Starting /dee2/code/volunteer_pipeline.sh SRR926848 current disk space = 3058657443840 free memory = 1580135472 SRR926848 SRAfilesize 1b52a36cd21264cb2e870f3d474d38cf SRR926848.sra SRR926848.sra file validated SRR926848 is single end SRR926848 is conventional basespace SRR926848 read1 length is 49 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR926848_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 49 %GC 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 37.57125 38.0 37.0 39.0 35.0 39.0 2 37.362 38.0 37.0 39.0 35.0 39.0 3 37.32225 38.0 37.0 39.0 35.0 39.0 4 37.272 38.0 37.0 39.0 35.0 39.0 5 36.714 38.0 37.0 39.0 34.0 39.0 6 37.16725 38.0 37.0 39.0 34.0 39.0 7 36.9885 38.0 37.0 39.0 34.0 39.0 8 36.97625 38.0 36.0 39.0 34.0 39.0 9 36.97325 38.0 36.0 39.0 34.0 39.0 10 36.84625 38.0 36.0 39.0 33.0 39.0 11 36.58025 38.0 36.0 39.0 33.0 39.0 12 36.652 38.0 36.0 39.0 33.0 39.0 13 36.73025 38.0 36.0 39.0 33.0 39.0 14 36.51225 38.0 36.0 39.0 33.0 39.0 15 36.25025 38.0 36.0 39.0 31.0 39.0 16 36.177 37.0 36.0 39.0 32.0 39.0 17 36.1685 38.0 36.0 39.0 32.0 39.0 18 36.19075 37.0 36.0 39.0 32.0 39.0 19 35.81375 37.0 35.0 39.0 31.0 39.0 20 35.8325 37.0 35.0 39.0 31.0 39.0 21 35.2975 37.0 35.0 39.0 30.0 39.0 22 35.40125 37.0 35.0 38.0 30.0 39.0 23 34.8195 37.0 33.0 38.0 28.0 39.0 24 35.0805 37.0 34.0 38.0 30.0 39.0 25 34.18475 36.0 33.0 38.0 27.0 39.0 26 34.49675 37.0 34.0 38.0 28.0 39.0 27 33.02575 35.0 31.0 37.0 24.0 39.0 28 34.09525 36.0 33.0 38.0 27.0 39.0 29 34.144 36.0 33.0 38.0 28.0 39.0 30 33.354 36.0 33.0 38.0 25.0 39.0 31 33.71725 36.0 33.0 38.0 27.0 39.0 32 33.374 36.0 33.0 38.0 26.0 39.0 33 33.60225 36.0 33.0 38.0 27.0 39.0 34 32.3505 35.0 31.0 37.0 23.0 38.0 35 32.23675 35.0 31.0 37.0 22.0 38.0 36 33.2265 36.0 33.0 37.0 25.0 39.0 37 32.484 36.0 31.0 37.0 22.0 38.0 38 31.6375 35.0 30.0 37.0 19.0 38.0 39 31.046 34.0 29.0 37.0 19.0 38.0 40 30.37875 34.0 28.0 36.0 17.0 37.0 41 30.26 34.0 28.0 37.0 13.0 38.0 42 30.869 34.0 29.0 36.0 19.0 38.0 43 30.06325 33.0 27.0 36.0 15.0 38.0 44 30.343 34.0 28.0 36.0 17.0 37.0 45 29.10475 33.0 26.0 36.0 13.0 37.0 46 30.594 34.0 29.0 37.0 14.0 38.0 47 31.8525 35.0 32.0 37.0 20.0 38.0 48 31.4775 35.0 31.0 37.0 19.0 38.0 49 30.81675 35.0 30.0 36.0 13.0 37.0 >>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 1101 47 0.0 1101 48 0.0 1101 49 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 1.0 14 6.0 15 4.0 16 11.0 17 12.0 18 13.0 19 19.0 20 20.0 21 19.0 22 20.0 23 15.0 24 24.0 25 22.0 26 34.0 27 60.0 28 82.0 29 102.0 30 129.0 31 187.0 32 233.0 33 318.0 34 417.0 35 555.0 36 770.0 37 752.0 38 174.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 11.725 30.85 44.125 13.3 2 23.25 38.0 20.9 17.849999999999998 3 28.414207103551774 23.56178089044522 18.209104552276138 29.814907453726864 4 28.553553553553552 24.2992992992993 18.01801801801802 29.129129129129126 5 23.23053589484328 27.502527805864506 35.9201213346815 13.346814964610717 6 36.125 22.525000000000002 21.925 19.425 7 39.900000000000006 21.4 20.599999999999998 18.099999999999998 8 24.15 23.724999999999998 39.425 12.7 9 26.8 22.35 36.65 14.2 10 44.275 22.95 18.325 14.45 11 24.625 38.0 19.0 18.375 12 22.8 22.900000000000002 39.900000000000006 14.399999999999999 13 24.875 21.7 20.599999999999998 32.824999999999996 14 20.575 27.750000000000004 18.675 33.0 15 23.525 27.450000000000003 34.0 15.024999999999999 16 39.550000000000004 25.900000000000002 21.05 13.5 17 22.325 21.725 24.625 31.324999999999996 18 25.874999999999996 20.349999999999998 19.05 34.725 19 24.175 36.75 19.75 19.325 20 39.7 20.5 21.65 18.15 21 20.7 20.925 38.75 19.625 22 19.825 34.175 32.05 13.950000000000001 23 33.225 14.224999999999998 26.900000000000002 25.650000000000002 24 29.849999999999998 11.475 38.224999999999994 20.45 25 15.75 4.324999999999999 55.875 24.05 26 23.95 18.05 18.65 39.35 27 41.225 13.950000000000001 40.125 4.7 28 20.275000000000002 21.95 51.87500000000001 5.8999999999999995 29 15.45 36.975 24.9 22.675 30 25.924999999999997 1.6 39.975 32.5 31 54.75 0.65 7.3 37.3 32 15.375 0.525 20.3 63.800000000000004 33 22.825 0.325 19.5 57.35 34 38.324999999999996 0.3 43.85 17.525 35 3.125 0.35000000000000003 68.625 27.900000000000002 36 2.0500000000000003 0.44999999999999996 41.475 56.025000000000006 37 4.05 0.375 78.525 17.05 38 18.7 0.625 54.725 25.95 39 14.725 1.7000000000000002 28.775000000000002 54.800000000000004 40 23.400000000000002 2.6 58.375 15.625 41 39.625 4.025 33.650000000000006 22.7 42 19.0 7.449999999999999 36.1 37.45 43 13.950000000000001 24.65 59.275 2.125 44 22.400000000000002 37.974999999999994 38.75 0.8750000000000001 45 36.55 59.875 2.8000000000000003 0.775 46 1.875 96.075 1.3 0.75 47 0.42500000000000004 97.975 0.8250000000000001 0.775 48 0.42500000000000004 98.075 0.475 1.0250000000000001 49 0.42500000000000004 98.4 0.27499999999999997 0.8999999999999999 >>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 0.0 24 0.0 25 0.0 26 0.0 27 0.0 28 0.0 29 0.0 30 2.5 31 5.0 32 10.5 33 16.0 34 42.5 35 69.0 36 102.5 37 136.0 38 227.5 39 319.0 40 375.5 41 432.0 42 517.0 43 602.0 44 601.5 45 601.0 46 821.0 47 1041.0 48 748.5 49 456.0 50 314.0 51 172.0 52 125.0 53 78.0 54 56.0 55 34.0 56 27.5 57 21.0 58 12.5 59 4.0 60 5.5 61 7.0 62 5.5 63 4.0 64 2.5 65 1.0 66 1.5 67 2.0 68 1.0 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 0.05 4 0.1 5 1.0999999999999999 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 47 0.0 48 0.0 49 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 49 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 74.675 #Duplication Level Percentage of deduplicated Percentage of total 1 95.94911282222967 71.65 2 2.2765316370940742 3.4000000000000004 3 0.7030465349849347 1.575 4 0.2008704385671242 0.6 5 0.2678272514228323 1.0 6 0.2343488449949782 1.05 7 0.03347840642785404 0.17500000000000002 8 0.06695681285570808 0.4 9 0.03347840642785404 0.22499999999999998 >10 0.16739203213927017 1.8499999999999999 >50 0.0 0.0 >100 0.03347840642785404 2.875 >500 0.03347840642785404 15.2 >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 TACCTGGTTGATCCTGCCAGTAGTCGTATGCCGTCTTCTGCTTGAAAAA 608 15.2 Illumina Single End Adapter 1 (95% over 22bp) TCGGACCAGGCTTCATTCCCCTCGTATGCCGTCTTCTGCTTGAAAAAAA 115 2.875 TruSeq Adapter, Index 16 (96% over 25bp) TGGTATGGGCGAGTTGGGAAGTCGTATGCCGTCTTCTGCTTGAAAAAAA 22 0.5499999999999999 Illumina Single End Adapter 2 (95% over 22bp) GGGGATGTAGCTCAGATGGTTCGTATGCCGTCTTCTGCTTGAAAAAAAA 15 0.375 Illumina Single End Adapter 2 (95% over 23bp) GTGTCGCTCCGATTCGTTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAA 13 0.325 Illumina Single End Adapter 2 (95% over 23bp) GGCGGATGTAGCCAAGTGGATCGTATGCCGTCTTCTGCTTGAAAAAAAA 13 0.325 Illumina Single End Adapter 2 (95% over 23bp) TCTTTCCTAGTCCTCCCATTCCTCGTATGCCGTCTTCTGCTTGAAAAAA 11 0.27499999999999997 Illumina Single End Adapter 2 (95% over 23bp) TTATACAGAGTAATCACGGTCGTCGTATGCCGTCTTCTGCTTGAAAAAA 9 0.22499999999999998 Illumina Single End Adapter 2 (95% over 22bp) GGGGATGTAGCTCAGATGGTATCGTATGCCGTCTTCTGCTTGAAAAAAA 8 0.2 TruSeq Adapter, Index 14 (95% over 24bp) TGAAGCTGCCAGCATGATCTATCGTATGCCGTCTTCTGCTTGAAAAAAA 8 0.2 TruSeq Adapter, Index 13 (95% over 24bp) TCGCTTGGTGCAGGTCGGGAATCGTATGCCGTCTTCTGCTTGAAAAAAA 7 0.17500000000000002 Illumina Single End Adapter 1 (95% over 22bp) TGTAATTGGACAAGACCGCACTCGTATGCCGTCTTCTGCTTGAAAAAAA 6 0.15 TruSeq Adapter, Index 13 (95% over 24bp) TCGGACCAGGCTTCATTCCCGTCGTATGCCGTCTTCTGCTTGAAAAAAA 6 0.15 Illumina Single End Adapter 2 (95% over 22bp) AACAACTGTGGAGTACGTATTATATCGTATGCCGTCTTCTGCTTGAAAA 6 0.15 Illumina PCR Primer Index 10 (96% over 26bp) TGACGATGCAGGACAGCAAGATCGTATGCCGTCTTCTGCTTGAAAAAAA 6 0.15 Illumina Single End Adapter 2 (95% over 24bp) GGAATGGGCTGTTTGGGATGATCGTATGCCGTCTTCTGCTTGAAAAAAA 6 0.15 Illumina Single End Adapter 1 (95% over 23bp) TACCNGGTTGATCCTGCCAGTAGTCGTATGCCGTCTTCTGCTTGAAAAA 6 0.15 Illumina Single End Adapter 1 (95% over 22bp) AATGGGAAGATAGGAAAGAACTCGTATGCCGTCTTCTGCTTGAAAAAAA 6 0.15 Illumina Single End Adapter 2 (96% over 27bp) GGAATGTTGTCTGGCTCGAGGTCGTATGCCGTCTTCTGCTTGAAAAAAA 5 0.125 Illumina Single End Adapter 1 (96% over 25bp) TTGCATATCTCAGGAGCTGCTCGTATGCCGTCTTCTGCTTGAAAAAAAA 5 0.125 TruSeq Adapter, Index 23 (96% over 25bp) TTGCCAATTCCACCCATTCCAATCGTATGCCGTCTTCTGCTTGAAAAAA 5 0.125 Illumina Single End Adapter 2 (95% over 22bp) TGGAGAAGCAGGGCACGTGCATCGTATGCCGTCTTCTGCTTGAAAAAAA 5 0.125 Illumina Single End Adapter 2 (95% over 22bp) GGCGGATGTAGCCAAGTGGATCGTATGCCGTCTTCTGCTTTAAAAAAAA 5 0.125 Illumina Single End Adapter 2 (95% over 22bp) GGGGATGTAGCTCAGATGGTAGATCGTATGCCGTCTTCTGCTTGAAAAA 5 0.125 Illumina Single End Adapter 2 (95% over 24bp) AAGCTCAGGAGGGATAGCGCCTCGTATGCCGTCTTCTGCTTGAAAAAAA 5 0.125 Illumina Single End Adapter 2 (95% over 23bp) AAGCTCAGGAGGGATAGCACCTCGTATGCCGTCTTCTGCTTGAAAAAAA 5 0.125 RNA PCR Primer, Index 24 (96% over 28bp) >>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 35 0.0 0.0 0.0 0.0 0.0 36 0.0 0.0 0.0 0.0 0.0 37 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 GTTGATC 55 1.8189894E-12 43.0 7 TGGTTGA 55 1.8189894E-12 43.0 5 GGTTGAT 55 1.8189894E-12 43.0 6 CCAGTAG 55 1.8189894E-12 43.0 17 CCTGCCA 55 1.8189894E-12 43.0 13 CAGTAGT 55 1.8189894E-12 43.0 18 TGATCCT 55 1.8189894E-12 43.0 9 GCCAGTA 55 1.8189894E-12 43.0 16 CTGGTTG 55 1.8189894E-12 43.0 4 ACCTGGT 55 1.8189894E-12 43.0 2 TGCCAGT 55 1.8189894E-12 43.0 15 TTGATCC 55 1.8189894E-12 43.0 8 TACCTGG 55 1.8189894E-12 43.0 1 TCCTGCC 55 1.8189894E-12 43.0 12 CCTGGTT 55 1.8189894E-12 43.0 3 ATCCTGC 60 1.8189894E-12 39.416664 11 AGTAGTC 60 1.8189894E-12 39.416664 19 TAGTCGT 60 1.8189894E-12 39.416664 21 GATCCTG 60 1.8189894E-12 39.416664 10 AGTCGTA 60 1.8189894E-12 39.416664 22 >>END_MODULE Read 875717 spots for SRR926848.sra Written 875717 spots for SRR926848.sra Read 875717 spots for SRR926848.sra Written 875717 spots for SRR926848.sra Read 875717 spots for SRR926848.sra Written 875717 spots for SRR926848.sra Read 875717 spots for SRR926848.sra Written 875717 spots for SRR926848.sra Read 875717 spots for SRR926848.sra Written 875717 spots for SRR926848.sra Read 875717 spots for SRR926848.sra Written 875717 spots for SRR926848.sra Read 875717 spots for SRR926848.sra Written 875717 spots for SRR926848.sra Read 875717 spots for SRR926848.sra Written 875717 spots for SRR926848.sra Read 875717 spots for SRR926848.sra Written 875717 spots for SRR926848.sra Read 875717 spots for SRR926848.sra Written 875717 spots for SRR926848.sra Read 875717 spots for SRR926848.sra Written 875717 spots for SRR926848.sra Read 875717 spots for SRR926848.sra Written 875717 spots for SRR926848.sra Read 875717 spots for SRR926848.sra Written 875717 spots for SRR926848.sra Read 875717 spots for SRR926848.sra Written 875717 spots for SRR926848.sra Read 875717 spots for SRR926848.sra Written 875717 spots for SRR926848.sra Read 875734 spots for SRR926848.sra Written 875734 spots for SRR926848.sra Read 875717 spots for SRR926848.sra Written 875717 spots for SRR926848.sra Read 875717 spots for SRR926848.sra Written 875717 spots for SRR926848.sra Read 875717 spots for SRR926848.sra Written 875717 spots for SRR926848.sra Read 875717 spots for SRR926848.sra Written 875717 spots for SRR926848.sra SRR ids: ['SRR926848.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_7z12gjjo SRR926848.sra spots: 17514357 blocks: [[1, 875717], [875718, 1751434], [1751435, 2627151], [2627152, 3502868], [3502869, 4378585], [4378586, 5254302], [5254303, 6130019], [6130020, 7005736], [7005737, 7881453], [7881454, 8757170], [8757171, 9632887], [9632888, 10508604], [10508605, 11384321], [11384322, 12260038], [12260039, 13135755], [13135756, 14011472], [14011473, 14887189], [14887190, 15762906], [15762907, 16638623], [16638624, 17514357]] SRR926848 file size 2777820 SRR926848 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 SRR926848 SRR926848_1.fastq Input file: SRR926848_1.fastq trimmed: SRR926848-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 12:42:24 2025 >> started Mon Feb 10 12:42:31 2025 >> done (7.214s) 17514357 reads processed; of these: 21147 ( 0.12%) short reads filtered out after trimming by size control 1980 ( 0.01%) empty reads filtered out after trimming by size control 17491230 (99.87%) reads available; of these: 1152786 ( 6.59%) trimmed reads available after processing 16338444 (93.41%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 6455 0.04% 19 15501 0.09% 20 23305 0.13% 21 11376 0.07% 22 16016 0.09% 23 26544 0.15% 24 54824 0.31% 25 67823 0.39% 26 37348 0.21% 27 17628 0.10% 28 15105 0.09% 29 20765 0.12% 30 28262 0.16% 31 5030 0.03% 32 8673 0.05% 33 17388 0.10% 34 18747 0.11% 35 20259 0.12% 36 10258 0.06% 37 16687 0.10% 38 41068 0.23% 39 32055 0.18% 40 64654 0.37% 41 18712 0.11% 42 34694 0.20% 43 55896 0.32% 44 123207 0.70% 45 155122 0.89% 46 48303 0.28% 47 62674 0.36% 48 78407 0.45% 49 16338444 93.41% 17491230 reads passed initial QC criterion=sequence-density sequence-density=95.11 sequence-density-rank=1 fanout-score=23.90 fanout-score-rank=4 prefix-density=96.68 prefix-fanout=23.5 sequence=TCGTATGCCGTCTTCTGCTTGAAAAACA criterion=fanout-score sequence-density=6.47 sequence-density-rank=2 fanout-score=43.69 fanout-score-rank=1 prefix-density=6.50 prefix-fanout=43.5 sequence=GGTCGTATGCCG 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 SRR926848 - Input file: STDIN trimmed: SRR926848-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 Mon Feb 10 12:42:57 2025 >> started Mon Feb 10 12:43:10 2025 >> done (12.726s) 17126830 reads processed; of these: 200962 ( 1.17%) short reads filtered out after trimming by size control 4929 ( 0.03%) empty reads filtered out after trimming by size control 16920939 (98.80%) reads available; of these: 16618162 (98.21%) trimmed reads available after processing 302777 ( 1.79%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 162606 0.96% 19 282918 1.67% 20 649134 3.84% 21 3059961 18.08% 22 2413756 14.26% 23 3481456 20.57% 24 6250279 36.94% 25 295906 1.75% 26 110737 0.65% 27 54594 0.32% 28 29645 0.18% 29 21365 0.13% 30 16974 0.10% 31 9282 0.05% 32 14113 0.08% 33 11383 0.07% 34 9805 0.06% 35 4459 0.03% 36 2040 0.01% 37 1237 0.01% 38 816 0.00% 39 507 0.00% 40 697 0.00% 41 164 0.00% 42 144 0.00% 43 180 0.00% 44 270 0.00% 45 307 0.00% 46 93 0.00% 47 149 0.00% 48 349 0.00% 49 35613 0.21% criterion=sequence-density sequence-density=1.83 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=15 prefix-density=0.00 prefix-fanout=1.0 sequence=GGGGATGTAGCTCAGATGGTAGAGC criterion=fanout-score sequence-density=0.01 sequence-density-rank=46 fanout-score=14.83 fanout-score-rank=1 prefix-density=0.08 prefix-fanout=1.0 sequence=AGGGCACGTCTGCCTGGGTGTCACGCA Started job on | Feb 10 12:43:28 Started mapping on | Feb 10 12:43:29 Finished on | Feb 10 12:44:55 Mapping speed, Million of reads per hour | 723.57 Number of input reads | 17285339 Average input read length | 23 UNIQUE READS: Uniquely mapped reads number | 3376983 Uniquely mapped reads % | 19.54% Average mapped length | 20.08 Number of splices: Total | 1031835 Number of splices: Annotated (sjdb) | 38030 Number of splices: GT/AG | 1012944 Number of splices: GC/AG | 18464 Number of splices: AT/AC | 30 Number of splices: Non-canonical | 397 Mismatch rate per base, % | 3.57% Deletion rate per base | 0.00% Deletion average length | 2.28 Insertion rate per base | 0.00% Insertion average length | 1.05 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 6118820 % of reads mapped to multiple loci | 35.40% Number of reads mapped to too many loci | 4909601 % of reads mapped to too many loci | 28.40% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 16.55% % of reads unmapped: other | 0.11% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 7789536 7789536 7789536 N_multimapping 6118820 6118820 6118820 N_noFeature 2271526 2750647 2858939 N_ambiguous 80786 25496 17153 UnstrandedReadsAssigned:1024671 PositiveStrandReadsAssigned:600840 NegativeStrandReadsAssigned:500891 Dataset is classified unstranded MeadianReadLen=23 20thPercentileLength=21 echo kmer=19 SRR926848 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: SRR926848-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 17,285,339 reads, 4,580,114 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 925 rounds 52401 SRR926848.ke.tsv 34699 SRR926848.se.tsv 87100 total ==> SRR926848.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 1 0.138597 Potri.005G024800.1.v4.1 1035 936 0 0 Potri.004G059700.1.v4.1 961 862 2 0.617095 Potri.007G009000.2.v4.1 1416 1317 8 1.6156 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 1 0.571975 Potri.010G195200.1.v4.1 1773 1674 1 0.158882 Potri.012G127500.1.v4.1 977 878 1 0.302925 ==> SRR926848.se.tsv <== Potri.001G166300.v4.1 26 Potri.001G448400.v4.1 29 Potri.001G233950.v4.1 111 Potri.001G122700.v4.1 9 Potri.001G212900.v4.1 6 Potri.001G182400.v4.1 46 Potri.001G256600.v4.1 4 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 49 Potri.001G452600.v4.1 3 SRR926848 completed mapping pipeline successfully