Starting /dee2/code/volunteer_pipeline.sh SRR6941565 current disk space = 1551554015232 free memory = 1598857484 SRR6941565 SRAfilesize b2beb64053c70b28175afe3a829c2f7a SRR6941565.sra SRR6941565.sra file validated SRR6941565 is single end SRR6941565 is conventional basespace SRR6941565 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6941565_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 47 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.277 34.0 33.0 34.0 33.0 34.0 2 33.36475 34.0 33.0 34.0 33.0 34.0 3 33.25875 34.0 33.0 34.0 33.0 34.0 4 33.3155 34.0 33.0 34.0 33.0 34.0 5 33.273 34.0 33.0 34.0 33.0 34.0 6 37.03725 38.0 37.0 38.0 36.0 38.0 7 37.345 38.0 38.0 38.0 37.0 38.0 8 37.5445 38.0 38.0 38.0 37.0 38.0 9 37.57675 38.0 38.0 38.0 38.0 38.0 10-11 37.559375 38.0 38.0 38.0 38.0 38.0 12-13 37.52575 38.0 38.0 38.0 38.0 38.0 14-15 37.5355 38.0 38.0 38.0 37.5 38.0 16-17 35.90175 38.0 36.5 38.0 27.0 38.0 18-19 36.736 38.0 37.5 38.0 33.5 38.0 20-21 36.129875 38.0 37.5 38.0 29.5 38.0 22-23 37.320499999999996 38.0 38.0 38.0 36.5 38.0 24-25 37.43475 38.0 38.0 38.0 37.0 38.0 26-27 37.40875 38.0 38.0 38.0 37.0 38.0 28-29 37.4495 38.0 38.0 38.0 37.0 38.0 30-31 37.36375 38.0 38.0 38.0 37.5 38.0 32-33 37.280125 38.0 38.0 38.0 37.0 38.0 34-35 37.304625 38.0 38.0 38.0 37.0 38.0 36-37 37.226749999999996 38.0 38.0 38.0 37.0 38.0 38-39 37.183375 38.0 38.0 38.0 37.0 38.0 40-41 37.156875 38.0 38.0 38.0 37.0 38.0 42-43 37.156625000000005 38.0 38.0 38.0 37.0 38.0 44-45 37.1205 38.0 38.0 38.0 37.0 38.0 46-47 37.09125 38.0 38.0 38.0 36.5 38.0 48-49 37.248999999999995 38.0 38.0 38.0 37.0 38.0 50-51 37.09587500000001 38.0 38.0 38.0 36.0 38.0 52-53 37.126999999999995 38.0 38.0 38.0 36.5 38.0 54-55 37.17275 38.0 38.0 38.0 37.0 38.0 56-57 37.019375 38.0 38.0 38.0 36.0 38.0 58-59 37.173249999999996 38.0 38.0 38.0 37.0 38.0 60-61 37.124875 38.0 38.0 38.0 36.5 38.0 62-63 36.86825 38.0 38.0 38.0 35.5 38.0 64-65 36.467875 38.0 37.5 38.0 33.5 38.0 66-67 36.338499999999996 38.0 37.5 38.0 33.5 38.0 68-69 36.64 38.0 38.0 38.0 34.0 38.0 70-71 36.370125 38.0 37.5 38.0 33.0 38.0 72-73 36.072874999999996 38.0 37.0 38.0 32.0 38.0 74-75 36.106125 38.0 37.0 38.0 32.0 38.0 76-77 36.176874999999995 38.0 37.0 38.0 33.0 38.0 78-79 36.429375 38.0 38.0 38.0 34.0 38.0 80-81 36.647375 38.0 38.0 38.0 35.5 38.0 82-83 36.70675 38.0 38.0 38.0 35.5 38.0 84-85 36.6205 38.0 38.0 38.0 35.0 38.0 86-87 36.548125 38.0 38.0 38.0 35.0 38.0 88-89 36.522875 38.0 38.0 38.0 35.0 38.0 90-91 36.509625 38.0 38.0 38.0 34.5 38.0 92-93 36.43325 38.0 38.0 38.0 34.5 38.0 94-95 36.076125 38.0 38.0 38.0 34.0 38.0 96-97 34.619375000000005 38.0 37.0 38.0 28.0 38.0 98-99 32.454625 38.0 35.0 38.0 8.5 38.0 100-101 29.669249999999998 38.0 25.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 5 1.0 6 0.0 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 1.0 16 1.0 17 0.0 18 0.0 19 1.0 20 0.0 21 1.0 22 2.0 23 3.0 24 7.0 25 7.0 26 12.0 27 23.0 28 36.0 29 18.0 30 28.0 31 41.0 32 56.0 33 91.0 34 158.0 35 360.0 36 764.0 37 2388.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 29.025000000000002 22.275 15.225 33.475 2 25.268951713785338 39.60470352764573 17.112834625969477 18.01351013259945 3 27.450000000000003 17.65 35.3 19.6 4 23.20580145036259 26.78169542385596 14.20355088772193 35.80895223805952 5 47.225 17.75 18.4 16.625 6 19.625 41.699999999999996 21.2 17.474999999999998 7 47.55 20.4 19.025 13.025 8 18.075 14.975 48.85 18.099999999999998 9 17.349999999999998 47.825 17.95 16.875 10-11 36.325 29.7875 17.875 16.0125 12-13 17.9125 16.037499999999998 20.7375 45.3125 14-15 18.7375 31.2375 34.75 15.275 16-17 29.675 19.6375 36.825 13.8625 18-19 32.525 26.3125 27.575 13.5875 20-21 14.774999999999999 24.4 42.2375 18.587500000000002 22-23 34.025 24.4 26.900000000000002 14.674999999999999 24-25 32.487500000000004 30.5375 22.037499999999998 14.9375 26-27 39.3375 28.1125 18.4875 14.0625 28-29 16.8875 38.550000000000004 26.4625 18.099999999999998 30-31 19.5875 13.8125 43.6875 22.912499999999998 32-33 30.2375 13.9125 32.625 23.225 34-35 34.725 24.9375 24.9125 15.425 36-37 37.5 20.6125 30.0 11.8875 38-39 24.275 17.724999999999998 36.5 21.5 40-41 24.587500000000002 13.4125 25.825 36.175000000000004 42-43 38.2 22.2125 18.1125 21.475 44-45 51.15 14.1875 16.950000000000003 17.712500000000002 46-47 31.662499999999998 25.525 15.0625 27.750000000000004 48-49 22.125 27.875 16.175 33.825 50-51 29.075 27.8375 8.387500000000001 34.699999999999996 52-53 29.4 42.449999999999996 7.35 20.8 54-55 20.599999999999998 28.825 18.6875 31.887500000000003 56-57 15.787499999999998 28.3375 13.175 42.699999999999996 58-59 28.3375 22.7 15.4875 33.475 60-61 16.3 21.175 23.2125 39.3125 62-63 15.675 29.062500000000004 17.4 37.8625 64-65 23.775 23.6875 21.4875 31.05 66-67 22.112499999999997 15.312500000000002 25.55 37.025000000000006 68-69 22.5875 21.0 21.0125 35.4 70-71 13.1625 28.475 31.3 27.0625 72-73 15.587500000000002 18.45 34.3125 31.65 74-75 16.6375 11.25 29.1625 42.95 76-77 21.224999999999998 12.5125 40.112500000000004 26.150000000000002 78-79 20.1875 10.75 41.0125 28.050000000000004 80-81 20.3625 9.0 34.75 35.8875 82-83 27.500000000000004 5.6375 37.525 29.3375 84-85 19.412499999999998 5.8375 39.6 35.15 86-87 18.525 11.425 43.5625 26.487500000000004 88-89 15.037500000000001 27.975 36.162499999999994 20.825 90-91 13.0 33.625 32.75 20.625 92-93 16.9625 40.425 28.475 14.1375 94-95 12.75 59.275 19.900000000000002 8.075000000000001 96-97 8.725 75.8625 11.875 3.5374999999999996 98-99 4.5375 87.8125 5.0375000000000005 2.6125 100-101 2.1375 91.9375 3.3875 2.5375 >>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 0.5 35 1.5 36 3.5 37 3.5 38 1.5 39 1.5 40 9.5 41 15.5 42 35.0 43 92.0 44 199.0 45 517.0 46 710.0 47 462.5 48 333.5 49 312.0 50 208.5 51 230.0 52 271.0 53 227.0 54 133.0 55 60.0 56 58.0 57 52.0 58 17.5 59 17.5 60 14.0 61 4.5 62 4.0 63 3.0 64 1.5 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 0.0 2 0.075 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 warn #Total Deduplicated Percentage 52.949999999999996 #Duplication Level Percentage of deduplicated Percentage of total 1 88.24362606232295 46.725 2 4.53257790368272 4.8 3 1.7469310670443814 2.775 4 1.2747875354107647 2.7 5 0.6137865911237016 1.625 6 0.5193578847969783 1.6500000000000001 7 0.141643059490085 0.525 8 0.6137865911237016 2.6 9 0.28328611898017 1.35 >10 1.6052880075542966 15.75 >50 0.3777148253068933 15.049999999999999 >100 0.047214353163361665 4.45 >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 CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 178 4.45 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTGGAATTCTCGGGTGCCA 98 2.45 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTGGAATTCTCGGGTGCCAA 96 2.4 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 88 2.1999999999999997 Illumina Small RNA Adapter 2 (100% over 21bp) GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 84 2.1 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 79 1.975 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 54 1.35 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTTGGAATTCTCGGGTGC 52 1.3 No Hit TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 51 1.275 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTTGGAATTCTCGGGTG 47 1.175 No Hit TCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTC 39 0.975 RNA PCR Primer, Index 1 (100% over 26bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 37 0.9249999999999999 No Hit CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 34 0.8500000000000001 RNA PCR Primer, Index 1 (100% over 28bp) TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 28 0.7000000000000001 RNA PCR Primer, Index 1 (100% over 29bp) CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 28 0.7000000000000001 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTTGGAATTCTCGGGTGCCA 28 0.7000000000000001 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTTGGAATTCTCGGGTGCCAAG 26 0.65 No Hit GAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTGC 25 0.625 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATGGAATTCTCGGGTGCCAAGGA 22 0.5499999999999999 RNA PCR Primer, Index 1 (100% over 22bp) ACCTGCTCTGATACCATGTTGTGATGGAATTCTCGGGTGCCAAGGAACTC 19 0.475 RNA PCR Primer, Index 1 (100% over 26bp) CATCGAGTAGACCTTGTTATTGTGAGAATTATGGAATTCTCGGGTGCCAA 19 0.475 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATGGAATTCTCGGGTG 17 0.42500000000000004 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATACTCTGGAATTCTCGGGTGCCAAG 16 0.4 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 15 0.375 No Hit CGGTCGAGGGCACGCCTGCCTGGGCGTCACGCTGGAATTCTCGGGTGCCA 15 0.375 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGGAATTCTCGGGTGCCA 15 0.375 No Hit AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 15 0.375 Illumina Small RNA Adapter 2 (100% over 21bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTTTGGAATTCTCGGGTGCC 14 0.35000000000000003 No Hit ACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCCA 14 0.35000000000000003 RNA PCR Primer, Index 1 (100% over 28bp) AGAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTG 13 0.325 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTTGGAATTCTCGGGTGC 13 0.325 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTAATGGAATTCTCGGGTGC 13 0.325 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGTGGAATTCTCGGGTGCC 13 0.325 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 12 0.3 Illumina Small RNA Adapter 2 (100% over 21bp) AGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCC 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 27bp) TTGACAGAAGAGAGTGAGCACTGGAATTCTCGGGTGCCAAGGAACTCCAG 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 29bp) TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGCTACATCTCGTATGC 11 0.27499999999999997 RNA PCR Primer, Index 11 (100% over 50bp) TGTCGTGCCAATTCAACATAAACCCCTTGGAATTCTCGGGTGCCAAGGAA 10 0.25 RNA PCR Primer, Index 1 (100% over 23bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTATGGAATTCTCGGGTGCC 10 0.25 No Hit GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTTGGAATTCTCGGGTGC 10 0.25 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTGGAATTCTCGGGTGCCAAGG 10 0.25 Illumina Small RNA Adapter 2 (100% over 21bp) ATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACT 10 0.25 RNA PCR Primer, Index 1 (100% over 25bp) CTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCA 10 0.25 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTGGAATTCTCGGGTG 9 0.22499999999999998 No Hit CATCGAGTAGACCTTGTTAATGTGAGAATTGGAATTCTCGGGTGCCAAGG 9 0.22499999999999998 Illumina Small RNA Adapter 2 (100% over 21bp) ACGAACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAAC 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 24bp) CATCGAGTAGACCTTGTTAATGTGAGAATTCTGGAATTCTCGGGTGCCAA 9 0.22499999999999998 No Hit CAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTC 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 26bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTAAATGGAATTCTCGGGTG 9 0.22499999999999998 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAATGGAATTCTCGGGTGCCA 8 0.2 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTAATCTGGAATTCT 8 0.2 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAAATGGAATTCTCGGGT 8 0.2 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGGAATTCTCGGGTGC 8 0.2 No Hit GACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 8 0.2 RNA PCR Primer, Index 1 (100% over 23bp) GACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAAC 8 0.2 RNA PCR Primer, Index 1 (100% over 24bp) TGTCGTGCCAATTCAACATAAACCCTGGAATTCTCGGGTGCCAAGGAACT 8 0.2 RNA PCR Primer, Index 1 (100% over 25bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTGAATCTGGAATTC 8 0.2 No Hit ATGCAGTTACTAATTCATGATCTGGCTGGAATTCTCGGGTGCCAAGGAAC 8 0.2 RNA PCR Primer, Index 1 (100% over 24bp) TGTCGTGCCAATTCAACATAAACCCCTGGAATTCTCGGGTGCCAAGGAAC 8 0.2 RNA PCR Primer, Index 1 (100% over 24bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCAAATGGAATTCTCGGGTGC 8 0.2 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTGGAATTCTCGGGT 8 0.2 No Hit GCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAA 8 0.2 RNA PCR Primer, Index 1 (100% over 23bp) GAACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 26bp) CATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAAC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 24bp) GACACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACT 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 25bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 6 0.15 Illumina Small RNA Adapter 2 (100% over 21bp) GGGATTGTAGTTCAATTGGACAGAGCACCGCCCTGGAATTCTCGGGTGCC 6 0.15 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCTGGAATTCTCGGG 6 0.15 No Hit ATATATTTCAAGTTATTTCGGATCTTGGAATTCTCGGGTGCCAAGGAACT 6 0.15 RNA PCR Primer, Index 1 (100% over 25bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCAATGGAATTCTCGGGTGCC 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATTTGGAATTCTCGGG 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTAAAATGGAATTCTCGGGT 6 0.15 No Hit CATCGAGTAGACCTTGTTAATGTGAGAATTCTTGGAATTCTCGGGTGCCA 6 0.15 No Hit CATCGAGTAGACCTTGATATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 6 0.15 No Hit CCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACT 6 0.15 RNA PCR Primer, Index 1 (100% over 25bp) ATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAA 6 0.15 RNA PCR Primer, Index 1 (100% over 23bp) CGAACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGAGTGGAATTCT 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCATGGAATTCTCGGGTGCCA 5 0.125 No Hit TAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAG 5 0.125 RNA PCR Primer, Index 1 (100% over 29bp) CCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCC 5 0.125 RNA PCR Primer, Index 1 (100% over 27bp) ATATTGGGTAGGTTGTGGTATTTCATTGCTATGGAATTCTCGGGTGCCAA 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTAAATGGAATTCTCGGGTGCC 5 0.125 No Hit CCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT 5 0.125 RNA PCR Primer, Index 1 (100% over 30bp) GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGGAATTCTCGGGTGCC 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTAATGGAATTCTCGGGTGCCA 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAAAATGGAATTCTCGGGTGCCAAG 5 0.125 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGATGGAATTCTC 5 0.125 No Hit TCGCTTGGTGCAGATCGGGACTGGAATTCTCGGGTGCCAAGGAACTCCAG 5 0.125 RNA PCR Primer, Index 1 (100% over 29bp) >>END_MODULE >>Adapter Content fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.375 0.0 0.0 0.0 2 0.0 0.375 0.0 0.0 0.0 3 0.0 0.375 0.0 0.0 0.0 4 0.0 0.375 0.0 0.0 0.0 5 0.0 0.375 0.0 0.0 0.0 6 0.0 0.375 0.0 0.0 0.0 7 0.0 0.375 0.0 0.0 0.0 8 0.0 0.375 0.0 0.0 0.0 9 0.0 0.375 0.0 0.0 0.0 10-11 0.0 0.3875 0.0 0.0 0.0 12-13 0.0 0.425 0.0 0.0 0.0 14-15 0.0 0.425 0.0 0.0 0.0 16-17 0.0 0.525 0.0 0.0 0.0 18-19 0.0 0.8875 0.0 0.0 0.0 20-21 0.0 1.875 0.0 0.0 0.0 22-23 0.0 7.375 0.0 0.0 0.0 24-25 0.0 18.325 0.0 0.0 0.0 26-27 0.0 29.8875 0.0 0.0 0.0 28-29 0.0 35.5625 0.0 0.0 0.0 30-31 0.0 48.400000000000006 0.0 0.0 0.0 32-33 0.0 66.725 0.0 0.0 0.0 34-35 0.0 81.7875 0.0 0.0 0.0 36-37 0.0 90.775 0.0 0.0 0.0 38-39 0.0 93.8875 0.0 0.0 0.0 40-41 0.0 95.3625 0.0 0.0 0.0 42-43 0.0 96.6375 0.0 0.0 0.0 44-45 0.0 97.19999999999999 0.0 0.0 0.0 46-47 0.0 97.3875 0.0 0.0 0.0 48-49 0.0 97.4125 0.0 0.0 0.0 50-51 0.0 97.425 0.0 0.0 0.0 52-53 0.0 97.425 0.0 0.0 0.0 54-55 0.0 97.425 0.0 0.0 0.0 56-57 0.0 97.425 0.0 0.0 0.0 58-59 0.0 97.425 0.0 0.0 0.0 60-61 0.0 97.425 0.0 0.0 0.0 62-63 0.0 97.425 0.0 0.0 0.0 64-65 0.0 97.425 0.0 0.0 0.0 66-67 0.0 97.425 0.0 0.0 0.0 68-69 0.0 97.425 0.0 0.0 0.0 70-71 0.0 97.425 0.0 0.0 0.0 72-73 0.0 97.425 0.0 0.0 0.0 74-75 0.0 97.425 0.0 0.0 0.0 76-77 0.0 97.425 0.0 0.0 0.0 78-79 0.0 97.425 0.0 0.0 0.0 80-81 0.0 97.425 0.0 0.0 0.0 82-83 0.0 97.425 0.0 0.0 0.0 84-85 0.0 97.425 0.0 0.0 0.0 86-87 0.0 97.425 0.0 0.0 0.0 88-89 0.0 97.425 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGATTGT 20 1.445552E-5 96.177216 2 GGGATTG 20 1.445552E-5 96.177216 1 CGAGCGT 30 8.652933E-9 96.177216 2 GCGAGCG 30 8.652933E-9 96.177216 1 GTAGACC 70 0.0 94.975 7 TTGTAGT 20 1.5412463E-5 94.975 5 GATTGTA 20 1.5412463E-5 94.975 3 TAGTTCA 50 0.0 94.975 8 GAGTAGA 70 0.0 94.975 5 ATTGTAG 20 1.5412463E-5 94.975 4 TGTAGTT 20 1.5412463E-5 94.975 6 CGAGTAG 70 0.0 94.975 4 AGACCTT 70 0.0 94.975 9 TCGAGTA 70 0.0 94.975 3 AGTTCAA 50 0.0 94.975 9 TAGACCT 70 0.0 94.975 8 GAGCGTA 30 9.476935E-9 94.97499 3 GCGTAGT 30 9.476935E-9 94.97499 5 AGCGTAG 30 9.476935E-9 94.97499 4 ATCGAGT 75 0.0 89.76541 2 >>END_MODULE Rejected 331312 READS because READLEN < 1 Read 331312 spots for SRR6941565.sra Written 331312 spots for SRR6941565.sra Rejected 331312 READS because READLEN < 1 Read 331312 spots for SRR6941565.sra Written 331312 spots for SRR6941565.sra Rejected 331312 READS because READLEN < 1 Read 331312 spots for SRR6941565.sra Written 331312 spots for SRR6941565.sra Rejected 331312 READS because READLEN < 1 Read 331312 spots for SRR6941565.sra Written 331312 spots for SRR6941565.sra Rejected 331312 READS because READLEN < 1 Read 331312 spots for SRR6941565.sra Written 331312 spots for SRR6941565.sra Rejected 331312 READS because READLEN < 1 Read 331312 spots for SRR6941565.sra Written 331312 spots for SRR6941565.sra Rejected 331312 READS because READLEN < 1 Read 331312 spots for SRR6941565.sra Written 331312 spots for SRR6941565.sra Rejected 331312 READS because READLEN < 1 Read 331312 spots for SRR6941565.sra Written 331312 spots for SRR6941565.sra Rejected 331312 READS because READLEN < 1 Read 331312 spots for SRR6941565.sra Written 331312 spots for SRR6941565.sra Rejected 331312 READS because READLEN < 1 Read 331312 spots for SRR6941565.sra Written 331312 spots for SRR6941565.sra Rejected 331312 READS because READLEN < 1 Read 331312 spots for SRR6941565.sra Written 331312 spots for SRR6941565.sra Rejected 331312 READS because READLEN < 1 Read 331312 spots for SRR6941565.sra Written 331312 spots for SRR6941565.sra Rejected 331312 READS because READLEN < 1 Read 331312 spots for SRR6941565.sra Written 331312 spots for SRR6941565.sra Rejected 331312 READS because READLEN < 1 Read 331312 spots for SRR6941565.sra Written 331312 spots for SRR6941565.sra Rejected 331312 READS because READLEN < 1 Read 331312 spots for SRR6941565.sra Written 331312 spots for SRR6941565.sra Rejected 331312 READS because READLEN < 1 Read 331312 spots for SRR6941565.sra Written 331312 spots for SRR6941565.sra Rejected 331312 READS because READLEN < 1 Read 331312 spots for SRR6941565.sra Written 331312 spots for SRR6941565.sra Rejected 331312 READS because READLEN < 1 Read 331312 spots for SRR6941565.sra Written 331312 spots for SRR6941565.sra Rejected 331322 READS because READLEN < 1 Read 331322 spots for SRR6941565.sra Written 331322 spots for SRR6941565.sra Rejected 331312 READS because READLEN < 1 Read 331312 spots for SRR6941565.sra Written 331312 spots for SRR6941565.sra SRR ids: ['SRR6941565.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_9c8ww28q SRR6941565.sra spots: 6626250 blocks: [[1, 331312], [331313, 662624], [662625, 993936], [993937, 1325248], [1325249, 1656560], [1656561, 1987872], [1987873, 2319184], [2319185, 2650496], [2650497, 2981808], [2981809, 3313120], [3313121, 3644432], [3644433, 3975744], [3975745, 4307056], [4307057, 4638368], [4638369, 4969680], [4969681, 5300992], [5300993, 5632304], [5632305, 5963616], [5963617, 6294928], [6294929, 6626250]] SRR6941565 file size 1583212 SRR6941565 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 SRR6941565 SRR6941565_1.fastq Input file: SRR6941565_1.fastq trimmed: SRR6941565-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 11:31:02 2024 >> started Fri Dec 6 11:31:06 2024 >> done (4.377s) 6626250 reads processed; of these: 98 ( 0.00%) short reads filtered out after trimming by size control 18 ( 0.00%) empty reads filtered out after trimming by size control 6626134 (100.00%) reads available; of these: 951608 (14.36%) trimmed reads available after processing 5674526 (85.64%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 15 0.00% 19 12 0.00% 20 11 0.00% 21 18 0.00% 22 18 0.00% 23 12 0.00% 24 22 0.00% 25 24 0.00% 26 17 0.00% 27 30 0.00% 28 60 0.00% 29 63 0.00% 30 97 0.00% 31 46 0.00% 32 68 0.00% 33 55 0.00% 34 90 0.00% 35 87 0.00% 36 82 0.00% 37 82 0.00% 38 96 0.00% 39 101 0.00% 40 132 0.00% 41 119 0.00% 42 121 0.00% 43 143 0.00% 44 134 0.00% 45 159 0.00% 46 145 0.00% 47 111 0.00% 48 92 0.00% 49 99 0.00% 50 98 0.00% 51 99 0.00% 52 122 0.00% 53 116 0.00% 54 79 0.00% 55 82 0.00% 56 93 0.00% 57 96 0.00% 58 95 0.00% 59 123 0.00% 60 140 0.00% 61 118 0.00% 62 119 0.00% 63 116 0.00% 64 113 0.00% 65 84 0.00% 66 128 0.00% 67 123 0.00% 68 205 0.00% 69 208 0.00% 70 292 0.00% 71 284 0.00% 72 400 0.01% 73 929 0.01% 74 4742 0.07% 75 3563 0.05% 76 1311 0.02% 77 473 0.01% 78 572 0.01% 79 542 0.01% 80 669 0.01% 81 648 0.01% 82 696 0.01% 83 880 0.01% 84 1199 0.02% 85 1441 0.02% 86 1555 0.02% 87 2021 0.03% 88 2506 0.04% 89 3733 0.06% 90 5525 0.08% 91 8277 0.12% 92 11882 0.18% 93 22783 0.34% 94 40785 0.62% 95 96102 1.45% 96 102992 1.55% 97 113492 1.71% 98 190654 2.88% 99 225493 3.40% 100 100449 1.52% 101 5674526 85.64% 6626134 reads passed initial QC criterion=sequence-density sequence-density=97.63 sequence-density-rank=1 fanout-score=28.86 fanout-score-rank=1 prefix-density=97.83 prefix-fanout=28.8 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGCTACATCTCGTATGCCGTCTTCTGCTTGAAAAAA criterion=fanout-score sequence-density=97.63 sequence-density-rank=1 fanout-score=28.86 fanout-score-rank=1 prefix-density=97.83 prefix-fanout=28.8 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGCTACATCTCGTATGCCGTCTTCTGCTTGAAAAAA 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGCTACATCTCGTATGCCGTCTTCTGCTTGAAAAAA -o SRR6941565 - Input file: STDIN trimmed: SRR6941565-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGCTACATCTCGTATGCCGTCTTCTGCTTGA -- 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 11:31:24 2024 >> started Fri Dec 6 11:31:32 2024 >> done (8.188s) 6490907 reads processed; of these: 29599 ( 0.46%) short reads filtered out after trimming by size control 17656 ( 0.27%) empty reads filtered out after trimming by size control 6443652 (99.27%) reads available; of these: 6402606 (99.36%) trimmed reads available after processing 41046 ( 0.64%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 15216 0.24% 19 36891 0.57% 20 53088 0.82% 21 237488 3.69% 22 185136 2.87% 23 165086 2.56% 24 953585 14.80% 25 201293 3.12% 26 185029 2.87% 27 170581 2.65% 28 173858 2.70% 29 431920 6.70% 30 781743 12.13% 31 517511 8.03% 32 534326 8.29% 33 517558 8.03% 34 373459 5.80% 35 309943 4.81% 36 168336 2.61% 37 100515 1.56% 38 61254 0.95% 39 45698 0.71% 40 50563 0.78% 41 50751 0.79% 42 40240 0.62% 43 11352 0.18% 44 14160 0.22% 45 6720 0.10% 46 2453 0.04% 47 2472 0.04% 48 1085 0.02% 49 665 0.01% 50 327 0.01% 51 294 0.00% 52 160 0.00% 53 143 0.00% 54 82 0.00% 55 87 0.00% 56 63 0.00% 57 69 0.00% 58 55 0.00% 59 58 0.00% 60 61 0.00% 61 52 0.00% 62 52 0.00% 63 50 0.00% 64 42 0.00% 65 42 0.00% 66 48 0.00% 67 40 0.00% 68 65 0.00% 69 60 0.00% 70 114 0.00% 71 67 0.00% 72 47 0.00% 73 65 0.00% 74 59 0.00% 75 75 0.00% 76 130 0.00% 77 515 0.01% 78 99 0.00% 79 140 0.00% 80 399 0.01% 81 167 0.00% 82 260 0.00% 83 290 0.00% 84 141 0.00% 85 135 0.00% 86 160 0.00% 87 226 0.00% 88 114 0.00% 89 123 0.00% 90 161 0.00% 91 299 0.00% 92 221 0.00% 93 256 0.00% 94 294 0.00% 95 354 0.01% 96 336 0.01% 97 418 0.01% 98 795 0.01% 99 569 0.01% 100 624 0.01% 101 34174 0.53% criterion=sequence-density sequence-density=23.29 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=16 prefix-density=0.00 prefix-fanout=1.0 sequence=CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAA criterion=fanout-score sequence-density=0.48 sequence-density-rank=13 fanout-score=47.85 fanout-score-rank=1 prefix-density=22.97 prefix-fanout=1.0 sequence=ATTGTGAGAATAAAAAA Started job on | Dec 06 11:31:48 Started mapping on | Dec 06 11:31:48 Finished on | Dec 06 11:32:10 Mapping speed, Million of reads per hour | 1076.54 Number of input reads | 6578879 Average input read length | 31 UNIQUE READS: Uniquely mapped reads number | 1057480 Uniquely mapped reads % | 16.07% Average mapped length | 25.64 Number of splices: Total | 6056 Number of splices: Annotated (sjdb) | 3284 Number of splices: GT/AG | 5719 Number of splices: GC/AG | 186 Number of splices: AT/AC | 2 Number of splices: Non-canonical | 149 Mismatch rate per base, % | 0.12% Deletion rate per base | 0.00% Deletion average length | 1.68 Insertion rate per base | 0.00% Insertion average length | 1.01 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 4141140 % of reads mapped to multiple loci | 62.95% Number of reads mapped to too many loci | 1135023 % of reads mapped to too many loci | 17.25% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.16% % of reads unmapped: other | 0.57% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1380259 1380259 1380259 N_multimapping 4141140 4141140 4141140 N_noFeature 757327 868985 942504 N_ambiguous 8217 4695 244 UnstrandedReadsAssigned:291936 PositiveStrandReadsAssigned:183800 NegativeStrandReadsAssigned:114732 Dataset is classified unstranded MeadianReadLen=30 20thPercentileLength=24 echo kmer=19 SRR6941565 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: SRR6941565-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 6,578,879 reads, 3,154,107 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 979 rounds 52973 SRR6941565.ke.tsv 35125 SRR6941565.se.tsv 88098 total ==> SRR6941565.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 0 0 KQK14071 474 375 2.1086 1.15801 ==> SRR6941565.se.tsv <== BRADI_1g14170v3 25 BRADI_1g53295v3 0 BRADI_1g59795v3 0 BRADI_1g07683v3 1 BRADI_1g00485v3 1 BRADI_1g20270v3 1 BRADI_1g74790v3 23 BRADI_1g09890v3 1 BRADI_1g77505v3 0 BRADI_1g48960v3 0 SRR6941565 completed mapping pipeline successfully