Starting /dee2/code/volunteer_pipeline.sh SRR8846530 current disk space = 1515385487360 free memory = 1570800576 SRR8846530 SRAfilesize 666206243a219bc8076a303a9c30322c SRR8846530.sra SRR8846530.sra file validated SRR8846530 is single end SRR8846530 is conventional basespace SRR8846530 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8846530_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 34.0345 35.0 35.0 35.0 32.0 35.0 2 34.46525 35.0 35.0 35.0 34.0 35.0 3 34.53675 35.0 35.0 35.0 35.0 35.0 4 34.6115 35.0 35.0 35.0 35.0 35.0 5 34.56475 35.0 35.0 35.0 34.0 35.0 6 39.1835 40.0 40.0 40.0 39.0 40.0 7 39.18925 40.0 40.0 40.0 39.0 40.0 8 39.25575 40.0 40.0 40.0 39.0 40.0 9 39.27725 40.0 40.0 40.0 39.0 40.0 10-14 39.30145 40.0 40.0 40.0 39.0 40.0 15-19 39.1851 40.0 39.8 40.0 38.8 40.0 20-24 38.9759 40.0 39.4 40.0 38.0 40.0 25-29 38.846999999999994 40.0 40.0 40.0 37.6 40.0 30-34 38.800149999999995 40.0 40.0 40.0 37.8 40.0 35-39 38.583800000000004 40.0 40.0 40.0 37.0 40.0 40-44 38.42815 40.0 39.6 40.0 36.8 40.0 45-49 38.282999999999994 40.0 39.2 40.0 36.0 40.0 50-54 38.219899999999996 40.0 39.0 40.0 36.0 40.0 55-59 38.11 40.0 39.0 40.0 36.0 40.0 60-64 37.9479 40.0 39.0 40.0 36.0 40.0 65-69 37.9276 40.0 39.0 40.0 36.0 40.0 70-74 37.71704999999999 40.0 39.0 40.0 34.8 40.0 75-79 37.749050000000004 40.0 39.0 40.0 35.6 40.0 80-84 37.68104999999999 40.0 39.0 40.0 34.6 40.0 85-89 37.77720000000001 40.0 39.0 40.0 35.6 40.0 90-94 37.707800000000006 40.0 39.0 40.0 35.2 40.0 95-99 37.525099999999995 40.0 39.0 40.0 34.4 40.0 100-104 35.065749999999994 37.0 35.4 38.4 30.6 38.6 105-109 37.36835 39.8 39.0 40.0 34.4 40.0 110-114 37.5062 40.0 39.0 40.0 34.8 40.0 115-119 37.26145 40.0 39.0 40.0 34.2 40.0 120-124 37.0168 40.0 39.0 40.0 34.0 40.0 125-129 36.7149 40.0 39.0 40.0 32.2 40.0 130-134 36.178599999999996 40.0 38.4 40.0 29.4 40.0 135-139 35.70354999999999 39.8 38.2 40.0 26.4 40.0 140-144 35.04515 39.0 37.8 40.0 14.8 40.0 145-149 34.116150000000005 39.0 36.6 40.0 4.2 40.0 150-151 26.614625000000004 33.0 19.0 38.0 2.0 39.5 >>END_MODULE >>Per sequence quality scores pass #Quality Count 5 1.0 6 4.0 7 5.0 8 7.0 9 10.0 10 15.0 11 15.0 12 15.0 13 12.0 14 10.0 15 5.0 16 1.0 17 4.0 18 5.0 19 2.0 20 5.0 21 5.0 22 10.0 23 5.0 24 16.0 25 12.0 26 19.0 27 21.0 28 26.0 29 32.0 30 31.0 31 45.0 32 54.0 33 72.0 34 95.0 35 94.0 36 146.0 37 228.0 38 501.0 39 2472.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 38.59077231695085 37.587763289869606 1.2788365095285856 22.542627883650955 2 19.875 38.95 23.25 17.925 3 14.85 38.425 27.200000000000003 19.525000000000002 4 17.549999999999997 35.449999999999996 26.6 20.4 5 15.725 39.525 25.174999999999997 19.575 6 15.0 44.574999999999996 23.575 16.85 7 14.45 45.824999999999996 23.025000000000002 16.7 8 13.075000000000001 45.225 23.625 18.075 9 14.774999999999999 43.125 25.775 16.325 10-14 15.545 34.260000000000005 30.06 20.135 15-19 14.485000000000001 30.65 35.49 19.375 20-24 12.475 31.240000000000002 37.945 18.34 25-29 15.055752787639381 34.13670683534177 32.916645832291614 17.89089454472724 30-34 16.377456618492776 34.98524778716808 29.03435515327299 19.60294044106616 35-39 16.818363672734545 35.522104420884176 27.2004400880176 20.459091818363675 40-44 17.776221677587156 35.612464362526886 26.06912419346771 20.542189766418247 45-49 18.386838683868387 34.84348434843484 25.722572257225725 21.04710471047105 50-54 17.722088835534215 34.94897959183674 25.730292116846737 21.598639455782312 55-59 16.833416708354175 36.7783891945973 24.71735867933967 21.670835417708854 60-64 16.990097029108732 35.47564269280784 24.397319195758726 23.136941082324697 65-69 18.658731746349268 35.087017403480694 23.419683936787358 22.834566913382677 70-74 17.513756878439217 35.5927963981991 23.75687843921961 23.13656828414207 75-79 18.46238495398159 34.61384553821529 23.149259703881555 23.774509803921568 80-84 18.232292917166866 36.394557823129254 21.82873149259704 23.544417767106843 85-89 18.529999999999998 35.58 21.495 24.395 90-94 17.875 35.46 21.755 24.91 95-99 17.845 35.57 21.490000000000002 25.095 100-104 18.045 36.015 20.97 24.97 105-109 18.18 36.61 20.54 24.67 110-114 18.44 34.845 21.16 25.555 115-119 18.709999999999997 34.83 21.015 25.445 120-124 18.790000000000003 34.36 20.915 25.935000000000002 125-129 19.189999999999998 33.135 21.26 26.415 130-134 18.825 33.71 21.23 26.235000000000003 135-139 19.115 33.125 21.404999999999998 26.355 140-144 18.02 33.01 21.735 27.235 145-149 17.965 33.64 21.905 26.490000000000002 150-151 15.262500000000001 35.2625 20.8 28.675 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.5 4 0.5 5 0.5 6 1.0 7 1.5 8 2.0 9 1.5 10 1.0 11 1.0 12 2.5 13 3.5 14 2.0 15 3.5 16 4.5 17 3.5 18 5.0 19 7.5 20 6.5 21 6.0 22 7.0 23 4.5 24 7.5 25 12.0 26 12.0 27 28.5 28 45.5 29 48.0 30 51.0 31 67.5 32 96.5 33 133.5 34 157.0 35 175.0 36 236.0 37 295.0 38 316.0 39 305.0 40 281.5 41 293.0 42 266.0 43 227.5 44 213.5 45 176.0 46 147.0 47 108.5 48 68.5 49 56.0 50 43.0 51 22.5 52 17.0 53 13.5 54 6.5 55 1.5 56 1.5 57 2.0 58 0.5 59 0.5 60 0.5 61 0.0 62 0.0 63 0.5 64 1.0 65 0.5 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 0.3 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 0.015 35-39 0.02 40-44 0.034999999999999996 45-49 0.01 50-54 0.04 55-59 0.05 60-64 0.03 65-69 0.02 70-74 0.05 75-79 0.04 80-84 0.04 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 84.65 #Duplication Level Percentage of deduplicated Percentage of total 1 92.20318960425281 78.05 2 4.90253987005316 8.3 3 1.447135262847017 3.675 4 0.5020673360897815 1.7000000000000002 5 0.29533372711163614 1.25 6 0.08860011813349085 0.44999999999999996 7 0.0 0.0 8 0.08860011813349085 0.6 9 0.05906674542232723 0.44999999999999996 >10 0.4134672179562906 5.525 >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 36 0.8999999999999999 No Hit CAAACATGTGGTAGATAAATATCAAGAGATGTGTAGCACATGACGTGTCT 21 0.525 No Hit ATTTAGACCTTCTTCATATTTAGTTTTATCTATTAATCGATAGTATCTAC 18 0.44999999999999996 No Hit GTAAAATTAACTTCAACTATTTGTATTATATCAAAATACTTCGGAGTTGA 17 0.42500000000000004 No Hit AACAAAAAGAGGTGTGTGTGTATATATAGTCCATAAACACGGGAAGTGGA 17 0.42500000000000004 No Hit GAAGAACAAAGATGCCCGGATTCATCTCACAAATAACCGAGGGATATTAC 16 0.4 No Hit GGCAGGGTAGCTTGGATGATTAATAAAGTTGAGCACACATACATAGAGAT 15 0.375 No Hit GTATAACAAACACTTTTATTCCACGTATACCCAATGTATATGCATGTACA 14 0.35000000000000003 No Hit GCAGCAAATTTTCTCTTCCCGCTGATTTTCAATACCAAACGATAACAGAG 13 0.325 No Hit GTTTCTTTTTATTTAGACCTTCTTCATATTTAGTTTTATCTATTAATCGA 12 0.3 No Hit CTTTATTCTGTCCCCTTATCTTTCATTCAGAAAAAGGAATGAATGGCTCG 11 0.27499999999999997 No Hit ATTTTGTTTCTTTTTATTTAGACCTTCTTCATATTTAGTTTTATCTATTA 11 0.27499999999999997 No Hit GTATAATATTACATGTATATGTGTGTATATGTGTAGTCAGGGTTCAAATG 10 0.25 No Hit AAACATGTGGTAGATAAATATCAAGAGATGTGTAGCACATGACGTGTCTC 10 0.25 No Hit CTAAATATTCAGTTAAGACCATTCCAAGGCTCCTTTTCGCCATGCATAAA 9 0.22499999999999998 No Hit AGACAGACAAACAGAGCCTCTGCCTTTCTTATATACTGATGGTTGGTTCA 9 0.22499999999999998 No Hit ATTCTGTCCCCTTATCTTTCATTCAGAAAAAGGAATGAATGGCTCGGCTA 8 0.2 No Hit AGCACACAATTGGATGATTTATTATACAGACTGTATGTAGGAGTAAGTAC 8 0.2 No Hit GAAACAACTAAATAACCTTTTTATTCGCTCCTCTAGTCCCAGAAGGATCC 8 0.2 No Hit GATGAAAATGGTATTATAATTATATAGTTGATGTCTTTTGGTCACAAGAT 6 0.15 No Hit GCTATGGCTATTTCCATATCTTTTTTTTAAGTAATGAGCCTATCCTCTCT 6 0.15 No Hit AAAGCAAATGTAGCGCATCACATCACAGATTCACAAAGTTCAACAGTACA 6 0.15 No Hit ACTTCAAAATCTGACAATCTTTTGTTCATAAGATCCTCGTAATTAATTTA 5 0.125 No Hit AGAACAAAGATGCCCGGATTCATCTCACAAATAACCGAGGGATATTACAC 5 0.125 No Hit ACCGGTAAATTATCATAATCAGAATTTGTCGACGAATTTGATATTCTTTT 5 0.125 No Hit CCTTTTCGAAATATACAATATTGCATTGGTCCATGTGTAAATCGATTTCA 5 0.125 No Hit GAAAACTCGAACCTGTGCTTGAAATTGTCCTTTACCGTTTCAATCCGATT 5 0.125 No Hit AAGAAAACATAACTACTTATGGAGTATTATTAGATAATTATTGCCGGCCT 5 0.125 No Hit CAACGATGAGAATATAGCTTCGATCTAAACGTATCCATTTTTTACATTGG 5 0.125 No Hit AAACAACTAAATAACCTTTTTATTCGCTCCTCTAGTCCCAGAAGGATCCA 5 0.125 No Hit AAGTTCAAACTTCACTTATTCATTGTACTTTAACCATACTGCCATACCAA 5 0.125 No Hit CGTTGCACATCATGGAATGGATTATTGACCAGTAATCACAGAGCTGCAAA 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 0.0 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 10-11 0.0 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 0.05 0.0 0.0 0.0 0.0 22-23 0.05 0.0 0.0 0.0 0.0 24-25 0.05 0.0 0.0 0.0 0.0 26-27 0.1 0.0 0.0 0.0 0.0 28-29 0.125 0.0 0.0 0.0 0.0 30-31 0.15 0.0 0.0 0.0 0.0 32-33 0.175 0.0 0.0 0.0 0.0 34-35 0.2 0.0 0.0 0.0 0.0 36-37 0.2625 0.0 0.0 0.0 0.0 38-39 0.32499999999999996 0.0 0.0 0.0 0.0 40-41 0.4125 0.0 0.0 0.0 0.0 42-43 0.525 0.0 0.0 0.0 0.0 44-45 0.6375 0.0 0.0 0.0 0.0 46-47 0.7 0.0 0.0 0.0 0.0 48-49 0.8 0.0 0.0 0.0 0.0 50-51 0.8625 0.0 0.0 0.0 0.0 52-53 0.9625 0.0 0.0 0.0 0.0 54-55 1.0750000000000002 0.0 0.0 0.0 0.0 56-57 1.3375 0.0 0.0 0.0 0.0 58-59 1.6125 0.0 0.0 0.0 0.0 60-61 1.8875000000000002 0.0 0.0 0.0 0.0 62-63 2.2875 0.0 0.0 0.0 0.0 64-65 2.5 0.0 0.0 0.0 0.0 66-67 2.8625 0.0 0.0 0.0 0.0 68-69 3.325 0.0 0.0 0.0 0.0 70-71 3.5999999999999996 0.0 0.0 0.0 0.0 72-73 4.0125 0.0 0.0 0.0 0.0 74-75 4.6375 0.0 0.0 0.0 0.0 76-77 5.237500000000001 0.0 0.0 0.0 0.0 78-79 5.875 0.0 0.0 0.0 0.0 80-81 6.5 0.0 0.0 0.0 0.0 82-83 7.4125 0.0 0.0 0.0 0.0 84-85 8.375 0.0 0.0 0.0 0.0 86-87 9.4 0.0 0.0 0.0 0.0 88-89 10.025 0.0 0.0 0.0 0.0 90-91 10.8625 0.0 0.0 0.0 0.0 92-93 11.75 0.0 0.0 0.0 0.0 94-95 12.8 0.0 0.0 0.0 0.0 96-97 14.0625 0.0 0.0 0.0 0.0 98-99 15.4 0.0 0.0 0.0 0.0 100-101 16.799999999999997 0.0 0.0 0.0 0.0 102-103 18.2375 0.0 0.0 0.0 0.0 104-105 19.3125 0.0 0.0 0.0 0.0 106-107 20.875 0.0 0.0 0.0 0.0 108-109 22.65 0.0 0.0 0.0 0.0 110-111 24.012500000000003 0.0 0.0 0.0 0.0 112-113 25.5875 0.0 0.0 0.0 0.0 114-115 26.9625 0.0 0.0 0.0 0.0 116-117 28.35 0.0 0.0 0.0 0.0 118-119 30.1 0.0 0.0 0.0 0.0 120-121 31.525 0.0 0.0 0.0 0.0 122-123 32.925 0.0 0.0 0.0 0.0 124-125 34.25 0.0 0.0 0.0 0.0 126-127 35.575 0.0 0.0 0.0 0.0 128-129 36.8125 0.0 0.0 0.0 0.0 130-131 38.3875 0.0 0.0 0.0 0.0 132-133 39.825 0.0 0.0 0.0 0.0 134-135 40.95 0.0 0.0 0.0 0.0 136-137 41.8 0.0 0.0 0.0 0.0 138-139 42.925 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TATCTCC 20 1.8793453E-6 145.0 145 CCAGTAT 115 0.0025531333 10.086957 140-144 CAGTATC 120 0.0036335043 9.666667 140-144 CACACCA 125 0.005090842 9.28 135-139 TCACACC 125 0.005090842 9.28 135-139 CCAGTCA 135 0.009581293 8.592592 130-134 TCCAGTC 135 0.009581293 8.592592 130-134 >>END_MODULE Rejected 1084553 READS because READLEN < 1 Read 1084553 spots for SRR8846530.sra Written 1084553 spots for SRR8846530.sra Rejected 1084553 READS because READLEN < 1 Read 1084553 spots for SRR8846530.sra Written 1084553 spots for SRR8846530.sra Rejected 1084553 READS because READLEN < 1 Read 1084553 spots for SRR8846530.sra Written 1084553 spots for SRR8846530.sra Rejected 1084553 READS because READLEN < 1 Read 1084553 spots for SRR8846530.sra Written 1084553 spots for SRR8846530.sra Rejected 1084553 READS because READLEN < 1 Read 1084553 spots for SRR8846530.sra Written 1084553 spots for SRR8846530.sra Rejected 1084553 READS because READLEN < 1 Read 1084553 spots for SRR8846530.sra Written 1084553 spots for SRR8846530.sra Rejected 1084553 READS because READLEN < 1 Read 1084553 spots for SRR8846530.sra Written 1084553 spots for SRR8846530.sra Rejected 1084553 READS because READLEN < 1 Read 1084553 spots for SRR8846530.sra Written 1084553 spots for SRR8846530.sra Rejected 1084553 READS because READLEN < 1 Read 1084553 spots for SRR8846530.sra Written 1084553 spots for SRR8846530.sra Rejected 1084564 READS because READLEN < 1 Read 1084564 spots for SRR8846530.sra Written 1084564 spots for SRR8846530.sra Rejected 1084553 READS because READLEN < 1 Read 1084553 spots for SRR8846530.sra Written 1084553 spots for SRR8846530.sra Rejected 1084553 READS because READLEN < 1 Read 1084553 spots for SRR8846530.sra Written 1084553 spots for SRR8846530.sra Rejected 1084553 READS because READLEN < 1 Read 1084553 spots for SRR8846530.sra Written 1084553 spots for SRR8846530.sra Rejected 1084553 READS because READLEN < 1 Read 1084553 spots for SRR8846530.sra Written 1084553 spots for SRR8846530.sra Rejected 1084553 READS because READLEN < 1 Read 1084553 spots for SRR8846530.sra Written 1084553 spots for SRR8846530.sra Rejected 1084553 READS because READLEN < 1 Read 1084553 spots for SRR8846530.sra Written 1084553 spots for SRR8846530.sra Rejected 1084553 READS because READLEN < 1 Read 1084553 spots for SRR8846530.sra Written 1084553 spots for SRR8846530.sra Rejected 1084553 READS because READLEN < 1 Read 1084553 spots for SRR8846530.sra Written 1084553 spots for SRR8846530.sra Rejected 1084553 READS because READLEN < 1 Read 1084553 spots for SRR8846530.sra Written 1084553 spots for SRR8846530.sra Rejected 1084553 READS because READLEN < 1 Read 1084553 spots for SRR8846530.sra Written 1084553 spots for SRR8846530.sra SRR ids: ['SRR8846530.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_hi3wcc9i SRR8846530.sra spots: 21691071 blocks: [[1, 1084553], [1084554, 2169106], [2169107, 3253659], [3253660, 4338212], [4338213, 5422765], [5422766, 6507318], [6507319, 7591871], [7591872, 8676424], [8676425, 9760977], [9760978, 10845530], [10845531, 11930083], [11930084, 13014636], [13014637, 14099189], [14099190, 15183742], [15183743, 16268295], [16268296, 17352848], [17352849, 18437401], [18437402, 19521954], [19521955, 20606507], [20606508, 21691071]] SRR8846530 file size 7328691 SRR8846530 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 SRR8846530 SRR8846530_1.fastq Input file: SRR8846530_1.fastq trimmed: SRR8846530-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 Thu Dec 12 02:56:51 2024 >> started Thu Dec 12 02:57:05 2024 >> done (13.692s) 21691071 reads processed; of these: 13892 ( 0.06%) short reads filtered out after trimming by size control 3095 ( 0.01%) empty reads filtered out after trimming by size control 21674084 (99.92%) reads available; of these: 13346430 (61.58%) trimmed reads available after processing 8327654 (38.42%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 2668 0.01% 19 7827 0.04% 20 2966 0.01% 21 3532 0.02% 22 4476 0.02% 23 5848 0.03% 24 7668 0.04% 25 9314 0.04% 26 10332 0.05% 27 10757 0.05% 28 12845 0.06% 29 13503 0.06% 30 15588 0.07% 31 19125 0.09% 32 20019 0.09% 33 21585 0.10% 34 23017 0.11% 35 24134 0.11% 36 27363 0.13% 37 25968 0.12% 38 27644 0.13% 39 29190 0.13% 40 29797 0.14% 41 31157 0.14% 42 31136 0.14% 43 31545 0.15% 44 32697 0.15% 45 32039 0.15% 46 33172 0.15% 47 33484 0.15% 48 33401 0.15% 49 34411 0.16% 50 34589 0.16% 51 34972 0.16% 52 36013 0.17% 53 36864 0.17% 54 37464 0.17% 55 38347 0.18% 56 39665 0.18% 57 42005 0.19% 58 43136 0.20% 59 43687 0.20% 60 45400 0.21% 61 47003 0.22% 62 48953 0.23% 63 49317 0.23% 64 50744 0.23% 65 52733 0.24% 66 52328 0.24% 67 53708 0.25% 68 55924 0.26% 69 58524 0.27% 70 61670 0.28% 71 64983 0.30% 72 67613 0.31% 73 72278 0.33% 74 75605 0.35% 75 79004 0.36% 76 79973 0.37% 77 83606 0.39% 78 84758 0.39% 79 88678 0.41% 80 90493 0.42% 81 90676 0.42% 82 92291 0.43% 83 96091 0.44% 84 99322 0.46% 85 102869 0.47% 86 106782 0.49% 87 109513 0.51% 88 112479 0.52% 89 115107 0.53% 90 114512 0.53% 91 116535 0.54% 92 118968 0.55% 93 121300 0.56% 94 124424 0.57% 95 128571 0.59% 96 132687 0.61% 97 137377 0.63% 98 140715 0.65% 99 144889 0.67% 100 148162 0.68% 101 155016 0.72% 102 150932 0.70% 103 151869 0.70% 104 156298 0.72% 105 157697 0.73% 106 158933 0.73% 107 163409 0.75% 108 161864 0.75% 109 165950 0.77% 110 164783 0.76% 111 167870 0.77% 112 164782 0.76% 113 166519 0.77% 114 162694 0.75% 115 164139 0.76% 116 163933 0.76% 117 163237 0.75% 118 158598 0.73% 119 151865 0.70% 120 5271 0.02% 121 5394 0.02% 122 5862 0.03% 123 5965 0.03% 124 6021 0.03% 125 6276 0.03% 126 6758 0.03% 127 7388 0.03% 128 7620 0.04% 129 8041 0.04% 130 8465 0.04% 131 8920 0.04% 132 9332 0.04% 133 9689 0.04% 134 10450 0.05% 135 11199 0.05% 136 12915 0.06% 137 13540 0.06% 138 16778 0.08% 139 16481 0.08% 140 19208 0.09% 141 22321 0.10% 142 24826 0.11% 143 29832 0.14% 144 37586 0.17% 145 50023 0.23% 146 62777 0.29% 147 85849 0.40% 148 151525 0.70% 149 298611 1.38% 150 4579604 21.13% 151 8327654 38.42% 21674084 reads passed initial QC criterion=sequence-density sequence-density=11.44 sequence-density-rank=1 fanout-score=35.35 fanout-score-rank=7 prefix-density=12.69 prefix-fanout=31.9 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACACCAGTATCTCGTATGCCGTCTTCTGCTTGAAAA criterion=fanout-score sequence-density=0.01 sequence-density-rank=15 fanout-score=187.59 fanout-score-rank=1 prefix-density=0.35 prefix-fanout=5.8 sequence=GAAACACACAAACACGTACCGGTAAATTATCATAATCAGAATTTGTCGACGAATTTGATATTCTTTTACAAAATATACTTATCTTAATATGTATAACCGGAGTTTATATTACATGCCCCTCTCCCAACGATAGTTGTAGTACTCTTATAATAGTAGTACTCATGAATACAGTTAATCCGGGTTGTTGGGAGAGATCACATGCATAAATACAACATGAAACAAACGTGTGAAAAAGGTACATAAAATCGGTGTGACCCGTTCTTGTATTATAAGAAATCAACTTGCTTAGGCCTTGCCGGACTCCTCACAACCCGGTGGCTTGAAGGCGATGAAGCTGATGCACTGCACTTGCCTGGTGTTGTCGAAGCCGATGATGCGGACATAGGC 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACACCAGTATCTCGTATGCCGTCTTCTGCTTGAAAA -o SRR8846530 - Input file: STDIN trimmed: SRR8846530-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACACCAGTATCTCGTATGCCGTCTTCTGCTTG -- 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 Thu Dec 12 02:58:13 2024 >> started Thu Dec 12 02:58:35 2024 >> done (21.690s) 18061737 reads processed; of these: 222 ( 0.00%) short reads filtered out after trimming by size control 4 ( 0.00%) empty reads filtered out after trimming by size control 18061511 (100.00%) reads available; of these: 3767551 (20.86%) trimmed reads available after processing 14293960 (79.14%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 2244 0.01% 19 6560 0.04% 20 2471 0.01% 21 2979 0.02% 22 3730 0.02% 23 4892 0.03% 24 6451 0.04% 25 7802 0.04% 26 8681 0.05% 27 8979 0.05% 28 10759 0.06% 29 11318 0.06% 30 13151 0.07% 31 16027 0.09% 32 16822 0.09% 33 18033 0.10% 34 19296 0.11% 35 20207 0.11% 36 22844 0.13% 37 21756 0.12% 38 23178 0.13% 39 24413 0.14% 40 24991 0.14% 41 26208 0.15% 42 26182 0.14% 43 26528 0.15% 44 27305 0.15% 45 26899 0.15% 46 27726 0.15% 47 28117 0.16% 48 28005 0.16% 49 28757 0.16% 50 29019 0.16% 51 29332 0.16% 52 30240 0.17% 53 30922 0.17% 54 31385 0.17% 55 32246 0.18% 56 33222 0.18% 57 35492 0.20% 58 36369 0.20% 59 36765 0.20% 60 37998 0.21% 61 39455 0.22% 62 41236 0.23% 63 41568 0.23% 64 42875 0.24% 65 44342 0.25% 66 43917 0.24% 67 45305 0.25% 68 46821 0.26% 69 49316 0.27% 70 51781 0.29% 71 54624 0.30% 72 56769 0.31% 73 60683 0.34% 74 63525 0.35% 75 66562 0.37% 76 67405 0.37% 77 70336 0.39% 78 71355 0.40% 79 74744 0.41% 80 76057 0.42% 81 76771 0.43% 82 77759 0.43% 83 80996 0.45% 84 83271 0.46% 85 86450 0.48% 86 89732 0.50% 87 91913 0.51% 88 95209 0.53% 89 96675 0.54% 90 95908 0.53% 91 97839 0.54% 92 100036 0.55% 93 102326 0.57% 94 104420 0.58% 95 108283 0.60% 96 111603 0.62% 97 115450 0.64% 98 117867 0.65% 99 121822 0.67% 100 124748 0.69% 101 130246 0.72% 102 126677 0.70% 103 127963 0.71% 104 132149 0.73% 105 132381 0.73% 106 133895 0.74% 107 136587 0.76% 108 135960 0.75% 109 138648 0.77% 110 137930 0.76% 111 140867 0.78% 112 139583 0.77% 113 140391 0.78% 114 136300 0.75% 115 136248 0.75% 116 136142 0.75% 117 133550 0.74% 118 130693 0.72% 119 128533 0.71% 120 132511 0.73% 121 133817 0.74% 122 132775 0.74% 123 136389 0.76% 124 141230 0.78% 125 137349 0.76% 126 137575 0.76% 127 134103 0.74% 128 133888 0.74% 129 131065 0.73% 130 127807 0.71% 131 126347 0.70% 132 125055 0.69% 133 121065 0.67% 134 116596 0.65% 135 116198 0.64% 136 116357 0.64% 137 116566 0.65% 138 118154 0.65% 139 116571 0.65% 140 117828 0.65% 141 119037 0.66% 142 123221 0.68% 143 125765 0.70% 144 128521 0.71% 145 136882 0.76% 146 157077 0.87% 147 229853 1.27% 148 351565 1.95% 149 180310 1.00% 150 2560934 14.18% 151 4730302 26.19% criterion=sequence-density sequence-density=0.77 sequence-density-rank=1 fanout-score=3.18 fanout-score-rank=40 prefix-density=0.91 prefix-fanout=2.7 sequence=TTCAAATGTACA criterion=fanout-score sequence-density=0.01 sequence-density-rank=31 fanout-score=218.28 fanout-score-rank=1 prefix-density=0.34 prefix-fanout=6.0 sequence=GAAACACACAAACACGTACCGGTAAATTATCATAATCAGAATTTGTCGACGAATTTGATATTCTTTTACAAAATATACTTATCTTAATATGTATAACCGGAGTTTATATTACATGCCCCTCTCCCAACGATAGTTGTAGTACTCTTATAATAGTAGTACTCATGAATACAGTTAATCCGGGTTGTTGGGAGAGATCACATGCATAAATACAACATGAAACAAACGTGTGAAAAAGGTACATAAAATCGGTGTGACCCGTTCTTGTATTATAAGAAATCAACTTGCTTAGGCCTTGCCGGACTCCTCACAACCCGGTGGCTTGAAGGCGATGAAGCTGATGCACTGCACTTGCCTGGTGTTGTCGAAGCCGATGATGCGGACATAGGC Started job on | Dec 12 02:59:04 Started mapping on | Dec 12 02:59:04 Finished on | Dec 12 02:59:29 Mapping speed, Million of reads per hour | 3121.04 Number of input reads | 21673858 Average input read length | 125 UNIQUE READS: Uniquely mapped reads number | 20040555 Uniquely mapped reads % | 92.46% Average mapped length | 126.05 Number of splices: Total | 116337 Number of splices: Annotated (sjdb) | 22890 Number of splices: GT/AG | 57635 Number of splices: GC/AG | 5494 Number of splices: AT/AC | 160 Number of splices: Non-canonical | 53048 Mismatch rate per base, % | 0.26% Deletion rate per base | 0.00% Deletion average length | 1.31 Insertion rate per base | 0.00% Insertion average length | 1.11 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1097325 % of reads mapped to multiple loci | 5.06% Number of reads mapped to too many loci | 167065 % of reads mapped to too many loci | 0.77% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.66% % of reads unmapped: other | 0.04% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 535978 535978 535978 N_multimapping 1097325 1097325 1097325 N_noFeature 929672 19244009 1169303 N_ambiguous 623574 1390 73214 UnstrandedReadsAssigned:18487309 PositiveStrandReadsAssigned:795156 NegativeStrandReadsAssigned:18798038 Dataset is classified negative stranded MeadianReadLen=139 20thPercentileLength=97 echo kmer=93 SRR8846530 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: SRR8846530-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 21,673,858 reads, 19,339,377 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,182 rounds 52973 SRR8846530.ke.tsv 35125 SRR8846530.se.tsv 88098 total ==> SRR8846530.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 544 26.8351 PNS24243 293 194 0 0 KQK14069 1603 1504 5991 269.594 KQK14071 474 375 0 0 ==> SRR8846530.se.tsv <== BRADI_1g14170v3 5966 BRADI_1g53295v3 73 BRADI_1g59795v3 121 BRADI_1g07683v3 0 BRADI_1g00485v3 18 BRADI_1g20270v3 905 BRADI_1g74790v3 127 BRADI_1g09890v3 19 BRADI_1g77505v3 319 BRADI_1g48960v3 1 SRR8846530 completed mapping pipeline successfully