Starting /dee2/code/volunteer_pipeline.sh SRR1033811 current disk space = 1548079300608 free memory = 1601815816 SRR1033811 SRAfilesize 76285d77a51d1bffaa4addbf61430d21 SRR1033811.sra SRR1033811.sra file validated SRR1033811 is single end SRR1033811 is conventional basespace SRR1033811 read1 length is 36 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR1033811_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 36 %GC 52 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.7 33.0 33.0 33.0 32.0 33.0 2 31.99325 33.0 32.0 34.0 30.0 34.0 3 30.9205 32.0 30.0 33.0 26.0 33.0 4 30.41425 32.0 30.0 33.0 26.0 33.0 5 30.864 32.0 30.0 33.0 26.0 33.0 6 31.3895 33.0 31.0 33.0 28.0 34.0 7 30.91775 32.0 30.0 33.0 26.0 33.0 8 30.213 32.0 29.0 33.0 24.0 33.0 9 29.95325 32.0 29.0 33.0 23.0 33.0 10 29.19575 31.0 28.0 33.0 22.0 33.0 11 30.3895 32.0 30.0 33.0 25.0 33.0 12 30.8145 32.0 30.0 33.0 26.0 33.0 13 30.76225 32.0 30.0 33.0 26.0 34.0 14 29.861 32.0 29.0 33.0 24.0 33.0 15 29.704 32.0 29.0 33.0 23.0 33.0 16 28.0685 30.0 26.0 32.0 20.0 33.0 17 28.43525 30.0 27.0 33.0 21.0 33.0 18 28.653 31.0 27.0 33.0 21.0 33.0 19 28.20275 30.0 27.0 32.0 21.0 33.0 20 27.56375 30.0 26.0 32.0 19.0 33.0 21 28.37075 31.0 28.0 33.0 20.0 33.0 22 27.20525 30.0 26.0 32.0 17.0 33.0 23 25.59125 29.0 23.0 31.0 13.0 33.0 24 25.03075 28.0 22.0 31.0 10.0 33.0 25 23.88725 27.0 20.0 30.0 4.0 32.0 26 24.08625 27.0 21.0 30.0 4.0 32.0 27 21.92375 24.0 18.0 28.0 4.0 31.0 28 20.4765 22.0 16.0 27.0 4.0 30.0 29 22.35775 25.0 18.0 29.0 4.0 31.0 30 23.92875 28.0 21.0 31.0 4.0 32.0 31 22.449 26.0 18.0 30.0 4.0 32.0 32 21.47475 25.0 16.0 29.0 4.0 31.0 33 21.01925 25.0 14.0 29.0 4.0 31.0 34 20.4115 25.0 4.0 30.0 4.0 32.0 35 16.5505 19.0 4.0 27.0 4.0 30.0 36 14.13325 4.0 4.0 25.0 4.0 30.0 >>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 >>END_MODULE >>Per sequence quality scores pass #Quality Count 4 14.0 5 0.0 6 1.0 7 2.0 8 4.0 9 4.0 10 7.0 11 16.0 12 19.0 13 29.0 14 39.0 15 33.0 16 49.0 17 66.0 18 62.0 19 70.0 20 84.0 21 70.0 22 103.0 23 143.0 24 169.0 25 248.0 26 333.0 27 452.0 28 513.0 29 555.0 30 520.0 31 303.0 32 88.0 33 4.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 16.807151979565774 27.739463601532567 43.83141762452107 11.621966794380588 2 32.95795795795796 20.245245245245243 17.792792792792792 29.004004004004003 3 41.335333833458364 26.081520380095025 14.628657164291074 17.95448862215554 4 24.50612653163291 24.48112028007002 14.653663415853963 36.35908977244311 5 21.215911933950462 29.647235426569928 28.621466099574683 20.515386539904927 6 28.23911955977989 21.46073036518259 33.19159579789895 17.10855427713857 7 38.54427213606804 28.58929464732366 18.459229614807406 14.4072036018009 8 33.91695847923962 27.888944472236116 18.10905452726363 20.08504252126063 9 28.95 21.775 35.05 14.224999999999998 10 42.57128564282141 26.413206603301653 12.981490745372687 18.034017008504254 11 30.975 20.9 16.825000000000003 31.3 12 28.307076769192296 42.36059014753689 14.428607151787947 14.90372593148287 13 46.73505128846635 24.36827620715537 11.708781586189643 17.187890918188643 14 24.256064016004 39.90997749437359 21.48037009252313 14.353588397099276 15 31.765882941470736 21.360680340170084 32.54127063531766 14.33216608304152 16 24.15603900975244 29.107276819204802 14.47861965491373 32.25806451612903 17 46.93673418354589 23.15578894723681 17.27931982995749 12.628157039259817 18 43.425000000000004 17.125 14.475 24.975 19 38.213213213213216 25.2002002002002 18.41841841841842 18.16816816816817 20 19.23461730865433 36.418209104552275 19.50975487743872 24.83741870935468 21 20.40510127531883 18.904726181545385 26.78169542385596 33.908477119279816 22 17.45872936468234 14.157078539269635 43.39669834917459 24.987493746873437 23 25.137568784392194 20.260130065032516 18.384192096048025 36.21810905452726 24 34.550913184888664 13.184888666499875 37.55316487365524 14.711033274956216 25 11.555777888944473 13.906953476738368 60.630315157578785 13.906953476738368 26 12.887887887887889 26.75175175175175 23.423423423423422 36.93693693693694 27 44.269269269269266 5.8308308308308305 37.687687687687685 12.212212212212211 28 34.0 9.3 38.875 17.825 29 10.36036036036036 30.48048048048048 18.61861861861862 40.54054054054054 30 22.061030515257627 4.927463731865933 37.31865932966483 35.692846423211606 31 56.864216054013504 2.2755688922230557 23.380845211302827 17.479369842460617 32 10.8 0.625 35.725 52.849999999999994 33 12.106053026513257 0.3501750875437719 23.13656828414207 64.4072036018009 34 32.16608304152076 0.2001000500250125 52.10105052526263 15.532766383191596 35 9.60720540405304 0.2752064048036027 65.17388041030773 24.943707780835627 36 5.1538653990492875 0.2752064048036027 40.65549161871404 53.91543657743307 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 2.0 1 1.0 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 0.5 27 1.0 28 1.0 29 3.0 30 5.0 31 5.0 32 5.5 33 6.0 34 6.0 35 8.5 36 11.0 37 11.0 38 24.5 39 38.0 40 92.5 41 147.0 42 147.0 43 204.0 44 261.0 45 261.0 46 306.0 47 351.0 48 351.0 49 609.0 50 867.0 51 733.0 52 599.0 53 599.0 54 622.0 55 645.0 56 645.0 57 710.5 58 776.0 59 776.0 60 453.5 61 131.0 62 131.0 63 107.0 64 83.0 65 61.0 66 39.0 67 39.0 68 31.0 69 23.0 70 23.0 71 16.0 72 9.0 73 9.0 74 6.0 75 3.0 76 2.0 77 1.0 78 1.0 79 0.5 80 0.0 81 0.0 82 0.5 83 1.0 84 1.0 85 0.5 86 0.0 87 0.0 88 0.0 89 0.0 90 0.5 91 1.0 92 1.0 93 0.5 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 2.125 2 0.1 3 0.025 4 0.025 5 0.075 6 0.05 7 0.05 8 0.05 9 0.0 10 0.05 11 0.0 12 0.025 13 0.075 14 0.025 15 0.05 16 0.025 17 0.025 18 0.0 19 0.1 20 0.05 21 0.025 22 0.05 23 0.05 24 0.075 25 0.05 26 0.1 27 0.1 28 0.0 29 0.1 30 0.05 31 0.025 32 0.0 33 0.05 34 0.05 35 0.075 36 0.075 >>END_MODULE >>Sequence Length Distribution pass #Length Count 36 4000.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 64.25 #Duplication Level Percentage of deduplicated Percentage of total 1 93.61867704280155 60.150000000000006 2 3.151750972762646 4.05 3 1.0894941634241244 2.1 4 0.5058365758754864 1.3 5 0.2723735408560311 0.8750000000000001 6 0.1556420233463035 0.6 7 0.23346303501945526 1.05 8 0.2723735408560311 1.4000000000000001 9 0.11673151750972763 0.675 >10 0.42801556420233466 5.0 >50 0.07782101167315175 4.075 >100 0.07782101167315175 18.725 >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 TCGCTTGGTGCAGATCGGGACTCGTATGCCGTCTTC 472 11.799999999999999 No Hit TGACAGAAGAGAGTGAGCACTCGTATGCCGTCTTCT 277 6.925000000000001 No Hit TTGACAGAAGAGAGTGAGCACTCGTATGCCGTCTTC 97 2.4250000000000003 No Hit TCGCTTGGTGCAGATCGGGACTCGTATGCCGTCTTT 66 1.6500000000000001 No Hit TTCTACAGTCCGACGATCTCGTATGCCGTCTTCTGC 39 0.975 RNA PCR Primer, Index 47 (96% over 26bp) CACGACTCTCGGCAACGGATATCTTCGTATGCCGTC 31 0.775 No Hit AGTTCTACAGTCCGACGATCTCGTATGCCGTCTTCT 22 0.5499999999999999 Illumina PCR Primer Index 1 (95% over 23bp) GACACGACTCTCGGCAACGGATATTCGTATGCCGTC 20 0.5 No Hit TCTACAGTCCGACGATCTCGTATGCCGTCTTCTGCT 20 0.5 RNA PCR Primer, Index 47 (96% over 27bp) AGAATCTTGATGATGCTGCATTCGTATGCCGTCTTC 13 0.325 No Hit TTGACAGAAGAGAGTGAGCACTCGTATGCCGTCTTT 12 0.3 No Hit TGAAGCTGCCAGCATGATCTGATCGTATGCCGTCTT 11 0.27499999999999997 No Hit CACGACTCTCGGCAACGGATATCTCTCGTATGCCGT 11 0.27499999999999997 No Hit NCGCTTGGTGCAGATCGGGACTCGTATGCCGTCTTC 11 0.27499999999999997 No Hit GGTAGTTCGACCGCGGAATTTTCGTATGCCGTCTTC 10 0.25 No Hit CACGACTCTCGGCAACGGATATCTCGTATGCCGTCT 9 0.22499999999999998 No Hit GACACGACTCTCGGCAACGGATATCTTCGTATGCCG 9 0.22499999999999998 No Hit NGACAGAAGAGAGTGAGCACTCGTATGCCGTCTTCT 9 0.22499999999999998 No Hit ACACGACTCTCGGCAACGGATATCTTCGTATGCCGT 8 0.2 No Hit TAGTTCTACAGTCCGACGATCTCGTATGCCGTCTTC 8 0.2 RNA PCR Primer, Index 47 (95% over 23bp) TCGCTTGGTGCAGATCGGGACTCGTATTCCGTCTTC 8 0.2 No Hit ACGACTCTCGGCAACGGATATCTTCGTATGCCGTCT 8 0.2 No Hit CACGACTCTCGGCAACGGATATTCGTATGCCGTCTT 8 0.2 No Hit CACGTCGCACGGATTCGTTCGTATGCCGTCTTCTGC 8 0.2 No Hit GGGGATGTAGCTCAGATGGTAGAGTCGTATGCCGTC 8 0.2 No Hit TGACAGAAGAGAGTGAGCACTCGTATGCCGTCTTTT 7 0.17500000000000002 No Hit GGGGATGTAGCTCAGATGGTTCGTATGCCGTCTTCT 7 0.17500000000000002 No Hit GACACGACTCTCGGCAACGGATATCGTATGCCGTCT 7 0.17500000000000002 No Hit GGTAGTTCGACCGCGGAATTTTCGTATGCCGTCTTT 7 0.17500000000000002 No Hit GACACGACTCTCGGCAACGGATTCGTATGCCGTCTT 7 0.17500000000000002 No Hit TTGCTTGGTGCAGATCGGGACTCGTATGCCGTCTTC 7 0.17500000000000002 No Hit GACACGACTCTCGGCAACGGATATCTCGTATGCCGT 6 0.15 No Hit CTAACGAACGAACGATTTGAACTCGTATGCCGTCTT 6 0.15 No Hit TCGCTTGGTGCAGATCTGGACTCGTATGCCGTCTTC 6 0.15 No Hit GGGGATGTAGCTCAGATGGTATCGTATGCCGTCTTC 6 0.15 No Hit AGCCCCACGTCGCACGGATTCGTTCGTATGCCGTCT 5 0.125 No Hit ACGTCGCACGGATTCGTTCGTATGCCGTCTTCTGCT 5 0.125 Illumina Single End Adapter 2 (95% over 21bp) CCTGCGGAAGGATCATTGTCGTATGCCGTCTTCTGC 5 0.125 TruSeq Adapter, Index 23 (95% over 21bp) GGGGATGTAGCTCAGATGGTAGATCGTATGCCGTCT 5 0.125 No Hit GGTAGTTCGACCGCGGAATTTATCGTATGCCGTCTT 5 0.125 No Hit CTGACAGAAGAGAGTGAGCACTCGTATGCCGTCTTC 5 0.125 No Hit CGAACGAACGATTTGAACTCGTATGCCGTCTTCTGC 5 0.125 Illumina PCR Primer Index 5 (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 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GACACGA 20 0.004355815 30.278482 1 GGACTCG 75 0.0 30.27848 18 TCGCTTG 75 0.0 30.27848 1 CGGGACT 75 0.0 30.27848 16 GGGACTC 75 0.0 30.27848 17 GACTCGT 75 0.0 30.27848 19 CTTCTGC 20 0.004639747 29.900002 30 GTGCAGA 65 0.0 29.9 8 CTTGGTG 65 0.0 29.9 4 GCAGATC 70 0.0 29.9 10 GCTTGGT 70 0.0 29.9 3 TTGGTGC 65 0.0 29.9 5 TGGTGCA 65 0.0 29.9 6 TGCAGAT 65 0.0 29.9 9 GGTGCAG 65 0.0 29.9 7 CGCTTGG 75 0.0 29.899998 2 GATCGGG 75 0.0 29.899998 13 ATCGGGA 75 0.0 29.899998 14 CAGATCG 75 0.0 29.899998 11 AGATCGG 75 0.0 29.899998 12 >>END_MODULE Read 461877 spots for SRR1033811.sra Written 461877 spots for SRR1033811.sra Read 461877 spots for SRR1033811.sra Written 461877 spots for SRR1033811.sra Read 461877 spots for SRR1033811.sra Written 461877 spots for SRR1033811.sra Read 461877 spots for SRR1033811.sra Written 461877 spots for SRR1033811.sra Read 461877 spots for SRR1033811.sra Written 461877 spots for SRR1033811.sra Read 461877 spots for SRR1033811.sra Written 461877 spots for SRR1033811.sra Read 461877 spots for SRR1033811.sra Written 461877 spots for SRR1033811.sra Read 461877 spots for SRR1033811.sra Written 461877 spots for SRR1033811.sra Read 461877 spots for SRR1033811.sra Written 461877 spots for SRR1033811.sra Read 461877 spots for SRR1033811.sra Written 461877 spots for SRR1033811.sra Read 461877 spots for SRR1033811.sra Written 461877 spots for SRR1033811.sra Read 461877 spots for SRR1033811.sra Written 461877 spots for SRR1033811.sra Read 461877 spots for SRR1033811.sra Written 461877 spots for SRR1033811.sra Read 461877 spots for SRR1033811.sra Written 461877 spots for SRR1033811.sra Read 461877 spots for SRR1033811.sra Written 461877 spots for SRR1033811.sra Read 461877 spots for SRR1033811.sra Written 461877 spots for SRR1033811.sra Read 461877 spots for SRR1033811.sra Written 461877 spots for SRR1033811.sra Read 461877 spots for SRR1033811.sra Written 461877 spots for SRR1033811.sra Read 461877 spots for SRR1033811.sra Written 461877 spots for SRR1033811.sra Read 461883 spots for SRR1033811.sra Written 461883 spots for SRR1033811.sra SRR ids: ['SRR1033811.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_un6kri1v SRR1033811.sra spots: 9237546 blocks: [[1, 461877], [461878, 923754], [923755, 1385631], [1385632, 1847508], [1847509, 2309385], [2309386, 2771262], [2771263, 3233139], [3233140, 3695016], [3695017, 4156893], [4156894, 4618770], [4618771, 5080647], [5080648, 5542524], [5542525, 6004401], [6004402, 6466278], [6466279, 6928155], [6928156, 7390032], [7390033, 7851909], [7851910, 8313786], [8313787, 8775663], [8775664, 9237546]] SRR1033811 file size 1196632 SRR1033811 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 SRR1033811 SRR1033811_1.fastq Input file: SRR1033811_1.fastq trimmed: SRR1033811-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 00:59:16 2024 >> started Sat Dec 7 00:59:22 2024 >> done (6.299s) 9237546 reads processed; of these: 181192 ( 1.96%) short reads filtered out after trimming by size control 30326 ( 0.33%) empty reads filtered out after trimming by size control 9026028 (97.71%) reads available; of these: 4723803 (52.34%) trimmed reads available after processing 4302225 (47.66%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 69090 0.77% 19 89142 0.99% 20 116265 1.29% 21 126823 1.41% 22 95198 1.05% 23 93303 1.03% 24 92975 1.03% 25 89738 0.99% 26 83749 0.93% 27 107948 1.20% 28 95311 1.06% 29 109445 1.21% 30 179786 1.99% 31 260819 2.89% 32 289494 3.21% 33 450968 5.00% 34 1170716 12.97% 35 1203033 13.33% 36 4302225 47.66% 9026028 reads passed initial QC criterion=sequence-density sequence-density=49.61 sequence-density-rank=1 fanout-score=20.54 fanout-score-rank=3 prefix-density=74.50 prefix-fanout=13.7 sequence=TCGTATGCCGTCTTCTGCTTGAAAAA criterion=fanout-score sequence-density=1.50 sequence-density-rank=3 fanout-score=67.87 fanout-score-rank=1 prefix-density=2.21 prefix-fanout=46.1 sequence=GCTCGTATGCCG 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 TCGTATGCCGTCTTCTGCTTGAAAAA -o SRR1033811 - Input file: STDIN trimmed: SRR1033811-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TCGTATGCCGTCTTCTGCTTGAAAAA -- 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 00:59:36 2024 >> started Sat Dec 7 00:59:46 2024 >> done (9.618s) 8664987 reads processed; of these: 204847 ( 2.36%) short reads filtered out after trimming by size control 11393 ( 0.13%) empty reads filtered out after trimming by size control 8448747 (97.50%) reads available; of these: 7709857 (91.25%) trimmed reads available after processing 738890 ( 8.75%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 364665 4.32% 19 326722 3.87% 20 1175416 13.91% 21 2292128 27.13% 22 578040 6.84% 23 733747 8.68% 24 2313526 27.38% 25 396114 4.69% 26 196044 2.32% 27 32219 0.38% 28 5886 0.07% 29 2110 0.02% 30 1415 0.02% 31 1530 0.02% 32 1434 0.02% 33 1716 0.02% 34 2655 0.03% 35 3249 0.04% 36 20131 0.24% criterion=sequence-density sequence-density=15.31 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=11 prefix-density=0.00 prefix-fanout=1.0 sequence=TCGCTTGGTGCAGATCGGGACTCGTATGCCG criterion=fanout-score sequence-density=0.15 sequence-density-rank=13 fanout-score=105.65 fanout-score-rank=1 prefix-density=15.56 prefix-fanout=1.0 sequence=TGGTGCAGATCTGGAC Started job on | Dec 07 01:00:01 Started mapping on | Dec 07 01:00:02 Finished on | Dec 07 01:00:31 Mapping speed, Million of reads per hour | 1093.63 Number of input reads | 8809788 Average input read length | 22 UNIQUE READS: Uniquely mapped reads number | 3768294 Uniquely mapped reads % | 42.77% Average mapped length | 22.08 Number of splices: Total | 48320 Number of splices: Annotated (sjdb) | 4700 Number of splices: GT/AG | 47208 Number of splices: GC/AG | 738 Number of splices: AT/AC | 3 Number of splices: Non-canonical | 371 Mismatch rate per base, % | 0.27% 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 | 2722416 % of reads mapped to multiple loci | 30.90% Number of reads mapped to too many loci | 1966289 % of reads mapped to too many loci | 22.32% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.90% % of reads unmapped: other | 1.10% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 2319078 2319078 2319078 N_multimapping 2722416 2722416 2722416 N_noFeature 2055560 2184452 3632833 N_ambiguous 9755 2553 785 UnstrandedReadsAssigned:1702979 PositiveStrandReadsAssigned:1581289 NegativeStrandReadsAssigned:134676 Dataset is classified positive stranded MeadianReadLen=22 20thPercentileLength=20 echo kmer=19 SRR1033811 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: SRR1033811-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 8,809,788 reads, 3,045,422 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 964 rounds 52973 SRR1033811.ke.tsv 35125 SRR1033811.se.tsv 88098 total ==> SRR1033811.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 3 0.219481 PNS24247 1044 945 0 0 PNS24249 1928 1829 0 0 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 0 0 PNS24243 293 194 0 0 KQK14069 1603 1504 42.157 1.71642 KQK14071 474 375 15.1076 2.46697 ==> SRR1033811.se.tsv <== BRADI_1g14170v3 64 BRADI_1g53295v3 1 BRADI_1g59795v3 1 BRADI_1g07683v3 1 BRADI_1g00485v3 0 BRADI_1g20270v3 4 BRADI_1g74790v3 16 BRADI_1g09890v3 0 BRADI_1g77505v3 0 BRADI_1g48960v3 0 SRR1033811 completed mapping pipeline successfully