Starting /dee2/code/volunteer_pipeline.sh SRR6892959 current disk space = 1550911873024 free memory = 1603368576 SRR6892959 SRAfilesize f0cce1e6605098f8bd0c3087df5b9b91 SRR6892959.sra SRR6892959.sra file validated SRR6892959 is single end SRR6892959 is conventional basespace SRR6892959 read1 length is 50 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6892959_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 50 %GC 53 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.303 33.0 31.0 34.0 31.0 34.0 2 32.5035 34.0 31.0 34.0 31.0 34.0 3 32.606 34.0 31.0 34.0 31.0 34.0 4 36.0505 37.0 35.0 37.0 35.0 37.0 5 36.09225 37.0 35.0 37.0 35.0 37.0 6 36.0005 37.0 35.0 37.0 35.0 37.0 7 36.03575 37.0 35.0 37.0 35.0 37.0 8 35.9065 37.0 35.0 37.0 35.0 37.0 9 37.7965 39.0 37.0 39.0 35.0 39.0 10 37.6265 39.0 37.0 39.0 35.0 39.0 11 37.6645 39.0 37.0 39.0 35.0 39.0 12 37.4185 39.0 37.0 39.0 34.0 39.0 13 37.56975 39.0 37.0 39.0 35.0 39.0 14 39.015 40.0 38.0 41.0 36.0 41.0 15 39.0445 40.0 38.0 41.0 36.0 41.0 16 38.95425 40.0 38.0 41.0 36.0 41.0 17 38.9155 40.0 38.0 41.0 35.0 41.0 18 38.87175 40.0 38.0 41.0 35.0 41.0 19 38.79525 40.0 38.0 41.0 34.0 41.0 20 38.904 40.0 38.0 41.0 35.0 41.0 21 38.6985 40.0 38.0 41.0 35.0 41.0 22 38.51475 40.0 38.0 41.0 34.0 41.0 23 39.58425 40.0 39.0 41.0 37.0 41.0 24 39.08725 40.0 39.0 41.0 36.0 41.0 25 40.00125 41.0 40.0 41.0 38.0 41.0 26 39.66975 41.0 40.0 41.0 37.0 41.0 27 40.274 41.0 40.0 41.0 39.0 41.0 28 39.33875 41.0 40.0 41.0 36.0 41.0 29 38.52925 40.0 38.0 41.0 34.0 41.0 30 38.561 40.0 38.0 41.0 34.0 41.0 31 38.682 41.0 38.0 41.0 34.0 41.0 32 39.91075 41.0 40.0 41.0 38.0 41.0 33 40.29325 41.0 40.0 41.0 40.0 41.0 34 34.25225 37.0 30.0 41.0 23.0 41.0 35 33.508 35.0 31.0 38.0 25.0 39.0 36 36.467 38.0 36.0 39.0 30.0 40.0 37 38.653 40.0 39.0 40.0 35.0 41.0 38 38.838 40.0 39.0 41.0 35.0 41.0 39 39.5225 40.0 39.0 41.0 37.0 41.0 40 39.12875 41.0 39.0 41.0 35.0 41.0 41 39.8495 41.0 40.0 41.0 37.0 41.0 42 39.11775 41.0 39.0 41.0 35.0 41.0 43 39.6765 41.0 40.0 41.0 37.0 41.0 44 39.19475 41.0 40.0 41.0 36.0 41.0 45 38.98625 41.0 39.0 41.0 35.0 41.0 46 38.93625 41.0 39.0 41.0 35.0 41.0 47 39.43525 41.0 40.0 41.0 36.0 41.0 48 38.8235 41.0 39.0 41.0 35.0 41.0 49 38.47975 40.0 38.0 41.0 34.0 41.0 50 37.48125 39.0 37.0 41.0 33.0 41.0 >>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 1101 50 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 1.0 14 1.0 15 0.0 16 1.0 17 3.0 18 0.0 19 1.0 20 0.0 21 0.0 22 3.0 23 4.0 24 6.0 25 8.0 26 2.0 27 14.0 28 8.0 29 22.0 30 34.0 31 41.0 32 57.0 33 69.0 34 116.0 35 192.0 36 258.0 37 443.0 38 670.0 39 2046.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 18.075 22.3 28.625 31.0 2 17.675 26.275 23.65 32.4 3 24.25 20.674999999999997 22.6 32.475 4 24.85 25.05 19.725 30.375000000000004 5 24.025 27.150000000000002 25.85 22.975 6 28.749999999999996 22.825 23.35 25.074999999999996 7 31.35 21.625 25.224999999999998 21.8 8 22.2 22.7 30.55 24.55 9 27.224999999999998 21.475 29.275000000000002 22.025 10 34.150000000000006 20.724999999999998 20.875 24.25 11 27.875 28.525 21.0 22.6 12 28.675 21.275 26.174999999999997 23.875 13 25.5 22.425 20.75 31.324999999999996 14 25.45 23.425 22.6 28.525 15 27.474999999999998 22.975 27.725 21.825 16 31.724999999999998 21.875 21.325 25.074999999999996 17 26.875 20.5 24.474999999999998 28.15 18 32.300000000000004 19.075 21.5 27.125 19 31.75 32.175 15.950000000000001 20.125 20 31.974999999999998 23.925 20.025000000000002 24.075 21 10.325 10.65 65.525 13.5 22 54.025 0.5499999999999999 45.35 0.075 23 98.7452948557089 0.6775407779171895 0.5018820577164366 0.0752823086574655 24 45.5955955955956 53.77877877877878 0.5005005005005005 0.12512512512512514 25 0.22499999999999998 98.85000000000001 0.625 0.3 26 0.1 45.5 54.1 0.3 27 0.125 0.17500000000000002 99.075 0.625 28 0.375 0.025 46.075 53.525 29 0.5499999999999999 0.075 53.574999999999996 45.800000000000004 30 0.9249999999999999 0.05 45.324999999999996 53.7 31 54.125 0.05 0.44999999999999996 45.375 32 99.375 0.1 0.25 0.27499999999999997 33 99.125 0.125 0.4 0.35000000000000003 34 48.8 0.125 50.55 0.525 35 55.05 0.375 43.775 0.8 36 45.275 0.5499999999999999 0.27499999999999997 53.900000000000006 37 0.525 0.8500000000000001 0.05 98.575 38 0.6 54.025 0.05 45.324999999999996 39 0.975 98.6 0.125 0.3 40 53.974999999999994 45.775 0.05 0.2 41 98.2 1.3 0.125 0.375 42 45.175 54.0 0.42500000000000004 0.4 43 0.325 97.975 0.35000000000000003 1.35 44 0.05 45.1 0.975 53.87499999999999 45 0.15 0.675 53.125 46.050000000000004 46 0.35000000000000003 0.42500000000000004 44.775 54.449999999999996 47 0.325 1.125 0.675 97.875 48 1.125 53.025 0.475 45.375 49 53.025 45.050000000000004 1.0999999999999999 0.8250000000000001 50 44.800000000000004 0.75 52.925 1.525 >>END_MODULE >>Per sequence GC content pass #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 0.0 31 0.0 32 0.0 33 0.5 34 1.0 35 1.0 36 1.0 37 3.5 38 6.0 39 10.0 40 14.0 41 33.0 42 52.0 43 77.5 44 103.0 45 147.0 46 191.0 47 283.5 48 376.0 49 431.0 50 486.0 51 497.5 52 509.0 53 610.0 54 711.0 55 630.0 56 549.0 57 454.0 58 359.0 59 310.5 60 262.0 61 210.0 62 158.0 63 144.5 64 131.0 65 91.5 66 52.0 67 39.0 68 26.0 69 18.0 70 10.0 71 5.5 72 1.0 73 1.5 74 2.0 75 1.0 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 0.0 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 0.375 24 0.1 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 50 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 50 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 86.875 #Duplication Level Percentage of deduplicated Percentage of total 1 98.58992805755395 85.65 2 0.6906474820143885 1.2 3 0.08633093525179857 0.22499999999999998 4 0.08633093525179857 0.3 5 0.08633093525179857 0.375 6 0.05755395683453237 0.3 7 0.028776978417266185 0.17500000000000002 8 0.028776978417266185 0.2 9 0.05755395683453237 0.44999999999999996 >10 0.17266187050359713 2.9749999999999996 >50 0.08633093525179857 5.3 >100 0.028776978417266185 2.85 >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 TACCTGGTTGATCCTGCCAGTGGAATTCTCGGGTGCCAAGGAACTCCAGT 114 2.85 RNA PCR Primer, Index 1 (100% over 30bp) TACCTGGTTGATCCTGCCAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG 81 2.025 RNA PCR Primer, Index 1 (100% over 29bp) CACGACTCTCGGCAACGGATTGGAATTCTCGGGTGCCAAGGAACTCCAGT 79 1.975 RNA PCR Primer, Index 1 (100% over 30bp) TCAAAAGAGGAAAGGCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAGT 52 1.3 RNA PCR Primer, Index 1 (100% over 30bp) CATCGAGTAGACCTTGTTATTGGAATTCTCGGGTGCCAAGGAACTCCAGT 47 1.175 RNA PCR Primer, Index 1 (100% over 30bp) GCGACCCCAGGTCAGGCGGGATGGAATTCTCGGGTGCCAAGGAACTCCAG 26 0.65 RNA PCR Primer, Index 1 (100% over 29bp) GACACGACTCTCGGCAACGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT 13 0.325 RNA PCR Primer, Index 1 (100% over 30bp) CGACACGACTCTCGGCAACGGTGGAATTCTCGGGTGCCAAGGAACTCCAG 12 0.3 RNA PCR Primer, Index 1 (100% over 29bp) CATCGAGTAGACCTTGTTATTTGGAATTCTCGGGTGCCAAGGAACTCCAG 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 29bp) ACACGACTCTCGGCAACGGATTGGAATTCTCGGGTGCCAAGGAACTCCAG 10 0.25 RNA PCR Primer, Index 1 (100% over 29bp) TCTCATGGAGAGTTCGATCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 29bp) GACACGACTCTCGGCAACGGATGGAATTCTCGGGTGCCAAGGAACTCCAG 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 29bp) ACACCGATGACGACTGTGAATGGAATTCTCGGGTGCCAAGGAACTCCAGT 8 0.2 RNA PCR Primer, Index 1 (100% over 30bp) ACACCGATGACGACTGTGAAGTGGAATTCTCGGGTGCCAAGGAACTCCAG 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 29bp) ACGACTCTCGGCAACGGATATTGGAATTCTCGGGTGCCAAGGAACTCCAG 6 0.15 RNA PCR Primer, Index 1 (100% over 29bp) ACACGACTCTCGGCAACGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT 6 0.15 RNA PCR Primer, Index 1 (100% over 30bp) TACCTGGTTGATCCTGCCAGTGGAATTCTCGGGGGCCAAGGAACTCCAGT 5 0.125 RNA PCR Primer, Index 1 (96% over 30bp) GCGACCCCAGGTCAGGCGGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT 5 0.125 RNA PCR Primer, Index 1 (100% over 30bp) CCATATGTTCCTTGCCAACCGTGGAATTCTCGGGTGCCAAGGAACTCCAG 5 0.125 RNA PCR Primer, Index 1 (100% over 29bp) >>END_MODULE >>Adapter Content fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.025 0.0 0.0 0.0 2 0.0 0.025 0.0 0.0 0.0 3 0.0 0.025 0.0 0.0 0.0 4 0.0 0.025 0.0 0.0 0.0 5 0.0 0.025 0.0 0.0 0.0 6 0.0 0.025 0.0 0.0 0.0 7 0.0 0.025 0.0 0.0 0.0 8 0.0 0.05 0.0 0.0 0.0 9 0.0 0.05 0.0 0.0 0.0 10 0.0 0.05 0.0 0.0 0.0 11 0.0 0.05 0.0 0.0 0.0 12 0.0 0.05 0.0 0.0 0.0 13 0.0 0.05 0.0 0.0 0.0 14 0.0 0.075 0.0 0.0 0.0 15 0.0 0.075 0.0 0.0 0.0 16 0.0 0.1 0.0 0.0 0.0 17 0.0 0.15 0.0 0.0 0.0 18 0.0 0.35 0.0 0.0 0.0 19 0.0 0.525 0.0 0.0 0.0 20 0.0 0.875 0.0 0.0 0.0 21 0.0 53.325 0.0 0.0 0.0 22 0.0 98.0 0.0 0.0 0.0 23 0.0 98.125 0.0 0.0 0.0 24 0.0 98.15 0.0 0.0 0.0 25 0.0 98.15 0.0 0.0 0.0 26 0.0 98.15 0.0 0.0 0.0 27 0.0 98.15 0.0 0.0 0.0 28 0.0 98.15 0.0 0.0 0.0 29 0.0 98.15 0.0 0.0 0.0 30 0.0 98.15 0.0 0.0 0.0 31 0.0 98.15 0.0 0.0 0.0 32 0.0 98.15 0.0 0.0 0.0 33 0.0 98.15 0.0 0.0 0.0 34 0.0 98.15 0.0 0.0 0.0 35 0.0 98.15 0.0 0.0 0.0 36 0.0 98.15 0.0 0.0 0.0 37 0.0 98.15 0.0 0.0 0.0 38 0.0 98.15 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CTCCAGT 195 0.0 43.912502 44 ATCCTGC 20 7.0206006E-4 43.9125 11 GTTGATC 20 7.0206006E-4 43.9125 7 TGGTTGA 20 7.0206006E-4 43.9125 5 GGTTGAT 20 7.0206006E-4 43.9125 6 CCTGCCA 20 7.0206006E-4 43.9125 13 TGATCCT 20 7.0206006E-4 43.9125 9 ACCTGGT 20 7.0206006E-4 43.9125 2 GATCCTG 20 7.0206006E-4 43.9125 10 TGCCAGT 20 7.0206006E-4 43.9125 15 TTGATCC 20 7.0206006E-4 43.9125 8 CTGCCAG 20 7.0206006E-4 43.9125 14 TACCTGG 20 7.0206006E-4 43.9125 1 TCCTGCC 20 7.0206006E-4 43.9125 12 CCTGGTT 20 7.0206006E-4 43.9125 3 ACTGGAA 35 5.2246633E-6 38.11573 19 CTGGTTG 25 0.002104782 35.13 4 CGGTGGA 40 1.3068204E-5 33.351265 19 GGTGGAA 55 8.009556E-8 32.340622 20 GATGGAA 30 0.004830434 29.64557 19 >>END_MODULE Read 2893614 spots for SRR6892959.sra Read 2893614 spots for SRR6892959.sra Written 2893614 spots for SRR6892959.sra Read 2893614 spots for SRR6892959.sra Written 2893614 spots for SRR6892959.sra Written 2893614 spots for SRR6892959.sra Read 2893614 spots for SRR6892959.sra Read 2893614 spots for SRR6892959.sra Written 2893614 spots for SRR6892959.sra Written 2893614 spots for SRR6892959.sra Read 2893614 spots for SRR6892959.sra Written 2893614 spots for SRR6892959.sra Read 2893614 spots for SRR6892959.sra Read 2893614 spots for SRR6892959.sra Written 2893614 spots for SRR6892959.sra Read 2893614 spots for SRR6892959.sra Written 2893614 spots for SRR6892959.sra Read 2893614 spots for SRR6892959.sra Written 2893614 spots for SRR6892959.sra Written 2893614 spots for SRR6892959.sra Read 2893614 spots for SRR6892959.sra Written 2893614 spots for SRR6892959.sra Read 2893614 spots for SRR6892959.sra Written 2893614 spots for SRR6892959.sra Read 2893614 spots for SRR6892959.sra Written 2893614 spots for SRR6892959.sra Read 2893614 spots for SRR6892959.sra Read 2893614 spots for SRR6892959.sra Written 2893614 spots for SRR6892959.sra Written 2893614 spots for SRR6892959.sra Read 2893614 spots for SRR6892959.sra Written 2893614 spots for SRR6892959.sra Read 2893614 spots for SRR6892959.sra Written 2893614 spots for SRR6892959.sra Read 2893614 spots for SRR6892959.sra Written 2893614 spots for SRR6892959.sra Read 2893614 spots for SRR6892959.sra Written 2893614 spots for SRR6892959.sra Read 2893622 spots for SRR6892959.sra Written 2893622 spots for SRR6892959.sra SRR ids: ['SRR6892959.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_usy2mohz SRR6892959.sra spots: 57872288 blocks: [[1, 2893614], [2893615, 5787228], [5787229, 8680842], [8680843, 11574456], [11574457, 14468070], [14468071, 17361684], [17361685, 20255298], [20255299, 23148912], [23148913, 26042526], [26042527, 28936140], [28936141, 31829754], [31829755, 34723368], [34723369, 37616982], [37616983, 40510596], [40510597, 43404210], [43404211, 46297824], [46297825, 49191438], [49191439, 52085052], [52085053, 54978666], [54978667, 57872288]] SRR6892959 file size 10020041 SRR6892959 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 SRR6892959 SRR6892959_1.fastq Input file: SRR6892959_1.fastq trimmed: SRR6892959-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 Fri Dec 6 13:40:46 2024 >> started Fri Dec 6 13:41:29 2024 >> done (43.650s) 57872288 reads processed; of these: 10552 ( 0.02%) short reads filtered out after trimming by size control 22 ( 0.00%) empty reads filtered out after trimming by size control 57861714 (99.98%) reads available; of these: 1749458 ( 3.02%) trimmed reads available after processing 56112256 (96.98%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 5608 0.01% 19 7805 0.01% 20 9351 0.02% 21 3304 0.01% 22 1483 0.00% 23 8441 0.01% 24 4134 0.01% 25 4999 0.01% 26 4876 0.01% 27 40055 0.07% 28 4144 0.01% 29 875 0.00% 30 1329 0.00% 31 2740 0.00% 32 5567 0.01% 33 40840 0.07% 34 54813 0.09% 35 22066 0.04% 36 11124 0.02% 37 25536 0.04% 38 18240 0.03% 39 26827 0.05% 40 9578 0.02% 41 72092 0.12% 42 25504 0.04% 43 306255 0.53% 44 77960 0.13% 45 19546 0.03% 46 38677 0.07% 47 433313 0.75% 48 287916 0.50% 49 174460 0.30% 50 56112256 96.98% 57861714 reads passed initial QC criterion=sequence-density sequence-density=98.15 sequence-density-rank=1 fanout-score=39.75 fanout-score-rank=2 prefix-density=98.54 prefix-fanout=39.6 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGCCAAT criterion=fanout-score sequence-density=4.41 sequence-density-rank=2 fanout-score=88.22 fanout-score-rank=1 prefix-density=98.56 prefix-fanout=3.9 sequence=GAATTCTCGGGGGCCAAGGAACT 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGCCAAT -o SRR6892959 - Input file: STDIN trimmed: SRR6892959-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGCCAAT -- 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 Fri Dec 6 13:42:58 2024 >> started Fri Dec 6 13:44:07 2024 >> done (68.931s) 56692791 reads processed; of these: 143164 ( 0.25%) short reads filtered out after trimming by size control 371 ( 0.00%) empty reads filtered out after trimming by size control 56549256 (99.75%) reads available; of these: 56231764 (99.44%) trimmed reads available after processing 317492 ( 0.56%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 150009 0.27% 19 222694 0.39% 20 29526308 52.21% 21 26247714 46.42% 22 80402 0.14% 23 26126 0.05% 24 5960 0.01% 25 2532 0.00% 26 1501 0.00% 27 5670 0.01% 28 878 0.00% 29 395 0.00% 30 449 0.00% 31 453 0.00% 32 772 0.00% 33 1186 0.00% 34 5949 0.01% 35 11051 0.02% 36 5101 0.01% 37 5073 0.01% 38 2523 0.00% 39 4344 0.01% 40 1180 0.00% 41 4374 0.01% 42 2666 0.00% 43 5045 0.01% 44 2534 0.00% 45 1730 0.00% 46 2616 0.00% 47 3471 0.01% 48 1843 0.00% 49 1152 0.00% 50 215555 0.38% criterion=sequence-density sequence-density=4.99 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=16 prefix-density=0.00 prefix-fanout=1.0 sequence=TACCTGGTTGATCCTGCCAGT criterion=fanout-score sequence-density=0.12 sequence-density-rank=8 fanout-score=64.08 fanout-score-rank=1 prefix-density=0.29 prefix-fanout=27.1 sequence=TGGAATTCTCGTATGCCGTCTTCTGCTTGA Started job on | Dec 06 13:44:32 Started mapping on | Dec 06 13:44:33 Finished on | Dec 06 13:46:11 Mapping speed, Million of reads per hour | 2120.26 Number of input reads | 57718179 Average input read length | 21 UNIQUE READS: Uniquely mapped reads number | 42858307 Uniquely mapped reads % | 74.25% Average mapped length | 20.42 Number of splices: Total | 1838562 Number of splices: Annotated (sjdb) | 1797835 Number of splices: GT/AG | 1820476 Number of splices: GC/AG | 17012 Number of splices: AT/AC | 998 Number of splices: Non-canonical | 76 Mismatch rate per base, % | 0.06% Deletion rate per base | 0.00% Deletion average length | 1.32 Insertion rate per base | 0.00% Insertion average length | 1.00 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 6761021 % of reads mapped to multiple loci | 11.71% Number of reads mapped to too many loci | 6586328 % of reads mapped to too many loci | 11.41% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.50% % of reads unmapped: other | 0.12% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 8098851 8098851 8098851 N_multimapping 6761021 6761021 6761021 N_noFeature 1765184 2059169 41859921 N_ambiguous 761507 58103 3745 UnstrandedReadsAssigned:40331616 PositiveStrandReadsAssigned:40741035 NegativeStrandReadsAssigned:994641 Dataset is classified positive stranded MeadianReadLen=20 20thPercentileLength=20 echo kmer=19 SRR6892959 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: SRR6892959-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 57,718,179 reads, 43,339,337 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,248 rounds 52973 SRR6892959.ke.tsv 35125 SRR6892959.se.tsv 88098 total ==> SRR6892959.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 7.91075 0.277376 PNS24249 1928 1829 186.729 3.38285 PNS24246 1044 945 7.91075 0.277376 PNS24248 1044 945 7.91075 0.277376 PNS24244 1471 1372 676.06 16.3273 PNS24243 293 194 2 0.341595 KQK14069 1603 1504 1730.5 38.1248 KQK14071 474 375 56.4162 4.98489 ==> SRR6892959.se.tsv <== BRADI_1g14170v3 1695 BRADI_1g53295v3 29 BRADI_1g59795v3 190 BRADI_1g07683v3 0 BRADI_1g00485v3 29 BRADI_1g20270v3 2903 BRADI_1g74790v3 327 BRADI_1g09890v3 22 BRADI_1g77505v3 567 BRADI_1g48960v3 1 SRR6892959 completed mapping pipeline successfully