Starting /dee2/code/volunteer_pipeline.sh SRR1033809 current disk space = 1548129669120 free memory = 1599454628 SRR1033809 SRAfilesize 0b60b343797a1c3476e0d562460b4336 SRR1033809.sra SRR1033809.sra file validated SRR1033809 is single end SRR1033809 is conventional basespace SRR1033809 read1 length is 35 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR1033809_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 35 %GC 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 70.99725 71.0 71.0 71.0 71.0 71.0 2 70.67175 71.0 71.0 71.0 71.0 71.0 3 70.69175 71.0 71.0 71.0 71.0 71.0 4 70.7975 71.0 71.0 71.0 71.0 71.0 5 70.69675 71.0 71.0 71.0 71.0 71.0 6 70.85125 71.0 71.0 71.0 71.0 71.0 7 70.72275 71.0 71.0 71.0 71.0 71.0 8 70.515 71.0 71.0 71.0 71.0 71.0 9 70.84675 71.0 71.0 71.0 71.0 71.0 10 70.67125 71.0 71.0 71.0 71.0 71.0 11 70.72225 71.0 71.0 71.0 71.0 71.0 12 70.31525 71.0 71.0 71.0 71.0 71.0 13 70.255 71.0 71.0 71.0 71.0 71.0 14 69.66925 71.0 71.0 71.0 71.0 71.0 15 70.34625 71.0 71.0 71.0 71.0 71.0 16 70.2595 71.0 71.0 71.0 71.0 71.0 17 70.08925 71.0 71.0 71.0 71.0 71.0 18 70.3485 71.0 71.0 71.0 71.0 71.0 19 70.33025 71.0 71.0 71.0 71.0 71.0 20 70.1375 71.0 71.0 71.0 71.0 71.0 21 70.324 71.0 71.0 71.0 71.0 71.0 22 70.295 71.0 71.0 71.0 71.0 71.0 23 69.918 71.0 71.0 71.0 71.0 71.0 24 70.056 71.0 71.0 71.0 71.0 71.0 25 69.87875 71.0 71.0 71.0 71.0 71.0 26 69.26725 71.0 71.0 71.0 70.0 71.0 27 69.9915 71.0 71.0 71.0 71.0 71.0 28 69.302 71.0 71.0 71.0 71.0 71.0 29 68.52725 71.0 71.0 71.0 61.0 71.0 30 70.0145 71.0 71.0 71.0 71.0 71.0 31 68.89675 71.0 71.0 71.0 65.0 71.0 32 69.99075 71.0 71.0 71.0 71.0 71.0 33 69.70375 71.0 71.0 71.0 71.0 71.0 34 69.2945 71.0 71.0 71.0 71.0 71.0 35 68.8265 71.0 71.0 71.0 64.0 71.0 >>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 >>END_MODULE >>Per sequence quality scores pass #Quality Count 42 1.0 43 0.0 44 1.0 45 0.0 46 0.0 47 0.0 48 0.0 49 0.0 50 0.0 51 0.0 52 2.0 53 0.0 54 1.0 55 0.0 56 1.0 57 0.0 58 1.0 59 1.0 60 5.0 61 10.0 62 11.0 63 17.0 64 25.0 65 54.0 66 51.0 67 137.0 68 241.0 69 491.0 70 1270.0 71 1680.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 40.949999999999996 58.95 0.075 0.025 2 30.049999999999997 30.8 19.275000000000002 19.875 3 38.275 22.175 20.200000000000003 19.35 4 33.7 31.5 19.1 15.7 5 24.05 31.7 17.2 27.05 6 25.6 21.224999999999998 37.4 15.775 7 29.599999999999998 28.749999999999996 20.549999999999997 21.099999999999998 8 20.3 19.55 37.075 23.075000000000003 9 23.525 31.924999999999997 27.275 17.275 10 39.25 19.275000000000002 20.025000000000002 21.45 11 24.25 17.549999999999997 31.775 26.424999999999997 12 24.675 19.3 28.075 27.950000000000003 13 31.81590795397699 25.41270635317659 16.58329164582291 26.18809404702351 14 28.57857857857858 36.53653653653654 20.145145145145147 14.73973973973974 15 31.73173173173173 26.601601601601605 18.543543543543546 23.123123123123122 16 26.876876876876878 36.93693693693694 19.344344344344343 16.84184184184184 17 27.988994497248626 24.96248124062031 31.21560780390195 15.832916458229116 18 36.66166166166166 23.523523523523522 17.792792792792792 22.02202202202202 19 40.965965965965964 17.34234234234234 25.900900900900904 15.79079079079079 20 29.87987987987988 21.57157157157157 32.78278278278278 15.765765765765765 21 23.48087021755439 28.257064266066518 30.857714428607153 17.404351087771943 22 27.224999999999998 18.375 28.349999999999998 26.05 23 27.888944472236116 28.23911955977989 25.912956478239117 17.958979489744873 24 22.025 18.075 39.35 20.549999999999997 25 13.356678339169584 15.08254127063532 52.32616308154077 19.23461730865433 26 18.734367183591797 11.755877938969485 29.139569784892444 40.37018509254627 27 49.0622655663916 8.802200550137535 26.356589147286826 15.778944736184048 28 18.70935467733867 11.605802901450724 47.148574287143575 22.536268134067033 29 17.983991995998 35.842921460730366 20.38519259629815 25.78789394697349 30 26.663331665832917 6.078039019509754 47.44872436218109 19.809904952476238 31 46.54827413706853 5.877938969484743 24.212106053026513 23.36168084042021 32 13.838838838838837 4.3043043043043046 23.84884884884885 58.008008008008005 33 16.966966966966968 1.9019019019019021 28.803803803803802 52.327327327327325 34 40.94094094094094 0.8758758758758759 34.80980980980981 23.373373373373376 35 10.11011011011011 0.2752752752752753 56.63163163163163 32.98298298298298 >>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 0.5 17 1.0 18 1.0 19 1.0 20 1.0 21 0.5 22 0.0 23 0.0 24 1.0 25 2.0 26 2.0 27 1.5 28 1.0 29 1.0 30 7.5 31 14.0 32 14.0 33 23.0 34 32.0 35 32.0 36 56.5 37 81.0 38 81.0 39 110.0 40 139.0 41 207.0 42 275.0 43 275.0 44 336.5 45 398.0 46 398.0 47 481.0 48 564.0 49 564.0 50 693.0 51 822.0 52 822.0 53 915.0 54 1008.0 55 1008.0 56 701.5 57 395.0 58 395.0 59 278.0 60 161.0 61 111.5 62 62.0 63 62.0 64 43.5 65 25.0 66 25.0 67 18.0 68 11.0 69 11.0 70 8.5 71 6.0 72 6.0 73 3.5 74 1.0 75 1.0 76 1.0 77 1.0 78 1.0 79 0.5 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 0.05 14 0.1 15 0.1 16 0.1 17 0.05 18 0.1 19 0.1 20 0.1 21 0.025 22 0.0 23 0.05 24 0.0 25 0.05 26 0.05 27 0.025 28 0.05 29 0.05 30 0.05 31 0.05 32 0.1 33 0.1 34 0.1 35 0.1 >>END_MODULE >>Sequence Length Distribution pass #Length Count 35 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 72.6 #Duplication Level Percentage of deduplicated Percentage of total 1 92.32093663911846 67.025 2 4.235537190082645 6.15 3 1.0674931129476584 2.325 4 0.7575757575757576 2.1999999999999997 5 0.30991735537190085 1.125 6 0.17217630853994492 0.75 7 0.03443526170798898 0.17500000000000002 8 0.10330578512396695 0.6 9 0.06887052341597796 0.44999999999999996 >10 0.7575757575757576 10.299999999999999 >50 0.13774104683195593 6.2 >100 0.03443526170798898 2.7 >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 GGGGATGTAGCTCAGATGGTTCGTATGCCGTCTTC 108 2.7 No Hit GACACGACTCTCGGCAACGGATATCTTCGTATGCC 78 1.95 No Hit AGTTCTACAGTCCGACGATCTCGTATGCCGTCTTC 68 1.7000000000000002 Illumina PCR Primer Index 1 (95% over 22bp) GACACGACTCTCGGCAACGGATATCTCTCGTATGC 51 1.275 No Hit GGGGATGTAGCTCAGATGGTATCGTATGCCGTCTT 51 1.275 No Hit ACGACTCTCGGCAACGGATATCTTCGTATGCCGTC 50 1.25 No Hit GACACGACTCTCGGCAACGGATATTCGTATGCCGT 30 0.75 No Hit GGGGATGTAGCTCAGATGGTAGAGTCGTATGCCGT 29 0.7250000000000001 No Hit AGAATCTTGATGATGCTGCATTCGTATGCCGTCTT 28 0.7000000000000001 No Hit GACACGACTCTCGGCAACGGATATCGTATGCCGTC 27 0.675 No Hit ACGACTCTCGGCAACGGATATCTCTCGTATGCCGT 24 0.6 No Hit GGGGATGTAGCTCAGATGGTCGTATGCCGTCTTCT 23 0.575 No Hit ACACGACTCTCGGCAACGGATATCTTCGTATGCCG 19 0.475 No Hit AACGAACGAACGATTTGAACTCGTATGCCGTCTTC 18 0.44999999999999996 No Hit GGGGATGTAGCTCAGATGGTAGATCGTATGCCGTC 18 0.44999999999999996 No Hit GGGGATGTAGCTCAGATGGTAGTCGTATGCCGTCT 16 0.4 No Hit GACACGACTCTCGGCAACGGATATCTCGTATGCCG 16 0.4 No Hit GGGGATGTAGCTCAAATGGTATCGTATGCCGTCTT 13 0.325 No Hit GCGTCTGTAGTCCAACGGTTTCGTATGCCGTCTTC 13 0.325 No Hit GACACGACTCTCGGCAACGGATTCGTATGCCGTCT 13 0.325 No Hit GGGGATGTAGCTCAGATGGTAGAGCTCGTATGCCG 13 0.325 No Hit AGGGCTATAGCTCAGTTCGGTCGTATGCCGTCTTC 11 0.27499999999999997 No Hit ACACGACTCTCGGCAACGGATATCTCTCGTATGCC 11 0.27499999999999997 No Hit GGGGATGTAGCTCAAATGGTAGAGTCGTATGCCGT 10 0.25 No Hit ACGACTCTCGGCAACGGATATCTCGTATGCCGTCT 10 0.25 TruSeq Adapter, Index 25 (95% over 22bp) ACGACTCTCGGCAACGGATATTCGTATGCCGTCTT 10 0.25 No Hit GGGGATGTAGCTCAAATGGTAGATCGTATGCCGTC 10 0.25 No Hit AGTTCTACAGTCCGACGATCATCGTATGCCGTCTT 9 0.22499999999999998 No Hit ACCTGCTCTGATACCATGTTGTGATCGTATGCCGT 9 0.22499999999999998 No Hit GCGTCTGTAGTCCAACGGTTATCGTATGCCGTCTT 8 0.2 No Hit ACACGACTCTCGGCAACGGATATTCGTATGCCGTC 8 0.2 No Hit ACGAACGAACGATTTGAACTCGTATGCCGTCTTCT 8 0.2 No Hit GGTAGTTCGACCGCGGAATTCGTATGCCGTCTTCT 7 0.17500000000000002 No Hit ACGACTCTCGGCAACGGATATCTCGTCGTATGCCG 6 0.15 No Hit GGGATGTAGCTCAGATGGTATCGTATGCCGTCTTC 6 0.15 No Hit GGGATGTAGCTCAGATGGTTCGTATGCCGTCTTCT 6 0.15 No Hit GGGGATGTAGCTCAAATGGTTCGTATGCCGTCTTC 6 0.15 No Hit GAAAAGAAACGAAGATCGCGTTCGTATGCCGTCTT 6 0.15 No Hit GGGATTGTAGTTCAATTGGTCAGAGTCGTATGCCG 5 0.125 No Hit ACCGGGCACATTAGTGTCTGTCGTATGCCGTCTTC 5 0.125 No Hit GCGTCTGTAGTCCAACGGTTAGTCGTATGCCGTCT 5 0.125 No Hit GGTGGCTGTAGTTTAGTGGTGAGAATCGTATGCCG 5 0.125 No Hit ACACGACTCTCGGCAACGGATATCTCGTATGCCGT 5 0.125 No Hit GGTGGCTGTAGTTTAGTGGTGAGATCGTATGCCGT 5 0.125 No Hit GGTGGCTGTAGTTTAGTGGTCGTATGCCGTCTTCT 5 0.125 No Hit GGTAGTTCGACCGCGGAATTTTCGTATGCCGTCTT 5 0.125 No Hit GTTCTACAGTCCGACGATTCGTATGCCGTCTTCTG 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 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AGCTCAG 20 0.005388326 29.0 9 GACACGA 25 4.303467E-4 29.0 1 TCAGATG 20 0.005388326 29.0 12 CTCAGAT 20 0.005388326 29.0 11 GGGGATG 20 0.005388326 29.0 1 GCTCAGA 20 0.005388326 29.0 10 ACACGAC 30 0.0012503903 24.166668 2 CACGACT 30 0.0012503903 24.166668 3 GATCGTA 35 0.0030680934 20.714287 23 ACTCGTA 40 0.0066521973 18.125 23 GGCAACG 40 0.0066521973 18.125 13 TCGGCAA 40 0.0066521973 18.125 11 CTCTCGG 40 0.0066521973 18.125 8 ACTCTCG 40 0.0066521973 18.125 7 GCAACGG 40 0.0066521973 18.125 14 TCTCGGC 40 0.0066521973 18.125 9 CTCGGCA 40 0.0066521973 18.125 10 ACGACTC 40 0.0066521973 18.125 4 CGGCAAC 40 0.0066521973 18.125 12 AACGGAT 40 0.0066521973 18.125 16 >>END_MODULE Read 371470 spots for SRR1033809.sra Written 371470 spots for SRR1033809.sra Read 371470 spots for SRR1033809.sra Written 371470 spots for SRR1033809.sra Read 371470 spots for SRR1033809.sra Written 371470 spots for SRR1033809.sra Read 371470 spots for SRR1033809.sra Written 371470 spots for SRR1033809.sra Read 371470 spots for SRR1033809.sra Written 371470 spots for SRR1033809.sra Read 371470 spots for SRR1033809.sra Written 371470 spots for SRR1033809.sra Read 371470 spots for SRR1033809.sra Written 371470 spots for SRR1033809.sra Read 371470 spots for SRR1033809.sra Written 371470 spots for SRR1033809.sra Read 371470 spots for SRR1033809.sra Written 371470 spots for SRR1033809.sra Read 371470 spots for SRR1033809.sra Written 371470 spots for SRR1033809.sra Read 371470 spots for SRR1033809.sra Written 371470 spots for SRR1033809.sra Read 371470 spots for SRR1033809.sra Written 371470 spots for SRR1033809.sra Read 371470 spots for SRR1033809.sra Written 371470 spots for SRR1033809.sra Read 371470 spots for SRR1033809.sra Written 371470 spots for SRR1033809.sra Read 371470 spots for SRR1033809.sra Written 371470 spots for SRR1033809.sra Read 371470 spots for SRR1033809.sra Written 371470 spots for SRR1033809.sra Read 371484 spots for SRR1033809.sra Written 371484 spots for SRR1033809.sra Read 371470 spots for SRR1033809.sra Written 371470 spots for SRR1033809.sra Read 371470 spots for SRR1033809.sra Written 371470 spots for SRR1033809.sra Read 371470 spots for SRR1033809.sra Written 371470 spots for SRR1033809.sra SRR ids: ['SRR1033809.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_ya11bgqa SRR1033809.sra spots: 7429414 blocks: [[1, 371470], [371471, 742940], [742941, 1114410], [1114411, 1485880], [1485881, 1857350], [1857351, 2228820], [2228821, 2600290], [2600291, 2971760], [2971761, 3343230], [3343231, 3714700], [3714701, 4086170], [4086171, 4457640], [4457641, 4829110], [4829111, 5200580], [5200581, 5572050], [5572051, 5943520], [5943521, 6314990], [6314991, 6686460], [6686461, 7057930], [7057931, 7429414]] SRR1033809 file size 1027402 SRR1033809 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 SRR1033809 SRR1033809_1.fastq Input file: SRR1033809_1.fastq trimmed: SRR1033809-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 00:57:02 2024 >> started Sat Dec 7 00:57:07 2024 >> done (4.457s) 7429414 reads processed; of these: 0 ( 0.00%) short reads filtered out after trimming by size control 0 ( 0.00%) empty reads filtered out after trimming by size control 7429414 (100.00%) reads available; of these: 7429414 (100.00%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 35 7429414 100.00% 7429414 reads passed initial QC criterion=sequence-density sequence-density=44.11 sequence-density-rank=1 fanout-score=35.50 fanout-score-rank=2 prefix-density=84.78 prefix-fanout=18.5 sequence=TCGTATGCCGTCTTCTGCTTGAAAA criterion=fanout-score sequence-density=4.63 sequence-density-rank=3 fanout-score=40.18 fanout-score-rank=1 prefix-density=5.56 prefix-fanout=33.4 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 TCGTATGCCGTCTTCTGCTTGAAAA -o SRR1033809 - Input file: STDIN trimmed: SRR1033809-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TCGTATGCCGTCTTCTGCTTGAAAA -- 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 00:57:19 2024 >> started Sat Dec 7 00:57:26 2024 >> done (7.420s) 7099218 reads processed; of these: 193163 ( 2.72%) short reads filtered out after trimming by size control 6401 ( 0.09%) empty reads filtered out after trimming by size control 6899654 (97.19%) reads available; of these: 6462791 (93.67%) trimmed reads available after processing 436863 ( 6.33%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 247032 3.58% 19 283052 4.10% 20 496213 7.19% 21 1538800 22.30% 22 395553 5.73% 23 611451 8.86% 24 1839637 26.66% 25 368303 5.34% 26 301960 4.38% 27 195295 2.83% 28 106195 1.54% 29 50907 0.74% 30 14568 0.21% 31 11370 0.16% 32 2455 0.04% 33 0 0.00% 34 0 0.00% 35 436863 6.33% criterion=sequence-density sequence-density=13.66 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=15 prefix-density=0.00 prefix-fanout=1.0 sequence=TCGCTTGGTGCAGATCGGGACTCGTATGCCG criterion=fanout-score sequence-density=0.19 sequence-density-rank=16 fanout-score=150.99 fanout-score-rank=1 prefix-density=1.33 prefix-fanout=21.7 sequence=CGTATGCCGTCTTC Started job on | Dec 07 00:57:42 Started mapping on | Dec 07 00:57:43 Finished on | Dec 07 00:58:05 Mapping speed, Million of reads per hour | 1183.07 Number of input reads | 7229850 Average input read length | 23 UNIQUE READS: Uniquely mapped reads number | 2871753 Uniquely mapped reads % | 39.72% Average mapped length | 22.19 Number of splices: Total | 56320 Number of splices: Annotated (sjdb) | 6259 Number of splices: GT/AG | 53852 Number of splices: GC/AG | 1388 Number of splices: AT/AC | 4 Number of splices: Non-canonical | 1076 Mismatch rate per base, % | 0.57% Deletion rate per base | 0.02% Deletion average length | 1.23 Insertion rate per base | 0.00% Insertion average length | 1.01 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1564621 % of reads mapped to multiple loci | 21.64% Number of reads mapped to too many loci | 2212010 % of reads mapped to too many loci | 30.60% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 7.00% % of reads unmapped: other | 1.04% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 2793476 2793476 2793476 N_multimapping 1564621 1564621 1564621 N_noFeature 1559433 1663059 2759901 N_ambiguous 11734 2681 1081 UnstrandedReadsAssigned:1300586 PositiveStrandReadsAssigned:1206013 NegativeStrandReadsAssigned:110771 Dataset is classified positive stranded MeadianReadLen=23 20thPercentileLength=21 echo kmer=19 SRR1033809 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: SRR1033809-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 7,229,850 reads, 1,602,585 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 940 rounds 52973 SRR1033809.ke.tsv 35125 SRR1033809.se.tsv 88098 total ==> SRR1033809.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 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 6 2.37492 KQK14071 474 375 0 0 ==> SRR1033809.se.tsv <== BRADI_1g14170v3 7 BRADI_1g53295v3 1 BRADI_1g59795v3 0 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 10 BRADI_1g74790v3 11 BRADI_1g09890v3 1 BRADI_1g77505v3 0 BRADI_1g48960v3 0 SRR1033809 completed mapping pipeline successfully