Starting /dee2/code/volunteer_pipeline.sh SRR8846500 current disk space = 1500801564672 free memory = 1354026196 SRR8846500 SRAfilesize 9988fe1328ea53c3f2f5b0513b4c1510 SRR8846500.sra SRR8846500.sra file validated SRR8846500 is single end SRR8846500 is conventional basespace SRR8846500 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8846500_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 fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.93925 33.0 33.0 34.0 28.0 34.0 2 32.80075 34.0 33.0 34.0 30.0 34.0 3 32.88375 34.0 33.0 34.0 32.0 34.0 4 32.94425 34.0 33.0 34.0 32.0 34.0 5 32.90125 34.0 33.0 34.0 32.0 34.0 6 36.5275 38.0 37.0 38.0 34.0 38.0 7 37.096 38.0 38.0 38.0 36.0 38.0 8 37.325 38.0 38.0 38.0 37.0 38.0 9 37.39775 38.0 38.0 38.0 37.0 38.0 10-11 37.40675 38.0 38.0 38.0 37.0 38.0 12-13 37.446875 38.0 38.0 38.0 37.0 38.0 14-15 37.411375 38.0 38.0 38.0 37.0 38.0 16-17 37.415499999999994 38.0 38.0 38.0 37.0 38.0 18-19 37.40575 38.0 38.0 38.0 37.0 38.0 20-21 37.3645 38.0 38.0 38.0 37.0 38.0 22-23 37.37825 38.0 38.0 38.0 37.0 38.0 24-25 37.418875 38.0 38.0 38.0 37.0 38.0 26-27 37.417875 38.0 38.0 38.0 37.0 38.0 28-29 37.283125 38.0 38.0 38.0 37.0 38.0 30-31 37.3885 38.0 38.0 38.0 37.0 38.0 32-33 37.361999999999995 38.0 38.0 38.0 37.0 38.0 34-35 37.170375 38.0 38.0 38.0 36.5 38.0 36-37 37.115875 38.0 38.0 38.0 36.0 38.0 38-39 37.19625 38.0 38.0 38.0 36.5 38.0 40-41 37.05 38.0 38.0 38.0 36.0 38.0 42-43 36.980000000000004 38.0 38.0 38.0 36.0 38.0 44-45 37.145375 38.0 38.0 38.0 36.5 38.0 46-47 37.140375 38.0 38.0 38.0 36.0 38.0 48-49 37.170625 38.0 38.0 38.0 36.5 38.0 50-51 37.242875 38.0 38.0 38.0 37.0 38.0 52-53 37.239000000000004 38.0 38.0 38.0 36.5 38.0 54-55 37.07875 38.0 38.0 38.0 36.5 38.0 56-57 36.821 38.0 38.0 38.0 35.5 38.0 58-59 36.56925 38.0 38.0 38.0 34.5 38.0 60-61 36.506125 38.0 38.0 38.0 34.0 38.0 62-63 35.947500000000005 38.0 37.0 38.0 30.0 38.0 64-65 35.578500000000005 38.0 36.5 38.0 29.0 38.0 66-67 35.28775 38.0 36.5 38.0 28.0 38.0 68-69 35.5835 38.0 37.0 38.0 28.5 38.0 70-71 35.995374999999996 38.0 37.0 38.0 31.0 38.0 72-73 35.9825 38.0 37.0 38.0 31.0 38.0 74-75 35.7545 38.0 37.0 38.0 29.0 38.0 76-77 35.727125 38.0 37.0 38.0 30.0 38.0 78-79 35.59725 38.0 37.0 38.0 29.5 38.0 80-81 35.632000000000005 38.0 37.0 38.0 30.0 38.0 82-83 35.603624999999994 38.0 37.0 38.0 29.0 38.0 84-85 35.446 38.0 37.0 38.0 29.0 38.0 86-87 35.855875 38.0 37.0 38.0 32.0 38.0 88-89 35.652125 38.0 37.0 38.0 32.0 38.0 90-91 35.376000000000005 38.0 37.0 38.0 30.0 38.0 92-93 35.08475 38.0 37.0 38.0 30.0 38.0 94-95 33.895125 38.0 36.0 38.0 21.0 38.0 96-97 31.31775 38.0 33.0 38.0 2.0 38.0 98-99 28.036499999999997 37.5 15.5 38.0 2.0 38.0 100-101 24.269125000000003 34.5 2.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 11 2.0 12 0.0 13 0.0 14 0.0 15 0.0 16 2.0 17 1.0 18 0.0 19 1.0 20 1.0 21 1.0 22 2.0 23 3.0 24 7.0 25 16.0 26 19.0 27 21.0 28 23.0 29 24.0 30 43.0 31 82.0 32 120.0 33 191.0 34 312.0 35 540.0 36 1032.0 37 1557.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 35.521028663273505 24.966514867398875 20.707206000535763 18.805250468791858 2 25.074999999999996 27.825 18.975 28.125 3 29.349999999999998 20.075000000000003 18.625 31.95 4 27.0 33.900000000000006 17.974999999999998 21.125 5 25.75 25.874999999999996 25.025 23.35 6 25.724999999999998 22.85 25.55 25.874999999999996 7 31.6 28.975 18.875 20.549999999999997 8 18.35 20.575 37.8 23.275000000000002 9 23.75 34.375 23.35 18.525 10-11 29.95 21.9375 26.6125 21.5 12-13 23.5375 20.525 25.8125 30.125 14-15 23.7625 36.8625 19.9625 19.412499999999998 16-17 23.95 26.487500000000004 33.675 15.8875 18-19 35.5625 21.3125 22.3875 20.7375 20-21 23.175 27.0875 28.249999999999996 21.4875 22-23 28.325 29.4875 26.6 15.587500000000002 24-25 27.474999999999998 26.0 27.6625 18.862499999999997 26-27 33.862500000000004 24.675 22.787499999999998 18.675 28-29 22.0125 31.362499999999997 24.4 22.225 30-31 25.087500000000002 18.637500000000003 37.075 19.2 32-33 24.212500000000002 15.162500000000001 35.0875 25.5375 34-35 35.6375 12.737499999999999 28.1875 23.4375 36-37 41.112500000000004 16.6125 23.425 18.85 38-39 35.55 17.3875 28.6375 18.425 40-41 28.749999999999996 16.6 21.7875 32.8625 42-43 30.5125 29.825000000000003 15.45 24.212500000000002 44-45 42.512499999999996 22.6375 12.25 22.6 46-47 29.1125 33.925 15.1125 21.85 48-49 23.5875 25.4 17.6125 33.4 50-51 20.3125 27.2625 13.8125 38.6125 52-53 28.000000000000004 30.975 12.662499999999998 28.3625 54-55 22.775000000000002 28.425 16.675 32.125 56-57 22.900000000000002 30.5125 15.475 31.112499999999997 58-59 27.712500000000002 27.9125 15.575 28.799999999999997 60-61 33.0 24.275 19.787499999999998 22.9375 62-63 37.6625 20.925 20.474999999999998 20.9375 64-65 25.775 25.124999999999996 27.224999999999998 21.875 66-67 27.6125 19.5625 27.825 25.0 68-69 30.95 17.1125 27.0875 24.85 70-71 29.062500000000004 19.075 31.1 20.7625 72-73 32.125 14.45 32.9625 20.4625 74-75 20.349999999999998 11.9375 30.85 36.8625 76-77 26.525 8.225 37.45 27.800000000000004 78-79 19.725 8.674999999999999 39.6125 31.9875 80-81 20.0375 8.4375 40.225 31.3 82-83 22.537499999999998 8.35 42.7125 26.400000000000002 84-85 19.875 12.587499999999999 38.2 29.3375 86-87 22.05 20.0625 35.712500000000006 22.175 88-89 12.537499999999998 40.2625 31.15 16.05 90-91 13.5625 50.925 23.5625 11.95 92-93 10.1125 60.45 17.5875 11.85 94-95 9.5625 67.4875 15.987499999999999 6.9625 96-97 6.7625 77.9375 11.075 4.2250000000000005 98-99 4.675 84.1125 7.625 3.5875 100-101 3.8125 86.3625 6.1875 3.6374999999999997 >>END_MODULE >>Per sequence GC content pass #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 2.0 36 3.5 37 3.5 38 5.0 39 10.5 40 31.5 41 60.5 42 134.0 43 209.5 44 249.5 45 322.5 46 355.5 47 403.0 48 431.0 49 380.5 50 307.0 51 294.0 52 275.5 53 170.0 54 106.0 55 78.0 56 73.5 57 51.0 58 17.5 59 9.5 60 6.0 61 3.5 62 2.5 63 1.0 64 1.0 65 0.5 66 0.5 67 0.5 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 warn #Base N-Count 1 6.675000000000001 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-11 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 60.699999999999996 #Duplication Level Percentage of deduplicated Percentage of total 1 87.0675453047776 52.849999999999994 2 5.766062602965404 7.000000000000001 3 2.471169686985173 4.5 4 0.9884678747940692 2.4 5 0.7825370675453047 2.375 6 0.5766062602965404 2.1 7 0.37067545304777594 1.575 8 0.16474464579901155 0.8 9 0.16474464579901155 0.8999999999999999 >10 1.4827018121911038 15.7 >50 0.08237232289950577 3.6249999999999996 >100 0.08237232289950577 6.175 >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 GACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 133 3.325 RNA PCR Primer, Index 1 (100% over 23bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 114 2.85 No Hit TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 86 2.15 RNA PCR Primer, Index 1 (100% over 29bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 59 1.4749999999999999 No Hit GGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 44 1.0999999999999999 RNA PCR Primer, Index 1 (100% over 22bp) CACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAACT 35 0.8750000000000001 RNA PCR Primer, Index 1 (100% over 25bp) GCCCACCCCAAGATGAGTGCTCTCTCTGGAATTCTCGGGTGCCAAGGAAC 34 0.8500000000000001 RNA PCR Primer, Index 1 (100% over 24bp) TCCGTCGTAGTCTAGGTGGTTAGGATATGGAATTCTCGGGTGCCAAGGAA 32 0.8 RNA PCR Primer, Index 1 (100% over 23bp) TCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 30 0.75 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 26 0.65 No Hit GCCTTGATGGTGAAATGGTAGACATGGAATTCTCGGGTGCCAAGGAACTC 25 0.625 RNA PCR Primer, Index 1 (100% over 26bp) GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGGAATTCTCGGGTGCCA 20 0.5 No Hit TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 20 0.5 No Hit GACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAAC 19 0.475 RNA PCR Primer, Index 1 (100% over 24bp) CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 19 0.475 No Hit AGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 18 0.44999999999999996 No Hit GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 17 0.42500000000000004 No Hit GCACCAGTGGTCTAGTGGTAGAATAGTACCTGGAATTCTCGGGTGCCAAG 16 0.4 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 16 0.4 Illumina Small RNA Adapter 2 (100% over 21bp) AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 16 0.4 Illumina Small RNA Adapter 2 (100% over 21bp) CTCTGATGATGATCAAACTAATACTTTCGTTCTTCTGGAATTCTCGGGTG 15 0.375 No Hit GACACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACT 15 0.375 RNA PCR Primer, Index 1 (100% over 25bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTTGGAATTCTCGGGTGCCA 15 0.375 No Hit CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 14 0.35000000000000003 RNA PCR Primer, Index 1 (100% over 28bp) AGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCC 13 0.325 RNA PCR Primer, Index 1 (100% over 27bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGATGGAATTCTC 13 0.325 No Hit ACCTGCTCTGATACCATGTTGTGATGGAATTCTCGGGTGCCAAGGAACTC 12 0.3 RNA PCR Primer, Index 1 (100% over 26bp) TCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTC 12 0.3 RNA PCR Primer, Index 1 (100% over 26bp) CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 12 0.3 No Hit TTCGGACCAGGCTTCATTCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 12 0.3 RNA PCR Primer, Index 1 (100% over 29bp) CGACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGA 12 0.3 RNA PCR Primer, Index 1 (100% over 22bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTTGGAATTCTCGGGTGCC 12 0.3 No Hit CAGGGTTCGTTTCCCTGGATGCGCACCATGGAATTCTCGGGTGCCAAGGA 12 0.3 RNA PCR Primer, Index 1 (100% over 22bp) ATAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAACT 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 25bp) NGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 11 0.27499999999999997 No Hit ACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAAC 10 0.25 RNA PCR Primer, Index 1 (100% over 24bp) ATATATTTCAAGTTATTTCGGATCTTGGAATTCTCGGGTGCCAAGGAACT 10 0.25 RNA PCR Primer, Index 1 (100% over 25bp) TCTCGGACCAGGCTTCATTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 10 0.25 RNA PCR Primer, Index 1 (100% over 29bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTGGAATTCTCGGGTGCCA 10 0.25 No Hit ATCAGCTGACACGAGCAAATCTGAACCCTGGAATTCTCGGGTGCCAAGGA 10 0.25 RNA PCR Primer, Index 1 (100% over 22bp) GCACCAGTGGTCTAGTGGTAGAATAGTATGGAATTCTCGGGTGCCAAGGA 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 22bp) TAATTCATGATCTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACG 9 0.22499999999999998 RNA PCR Primer, Index 6 (100% over 34bp) TAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAG 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 29bp) CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 23bp) TAATTCATGATCTGGCATGTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 8 0.2 RNA PCR Primer, Index 1 (100% over 31bp) CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 8 0.2 Illumina Small RNA Adapter 2 (100% over 21bp) GAAGTCCTCGTGTTGCATTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA 8 0.2 RNA PCR Primer, Index 1 (100% over 28bp) ACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCC 8 0.2 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATACTCTGGAATTCTCGGGTGCCAAG 7 0.17500000000000002 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTTGGAATTCT 7 0.17500000000000002 No Hit GCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCCA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 28bp) CATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAAC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 24bp) ATGCAGTTACTAATTCATGATCTGGCTGGAATTCTCGGGTGCCAAGGAAC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 24bp) CTTAGCGGATACTATGATAGCACCTGGAATTCTCGGGTGCCAAGGAACTC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 26bp) CAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 26bp) AGGGCTATAGCTCAGTTCGGTAGAGCAACTCGTTTACACCGAGATGGAAT 7 0.17500000000000002 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTTGGAATTCTCGGGTGC 7 0.17500000000000002 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 6 0.15 No Hit TCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) NACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAACT 6 0.15 RNA PCR Primer, Index 1 (100% over 25bp) GCACCAGTAGTCTAGTGGTAGAATAGTACCTGGAATTCTCGGGTGCCAAG 6 0.15 No Hit NCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 6 0.15 RNA PCR Primer, Index 1 (100% over 29bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCGTGGAATT 6 0.15 No Hit TGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAA 6 0.15 No Hit CACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACTCC 6 0.15 RNA PCR Primer, Index 1 (100% over 27bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTTGGAATTCTCGGGTG 6 0.15 No Hit TTTGGATTGAAGGGAGCTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG 6 0.15 RNA PCR Primer, Index 1 (100% over 29bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTCATGGAATTCTCGGGTG 6 0.15 No Hit GACACGACTCTCGGCAACGGATATTGGAATTCTCGGGTGCCAAGGAACTC 6 0.15 RNA PCR Primer, Index 1 (100% over 26bp) CAGGCTTTCTTGAACTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC 6 0.15 RNA PCR Primer, Index 1 (100% over 33bp) TCGCTTGGTGCAGATCGGGACTGGAATTCTCGGGTGCCAAGGAACTCCAG 6 0.15 RNA PCR Primer, Index 1 (100% over 29bp) NCCGTCGTAGTCTAGGTGGTTAGGATATGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) GACACGACTCTCGGCAACGGATATGGAATTCTCGGGTGCCAAGGAACTCC 5 0.125 RNA PCR Primer, Index 1 (100% over 27bp) GCTATGAGATCCGAGGGACTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 5 0.125 RNA PCR Primer, Index 1 (100% over 31bp) CATCGAGTAGACCTTGTTATTGTGAGAATGGAATTCTCGGGTGCCAAGGA 5 0.125 RNA PCR Primer, Index 1 (100% over 22bp) GACACGACTCTCGGCAACGTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 5 0.125 RNA PCR Primer, Index 1 (100% over 31bp) ATATATTTCAAGTTATTTCGGATCTGGAATTCTCGGGTGCCAAGGAACTC 5 0.125 RNA PCR Primer, Index 1 (100% over 26bp) GGGGATATGGCGAAATCGGTAGACGCTACGGACTTTGGAATTCTCGGGTG 5 0.125 No Hit CCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCC 5 0.125 RNA PCR Primer, Index 1 (100% over 27bp) CTCGGGTGCCAAGGAACTCCAGTCACGAGTGGATCTCGTATGCCGTCTTC 5 0.125 RNA PCR Primer, Index 23 (100% over 50bp) GCCTACTTAACTCAGTGGTTAGAGTATTGCTTTCATACGGCTGGAATTCT 5 0.125 No Hit TGCCACGATCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAAT 5 0.125 No Hit CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGG 5 0.125 No Hit TCGTGACCCTGACCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGAG 5 0.125 RNA PCR Primer, Index 7 (97% over 36bp) GCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) NACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGC 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTATGGAATTCTCGGGTGCCAA 5 0.125 No Hit TAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAACTC 5 0.125 RNA PCR Primer, Index 1 (100% over 26bp) CACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGC 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 0.075 0.0 0.0 0.0 2 0.0 0.075 0.0 0.0 0.0 3 0.0 0.075 0.0 0.0 0.0 4 0.0 0.075 0.0 0.0 0.0 5 0.0 0.075 0.0 0.0 0.0 6 0.0 0.075 0.0 0.0 0.0 7 0.0 0.075 0.0 0.0 0.0 8 0.0 0.1 0.0 0.0 0.0 9 0.0 0.175 0.0 0.0 0.0 10-11 0.0 0.275 0.0 0.0 0.0 12-13 0.0 0.4125 0.0 0.0 0.0 14-15 0.0 0.8374999999999999 0.0 0.0 0.0 16-17 0.0 1.8499999999999999 0.0 0.0 0.0 18-19 0.0 3.2375 0.0 0.0 0.0 20-21 0.0 6.0125 0.0 0.0 0.0 22-23 0.0 15.0375 0.0 0.0 0.0 24-25 0.0 28.55 0.0 0.0 0.0 26-27 0.0 43.425 0.0 0.0 0.0 28-29 0.0 55.3875 0.0 0.0 0.0 30-31 0.0 63.425000000000004 0.0 0.0 0.0 32-33 0.0 72.375 0.0 0.0 0.0 34-35 0.0 82.26249999999999 0.0 0.0 0.0 36-37 0.0 88.25 0.0 0.0 0.0 38-39 0.0 91.3875 0.0 0.0 0.0 40-41 0.0 92.98750000000001 0.0 0.0 0.0 42-43 0.0 94.6875 0.0 0.0 0.0 44-45 0.0 96.0375 0.0 0.0 0.0 46-47 0.0 96.475 0.0 0.0 0.0 48-49 0.0 96.55000000000001 0.0 0.0 0.0 50-51 0.0 96.6125 0.0 0.0 0.0 52-53 0.0 96.625 0.0 0.0 0.0 54-55 0.0 96.625 0.0 0.0 0.0 56-57 0.0 96.625 0.0 0.0 0.0 58-59 0.0 96.625 0.0 0.0 0.0 60-61 0.0 96.625 0.0 0.0 0.0 62-63 0.0 96.625 0.0 0.0 0.0 64-65 0.0 96.625 0.0 0.0 0.0 66-67 0.0 96.625 0.0 0.0 0.0 68-69 0.0 96.625 0.0 0.0 0.0 70-71 0.0 96.625 0.0 0.0 0.0 72-73 0.0 96.625 0.0 0.0 0.0 74-75 0.0 96.625 0.0 0.0 0.0 76-77 0.0 96.625 0.0 0.0 0.0 78-79 0.0 96.625 0.0 0.0 0.0 80-81 0.0 96.6375 0.0 0.0 0.0 82-83 0.0 96.65 0.0 0.0 0.0 84-85 0.0 96.7 0.0 0.0 0.0 86-87 0.0 96.725 0.0 0.0 0.0 88-89 0.0 96.725 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGATTG 20 1.038194E-5 102.62161 1 GTAGACC 25 3.8470353E-7 94.924995 7 ACACGAC 25 3.8470353E-7 94.924995 2 TTGTAGT 20 1.545283E-5 94.924995 5 AGTAGAC 25 3.8470353E-7 94.924995 6 CTCTCGG 25 3.8470353E-7 94.924995 8 GGATTGT 20 1.545283E-5 94.924995 2 ACTCTCG 25 3.8470353E-7 94.924995 7 CACGACT 25 3.8470353E-7 94.924995 3 GATTGTA 20 1.545283E-5 94.924995 3 TAGTTCA 20 1.545283E-5 94.924995 8 GAGTAGA 25 3.8470353E-7 94.924995 5 ATTGTAG 20 1.545283E-5 94.924995 4 TGTAGTT 20 1.545283E-5 94.924995 6 CGAGTAG 25 3.8470353E-7 94.924995 4 ACGACTC 25 3.8470353E-7 94.924995 4 AGACCTT 25 3.8470353E-7 94.924995 9 GACTCTC 25 3.8470353E-7 94.924995 6 TCGAGTA 25 3.8470353E-7 94.924995 3 AGTTCAA 20 1.545283E-5 94.924995 9 >>END_MODULE Rejected 917701 READS because READLEN < 1 Read 917701 spots for SRR8846500.sra Written 917701 spots for SRR8846500.sra Rejected 917701 READS because READLEN < 1 Read 917701 spots for SRR8846500.sra Written 917701 spots for SRR8846500.sra Rejected 917701 READS because READLEN < 1 Read 917701 spots for SRR8846500.sra Written 917701 spots for SRR8846500.sra Rejected 917701 READS because READLEN < 1 Read 917701 spots for SRR8846500.sra Written 917701 spots for SRR8846500.sra Rejected 917701 READS because READLEN < 1 Read 917701 spots for SRR8846500.sra Written 917701 spots for SRR8846500.sra Rejected 917701 READS because READLEN < 1 Read 917701 spots for SRR8846500.sra Written 917701 spots for SRR8846500.sra Rejected 917701 READS because READLEN < 1 Read 917701 spots for SRR8846500.sra Written 917701 spots for SRR8846500.sra Rejected 917701 READS because READLEN < 1 Read 917701 spots for SRR8846500.sra Written 917701 spots for SRR8846500.sra Rejected 917701 READS because READLEN < 1 Read 917701 spots for SRR8846500.sra Written 917701 spots for SRR8846500.sra Rejected 917701 READS because READLEN < 1 Read 917701 spots for SRR8846500.sra Written 917701 spots for SRR8846500.sra Rejected 917701 READS because READLEN < 1 Read 917701 spots for SRR8846500.sra Written 917701 spots for SRR8846500.sra Rejected 917701 READS because READLEN < 1 Read 917701 spots for SRR8846500.sra Written 917701 spots for SRR8846500.sra Rejected 917701 READS because READLEN < 1 Read 917701 spots for SRR8846500.sra Written 917701 spots for SRR8846500.sra Rejected 917701 READS because READLEN < 1 Read 917701 spots for SRR8846500.sra Written 917701 spots for SRR8846500.sra Rejected 917715 READS because READLEN < 1 Read 917715 spots for SRR8846500.sra Written 917715 spots for SRR8846500.sra Rejected 917701 READS because READLEN < 1 Read 917701 spots for SRR8846500.sra Written 917701 spots for SRR8846500.sra Rejected 917701 READS because READLEN < 1 Read 917701 spots for SRR8846500.sra Written 917701 spots for SRR8846500.sra Rejected 917701 READS because READLEN < 1 Read 917701 spots for SRR8846500.sra Written 917701 spots for SRR8846500.sra Rejected 917701 READS because READLEN < 1 Read 917701 spots for SRR8846500.sra Written 917701 spots for SRR8846500.sra Rejected 917701 READS because READLEN < 1 Read 917701 spots for SRR8846500.sra Written 917701 spots for SRR8846500.sra SRR ids: ['SRR8846500.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_z3zv000h SRR8846500.sra spots: 18354034 blocks: [[1, 917701], [917702, 1835402], [1835403, 2753103], [2753104, 3670804], [3670805, 4588505], [4588506, 5506206], [5506207, 6423907], [6423908, 7341608], [7341609, 8259309], [8259310, 9177010], [9177011, 10094711], [10094712, 11012412], [11012413, 11930113], [11930114, 12847814], [12847815, 13765515], [13765516, 14683216], [14683217, 15600917], [15600918, 16518618], [16518619, 17436319], [17436320, 18354034]] SRR8846500 file size 4405493 SRR8846500 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 SRR8846500 SRR8846500_1.fastq Input file: SRR8846500_1.fastq trimmed: SRR8846500-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 00:38:28 2024 >> started Mon Dec 9 00:39:18 2024 >> done (49.580s) 18354034 reads processed; of these: 573 ( 0.00%) short reads filtered out after trimming by size control 72 ( 0.00%) empty reads filtered out after trimming by size control 18353389 (100.00%) reads available; of these: 4831232 (26.32%) trimmed reads available after processing 13522157 (73.68%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 70 0.00% 19 55 0.00% 20 74 0.00% 21 67 0.00% 22 72 0.00% 23 80 0.00% 24 107 0.00% 25 119 0.00% 26 185 0.00% 27 235 0.00% 28 263 0.00% 29 396 0.00% 30 379 0.00% 31 360 0.00% 32 311 0.00% 33 269 0.00% 34 268 0.00% 35 227 0.00% 36 215 0.00% 37 210 0.00% 38 217 0.00% 39 234 0.00% 40 247 0.00% 41 295 0.00% 42 422 0.00% 43 468 0.00% 44 538 0.00% 45 588 0.00% 46 463 0.00% 47 364 0.00% 48 291 0.00% 49 307 0.00% 50 294 0.00% 51 301 0.00% 52 329 0.00% 53 374 0.00% 54 474 0.00% 55 458 0.00% 56 485 0.00% 57 547 0.00% 58 520 0.00% 59 581 0.00% 60 601 0.00% 61 701 0.00% 62 769 0.00% 63 968 0.01% 64 1243 0.01% 65 1314 0.01% 66 2573 0.01% 67 8723 0.05% 68 10337 0.06% 69 8184 0.04% 70 10036 0.05% 71 17377 0.09% 72 7793 0.04% 73 3870 0.02% 74 11097 0.06% 75 5352 0.03% 76 3287 0.02% 77 3018 0.02% 78 4012 0.02% 79 4821 0.03% 80 6731 0.04% 81 9456 0.05% 82 13793 0.08% 83 14475 0.08% 84 14588 0.08% 85 15960 0.09% 86 21223 0.12% 87 31419 0.17% 88 48518 0.26% 89 63122 0.34% 90 96416 0.53% 91 107933 0.59% 92 135898 0.74% 93 210456 1.15% 94 249022 1.36% 95 557482 3.04% 96 622574 3.39% 97 569209 3.10% 98 873141 4.76% 99 699340 3.81% 100 351641 1.92% 101 13522157 73.68% 18353389 reads passed initial QC criterion=sequence-density sequence-density=96.49 sequence-density-rank=1 fanout-score=34.50 fanout-score-rank=2 prefix-density=96.85 prefix-fanout=34.4 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGAGTGGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAT criterion=fanout-score sequence-density=2.07 sequence-density-rank=5 fanout-score=47.73 fanout-score-rank=1 prefix-density=97.88 prefix-fanout=1.0 sequence=CACGAGTGGATATCGTATGCCGT 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGAGTGGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAT -o SRR8846500 - Input file: STDIN trimmed: SRR8846500-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGAGTGGATCTCGTATGCCGTCTTCTGCTTGA -- 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 00:42:24 2024 >> started Mon Dec 9 00:43:54 2024 >> done (90.014s) 17974969 reads processed; of these: 508706 ( 2.83%) short reads filtered out after trimming by size control 22388 ( 0.12%) empty reads filtered out after trimming by size control 17443875 (97.05%) reads available; of these: 17220416 (98.72%) trimmed reads available after processing 223459 ( 1.28%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 154197 0.88% 19 279458 1.60% 20 274840 1.58% 21 1234338 7.08% 22 613209 3.52% 23 758641 4.35% 24 2771510 15.89% 25 810048 4.64% 26 870037 4.99% 27 1282584 7.35% 28 793411 4.55% 29 670547 3.84% 30 857970 4.92% 31 641503 3.68% 32 1237513 7.09% 33 931226 5.34% 34 659386 3.78% 35 592357 3.40% 36 459760 2.64% 37 256452 1.47% 38 188584 1.08% 39 150112 0.86% 40 160787 0.92% 41 165122 0.95% 42 157153 0.90% 43 78564 0.45% 44 90528 0.52% 45 24992 0.14% 46 16324 0.09% 47 8549 0.05% 48 5395 0.03% 49 3148 0.02% 50 1985 0.01% 51 1779 0.01% 52 1066 0.01% 53 793 0.00% 54 638 0.00% 55 374 0.00% 56 627 0.00% 57 307 0.00% 58 268 0.00% 59 339 0.00% 60 313 0.00% 61 413 0.00% 62 434 0.00% 63 568 0.00% 64 863 0.00% 65 900 0.01% 66 2065 0.01% 67 8105 0.05% 68 9517 0.05% 69 7242 0.04% 70 9084 0.05% 71 16028 0.09% 72 5941 0.03% 73 1181 0.01% 74 717 0.00% 75 513 0.00% 76 729 0.00% 77 1381 0.01% 78 647 0.00% 79 941 0.01% 80 3130 0.02% 81 1687 0.01% 82 1991 0.01% 83 4110 0.02% 84 1607 0.01% 85 1029 0.01% 86 954 0.01% 87 1083 0.01% 88 698 0.00% 89 809 0.00% 90 843 0.00% 91 851 0.00% 92 997 0.01% 93 1196 0.01% 94 1078 0.01% 95 1460 0.01% 96 1708 0.01% 97 2329 0.01% 98 3919 0.02% 99 2746 0.02% 100 3480 0.02% 101 132167 0.76% criterion=sequence-density sequence-density=3.46 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=12 prefix-density=0.00 prefix-fanout=1.0 sequence=CATCGAGTAGACCTTGTTATTGTGAGAAT criterion=fanout-score sequence-density=0.61 sequence-density-rank=8 fanout-score=10.82 fanout-score-rank=1 prefix-density=6.59 prefix-fanout=1.0 sequence=GAGCACCGCCCTGTCAAGG Started job on | Dec 09 00:46:17 Started mapping on | Dec 09 00:46:17 Finished on | Dec 09 00:52:50 Mapping speed, Million of reads per hour | 163.26 Number of input reads | 17822295 Average input read length | 30 UNIQUE READS: Uniquely mapped reads number | 3338097 Uniquely mapped reads % | 18.73% Average mapped length | 25.94 Number of splices: Total | 31126 Number of splices: Annotated (sjdb) | 19213 Number of splices: GT/AG | 29479 Number of splices: GC/AG | 1099 Number of splices: AT/AC | 17 Number of splices: Non-canonical | 531 Mismatch rate per base, % | 0.13% Deletion rate per base | 0.00% Deletion average length | 1.39 Insertion rate per base | 0.00% Insertion average length | 1.03 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 7370682 % of reads mapped to multiple loci | 41.36% Number of reads mapped to too many loci | 6233071 % of reads mapped to too many loci | 34.97% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.25% % of reads unmapped: other | 0.69% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 7113516 7113516 7113516 N_multimapping 7370682 7370682 7370682 N_noFeature 2172972 2423207 3071609 N_ambiguous 42583 25758 712 UnstrandedReadsAssigned:1122542 PositiveStrandReadsAssigned:889132 NegativeStrandReadsAssigned:265776 Dataset is classified unstranded MeadianReadLen=27 20thPercentileLength=24 echo kmer=19 SRR8846500 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: SRR8846500-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 17,822,295 reads, 5,516,594 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,141 rounds 52973 SRR8846500.ke.tsv 35125 SRR8846500.se.tsv 88098 total ==> SRR8846500.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0.620664 0.116396 PNS24249 1928 1829 4.13801 0.400951 PNS24246 1044 945 0.620664 0.116396 PNS24248 1044 945 0.620664 0.116396 PNS24244 1471 1372 0 0 PNS24243 293 194 0 0 KQK14069 1603 1504 83.632 9.85457 KQK14071 474 375 2.85666 1.35002 ==> SRR8846500.se.tsv <== BRADI_1g14170v3 163 BRADI_1g53295v3 2 BRADI_1g59795v3 4 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 28 BRADI_1g74790v3 49 BRADI_1g09890v3 0 BRADI_1g77505v3 7 BRADI_1g48960v3 0 SRR8846500 completed mapping pipeline successfully