Starting /dee2/code/volunteer_pipeline.sh SRR6941543 current disk space = 1551495688192 free memory = 1322515604 SRR6941543 SRAfilesize e16dbe5c9f9cf3845b48f98a52ec4b55 SRR6941543.sra SRR6941543.sra file validated SRR6941543 is single end SRR6941543 is conventional basespace SRR6941543 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6941543_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 101 %GC 48 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.2715 34.0 33.0 34.0 32.0 34.0 2 33.3475 34.0 33.0 34.0 33.0 34.0 3 33.0805 34.0 33.0 34.0 31.0 34.0 4 33.25425 34.0 33.0 34.0 32.0 34.0 5 33.2135 34.0 33.0 34.0 33.0 34.0 6 36.98075 38.0 37.0 38.0 36.0 38.0 7 37.3465 38.0 38.0 38.0 37.0 38.0 8 37.53425 38.0 38.0 38.0 37.0 38.0 9 37.515 38.0 38.0 38.0 38.0 38.0 10-11 37.556250000000006 38.0 38.0 38.0 38.0 38.0 12-13 37.5255 38.0 38.0 38.0 38.0 38.0 14-15 37.524 38.0 38.0 38.0 38.0 38.0 16-17 36.15575 38.0 37.5 38.0 27.0 38.0 18-19 36.851875 38.0 37.5 38.0 33.5 38.0 20-21 36.11 38.0 38.0 38.0 30.0 38.0 22-23 37.268625 38.0 38.0 38.0 36.5 38.0 24-25 37.45225 38.0 38.0 38.0 37.0 38.0 26-27 37.484875 38.0 38.0 38.0 37.5 38.0 28-29 37.510375 38.0 38.0 38.0 38.0 38.0 30-31 37.458625 38.0 38.0 38.0 38.0 38.0 32-33 37.353625 38.0 38.0 38.0 37.0 38.0 34-35 37.222125 38.0 38.0 38.0 37.0 38.0 36-37 37.177875 38.0 38.0 38.0 36.5 38.0 38-39 37.252875 38.0 38.0 38.0 37.0 38.0 40-41 37.174499999999995 38.0 38.0 38.0 37.0 38.0 42-43 37.138125 38.0 38.0 38.0 36.5 38.0 44-45 37.105125 38.0 38.0 38.0 36.0 38.0 46-47 36.979 38.0 38.0 38.0 36.0 38.0 48-49 37.1295 38.0 38.0 38.0 36.5 38.0 50-51 36.959500000000006 38.0 38.0 38.0 36.0 38.0 52-53 36.97475 38.0 38.0 38.0 36.0 38.0 54-55 37.133875 38.0 38.0 38.0 37.0 38.0 56-57 36.990750000000006 38.0 38.0 38.0 36.0 38.0 58-59 37.21 38.0 38.0 38.0 37.0 38.0 60-61 37.114999999999995 38.0 38.0 38.0 36.5 38.0 62-63 37.020875000000004 38.0 38.0 38.0 36.0 38.0 64-65 36.68537499999999 38.0 37.5 38.0 34.5 38.0 66-67 36.30225 38.0 37.5 38.0 32.5 38.0 68-69 36.689 38.0 38.0 38.0 35.0 38.0 70-71 36.253 38.0 37.5 38.0 33.5 38.0 72-73 36.168875 38.0 37.0 38.0 32.0 38.0 74-75 35.776624999999996 38.0 37.0 38.0 29.5 38.0 76-77 36.182249999999996 38.0 37.5 38.0 32.5 38.0 78-79 36.555875 38.0 38.0 38.0 34.5 38.0 80-81 36.815749999999994 38.0 38.0 38.0 36.0 38.0 82-83 36.842 38.0 38.0 38.0 36.0 38.0 84-85 36.841875 38.0 38.0 38.0 36.0 38.0 86-87 36.640249999999995 38.0 38.0 38.0 35.0 38.0 88-89 36.587875 38.0 38.0 38.0 35.0 38.0 90-91 36.53075 38.0 38.0 38.0 34.5 38.0 92-93 36.501625000000004 38.0 38.0 38.0 34.5 38.0 94-95 36.084500000000006 38.0 38.0 38.0 34.0 38.0 96-97 34.729375000000005 38.0 37.0 38.0 29.0 38.0 98-99 32.611000000000004 38.0 35.0 38.0 13.0 38.0 100-101 29.700625000000002 38.0 25.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 7 1.0 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 1.0 17 0.0 18 0.0 19 1.0 20 1.0 21 1.0 22 3.0 23 1.0 24 6.0 25 9.0 26 13.0 27 19.0 28 23.0 29 29.0 30 37.0 31 48.0 32 53.0 33 85.0 34 142.0 35 357.0 36 806.0 37 2364.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 39.65 24.25 13.05 23.05 2 33.39169584792396 30.64032016008004 19.334667333666832 16.633316658329164 3 32.425 17.95 28.249999999999996 21.375 4 25.85646411602901 32.808202050512634 14.57864466116529 26.756689172293076 5 43.175000000000004 15.9 24.5 16.425 6 22.400000000000002 33.2 26.474999999999998 17.925 7 46.550000000000004 20.75 20.45 12.25 8 21.825 13.475000000000001 49.725 14.975 9 17.150000000000002 48.199999999999996 20.275000000000002 14.374999999999998 10-11 38.4125 25.4875 19.45 16.650000000000002 12-13 15.725 14.224999999999998 26.674999999999997 43.375 14-15 20.3 39.275 27.875 12.55 16-17 27.737499999999997 16.3625 43.225 12.675 18-19 43.55 20.849999999999998 23.3 12.3 20-21 13.6875 26.087500000000002 40.2375 19.9875 22-23 34.387499999999996 29.212500000000002 22.3875 14.0125 24-25 30.1875 30.925000000000004 22.6375 16.25 26-27 38.35 25.5375 20.275000000000002 15.837499999999999 28-29 16.8125 38.1375 19.412499999999998 25.637500000000003 30-31 21.7375 13.1375 42.8 22.325 32-33 27.8125 11.774999999999999 31.125000000000004 29.2875 34-35 35.5625 21.637500000000003 27.55 15.25 36-37 42.762499999999996 21.2875 26.450000000000003 9.5 38-39 22.0625 21.087500000000002 38.1125 18.7375 40-41 20.9125 11.0625 28.625 39.4 42-43 33.550000000000004 23.1125 20.7625 22.575 44-45 57.99999999999999 10.487499999999999 14.387500000000001 17.125 46-47 33.2125 26.8125 15.812499999999998 24.1625 48-49 23.45 23.724999999999998 18.05 34.775 50-51 25.837500000000002 27.750000000000004 6.375 40.0375 52-53 31.7375 45.9875 5.3625 16.9125 54-55 22.875 27.987499999999997 19.5875 29.549999999999997 56-57 12.237499999999999 32.95 13.3125 41.5 58-59 24.637500000000003 17.5875 25.0625 32.7125 60-61 30.862499999999997 18.625 15.412500000000001 35.099999999999994 62-63 19.6875 19.5 17.1375 43.675000000000004 64-65 19.662499999999998 23.175 28.65 28.512500000000003 66-67 31.8125 10.15 24.025 34.0125 68-69 36.4625 9.5625 19.4875 34.4875 70-71 24.3 19.5 27.075 29.125 72-73 19.025 13.925 30.362499999999997 36.6875 74-75 15.049999999999999 9.525 29.262500000000003 46.1625 76-77 21.6125 10.7375 42.0125 25.637500000000003 78-79 22.2625 9.175 39.887499999999996 28.675 80-81 19.125 11.9625 35.699999999999996 33.2125 82-83 30.2125 5.3 35.7875 28.7 84-85 19.4875 4.75 37.1375 38.625 86-87 19.525000000000002 9.1875 44.7125 26.575 88-89 13.100000000000001 28.050000000000004 38.1625 20.6875 90-91 11.2125 31.837500000000002 34.7375 22.2125 92-93 19.725 38.025 26.937499999999996 15.312500000000002 94-95 11.9625 55.1625 24.2375 8.6375 96-97 11.525 73.55000000000001 11.9375 2.9875 98-99 4.45 89.8875 3.7624999999999997 1.9 100-101 1.6500000000000001 93.5 2.4 2.45 >>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 0.0 31 0.0 32 0.0 33 0.0 34 0.0 35 0.0 36 0.0 37 1.5 38 2.5 39 2.0 40 2.0 41 3.0 42 9.5 43 24.5 44 80.5 45 180.5 46 469.5 47 581.0 48 386.5 49 353.5 50 308.5 51 216.5 52 295.5 53 400.5 54 322.0 55 148.5 56 53.0 57 49.5 58 41.5 59 16.0 60 23.5 61 18.0 62 2.5 63 3.0 64 1.5 65 2.0 66 1.5 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 0.0 2 0.05 3 0.0 4 0.025 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-11 0.0 12-13 0.0 14-15 0.0 16-17 0.0 18-19 0.0 20-21 0.0 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.0 30-31 0.0 32-33 0.0 34-35 0.0 36-37 0.0 38-39 0.0 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0 54-55 0.0 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0 66-67 0.0 68-69 0.0 70-71 0.0 72-73 0.0 74-75 0.0 76-77 0.0 78-79 0.0 80-81 0.0 82-83 0.0 84-85 0.0 86-87 0.0 88-89 0.0 90-91 0.0 92-93 0.0 94-95 0.0 96-97 0.0 98-99 0.0 100-101 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 101 4000.0 >>END_MODULE >>Sequence Duplication Levels fail #Total Deduplicated Percentage 47.099999999999994 #Duplication Level Percentage of deduplicated Percentage of total 1 86.62420382165605 40.8 2 5.254777070063694 4.95 3 2.176220806794055 3.075 4 1.2738853503184715 2.4 5 1.2738853503184715 3.0 6 0.47770700636942676 1.35 7 0.2653927813163482 0.8750000000000001 8 0.15923566878980894 0.6 9 0.21231422505307856 0.8999999999999999 >10 1.7515923566878981 19.475 >50 0.3715498938428875 12.049999999999999 >100 0.15923566878980894 10.525 >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 GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 183 4.575 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 134 3.35 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 104 2.6 No Hit GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 90 2.25 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTGGAATTCTCGGGTGCCAA 75 1.875 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 73 1.825 Illumina Small RNA Adapter 2 (100% over 21bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTTGGAATTCTCGGGTG 69 1.725 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTTGGAATTCTCGGGTGC 66 1.6500000000000001 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 55 1.375 No Hit GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTTGGAATTCTCGGGTGC 54 1.35 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTTGGAATTCTCGGGTGCCA 50 1.25 No Hit TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 48 1.2 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTGGAATTCTCGGGTGCCA 48 1.2 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTGGAATTCTCGGGTGCCAAGG 47 1.175 Illumina Small RNA Adapter 2 (100% over 21bp) CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 43 1.075 RNA PCR Primer, Index 1 (100% over 28bp) ATATTGGGTAGGTTGTGGTATTTCATTGCTTGGAATTCTCGGGTGCCAAG 39 0.975 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 36 0.8999999999999999 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGGAATTCTCGGGTGCCA 36 0.8999999999999999 No Hit TCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTC 31 0.775 RNA PCR Primer, Index 1 (100% over 26bp) CGGTCGAGGGCACGCCTGCCTGGGCGTCACGCTGGAATTCTCGGGTGCCA 30 0.75 No Hit TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 30 0.75 RNA PCR Primer, Index 1 (100% over 29bp) CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 30 0.75 No Hit GGGTGTTTGGTCTAGTGGTATGATTCTCGCTTGGAATTCTCGGGTGCCAA 26 0.65 No Hit GAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTGC 21 0.525 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTTGGAATTCTCGGGTGC 21 0.525 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATACTCTGGAATTCTCGGGTGCCAAG 19 0.475 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATGGAATTCTCGGGTGCCAAGGA 19 0.475 RNA PCR Primer, Index 1 (100% over 22bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 18 0.44999999999999996 Illumina Small RNA Adapter 2 (100% over 21bp) GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGTGGAATTCTCGGGTG 18 0.44999999999999996 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACCTGGAATTCTCGGGTGCC 16 0.4 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 14 0.35000000000000003 Illumina Small RNA Adapter 2 (100% over 21bp) AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 14 0.35000000000000003 Illumina Small RNA Adapter 2 (100% over 21bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGGAATTCTCGGGTGC 13 0.325 No Hit GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGTTGGAATTCTCGGGT 13 0.325 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGGAATTCTCGGGTGCCAA 13 0.325 No Hit CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 12 0.3 RNA PCR Primer, Index 1 (100% over 23bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGATGGAATTCTC 12 0.3 No Hit AATATTGGGTAGGTTGTGGTATTTCATTGCTTGGAATTCTCGGGTGCCAA 11 0.27499999999999997 No Hit TCGGACCAGGCTTCGATCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 29bp) AGAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTG 10 0.25 No Hit TGTCGTGCCAATTCAACATAAACCCTGGAATTCTCGGGTGCCAAGGAACT 10 0.25 RNA PCR Primer, Index 1 (100% over 25bp) GTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTTGGAATTCTCGGGTGCC 10 0.25 No Hit ACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCCA 10 0.25 RNA PCR Primer, Index 1 (100% over 28bp) AATATTGGGTAGGTTGTGGTATTTCATTGCTGGAATTCTCGGGTGCCAAG 9 0.22499999999999998 No Hit GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGGAATTCTCGGGTGCC 9 0.22499999999999998 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTATGGAATTCTCGGGTGCCAA 9 0.22499999999999998 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCATGGAATTCTCGGGTGCC 9 0.22499999999999998 No Hit CATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAAC 8 0.2 RNA PCR Primer, Index 1 (100% over 24bp) TTGACAGAAGAGAGTGAGCACTGGAATTCTCGGGTGCCAAGGAACTCCAG 8 0.2 RNA PCR Primer, Index 1 (100% over 29bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATGGAATTCTCGGGTG 8 0.2 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTTGGAATTCTCGGGTGCCAA 7 0.17500000000000002 No Hit TCCTCAGTAGCTCAGTGGTAGAGCGGTCGGCTTGGAATTCTCGGGTGCCA 7 0.17500000000000002 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTATGGAATTCTCGGGTGCCAA 7 0.17500000000000002 No Hit CACGACTCTCGGCAACGGATATCTCGGCTTGGAATTCTCGGGTGCCAAGG 7 0.17500000000000002 Illumina Small RNA Adapter 2 (100% over 21bp) ATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACT 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 25bp) GGGATTGTAGTTCAATTGGACAGAGCACCGCCCTGGAATTCTCGGGTGCC 6 0.15 No Hit CGAACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACT 6 0.15 RNA PCR Primer, Index 1 (100% over 25bp) GGGCCTGTAGCTCAGAGGATGGAATTCTCGGGTGCCAAGGAACTCCAGTC 6 0.15 RNA PCR Primer, Index 1 (100% over 31bp) GGGCCTGTAGCTCAGAGGATTAGAGCACGTGGCTGGAATTCTCGGGTGCC 6 0.15 No Hit GTCAGGATAGCTCAGTTGGAAGAGCAGAGGACTTGGAATTCTCGGGTGCC 6 0.15 No Hit GGGATTGTAGTTCAATTGGCCAGAGCACCGCCCTGGAATTCTCGGGTGCC 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTAATGGAATTCTCGGGTGC 6 0.15 No Hit TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGGCCATCTCGTATGC 6 0.15 RNA PCR Primer, Index 20 (100% over 50bp) TCGCTTGGTGCAGATCGGGACTGGAATTCTCGGGTGCCAAGGAACTCCAG 6 0.15 RNA PCR Primer, Index 1 (100% over 29bp) CATCGAGTAGACCTTGTTATTGTGAGAATAAATGGAATTCTCGGGTGCCA 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTAAAATGGAATTCTCGGGTGC 5 0.125 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGATGGAATTCTCGGGTGC 5 0.125 No Hit AGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCC 5 0.125 RNA PCR Primer, Index 1 (100% over 27bp) CATCGAGTAGACCTTGTTATTGTGAGAATAAAAAATGGAATTCTCGGGTG 5 0.125 No Hit GGGATTGTAGTTCAATTGGACAGAGCACCGCCCTTGGAATTCTCGGGTGC 5 0.125 No Hit CATCGAGTAGACCTTGGTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 5 0.125 No Hit GAACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTC 5 0.125 RNA PCR Primer, Index 1 (100% over 26bp) GACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) TCTCATGGAGAGTTCGATCCTGGCTTGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) AATATTGGGTAGGTTGTGGTATTTCATTGCTATGGAATTCTCGGGTGCCA 5 0.125 No Hit GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGTGTGGAATTCTCGGG 5 0.125 No Hit AAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTGCC 5 0.125 No Hit GACACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) CATCGAGTAGACCTTGTTATTGTGAGAATTAAATGGAATTCTCGGGTGCC 5 0.125 No Hit ATGCAGTTACTAATTCATGATCTGGCTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGTGGAATTCTCGGGTGCC 5 0.125 No Hit TGTCGTGCCAATTCAACATAAACCCCTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) TTTCGTGCTTATCCTAGTTGTTGGTTTAGTTGGAATTCTCGGGTGCCAAG 5 0.125 No Hit GCGTCTGTAGTCCAACGGTTAGGATAATTGCCTTCCTGGAATTCTCGGGT 5 0.125 No Hit GCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) CAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTC 5 0.125 RNA PCR Primer, Index 1 (100% over 26bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTAAATGGAATTCTCGGGTG 5 0.125 No Hit ATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) >>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 0.2 0.0 0.0 0.0 2 0.0 0.2 0.0 0.0 0.0 3 0.0 0.2 0.0 0.0 0.0 4 0.0 0.2 0.0 0.0 0.0 5 0.0 0.2 0.0 0.0 0.0 6 0.0 0.2 0.0 0.0 0.0 7 0.0 0.2 0.0 0.0 0.0 8 0.0 0.2 0.0 0.0 0.0 9 0.0 0.2 0.0 0.0 0.0 10-11 0.0 0.2 0.0 0.0 0.0 12-13 0.0 0.2375 0.0 0.0 0.0 14-15 0.0 0.25 0.0 0.0 0.0 16-17 0.0 0.4625 0.0 0.0 0.0 18-19 0.0 0.8999999999999999 0.0 0.0 0.0 20-21 0.0 1.675 0.0 0.0 0.0 22-23 0.0 6.012499999999999 0.0 0.0 0.0 24-25 0.0 17.5 0.0 0.0 0.0 26-27 0.0 29.25 0.0 0.0 0.0 28-29 0.0 33.0 0.0 0.0 0.0 30-31 0.0 45.6375 0.0 0.0 0.0 32-33 0.0 62.3 0.0 0.0 0.0 34-35 0.0 82.9375 0.0 0.0 0.0 36-37 0.0 92.9625 0.0 0.0 0.0 38-39 0.0 95.275 0.0 0.0 0.0 40-41 0.0 96.3375 0.0 0.0 0.0 42-43 0.0 97.275 0.0 0.0 0.0 44-45 0.0 97.5875 0.0 0.0 0.0 46-47 0.0 97.7625 0.0 0.0 0.0 48-49 0.0 97.775 0.0 0.0 0.0 50-51 0.0 97.775 0.0 0.0 0.0 52-53 0.0 97.775 0.0 0.0 0.0 54-55 0.0 97.775 0.0 0.0 0.0 56-57 0.0 97.775 0.0 0.0 0.0 58-59 0.0 97.775 0.0 0.0 0.0 60-61 0.0 97.775 0.0 0.0 0.0 62-63 0.0 97.775 0.0 0.0 0.0 64-65 0.0 97.775 0.0 0.0 0.0 66-67 0.0 97.775 0.0 0.0 0.0 68-69 0.0 97.775 0.0 0.0 0.0 70-71 0.0 97.775 0.0 0.0 0.0 72-73 0.0 97.775 0.0 0.0 0.0 74-75 0.0 97.775 0.0 0.0 0.0 76-77 0.0 97.775 0.0 0.0 0.0 78-79 0.0 97.8 0.0 0.0 0.0 80-81 0.0 97.8 0.0 0.0 0.0 82-83 0.0 97.8 0.0 0.0 0.0 84-85 0.0 97.8 0.0 0.0 0.0 86-87 0.0 97.8 0.0 0.0 0.0 88-89 0.0 97.8 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGCTGTA 20 1.5392321E-5 95.00001 4 TAGTTTA 20 1.5392321E-5 95.00001 9 GCTGTAG 20 1.5392321E-5 95.00001 5 GTGGCTG 20 1.5392321E-5 95.00001 2 GGTGGCT 20 1.5392321E-5 95.00001 1 GTCAGGA 20 1.5392321E-5 95.00001 1 GTAGTTT 20 1.5392321E-5 95.00001 8 TGGCTGT 20 1.5392321E-5 95.00001 3 GTAGACC 90 0.0 95.0 7 AGCTCAG 25 3.8289727E-7 95.0 9 TTGTAGT 30 9.458745E-9 95.0 5 AGTAGAC 90 0.0 95.0 6 TAGCTCA 25 3.8289727E-7 95.0 8 GGATTGT 30 9.458745E-9 95.0 2 CGTAGTT 15 6.142176E-4 95.0 6 GATTGTA 30 9.458745E-9 95.0 3 TAGTTCA 45 0.0 95.0 8 GAGTAGA 90 0.0 95.0 5 ATTGTAG 30 9.458745E-9 95.0 4 GGGATTG 30 9.458745E-9 95.0 1 >>END_MODULE Rejected 273385 READS because READLEN < 1 Read 273385 spots for SRR6941543.sra Written 273385 spots for SRR6941543.sra Rejected 273385 READS because READLEN < 1 Read 273385 spots for SRR6941543.sra Written 273385 spots for SRR6941543.sra Rejected 273385 READS because READLEN < 1 Read 273385 spots for SRR6941543.sra Written 273385 spots for SRR6941543.sra Rejected 273385 READS because READLEN < 1 Read 273385 spots for SRR6941543.sra Written 273385 spots for SRR6941543.sra Rejected 273385 READS because READLEN < 1 Read 273385 spots for SRR6941543.sra Written 273385 spots for SRR6941543.sra Rejected 273385 READS because READLEN < 1 Read 273385 spots for SRR6941543.sra Written 273385 spots for SRR6941543.sra Rejected 273385 READS because READLEN < 1 Read 273385 spots for SRR6941543.sra Written 273385 spots for SRR6941543.sra Rejected 273385 READS because READLEN < 1 Read 273385 spots for SRR6941543.sra Written 273385 spots for SRR6941543.sra Rejected 273385 READS because READLEN < 1 Read 273385 spots for SRR6941543.sra Written 273385 spots for SRR6941543.sra Rejected 273404 READS because READLEN < 1 Read 273404 spots for SRR6941543.sra Written 273404 spots for SRR6941543.sra Rejected 273385 READS because READLEN < 1 Read 273385 spots for SRR6941543.sra Written 273385 spots for SRR6941543.sra Rejected 273385 READS because READLEN < 1 Read 273385 spots for SRR6941543.sra Written 273385 spots for SRR6941543.sra Rejected 273385 READS because READLEN < 1 Read 273385 spots for SRR6941543.sra Written 273385 spots for SRR6941543.sra Rejected 273385 READS because READLEN < 1 Read 273385 spots for SRR6941543.sra Written 273385 spots for SRR6941543.sra Rejected 273385 READS because READLEN < 1 Read 273385 spots for SRR6941543.sra Written 273385 spots for SRR6941543.sra Rejected 273385 READS because READLEN < 1 Read 273385 spots for SRR6941543.sra Written 273385 spots for SRR6941543.sra Rejected 273385 READS because READLEN < 1 Read 273385 spots for SRR6941543.sra Written 273385 spots for SRR6941543.sra Rejected 273385 READS because READLEN < 1 Read 273385 spots for SRR6941543.sra Written 273385 spots for SRR6941543.sra Rejected 273385 READS because READLEN < 1 Read 273385 spots for SRR6941543.sra Written 273385 spots for SRR6941543.sra Rejected 273385 READS because READLEN < 1 Read 273385 spots for SRR6941543.sra Written 273385 spots for SRR6941543.sra SRR ids: ['SRR6941543.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_t6jpwnmc SRR6941543.sra spots: 5467719 blocks: [[1, 273385], [273386, 546770], [546771, 820155], [820156, 1093540], [1093541, 1366925], [1366926, 1640310], [1640311, 1913695], [1913696, 2187080], [2187081, 2460465], [2460466, 2733850], [2733851, 3007235], [3007236, 3280620], [3280621, 3554005], [3554006, 3827390], [3827391, 4100775], [4100776, 4374160], [4374161, 4647545], [4647546, 4920930], [4920931, 5194315], [5194316, 5467719]] SRR6941543 file size 1306025 SRR6941543 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 SRR6941543 SRR6941543_1.fastq Input file: SRR6941543_1.fastq trimmed: SRR6941543-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 10:46:26 2024 >> started Fri Dec 6 10:46:30 2024 >> done (4.177s) 5467719 reads processed; of these: 97 ( 0.00%) short reads filtered out after trimming by size control 17 ( 0.00%) empty reads filtered out after trimming by size control 5467605 (100.00%) reads available; of these: 759270 (13.89%) trimmed reads available after processing 4708335 (86.11%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 6 0.00% 19 6 0.00% 20 7 0.00% 21 20 0.00% 22 10 0.00% 23 18 0.00% 24 17 0.00% 25 12 0.00% 26 23 0.00% 27 18 0.00% 28 37 0.00% 29 63 0.00% 30 60 0.00% 31 29 0.00% 32 56 0.00% 33 60 0.00% 34 60 0.00% 35 77 0.00% 36 65 0.00% 37 50 0.00% 38 114 0.00% 39 102 0.00% 40 91 0.00% 41 97 0.00% 42 76 0.00% 43 111 0.00% 44 68 0.00% 45 102 0.00% 46 117 0.00% 47 85 0.00% 48 88 0.00% 49 60 0.00% 50 59 0.00% 51 58 0.00% 52 54 0.00% 53 46 0.00% 54 48 0.00% 55 54 0.00% 56 70 0.00% 57 71 0.00% 58 52 0.00% 59 92 0.00% 60 109 0.00% 61 78 0.00% 62 65 0.00% 63 74 0.00% 64 74 0.00% 65 84 0.00% 66 107 0.00% 67 109 0.00% 68 192 0.00% 69 179 0.00% 70 310 0.01% 71 335 0.01% 72 433 0.01% 73 973 0.02% 74 4801 0.09% 75 3211 0.06% 76 1119 0.02% 77 479 0.01% 78 587 0.01% 79 560 0.01% 80 592 0.01% 81 621 0.01% 82 798 0.01% 83 924 0.02% 84 1331 0.02% 85 1472 0.03% 86 1673 0.03% 87 1955 0.04% 88 2206 0.04% 89 3329 0.06% 90 6352 0.12% 91 7800 0.14% 92 9322 0.17% 93 17433 0.32% 94 30027 0.55% 95 77115 1.41% 96 76452 1.40% 97 82872 1.52% 98 168841 3.09% 99 179484 3.28% 100 72383 1.32% 101 4708335 86.11% 5467605 reads passed initial QC criterion=sequence-density sequence-density=97.60 sequence-density-rank=1 fanout-score=27.18 fanout-score-rank=1 prefix-density=97.84 prefix-fanout=27.1 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGGCCATCTCGTATGCCGTCTTCTGCTTGAAAAAAA criterion=fanout-score sequence-density=97.60 sequence-density-rank=1 fanout-score=27.18 fanout-score-rank=1 prefix-density=97.84 prefix-fanout=27.1 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGGCCATCTCGTATGCCGTCTTCTGCTTGAAAAAAA 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGGCCATCTCGTATGCCGTCTTCTGCTTGAAAAAAA -o SRR6941543 - Input file: STDIN trimmed: SRR6941543-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGGCCATCTCGTATGCCGTCTTCTGCTTGA -- 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 10:46:49 2024 >> started Fri Dec 6 10:46:58 2024 >> done (8.108s) 5356021 reads processed; of these: 28719 ( 0.54%) short reads filtered out after trimming by size control 17138 ( 0.32%) empty reads filtered out after trimming by size control 5310164 (99.14%) reads available; of these: 5281795 (99.47%) trimmed reads available after processing 28369 ( 0.53%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 9051 0.17% 19 24788 0.47% 20 30261 0.57% 21 188464 3.55% 22 131903 2.48% 23 112230 2.11% 24 885653 16.68% 25 122505 2.31% 26 107440 2.02% 27 93362 1.76% 28 106748 2.01% 29 321352 6.05% 30 566876 10.68% 31 382414 7.20% 32 486326 9.16% 33 661636 12.46% 34 422757 7.96% 35 277464 5.23% 36 133390 2.51% 37 62773 1.18% 38 31090 0.59% 39 21642 0.41% 40 31593 0.59% 41 28058 0.53% 42 19435 0.37% 43 5478 0.10% 44 6545 0.12% 45 4545 0.09% 46 1522 0.03% 47 1443 0.03% 48 588 0.01% 49 267 0.01% 50 155 0.00% 51 133 0.00% 52 78 0.00% 53 65 0.00% 54 54 0.00% 55 48 0.00% 56 35 0.00% 57 54 0.00% 58 32 0.00% 59 44 0.00% 60 31 0.00% 61 24 0.00% 62 28 0.00% 63 27 0.00% 64 25 0.00% 65 27 0.00% 66 26 0.00% 67 33 0.00% 68 49 0.00% 69 42 0.00% 70 53 0.00% 71 55 0.00% 72 50 0.00% 73 66 0.00% 74 55 0.00% 75 84 0.00% 76 90 0.00% 77 411 0.01% 78 64 0.00% 79 93 0.00% 80 535 0.01% 81 182 0.00% 82 287 0.01% 83 246 0.00% 84 78 0.00% 85 79 0.00% 86 109 0.00% 87 217 0.00% 88 103 0.00% 89 82 0.00% 90 106 0.00% 91 174 0.00% 92 152 0.00% 93 230 0.00% 94 230 0.00% 95 272 0.01% 96 273 0.01% 97 286 0.01% 98 550 0.01% 99 398 0.01% 100 407 0.01% 101 23538 0.44% criterion=sequence-density sequence-density=15.22 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=11 prefix-density=0.00 prefix-fanout=1.0 sequence=CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAA criterion=fanout-score sequence-density=0.17 sequence-density-rank=23 fanout-score=87.03 fanout-score-rank=1 prefix-density=15.08 prefix-fanout=1.0 sequence=TATTGTGAGAAAAA Started job on | Dec 06 10:47:20 Started mapping on | Dec 06 10:47:21 Finished on | Dec 06 10:47:34 Mapping speed, Million of reads per hour | 1501.41 Number of input reads | 5421748 Average input read length | 31 UNIQUE READS: Uniquely mapped reads number | 822363 Uniquely mapped reads % | 15.17% Average mapped length | 25.71 Number of splices: Total | 20658 Number of splices: Annotated (sjdb) | 2125 Number of splices: GT/AG | 19920 Number of splices: GC/AG | 625 Number of splices: AT/AC | 4 Number of splices: Non-canonical | 109 Mismatch rate per base, % | 1.06% Deletion rate per base | 0.01% Deletion average length | 1.24 Insertion rate per base | 0.00% Insertion average length | 1.23 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 3602013 % of reads mapped to multiple loci | 66.44% Number of reads mapped to too many loci | 754554 % of reads mapped to too many loci | 13.92% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.85% % of reads unmapped: other | 0.63% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 997372 997372 997372 N_multimapping 3602013 3602013 3602013 N_noFeature 559905 656525 721676 N_ambiguous 9145 4610 542 UnstrandedReadsAssigned:253313 PositiveStrandReadsAssigned:161228 NegativeStrandReadsAssigned:100145 Dataset is classified unstranded MeadianReadLen=30 20thPercentileLength=24 echo kmer=19 SRR6941543 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: SRR6941543-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 5,421,748 reads, 2,532,444 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 929 rounds 52973 SRR6941543.ke.tsv 35125 SRR6941543.se.tsv 88098 total ==> SRR6941543.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 2 0.296511 PNS24243 293 194 3 3.14547 KQK14069 1603 1504 14.5871 1.97281 KQK14071 474 375 2.28099 1.23725 ==> SRR6941543.se.tsv <== BRADI_1g14170v3 61 BRADI_1g53295v3 4 BRADI_1g59795v3 1 BRADI_1g07683v3 0 BRADI_1g00485v3 1 BRADI_1g20270v3 2 BRADI_1g74790v3 7 BRADI_1g09890v3 24 BRADI_1g77505v3 0 BRADI_1g48960v3 0 SRR6941543 completed mapping pipeline successfully