Starting /dee2/code/volunteer_pipeline.sh SRR8846526 current disk space = 1508801413120 free memory = 1389308568 SRR8846526 SRAfilesize f8e782740de24932ad918a1ad86a1495 SRR8846526.sra SRR8846526.sra file validated SRR8846526 is single end SRR8846526 is conventional basespace SRR8846526 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8846526_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 40 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 34.0475 35.0 35.0 35.0 32.0 35.0 2 34.52675 35.0 35.0 35.0 35.0 35.0 3 34.5785 35.0 35.0 35.0 35.0 35.0 4 34.58225 35.0 35.0 35.0 35.0 35.0 5 34.598 35.0 35.0 35.0 34.0 35.0 6 39.37125 40.0 40.0 40.0 39.0 40.0 7 39.32075 40.0 40.0 40.0 39.0 40.0 8 39.37175 40.0 40.0 40.0 39.0 40.0 9 39.41175 40.0 40.0 40.0 39.0 40.0 10-14 39.36905 40.0 40.0 40.0 39.0 40.0 15-19 39.244150000000005 40.0 40.0 40.0 38.8 40.0 20-24 38.97025 40.0 39.4 40.0 38.0 40.0 25-29 38.82825 40.0 40.0 40.0 38.0 40.0 30-34 38.62819999999999 40.0 40.0 40.0 37.8 40.0 35-39 38.44045 40.0 40.0 40.0 37.0 40.0 40-44 38.285199999999996 40.0 39.8 40.0 36.8 40.0 45-49 38.02715 40.0 39.4 40.0 36.0 40.0 50-54 37.93545 40.0 39.2 40.0 36.0 40.0 55-59 37.8609 40.0 39.0 40.0 36.0 40.0 60-64 37.73865 40.0 39.0 40.0 35.6 40.0 65-69 37.610749999999996 40.0 39.0 40.0 35.2 40.0 70-74 37.458450000000006 40.0 39.0 40.0 34.8 40.0 75-79 37.491949999999996 40.0 39.0 40.0 35.0 40.0 80-84 37.45185 40.0 39.0 40.0 34.4 40.0 85-89 37.5098 40.0 39.0 40.0 34.8 40.0 90-94 37.513149999999996 40.0 39.0 40.0 35.2 40.0 95-99 37.25405 40.0 39.0 40.0 34.0 40.0 100-104 34.86715 37.0 35.4 38.4 30.2 38.6 105-109 37.11105 39.8 39.0 40.0 34.0 40.0 110-114 37.28995 40.0 39.0 40.0 34.4 40.0 115-119 37.015100000000004 40.0 39.0 40.0 33.4 40.0 120-124 36.82675 40.0 39.0 40.0 34.0 40.0 125-129 36.487700000000004 40.0 39.0 40.0 31.6 40.0 130-134 36.01975 40.0 38.6 40.0 29.2 40.0 135-139 35.4133 39.8 38.2 40.0 21.8 40.0 140-144 34.7875 39.2 37.6 40.0 10.8 40.0 145-149 33.73175 39.0 36.4 40.0 2.0 40.0 150-151 26.590375 33.5 19.0 38.0 2.0 39.5 >>END_MODULE >>Per sequence quality scores pass #Quality Count 6 4.0 7 11.0 8 14.0 9 19.0 10 19.0 11 20.0 12 23.0 13 10.0 14 5.0 15 6.0 16 3.0 17 5.0 18 3.0 19 3.0 20 3.0 21 11.0 22 9.0 23 5.0 24 13.0 25 8.0 26 19.0 27 21.0 28 25.0 29 27.0 30 33.0 31 53.0 32 64.0 33 49.0 34 67.0 35 104.0 36 142.0 37 210.0 38 541.0 39 2451.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 38.50401606425703 37.148594377510044 1.179718875502008 23.167670682730922 2 18.9 38.35 24.425 18.325 3 16.075 36.75 29.225 17.95 4 16.75 38.2 25.724999999999998 19.325 5 17.25 39.4 24.45 18.9 6 15.2 44.0 23.75 17.05 7 12.950000000000001 48.025 24.474999999999998 14.549999999999999 8 13.600000000000001 45.15 23.724999999999998 17.525 9 14.549999999999999 43.075 25.5 16.875 10-14 15.950000000000001 35.144999999999996 29.37 19.535 15-19 14.05 31.574999999999996 35.575 18.8 20-24 12.754999999999999 30.995 37.785000000000004 18.465 25-29 14.245712285614282 33.78668933446672 33.476673833691684 18.490924546227312 30-34 17.088417683536708 35.072014402880576 29.240848169633928 18.59871974394879 35-39 16.900070021006304 35.35060518155447 27.613283985195558 20.13604081224367 40-44 17.793006853083888 36.22129958481317 25.476464408984047 20.509229153118905 45-49 18.652797919687952 35.50032504875731 24.863729559433914 20.98314747212082 50-54 17.93896948474237 36.05302651325663 24.402201100550275 21.605802901450723 55-59 17.608804402201102 37.40870435217609 23.401700850425215 21.5807903951976 60-64 18.18636522782974 35.957585154804185 22.90801780623218 22.948031811133898 65-69 18.46553966189857 35.49064719415825 22.98189456837051 23.06191857557267 70-74 18.240032017609686 36.03481915053279 22.73250287658212 22.9926459552754 75-79 19.003551598219197 35.25586513931269 22.300035015757093 23.44054824671102 80-84 18.174087043521762 36.133066533266636 22.11105552776388 23.581790895447725 85-89 19.335 35.695 20.91 24.060000000000002 90-94 19.134999999999998 35.949999999999996 20.925 23.990000000000002 95-99 19.41 35.355 20.855 24.38 100-104 18.605 36.235 21.175 23.985 105-109 19.675 35.33 20.96 24.035 110-114 19.009999999999998 35.31 20.635 25.045 115-119 19.79 34.475 20.71 25.025 120-124 19.86 34.435 21.02 24.685000000000002 125-129 20.165 32.485 21.805 25.545 130-134 20.51 32.72 22.055 24.715 135-139 20.424999999999997 32.87 22.025 24.68 140-144 20.21 33.83 21.38 24.58 145-149 19.365 33.465 22.145 25.025 150-151 16.9125 35.462500000000006 21.099999999999998 26.525 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.5 2 1.0 3 1.0 4 1.0 5 0.5 6 2.5 7 3.0 8 2.0 9 2.0 10 2.0 11 2.0 12 2.5 13 4.0 14 5.0 15 4.5 16 4.5 17 6.0 18 7.5 19 6.5 20 3.5 21 7.5 22 9.0 23 7.0 24 7.0 25 8.5 26 12.0 27 29.0 28 42.5 29 38.0 30 50.5 31 74.0 32 97.0 33 129.0 34 154.5 35 173.5 36 218.5 37 277.5 38 296.0 39 291.5 40 304.0 41 286.5 42 266.0 43 254.0 44 205.5 45 165.0 46 135.5 47 110.0 48 91.5 49 72.5 50 50.0 51 25.5 52 16.0 53 11.5 54 4.5 55 2.5 56 3.5 57 4.0 58 2.5 59 2.0 60 2.0 61 0.5 62 0.5 63 0.5 64 0.0 65 0.0 66 0.0 67 0.0 68 0.0 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 0.4 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.005 30-34 0.02 35-39 0.03 40-44 0.045 45-49 0.015 50-54 0.05 55-59 0.05 60-64 0.034999999999999996 65-69 0.03 70-74 0.055 75-79 0.045 80-84 0.05 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 85.15 #Duplication Level Percentage of deduplicated Percentage of total 1 92.89489136817382 79.10000000000001 2 4.315913094539049 7.35 3 1.0569583088667058 2.7 4 0.7046388725778039 2.4 5 0.2935995302407516 1.25 6 0.1467997651203758 0.75 7 0.02935995302407516 0.17500000000000002 8 0.11743981209630064 0.8 9 0.08807985907222549 0.675 >10 0.35231943628890194 4.8 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source GCGAACAAAACTTTGCTCATTCTTTTTTCATTCATTCATAGGGATAGCGA 37 0.9249999999999999 No Hit CAAACATGTGGTAGATAAATATCAAGAGATGTGTAGCACATGACGTGTCT 29 0.7250000000000001 No Hit GTAAAATTAACTTCAACTATTTGTATTATATCAAAATACTTCGGAGTTGA 21 0.525 No Hit CTTTATTCTGTCCCCTTATCTTTCATTCAGAAAAAGGAATGAATGGCTCG 14 0.35000000000000003 No Hit AGTTAAACCAGGGCGATTTTATTTATGGGGGGTTACAAGCATGGCATGGG 13 0.325 No Hit ATATGTTAGCGGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCA 13 0.325 No Hit GATGAAAATGGTATTATAATTATATAGTTGATGTCTTTTGGTCACAAGAT 12 0.3 No Hit GCAGCAAATTTTCTCTTCCCGCTGATTTTCAATACCAAACGATAACAGAG 12 0.3 No Hit ATTCTGTCCCCTTATCTTTCATTCAGAAAAAGGAATGAATGGCTCGGCTA 11 0.27499999999999997 No Hit ATTTAGACCTTCTTCATATTTAGTTTTATCTATTAATCGATAGTATCTAC 10 0.25 No Hit CCATAATACCATCATTTTTAGCTGTGGAGTAGACAGTACAAGTTACCGAT 10 0.25 No Hit AGGGAAAGGAAAGCTGCGAATTCATCCATTATTACGAGTGATAGATCATT 10 0.25 No Hit GACAGCAAGTCGAAAGTTTCTCATAGCAGCAGCAGGATACATGGAAGGAA 9 0.22499999999999998 No Hit AAGAAAACATAACTACTTATGGAGTATTATTAGATAATTATTGCCGGCCT 9 0.22499999999999998 No Hit ATTTTGTTTCTTTTTATTTAGACCTTCTTCATATTTAGTTTTATCTATTA 9 0.22499999999999998 No Hit ACCGCTAAACCGAATATATTAATCAATCCACGTCGCAGAGACGTGGCACT 8 0.2 No Hit GTTTCTTTTTATTTAGACCTTCTTCATATTTAGTTTTATCTATTAATCGA 8 0.2 No Hit CTAAATATTCAGTTAAGACCATTCCAAGGCTCCTTTTCGCCATGCATAAA 8 0.2 No Hit AGATAGTAAGACCACACGATAAATTTCATTCCATGCAAACACGTACGGAC 8 0.2 No Hit AAGAAAGAAAGTGATTTTCTCAACTCTTTCAAACTTTTAGGAATTCACAT 7 0.17500000000000002 No Hit AATGAACCATTGCTGATTACTATTACTGATTGGAATGTAACACACATGGG 6 0.15 No Hit GGATAGTAAGACCACACGATAAATTTCATTCCATGCAAACACGTACGGAC 6 0.15 No Hit GATAGTAAGACCACACGATAAATTTCATTCCATGCAAACACGTACGGACT 6 0.15 No Hit AGCACACAATTGGATGATTTATTATACAGACTGTATGTAGGAGTAAGTAC 6 0.15 No Hit GAAACAACTAAATAACCTTTTTATTCGCTCCTCTAGTCCCAGAAGGATCC 6 0.15 No Hit GTATAATATTACATGTATATGTGTGTATATGTGTAGTCAGGGTTCAAATG 5 0.125 No Hit GAACAAAGCAAGATACGATCCAAATTAATTGCCACCACACAACAGACGTG 5 0.125 No Hit CTCAACTCTTTCAAACTTTTAGGAATTCACATATGCAAGCTAGCTCCTCG 5 0.125 No Hit AGACAACCACATAACATGCATAATAACAAAGGTGCCAAGCAACCACAGGT 5 0.125 No Hit CATCCTACCATTCCATTAGGGAATATCTTTTTGAAGATTAAGAAAGATCC 5 0.125 No Hit CACATAAACACTTGATATGTTTTTTCTTCTTGCGCTAATTAAAACCAGAC 5 0.125 No Hit CATCCATTATTACGAGTGATAGATCATTAAGCGGAATACAAGCAAAAGGT 5 0.125 No Hit GGAATTACATTACATATATATAAACTCCAGATAAAGATCTGACACAGATA 5 0.125 No Hit AAACCGAACGAGCGGATTTTTTTACCTCGTCACAACAATTACAATGACAC 5 0.125 No Hit CCAAAAGTTGTTTACTTAATTAGGGTGGTAAAACACAGTATACTTTCTGA 5 0.125 No Hit >>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 0.0 0.0 0.0 0.0 2 0.025 0.0 0.0 0.0 0.0 3 0.025 0.0 0.0 0.0 0.0 4 0.025 0.0 0.0 0.0 0.0 5 0.025 0.0 0.0 0.0 0.0 6 0.025 0.0 0.0 0.0 0.0 7 0.025 0.0 0.0 0.0 0.0 8 0.025 0.0 0.0 0.0 0.0 9 0.025 0.0 0.0 0.0 0.0 10-11 0.025 0.0 0.0 0.0 0.0 12-13 0.025 0.0 0.0 0.0 0.0 14-15 0.025 0.0 0.0 0.0 0.0 16-17 0.025 0.0 0.0 0.0 0.0 18-19 0.025 0.0 0.0 0.0 0.0 20-21 0.025 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.05 0.0 0.0 0.0 0.0 32-33 0.0875 0.0 0.0 0.0 0.0 34-35 0.1375 0.0 0.0 0.0 0.0 36-37 0.15 0.0 0.0 0.0 0.0 38-39 0.16249999999999998 0.0 0.0 0.0 0.0 40-41 0.2375 0.0 0.0 0.0 0.0 42-43 0.3375 0.0 0.0 0.0 0.0 44-45 0.4625 0.0 0.0 0.0 0.0 46-47 0.6125 0.0 0.0 0.0 0.0 48-49 0.65 0.0 0.0 0.0 0.0 50-51 0.825 0.0 0.0 0.0 0.0 52-53 1.075 0.0 0.0 0.0 0.0 54-55 1.2374999999999998 0.0 0.0 0.0 0.0 56-57 1.425 0.0 0.0 0.0 0.0 58-59 1.65 0.0 0.0 0.0 0.0 60-61 1.9125 0.0 0.0 0.0 0.0 62-63 2.2125 0.0 0.0 0.0 0.0 64-65 2.775 0.0 0.0 0.0 0.0 66-67 3.1625 0.0 0.0 0.0 0.0 68-69 3.6125 0.0 0.0 0.0 0.0 70-71 4.275 0.0 0.0 0.0 0.0 72-73 4.862500000000001 0.0 0.0 0.0 0.0 74-75 5.7125 0.0 0.0 0.0 0.0 76-77 6.375 0.0 0.0 0.0 0.0 78-79 7.0625 0.0 0.0 0.0 0.0 80-81 8.0125 0.0 0.0 0.0 0.0 82-83 8.7375 0.0 0.0 0.0 0.0 84-85 9.525 0.0 0.0 0.0 0.0 86-87 10.2375 0.0 0.0 0.0 0.0 88-89 11.0625 0.0 0.0 0.0 0.0 90-91 11.7375 0.0 0.0 0.0 0.0 92-93 12.725 0.0 0.0 0.0 0.0 94-95 13.8125 0.0 0.0 0.0 0.0 96-97 14.912500000000001 0.0 0.0 0.0 0.0 98-99 16.1375 0.0 0.0 0.0 0.0 100-101 17.8375 0.0 0.0 0.0 0.0 102-103 19.275 0.0 0.0 0.0 0.0 104-105 20.6625 0.0 0.0 0.0 0.0 106-107 21.9375 0.0 0.0 0.0 0.0 108-109 23.1625 0.0 0.0 0.0 0.0 110-111 24.262500000000003 0.0 0.0 0.0 0.0 112-113 25.799999999999997 0.0 0.0 0.0 0.0 114-115 27.3625 0.0 0.0 0.0 0.0 116-117 28.675 0.0 0.0 0.0 0.0 118-119 30.025 0.0 0.0 0.0 0.0 120-121 31.2125 0.0 0.0 0.0 0.0 122-123 32.45 0.0 0.0 0.0 0.0 124-125 34.075 0.0 0.0 0.0 0.0 126-127 35.7125 0.0 0.0 0.0 0.0 128-129 37.275 0.0 0.0 0.0 0.0 130-131 38.8 0.0 0.0 0.0 0.0 132-133 40.0125 0.0 0.0 0.0 0.0 134-135 41.4875 0.0 0.0 0.0 0.0 136-137 42.8625 0.0 0.0 0.0 0.0 138-139 44.05 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GCGAACA 10 0.006577216 146.82278 1 TAGCGGA 15 1.14152615E-4 144.9875 7 AAACTTT 15 1.14152615E-4 144.9875 8 TATGTTA 15 1.14152615E-4 144.9875 2 GCGGAAA 15 1.14152615E-4 144.9875 9 TGTTAGC 15 1.14152615E-4 144.9875 4 AACTTTG 15 1.14152615E-4 144.9875 9 CGAACAA 10 0.006832588 144.9875 2 GTTAGCG 15 1.14152615E-4 144.9875 5 ATGTTAG 15 1.14152615E-4 144.9875 3 TTAGCGG 15 1.14152615E-4 144.9875 6 AGCGGAA 20 3.5889345E-4 108.74062 8 ATATGTT 25 8.283309E-4 88.09367 1 CTTTTTT 65 8.415773E-6 56.4703 1 AAAAAAA 180 1.1807733E-5 9.665833 135-139 >>END_MODULE Rejected 1140641 READS because READLEN < 1 Read 1140641 spots for SRR8846526.sra Written 1140641 spots for SRR8846526.sra Rejected 1140641 READS because READLEN < 1 Read 1140641 spots for SRR8846526.sra Written 1140641 spots for SRR8846526.sra Rejected 1140641 READS because READLEN < 1 Read 1140641 spots for SRR8846526.sra Written 1140641 spots for SRR8846526.sra Rejected 1140641 READS because READLEN < 1 Read 1140641 spots for SRR8846526.sra Written 1140641 spots for SRR8846526.sra Rejected 1140641 READS because READLEN < 1 Read 1140641 spots for SRR8846526.sra Written 1140641 spots for SRR8846526.sra Rejected 1140641 READS because READLEN < 1 Read 1140641 spots for SRR8846526.sra Written 1140641 spots for SRR8846526.sra Rejected 1140641 READS because READLEN < 1 Read 1140641 spots for SRR8846526.sra Written 1140641 spots for SRR8846526.sra Rejected 1140641 READS because READLEN < 1 Read 1140641 spots for SRR8846526.sra Written 1140641 spots for SRR8846526.sra Rejected 1140641 READS because READLEN < 1 Read 1140641 spots for SRR8846526.sra Written 1140641 spots for SRR8846526.sra Rejected 1140641 READS because READLEN < 1 Read 1140641 spots for SRR8846526.sra Written 1140641 spots for SRR8846526.sra Rejected 1140641 READS because READLEN < 1 Read 1140641 spots for SRR8846526.sra Written 1140641 spots for SRR8846526.sra Rejected 1140641 READS because READLEN < 1 Read 1140641 spots for SRR8846526.sra Written 1140641 spots for SRR8846526.sra Rejected 1140641 READS because READLEN < 1 Read 1140641 spots for SRR8846526.sra Written 1140641 spots for SRR8846526.sra Rejected 1140641 READS because READLEN < 1 Read 1140641 spots for SRR8846526.sra Written 1140641 spots for SRR8846526.sra Rejected 1140641 READS because READLEN < 1 Read 1140641 spots for SRR8846526.sra Written 1140641 spots for SRR8846526.sra Rejected 1140645 READS because READLEN < 1 Read 1140645 spots for SRR8846526.sra Written 1140645 spots for SRR8846526.sra Rejected 1140641 READS because READLEN < 1 Read 1140641 spots for SRR8846526.sra Written 1140641 spots for SRR8846526.sra Rejected 1140641 READS because READLEN < 1 Read 1140641 spots for SRR8846526.sra Written 1140641 spots for SRR8846526.sra Rejected 1140641 READS because READLEN < 1 Read 1140641 spots for SRR8846526.sra Written 1140641 spots for SRR8846526.sra Rejected 1140641 READS because READLEN < 1 Read 1140641 spots for SRR8846526.sra Written 1140641 spots for SRR8846526.sra SRR ids: ['SRR8846526.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_knvucsbh SRR8846526.sra spots: 22812824 blocks: [[1, 1140641], [1140642, 2281282], [2281283, 3421923], [3421924, 4562564], [4562565, 5703205], [5703206, 6843846], [6843847, 7984487], [7984488, 9125128], [9125129, 10265769], [10265770, 11406410], [11406411, 12547051], [12547052, 13687692], [13687693, 14828333], [14828334, 15968974], [15968975, 17109615], [17109616, 18250256], [18250257, 19390897], [19390898, 20531538], [20531539, 21672179], [21672180, 22812824]] SRR8846526 file size 7708817 SRR8846526 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 SRR8846526 SRR8846526_1.fastq Input file: SRR8846526_1.fastq trimmed: SRR8846526-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 Dec 9 06:56:23 2024 >> started Mon Dec 9 06:57:52 2024 >> done (89.451s) 22812824 reads processed; of these: 9804 ( 0.04%) short reads filtered out after trimming by size control 3011 ( 0.01%) empty reads filtered out after trimming by size control 22800009 (99.94%) reads available; of these: 13994515 (61.38%) trimmed reads available after processing 8805494 (38.62%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 2464 0.01% 19 9584 0.04% 20 2547 0.01% 21 3232 0.01% 22 4140 0.02% 23 5804 0.03% 24 7953 0.03% 25 10008 0.04% 26 11095 0.05% 27 11605 0.05% 28 14278 0.06% 29 15075 0.07% 30 17778 0.08% 31 21143 0.09% 32 22438 0.10% 33 23971 0.11% 34 26089 0.11% 35 27221 0.12% 36 30730 0.13% 37 29708 0.13% 38 31670 0.14% 39 33259 0.15% 40 34231 0.15% 41 36153 0.16% 42 36236 0.16% 43 36752 0.16% 44 38528 0.17% 45 37455 0.16% 46 38869 0.17% 47 38886 0.17% 48 39421 0.17% 49 39849 0.17% 50 39959 0.18% 51 40219 0.18% 52 41130 0.18% 53 42180 0.18% 54 42831 0.19% 55 43678 0.19% 56 45331 0.20% 57 48064 0.21% 58 48733 0.21% 59 49976 0.22% 60 51238 0.22% 61 52280 0.23% 62 55204 0.24% 63 57731 0.25% 64 60006 0.26% 65 62564 0.27% 66 62161 0.27% 67 64634 0.28% 68 67957 0.30% 69 70471 0.31% 70 74002 0.32% 71 77748 0.34% 72 79700 0.35% 73 84475 0.37% 74 89075 0.39% 75 93180 0.41% 76 92645 0.41% 77 96020 0.42% 78 96775 0.42% 79 100933 0.44% 80 100834 0.44% 81 101487 0.45% 82 102707 0.45% 83 105271 0.46% 84 107556 0.47% 85 111637 0.49% 86 112270 0.49% 87 113570 0.50% 88 116231 0.51% 89 118916 0.52% 90 121111 0.53% 91 123519 0.54% 92 125613 0.55% 93 128390 0.56% 94 130443 0.57% 95 136003 0.60% 96 141574 0.62% 97 146696 0.64% 98 149785 0.66% 99 154766 0.68% 100 157411 0.69% 101 160385 0.70% 102 152318 0.67% 103 151107 0.66% 104 151167 0.66% 105 151889 0.67% 106 151860 0.67% 107 154354 0.68% 108 153140 0.67% 109 157754 0.69% 110 158582 0.70% 111 163915 0.72% 112 161476 0.71% 113 164071 0.72% 114 161870 0.71% 115 167232 0.73% 116 167863 0.74% 117 169461 0.74% 118 165790 0.73% 119 158735 0.70% 120 5304 0.02% 121 5383 0.02% 122 5730 0.03% 123 5941 0.03% 124 5939 0.03% 125 6201 0.03% 126 6732 0.03% 127 7296 0.03% 128 7440 0.03% 129 8053 0.04% 130 8523 0.04% 131 8936 0.04% 132 9345 0.04% 133 9787 0.04% 134 10489 0.05% 135 11136 0.05% 136 12691 0.06% 137 13558 0.06% 138 16686 0.07% 139 16587 0.07% 140 19176 0.08% 141 21749 0.10% 142 24455 0.11% 143 29596 0.13% 144 36940 0.16% 145 48688 0.21% 146 61905 0.27% 147 84323 0.37% 148 150453 0.66% 149 291468 1.28% 150 4746174 20.82% 151 8805494 38.62% 22800009 reads passed initial QC criterion=sequence-density sequence-density=11.34 sequence-density-rank=1 fanout-score=35.37 fanout-score-rank=5 prefix-density=12.64 prefix-fanout=31.7 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGTAGATCTCGTATGCCGTCTTCTGCTTGAAAA criterion=fanout-score sequence-density=0.01 sequence-density-rank=20 fanout-score=66.19 fanout-score-rank=1 prefix-density=0.09 prefix-fanout=4.0 sequence=TATTTTGTTTCTTTTTATTTAGACCTTCTTCATATTTAGTTTTATCTATTAATCGATAGTATCTACCGGCGCGAACTCGAATTTGATCGCCTTCCATACTTCACAAGCTGCGGCTAGTTCAGGACTCCATTTGCAAGCTGCTCGGATAATTTCATTACCTTCACGAGCAAGATCGCGCCCTTCGTTACGAGCTT 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGTAGATCTCGTATGCCGTCTTCTGCTTGAAAA -o SRR8846526 - Input file: STDIN trimmed: SRR8846526-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGTAGATCTCGTATGCCGTCTTCTGCTTG -- 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 Dec 9 07:02:35 2024 >> started Mon Dec 9 07:04:36 2024 >> done (121.740s) 19000008 reads processed; of these: 155 ( 0.00%) short reads filtered out after trimming by size control 4 ( 0.00%) empty reads filtered out after trimming by size control 18999849 (100.00%) reads available; of these: 4023008 (21.17%) trimmed reads available after processing 14976841 (78.83%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 2068 0.01% 19 8024 0.04% 20 2177 0.01% 21 2682 0.01% 22 3467 0.02% 23 4831 0.03% 24 6666 0.04% 25 8292 0.04% 26 9292 0.05% 27 9716 0.05% 28 11906 0.06% 29 12666 0.07% 30 14912 0.08% 31 17624 0.09% 32 18706 0.10% 33 20018 0.11% 34 21975 0.12% 35 22869 0.12% 36 25605 0.13% 37 24931 0.13% 38 26480 0.14% 39 27859 0.15% 40 28679 0.15% 41 30289 0.16% 42 30197 0.16% 43 30741 0.16% 44 32159 0.17% 45 31337 0.16% 46 32675 0.17% 47 32550 0.17% 48 32959 0.17% 49 33273 0.18% 50 33374 0.18% 51 33859 0.18% 52 34592 0.18% 53 35523 0.19% 54 35869 0.19% 55 36508 0.19% 56 38029 0.20% 57 40596 0.21% 58 41117 0.22% 59 42007 0.22% 60 42818 0.23% 61 43581 0.23% 62 46226 0.24% 63 48452 0.26% 64 50729 0.27% 65 52863 0.28% 66 52118 0.27% 67 54278 0.29% 68 56817 0.30% 69 59071 0.31% 70 61808 0.33% 71 65146 0.34% 72 66991 0.35% 73 71239 0.37% 74 74619 0.39% 75 78657 0.41% 76 77622 0.41% 77 80762 0.43% 78 80975 0.43% 79 84795 0.45% 80 84543 0.44% 81 85233 0.45% 82 86085 0.45% 83 88007 0.46% 84 90109 0.47% 85 93912 0.49% 86 94161 0.50% 87 95380 0.50% 88 97472 0.51% 89 99873 0.53% 90 101369 0.53% 91 103687 0.55% 92 105611 0.56% 93 107920 0.57% 94 109291 0.58% 95 114236 0.60% 96 118881 0.63% 97 122623 0.65% 98 125157 0.66% 99 129874 0.68% 100 132184 0.70% 101 134428 0.71% 102 127696 0.67% 103 126661 0.67% 104 127286 0.67% 105 127241 0.67% 106 128052 0.67% 107 128940 0.68% 108 128412 0.68% 109 131519 0.69% 110 132575 0.70% 111 136806 0.72% 112 136263 0.72% 113 137675 0.72% 114 135541 0.71% 115 139188 0.73% 116 139534 0.73% 117 138509 0.73% 118 135978 0.72% 119 132763 0.70% 120 138385 0.73% 121 142316 0.75% 122 141448 0.74% 123 148491 0.78% 124 157333 0.83% 125 151051 0.80% 126 151081 0.80% 127 145377 0.77% 128 142778 0.75% 129 140356 0.74% 130 133457 0.70% 131 131284 0.69% 132 131038 0.69% 133 127511 0.67% 134 123125 0.65% 135 122734 0.65% 136 123247 0.65% 137 123639 0.65% 138 126005 0.66% 139 126302 0.66% 140 127519 0.67% 141 126911 0.67% 142 131748 0.69% 143 131531 0.69% 144 134707 0.71% 145 144023 0.76% 146 165437 0.87% 147 238205 1.25% 148 361025 1.90% 149 173546 0.91% 150 2611428 13.74% 151 4977470 26.20% criterion=sequence-density sequence-density=0.85 sequence-density-rank=1 fanout-score=2.58 fanout-score-rank=37 prefix-density=0.92 prefix-fanout=2.4 sequence=TTCAAATGTACA criterion=fanout-score sequence-density=0.01 sequence-density-rank=33 fanout-score=142.04 fanout-score-rank=1 prefix-density=0.24 prefix-fanout=6.8 sequence=AAGCATAAAACTTCAGAATTAGGTGCTTAAAGTATTTGGAACTGAGAATAACAGGGTACGAATATCACATATGGTATTACTGATGCAGTTTCAGCATACTAAAAAATAACAGGACGACTGATAGAGCAAACTGCACAGCTATTGCAGTTTTAGACTCGAAAACGAAGGAAAACCACAAAAGATAACAAAAGACCCGACTAGTATAAACTCAGCACGTAACTC Started job on | Dec 09 07:07:39 Started mapping on | Dec 09 07:07:40 Finished on | Dec 09 07:11:31 Mapping speed, Million of reads per hour | 355.32 Number of input reads | 22799850 Average input read length | 124 UNIQUE READS: Uniquely mapped reads number | 20847274 Uniquely mapped reads % | 91.44% Average mapped length | 125.85 Number of splices: Total | 129957 Number of splices: Annotated (sjdb) | 25645 Number of splices: GT/AG | 63641 Number of splices: GC/AG | 5971 Number of splices: AT/AC | 198 Number of splices: Non-canonical | 60147 Mismatch rate per base, % | 0.26% Deletion rate per base | 0.00% Deletion average length | 1.35 Insertion rate per base | 0.00% Insertion average length | 1.11 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1294988 % of reads mapped to multiple loci | 5.68% Number of reads mapped to too many loci | 212921 % of reads mapped to too many loci | 0.93% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.90% % of reads unmapped: other | 0.05% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 657588 657588 657588 N_multimapping 1294988 1294988 1294988 N_noFeature 1030957 20112634 1259396 N_ambiguous 563639 1704 65056 UnstrandedReadsAssigned:19252678 PositiveStrandReadsAssigned:732936 NegativeStrandReadsAssigned:19522822 Dataset is classified negative stranded MeadianReadLen=138 20thPercentileLength=95 echo kmer=91 SRR8846526 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=31 [quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20 [index] k-mer length: 31 [index] number of targets: 52,972 [index] number of k-mers: 66,720,672 [index] number of equivalence classes: 111,837 [quant] running in single-end mode [quant] will process file 1: SRR8846526-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 22,799,850 reads, 20,236,045 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,195 rounds 52973 SRR8846526.ke.tsv 35125 SRR8846526.se.tsv 88098 total ==> SRR8846526.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 543 25.4581 PNS24243 293 194 0 0 KQK14069 1603 1504 30200.3 1291.65 KQK14071 474 375 0 0 ==> SRR8846526.se.tsv <== BRADI_1g14170v3 30095 BRADI_1g53295v3 156 BRADI_1g59795v3 509 BRADI_1g07683v3 0 BRADI_1g00485v3 17 BRADI_1g20270v3 1617 BRADI_1g74790v3 98 BRADI_1g09890v3 40 BRADI_1g77505v3 503 BRADI_1g48960v3 0 SRR8846526 completed mapping pipeline successfully