000000000002 Illumina Single End Adapter 1 (95% over 22bp) GGGGATGTAGCTCAGATGGTAGAGTCGTATGCCGTCTTCTGCTTGG 7 0.17500000000000002 Illumina Single End Adapter 2 (95% over 22bp) CAAGTCCCGGCGACGGAACCATCGTATGCCGTCTTCTGCTTGAAAA 7 0.17500000000000002 Illumina Single End Adapter 1 (95% over 22bp) GGTGAACCTGCGGAAGGATCATTGTCGTATGCCGTCTTCTGCTTGT 6 0.15 TruSeq Adapter, Index 20 (95% over 24bp) CACGACTCTCGGCAACGGATATTCGTATGCCGTCTTCTGCTTGAAA 6 0.15 Illumina Single End Adapter 1 (95% over 22bp) GACACGACTCTCGGCAACGGATATCGTATGCCGTCTTCTGCTTGAA 6 0.15 Illumina PCR Primer Index 5 (96% over 25bp) TCGGACCAGGCTTCATTCCCCTCGTATGCCGTCTTCTGCTTGAAAA 6 0.15 TruSeq Adapter, Index 16 (96% over 25bp) TCGCTTGGTGCAGATCGGGACTCGTATGCCGTCTTCTGCTTTAAAA 6 0.15 TruSeq Adapter, Index 15 (95% over 23bp) CAGGTCCCGGCGACGGAACCATCGTATGCCGTCTTCTGCTTGAAAA 6 0.15 Illumina Single End Adapter 1 (95% over 22bp) GACACGACTCTCGGCAACGGATATTCGTATGCCGTCTTCTGCTTGG 6 0.15 Illumina Single End Adapter 1 (95% over 22bp) NCGCTTGGTGCAGATCGGGACTCGTATGCCGTCTTCTGCTTGAAAA 6 0.15 TruSeq Adapter, Index 15 (95% over 24bp) ACGACTCTCGGCAACGGATATCTTCGTATGCCGTCTTCTGCTTGAA 6 0.15 Illumina Single End Adapter 1 (95% over 22bp) TAACGAACGAACGATTTGAACTCGTATGCCGTCTTCTGCTTGAAAA 6 0.15 Illumina PCR Primer Index 5 (96% over 26bp) TTCGTGACCTGTATGGGCCACCATCGTATGCCGTCTTCTGCTTGAA 6 0.15 Illumina Single End Adapter 2 (95% over 22bp) TTCTACAGTCCGACGATCTCGTATGCCGTCTTCTGCTTGAAAAAAA 5 0.125 RNA PCR Primer, Index 47 (96% over 29bp) AGTTCTACAGTCCGACGATCTCGTATGCCGTCTTCTGCTTGAAAAA 5 0.125 Illumina PCR Primer Index 1 (96% over 28bp) ACGAACGAACGATTTGAACTCGTATGCCGTCTTCTGCTTGAAAAAA 5 0.125 Illumina Single End Adapter 2 (96% over 25bp) GGGGATGTAGCTCAAATGGTAGATCGTATGCCGTCTTCTGCTTGAA 5 0.125 Illumina Single End Adapter 2 (95% over 24bp) GGGGATGTAGCTCAGATGGTCGTATGCCGTCTTCTGCTTGAAAAAA 5 0.125 Illumina Single End Adapter 2 (95% over 23bp) GGGGATGTAGCTCAAATGGTATCGTATGCCGTCTTCTGCTTGAAAA 5 0.125 TruSeq Adapter, Index 14 (95% over 24bp) TCCAGCCCCACGTCGCACGGATTCGTTCGTATGCCGTCTTCTGCTT 5 0.125 Illumina Single End Adapter 2 (95% over 22bp) TCAGGTCCCGGCGACGGAACCATCGTATGCCGTCTTCTGCTTGAAA 5 0.125 Illumina Single End Adapter 1 (95% over 22bp) CAGCCCCACGTCGCACGGATTCGTTCGTATGCCGTCTTCTGCTTGT 5 0.125 Illumina Single End Adapter 2 (95% over 23bp) >>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 CAGATCG 30 3.0468964E-6 41.18182 11 AGATCGG 30 3.0468964E-6 41.18182 12 GTGCAGA 30 3.3417637E-6 40.653847 8 TAGCTCA 20 0.0010231554 40.653847 8 GCAGATC 30 3.3417637E-6 40.653847 10 TGGTGCA 30 3.3417637E-6 40.653847 6 TGCAGAT 30 3.3417637E-6 40.653847 9 GGTGCAG 30 3.3417637E-6 40.653847 7 GATCGGG 30 3.660598E-6 40.13924 13 TCGCTTG 30 3.660598E-6 40.13924 1 ATCGGGA 30 3.660598E-6 40.13924 14 CGGGACT 30 3.660598E-6 40.13924 16 TTGACAG 20 0.0010911418 40.13924 1 GGGACTC 30 3.660598E-6 40.13924 17 TCGGGAC 30 3.660598E-6 40.13924 15 CGCTTGG 30 4.0049854E-6 39.6375 2 CTTGGTG 30 4.0049854E-6 39.6375 4 TGCTTGG 40 1.3387762E-8 39.6375 40 GCTTGGT 30 4.0049854E-6 39.6375 3 TTGGTGC 30 4.0049854E-6 39.6375 5 >>END_MODULE Read 613400 spots for SRR1033814.sra Written 613400 spots for SRR1033814.sra Read 613400 spots for SRR1033814.sra Written 613400 spots for SRR1033814.sra Read 613400 spots for SRR1033814.sra Written 613400 spots for SRR1033814.sra Read 613400 spots for SRR1033814.sra Written 613400 spots for SRR1033814.sra Read 613400 spots for SRR1033814.sra Written 613400 spots for SRR1033814.sra Read 613400 spots for SRR1033814.sra Written 613400 spots for SRR1033814.sra Read 613400 spots for SRR1033814.sra Written 613400 spots for SRR1033814.sra Read 613400 spots for SRR1033814.sra Written 613400 spots for SRR1033814.sra Read 613400 spots for SRR1033814.sra Written 613400 spots for SRR1033814.sra Read 613400 spots for SRR1033814.sra Written 613400 spots for SRR1033814.sra Read 613400 spots for SRR1033814.sra Written 613400 spots for SRR1033814.sra Read 613400 spots for SRR1033814.sra Written 613400 spots for SRR1033814.sra Read 613400 spots for SRR1033814.sra Written 613400 spots for SRR1033814.sra Read 613400 spots for SRR1033814.sra Written 613400 spots for SRR1033814.sra Read 613400 spots for SRR1033814.sra Written 613400 spots for SRR1033814.sra Read 613406 spots for SRR1033814.sra Written 613406 spots for SRR1033814.sra Read 613400 spots for SRR1033814.sra Written 613400 spots for SRR1033814.sra Read 613400 spots for SRR1033814.sra Written 613400 spots for SRR1033814.sra Read 613400 spots for SRR1033814.sra Written 613400 spots for SRR1033814.sra Read 613400 spots for SRR1033814.sra Written 613400 spots for SRR1033814.sra SRR ids: ['SRR1033814.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_326c7d1r SRR1033814.sra spots: 12268006 blocks: [[1, 613400], [613401, 1226800], [1226801, 1840200], [1840201, 2453600], [2453601, 3067000], [3067001, 3680400], [3680401, 4293800], [4293801, 4907200], [4907201, 5520600], [5520601, 6134000], [6134001, 6747400], [6747401, 7360800], [7360801, 7974200], [7974201, 8587600], [8587601, 9201000], [9201001, 9814400], [9814401, 10427800], [10427801, 11041200], [11041201, 11654600], [11654601, 12268006]] SRR1033814 file size 1831369 SRR1033814 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 SRR1033814 SRR1033814_1.fastq Input file: SRR1033814_1.fastq trimmed: SRR1033814-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 Sat Dec 7 01:09:39 2024 >> started Sat Dec 7 01:09:47 2024 >> done (8.832s) 12268006 reads processed; of these: 100218 ( 0.82%) short reads filtered out after trimming by size control 23125 ( 0.19%) empty reads filtered out after trimming by size control 12144663 (98.99%) reads available; of these: 5221751 (43.00%) trimmed reads available after processing 6922912 (57.00%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 25813 0.21% 19 37655 0.31% 20 50341 0.41% 21 51086 0.42% 22 47009 0.39% 23 40673 0.33% 24 52304 0.43% 25 39930 0.33% 26 46810 0.39% 27 51351 0.42% 28 36899 0.30% 29 33281 0.27% 30 46325 0.38% 31 65194 0.54% 32 38275 0.32% 33 52177 0.43% 34 52920 0.44% 35 54053 0.45% 36 85560 0.70% 37 156629 1.29% 38 191005 1.57% 39 152731 1.26% 40 296235 2.44% 41 328379 2.70% 42 356455 2.94% 43 586987 4.83% 44 1327850 10.93% 45 917824 7.56% 46 6922912 57.00% 12144663 reads passed initial QC criterion=sequence-density sequence-density=86.50 sequence-density-rank=1 fanout-score=22.05 fanout-score-rank=6 prefix-density=89.86 prefix-fanout=21.2 sequence=TCGTATGCCGTCTTCTGCTTGAAAAACA criterion=fanout-score sequence-density=1.35 sequence-density-rank=8 fanout-score=61.31 fanout-score-rank=1 prefix-density=82.04 prefix-fanout=1.0 sequence=TGCCGTCTTCTTCTTG 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 TCGTATGCCGTCTTCTGCTTGAAAAACA -o SRR1033814 - Input file: STDIN trimmed: SRR1033814-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TCGTATGCCGTCTTCTGCTTGAAAAACA -- 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 Sat Dec 7 01:10:01 2024 >> started Sat Dec 7 01:10:15 2024 >> done (14.406s) 11865475 reads processed; of these: 24011 ( 0.20%) short reads filtered out after trimming by size control 3456 ( 0.03%) empty reads filtered out after trimming by size control 11838008 (99.77%) reads available; of these: 11441371 (96.65%) trimmed reads available after processing 396637 ( 3.35%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 159254 1.35% 19 408500 3.45% 20 1970990 16.65% 21 2412598 20.38% 22 804584 6.80% 23 1135193 9.59% 24 3630022 30.66% 25 669371 5.65% 26 465985 3.94% 27 117106 0.99% 28 10092 0.09% 29 2907 0.02% 30 851 0.01% 31 870 0.01% 32 365 0.00% 33 406 0.00% 34 370 0.00% 35 418 0.00% 36 476 0.00% 37 696 0.01% 38 766 0.01% 39 620 0.01% 40 825 0.01% 41 793 0.01% 42 568 0.00% 43 794 0.01% 44 1405 0.01% 45 1087 0.01% 46 40096 0.34% criterion=sequence-density sequence-density=7.75 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=7 prefix-density=0.00 prefix-fanout=1.0 sequence=TCGCTTGGTGCAGATCGGGACTCG criterion=fanout-score sequence-density=0.53 sequence-density-rank=7 fanout-score=3.95 fanout-score-rank=1 prefix-density=2.07 prefix-fanout=1.0 sequence=GATGTAGCTCAAATGGTAGAGC Started job on | Dec 07 01:10:30 Started mapping on | Dec 07 01:10:30 Finished on | Dec 07 01:11:07 Mapping speed, Million of reads per hour | 1178.97 Number of input reads | 12117196 Average input read length | 22 UNIQUE READS: Uniquely mapped reads number | 4181035 Uniquely mapped reads % | 34.50% Average mapped length | 22.59 Number of splices: Total | 75511 Number of splices: Annotated (sjdb) | 8467 Number of splices: GT/AG | 74540 Number of splices: GC/AG | 804 Number of splices: AT/AC | 6 Number of splices: Non-canonical | 161 Mismatch rate per base, % | 0.36% Deletion rate per base | 0.00% Deletion average length | 1.09 Insertion rate per base | 0.00% Insertion average length | 1.00 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 3989479 % of reads mapped to multiple loci | 32.92% Number of reads mapped to too many loci | 3273081 % of reads mapped to too many loci | 27.01% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.57% % of reads unmapped: other | 1.99% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 3946682 3946682 3946682 N_multimapping 3989479 3989479 3989479 N_noFeature 2593764 2764536 4000168 N_ambiguous 14821 3753 1419 UnstrandedReadsAssigned:1572450 PositiveStrandReadsAssigned:1412746 NegativeStrandReadsAssigned:179448 Dataset is classified positive stranded MeadianReadLen=23 20thPercentileLength=20 echo kmer=19 SRR1033814 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: SRR1033814-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 12,117,196 reads, 3,581,685 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 992 rounds 52973 SRR1033814.ke.tsv 35125 SRR1033814.se.tsv 88098 total ==> SRR1033814.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 2.13262 0.0468696 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 2.9437 0.0862443 PNS24243 293 194 0 0 KQK14069 1603 1504 66.8792 1.78746 KQK14071 474 375 16.7519 1.79566 ==> SRR1033814.se.tsv <== BRADI_1g14170v3 88 BRADI_1g53295v3 2 BRADI_1g59795v3 2 BRADI_1g07683v3 1 BRADI_1g00485v3 1 BRADI_1g20270v3 9 BRADI_1g74790v3 27 BRADI_1g09890v3 1 BRADI_1g77505v3 1 BRADI_1g48960v3 0 SRR1033814 completed mapping pipeline successfully