Starting /dee2/code/volunteer_pipeline.sh SRR6941545 current disk space = 1551531008000 free memory = 1602322232 SRR6941545 SRAfilesize 8d91b00dd7ef9a5210d66f1377dc130a SRR6941545.sra SRR6941545.sra file validated SRR6941545 is single end SRR6941545 is conventional basespace SRR6941545 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6941545_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 46 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.15425 34.0 33.0 34.0 32.0 34.0 2 33.325 34.0 33.0 34.0 32.0 34.0 3 32.82125 34.0 33.0 34.0 31.0 34.0 4 33.10525 34.0 33.0 34.0 32.0 34.0 5 33.158 34.0 33.0 34.0 31.0 34.0 6 36.9865 38.0 37.0 38.0 36.0 38.0 7 37.28775 38.0 38.0 38.0 36.0 38.0 8 37.4905 38.0 38.0 38.0 37.0 38.0 9 37.51425 38.0 38.0 38.0 37.0 38.0 10-11 37.533625 38.0 38.0 38.0 37.0 38.0 12-13 37.442375 38.0 38.0 38.0 37.0 38.0 14-15 37.482625 38.0 38.0 38.0 37.0 38.0 16-17 36.2525 38.0 37.5 38.0 32.0 38.0 18-19 36.936499999999995 38.0 38.0 38.0 33.5 38.0 20-21 35.8765 38.0 37.5 38.0 29.5 38.0 22-23 37.139875 38.0 38.0 38.0 36.5 38.0 24-25 37.4075 38.0 38.0 38.0 37.0 38.0 26-27 37.38225 38.0 38.0 38.0 37.0 38.0 28-29 37.449625 38.0 38.0 38.0 37.0 38.0 30-31 37.3565 38.0 38.0 38.0 37.0 38.0 32-33 37.25825 38.0 38.0 38.0 37.0 38.0 34-35 37.211375000000004 38.0 38.0 38.0 37.0 38.0 36-37 37.052375 38.0 38.0 38.0 36.5 38.0 38-39 37.069375 38.0 38.0 38.0 36.5 38.0 40-41 37.103625 38.0 38.0 38.0 37.0 38.0 42-43 37.116 38.0 38.0 38.0 36.5 38.0 44-45 37.13075 38.0 38.0 38.0 36.5 38.0 46-47 36.991625 38.0 38.0 38.0 36.0 38.0 48-49 37.1235 38.0 38.0 38.0 36.5 38.0 50-51 36.954375 38.0 38.0 38.0 36.0 38.0 52-53 36.898624999999996 38.0 38.0 38.0 36.0 38.0 54-55 37.083375000000004 38.0 38.0 38.0 36.0 38.0 56-57 37.06325 38.0 38.0 38.0 36.0 38.0 58-59 37.18375 38.0 38.0 38.0 37.0 38.0 60-61 37.134625 38.0 38.0 38.0 37.0 38.0 62-63 36.909 38.0 38.0 38.0 36.0 38.0 64-65 36.606375 38.0 38.0 38.0 34.5 38.0 66-67 36.40325 38.0 37.5 38.0 33.5 38.0 68-69 36.901624999999996 38.0 38.0 38.0 36.0 38.0 70-71 36.42937499999999 38.0 38.0 38.0 33.5 38.0 72-73 36.223625 38.0 37.0 38.0 33.0 38.0 74-75 35.740375 38.0 37.0 38.0 29.5 38.0 76-77 35.76275 38.0 37.0 38.0 30.0 38.0 78-79 36.218625 38.0 37.5 38.0 33.5 38.0 80-81 36.608375 38.0 38.0 38.0 35.0 38.0 82-83 36.484125 38.0 38.0 38.0 35.0 38.0 84-85 36.4655 38.0 38.0 38.0 35.0 38.0 86-87 36.2545 38.0 38.0 38.0 34.0 38.0 88-89 36.402625 38.0 38.0 38.0 34.0 38.0 90-91 36.415875 38.0 38.0 38.0 34.5 38.0 92-93 36.374125 38.0 38.0 38.0 34.5 38.0 94-95 36.167 38.0 38.0 38.0 34.5 38.0 96-97 34.525125 38.0 37.5 38.0 27.5 38.0 98-99 31.597 38.0 34.0 38.0 2.0 38.0 100-101 28.598125 38.0 25.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 8 1.0 9 1.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 3.0 16 3.0 17 1.0 18 1.0 19 1.0 20 1.0 21 1.0 22 1.0 23 4.0 24 4.0 25 8.0 26 15.0 27 17.0 28 27.0 29 19.0 30 42.0 31 42.0 32 63.0 33 95.0 34 179.0 35 422.0 36 805.0 37 2244.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 40.775 25.775 13.725000000000001 19.725 2 34.99249624812406 27.063531765882942 18.78439219609805 19.15957978989495 3 31.35 19.825 23.599999999999998 25.224999999999998 4 29.232308077019255 30.707676919229808 16.62915728932233 23.43085771442861 5 39.65 19.475 25.025 15.85 6 22.5 32.574999999999996 25.424999999999997 19.5 7 41.4 22.0 23.575 13.025 8 25.45 14.649999999999999 44.925 14.975 9 20.125 41.349999999999994 23.225 15.299999999999999 10-11 37.8 24.7875 19.3625 18.05 12-13 18.05 14.575 25.924999999999997 41.449999999999996 14-15 20.3 41.4 23.1125 15.187500000000002 16-17 27.6375 15.662499999999998 42.25 14.45 18-19 43.475 19.8625 23.1875 13.475000000000001 20-21 13.825000000000001 27.8625 36.575 21.7375 22-23 30.0375 31.412499999999998 21.9375 16.6125 24-25 32.175 29.825000000000003 22.3125 15.687499999999998 26-27 39.7 23.9125 18.462500000000002 17.925 28-29 17.05 37.987500000000004 21.025 23.9375 30-31 22.975 9.9375 44.487500000000004 22.6 32-33 28.325 13.3875 29.5875 28.7 34-35 36.9625 18.5625 29.025000000000002 15.45 36-37 43.8 18.125 26.8125 11.262500000000001 38-39 23.799999999999997 22.662499999999998 33.6875 19.85 40-41 20.6375 16.287499999999998 26.25 36.825 42-43 32.7875 25.45 21.2 20.5625 44-45 53.6875 13.55 14.2125 18.55 46-47 31.2875 28.237499999999997 16.05 24.425 48-49 22.7375 21.587500000000002 20.7875 34.887499999999996 50-51 26.0125 25.0125 8.3625 40.612500000000004 52-53 29.65 43.9125 6.7 19.7375 54-55 21.1625 30.112499999999997 19.05 29.675 56-57 14.249999999999998 35.525 12.025 38.2 58-59 20.05 30.525000000000002 17.3875 32.0375 60-61 10.375 28.3125 22.675 38.6375 62-63 12.7 44.3125 16.575 26.4125 64-65 13.25 33.25 27.3125 26.187500000000004 66-67 12.15 25.1875 26.075 36.5875 68-69 20.7875 33.95 19.675 25.587500000000002 70-71 12.562499999999998 36.225 31.275 19.9375 72-73 16.150000000000002 29.012500000000003 28.712500000000002 26.125 74-75 14.0625 17.675 27.224999999999998 41.0375 76-77 19.2125 12.275 44.0375 24.474999999999998 78-79 19.112499999999997 9.7875 40.7125 30.3875 80-81 19.725 12.687499999999998 35.112500000000004 32.475 82-83 28.025 7.025 38.625 26.325 84-85 20.125 6.0375 37.55 36.2875 86-87 21.3125 13.850000000000001 39.787499999999994 25.05 88-89 12.3375 34.125 34.175 19.3625 90-91 9.9375 36.662499999999994 33.45 19.950000000000003 92-93 17.8875 41.949999999999996 24.55 15.6125 94-95 11.65 56.6625 22.025 9.6625 96-97 10.0625 71.1375 15.225 3.5749999999999997 98-99 5.525 86.6625 5.125 2.6875 100-101 2.2875 91.53750000000001 3.3875 2.7875 >>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 0.5 32 1.5 33 2.0 34 2.0 35 3.0 36 4.0 37 3.5 38 4.5 39 9.5 40 25.0 41 90.0 42 186.0 43 451.0 44 560.5 45 383.5 46 356.5 47 299.5 48 177.0 49 258.0 50 348.5 51 339.5 52 227.5 53 82.5 54 65.0 55 48.5 56 18.5 57 25.5 58 21.5 59 2.5 60 1.5 61 0.5 62 0.5 63 0.5 64 0.0 65 0.0 66 0.0 67 0.0 68 0.0 69 0.0 70 0.0 71 0.0 72 0.0 73 0.0 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 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 48.325 #Duplication Level Percentage of deduplicated Percentage of total 1 87.73926539058459 42.4 2 4.811174340403518 4.65 3 2.0175892395240558 2.9250000000000003 4 1.2415933781686497 2.4 5 0.5690636316606311 1.375 6 0.6207966890843248 1.7999999999999998 7 0.20693222969477496 0.7000000000000001 8 0.2586652871184687 1.0 9 0.1551991722710812 0.675 >10 1.7071908949818935 16.400000000000002 >50 0.46559751681324363 14.374999999999998 >100 0.20693222969477496 11.3 >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 GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTTGGAATTCTCGGGTG 123 3.075 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 111 2.775 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 109 2.725 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 109 2.725 No Hit GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 88 2.1999999999999997 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTGGAATTCTCGGGTGCCAA 68 1.7000000000000002 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTTGGAATTCTCGGGTGCCA 68 1.7000000000000002 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTTGGAATTCTCGGGTGC 65 1.625 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 61 1.525 Illumina Small RNA Adapter 2 (100% over 21bp) CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 59 1.4749999999999999 RNA PCR Primer, Index 1 (100% over 28bp) TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 59 1.4749999999999999 RNA PCR Primer, Index 1 (100% over 29bp) GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTTGGAATTCTCGGGTGC 54 1.35 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 53 1.325 Illumina Small RNA Adapter 2 (100% over 21bp) ATATTGGGTAGGTTGTGGTATTTCATTGCTGGAATTCTCGGGTGCCAAGG 47 1.175 Illumina Small RNA Adapter 2 (100% over 21bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 44 1.0999999999999999 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 38 0.95 No Hit TCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTC 38 0.95 RNA PCR Primer, Index 1 (100% over 26bp) ATATTGGGTAGGTTGTGGTATTTCATTGCTTGGAATTCTCGGGTGCCAAG 36 0.8999999999999999 No Hit CGGTCGAGGGCACGCCTGCCTGGGCGTCACGCTGGAATTCTCGGGTGCCA 32 0.8 No Hit AACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCC 31 0.775 RNA PCR Primer, Index 1 (100% over 27bp) TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 31 0.775 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTGGAATTCTCGGGTGCCA 30 0.75 No Hit ACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCCA 25 0.625 RNA PCR Primer, Index 1 (100% over 28bp) GAACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTC 20 0.5 RNA PCR Primer, Index 1 (100% over 26bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGGAATTCTCGGGTGC 18 0.44999999999999996 No Hit GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTTGGAATTCTCGGGTGC 18 0.44999999999999996 No Hit ACCTGCTCTGATACCATGTTGTGATGGAATTCTCGGGTGCCAAGGAACTC 17 0.42500000000000004 RNA PCR Primer, Index 1 (100% over 26bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTGAATCTGGAATTC 16 0.4 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGTGGAATTCTCGGGTGCC 16 0.4 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGGAATTCTCGGGTGCCAA 16 0.4 No Hit GAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTGC 15 0.375 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTGGAATTCTCGGGT 13 0.325 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTAATCTGGAATTCT 13 0.325 No Hit TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTCAAATCTCGTATGC 13 0.325 RNA PCR Primer, Index 13 (100% over 50bp) AGAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTG 12 0.3 No Hit TGTCGTGCCAATTCAACATAAACCCCTTGGAATTCTCGGGTGCCAAGGAA 12 0.3 RNA PCR Primer, Index 1 (100% over 23bp) CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 12 0.3 No Hit GTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTTGGAATTCTCGGGTGCC 12 0.3 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGTGGAATTCT 11 0.27499999999999997 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAATGGAATTCTCGGGTGCCA 10 0.25 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTTGGAATTCT 10 0.25 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGGAATTCTCGGGTGCCA 10 0.25 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTATGGAATTCTCGGGTGCCAA 10 0.25 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGATGGAATTCTC 10 0.25 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTGGAATTCTCGGGT 10 0.25 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACCTGGAATTCTCGGGTGCC 10 0.25 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATGGAATTCTCGGGTGCCAAGGA 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 22bp) AGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCC 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 27bp) CATCGAGTAGACCTTGTTATTGTGAGAATTATGGAATTCTCGGGTGCCAA 9 0.22499999999999998 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATACTCTGGAATTCTCGGGTGCCAAG 8 0.2 No Hit GGCGGATGTAGCCAAGTGGTTCAAGGCAGTGGATTTGGAATTCTCGGGTG 8 0.2 No Hit ACGAACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAAC 8 0.2 RNA PCR Primer, Index 1 (100% over 24bp) AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 8 0.2 Illumina Small RNA Adapter 2 (100% over 21bp) CTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCCAG 8 0.2 RNA PCR Primer, Index 1 (100% over 29bp) TTCGGACCAGGCTTCATTCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 29bp) CGAACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACT 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 25bp) CAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTG 7 0.17500000000000002 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCTGGAATTC 7 0.17500000000000002 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGTGGAATTCTCGGGTGCCAAGGA 6 0.15 RNA PCR Primer, Index 1 (100% over 22bp) CACCATGCGCGGGTTCAATTCCCGTCGTTCGCCCCATGGAATTCTCGGGT 6 0.15 No Hit GGGATTGTAGTTCAATTGGACAGAGCACCGCCCTGGAATTCTCGGGTGCC 6 0.15 No Hit GGGATTGTAGTTCAATTGGACAGAGCACCGCCCTTGGAATTCTCGGGTGC 6 0.15 No Hit AATATTGGGTAGGTTGTGGTATTTCATTGCTTGGAATTCTCGGGTGCCAA 6 0.15 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 6 0.15 Illumina Small RNA Adapter 2 (100% over 21bp) GCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCCA 6 0.15 RNA PCR Primer, Index 1 (100% over 28bp) AATATTGGGTAGGTTGTGGTATTTCATTGCTGGAATTCTCGGGTGCCAAG 6 0.15 No Hit GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGTGGAATTCTCGGGTG 6 0.15 No Hit AAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTGCC 6 0.15 No Hit GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGTTGGAATTCTCGGGT 6 0.15 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCATGGAATTCTCGGGTG 6 0.15 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTTGGAATTCTCGGGTGCCAA 5 0.125 No Hit CCGTTACTCGGAGGTTCGAATCCTTCCGTCCCAGCCATGGAATTCTCGGG 5 0.125 No Hit CCCTATAGAACTCCACATCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG 5 0.125 RNA PCR Primer, Index 1 (100% over 29bp) CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) CATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) TGTCGTGCCAATTCAACATAAACCCCTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) GAGGCATCCTAACGAAAGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 5 0.125 No Hit AAGCTGAAGCGGAAATGCAATTCTCGGGTGAGATGGAATTCTCGGGTGCC 5 0.125 No Hit TTGACAGAAGAGAGTGAGCACTGGAATTCTCGGGTGCCAAGGAACTCCAG 5 0.125 RNA PCR Primer, Index 1 (100% over 29bp) GCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) ATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) >>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 0.45 0.0 0.0 0.0 2 0.0 0.475 0.0 0.0 0.0 3 0.0 0.475 0.0 0.0 0.0 4 0.0 0.475 0.0 0.0 0.0 5 0.0 0.475 0.0 0.0 0.0 6 0.0 0.5 0.0 0.0 0.0 7 0.0 0.5 0.0 0.0 0.0 8 0.0 0.5 0.0 0.0 0.0 9 0.0 0.5 0.0 0.0 0.0 10-11 0.0 0.5 0.0 0.0 0.0 12-13 0.0 0.575 0.0 0.0 0.0 14-15 0.0 0.625 0.0 0.0 0.0 16-17 0.0 0.7 0.0 0.0 0.0 18-19 0.0 0.95 0.0 0.0 0.0 20-21 0.0 1.7374999999999998 0.0 0.0 0.0 22-23 0.0 9.0 0.0 0.0 0.0 24-25 0.0 22.75 0.0 0.0 0.0 26-27 0.0 34.125 0.0 0.0 0.0 28-29 0.0 37.2875 0.0 0.0 0.0 30-31 0.0 48.475 0.0 0.0 0.0 32-33 0.0 61.849999999999994 0.0 0.0 0.0 34-35 0.0 78.9 0.0 0.0 0.0 36-37 0.0 90.525 0.0 0.0 0.0 38-39 0.0 93.17500000000001 0.0 0.0 0.0 40-41 0.0 94.35 0.0 0.0 0.0 42-43 0.0 96.55 0.0 0.0 0.0 44-45 0.0 97.26249999999999 0.0 0.0 0.0 46-47 0.0 97.3875 0.0 0.0 0.0 48-49 0.0 97.425 0.0 0.0 0.0 50-51 0.0 97.4375 0.0 0.0 0.0 52-53 0.0 97.45 0.0 0.0 0.0 54-55 0.0 97.45 0.0 0.0 0.0 56-57 0.0 97.45 0.0 0.0 0.0 58-59 0.0 97.45 0.0 0.0 0.0 60-61 0.0 97.45 0.0 0.0 0.0 62-63 0.0 97.45 0.0 0.0 0.0 64-65 0.0 97.45 0.0 0.0 0.0 66-67 0.0 97.45 0.0 0.0 0.0 68-69 0.0 97.45 0.0 0.0 0.0 70-71 0.0 97.45 0.0 0.0 0.0 72-73 0.0 97.45 0.0 0.0 0.0 74-75 0.0 97.45 0.0 0.0 0.0 76-77 0.0 97.45 0.0 0.0 0.0 78-79 0.0 97.45 0.0 0.0 0.0 80-81 0.0 97.45 0.0 0.0 0.0 82-83 0.0 97.45 0.0 0.0 0.0 84-85 0.0 97.45 0.0 0.0 0.0 86-87 0.0 97.45 0.0 0.0 0.0 88-89 0.0 97.45 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGATGTA 40 5.456968E-12 95.00001 4 GATGTAG 40 5.456968E-12 95.00001 5 TAGCCAA 40 5.456968E-12 95.00001 9 TAGTTCA 40 5.456968E-12 95.00001 8 TGTAGCC 40 5.456968E-12 95.00001 7 ATGTAGC 40 5.456968E-12 95.00001 6 AGTTCAA 40 5.456968E-12 95.00001 9 GTAGTTC 40 5.456968E-12 95.00001 7 GTAGCCA 40 5.456968E-12 95.00001 8 GAGCGTA 25 3.8289727E-7 95.0 3 GTAGACC 50 0.0 95.0 7 TTGTAGT 15 6.142176E-4 95.0 5 AGTAGAC 50 0.0 95.0 6 GGACCAG 15 6.142176E-4 95.0 3 CGTAGTT 25 3.8289727E-7 95.0 6 CGGACCA 15 6.142176E-4 95.0 2 TCGGACC 15 6.142176E-4 95.0 1 GATTGTA 15 6.142176E-4 95.0 3 GAGTAGA 50 0.0 95.0 5 ATTGTAG 15 6.142176E-4 95.0 4 >>END_MODULE Rejected 257564 READS because READLEN < 1 Read 257564 spots for SRR6941545.sra Written 257564 spots for SRR6941545.sra Rejected 257564 READS because READLEN < 1 Read 257564 spots for SRR6941545.sra Written 257564 spots for SRR6941545.sra Rejected 257564 READS because READLEN < 1 Read 257564 spots for SRR6941545.sra Written 257564 spots for SRR6941545.sra Rejected 257564 READS because READLEN < 1 Read 257564 spots for SRR6941545.sra Written 257564 spots for SRR6941545.sra Rejected 257564 READS because READLEN < 1 Read 257564 spots for SRR6941545.sra Written 257564 spots for SRR6941545.sra Rejected 257564 READS because READLEN < 1 Read 257564 spots for SRR6941545.sra Written 257564 spots for SRR6941545.sra Rejected 257564 READS because READLEN < 1 Read 257564 spots for SRR6941545.sra Written 257564 spots for SRR6941545.sra Rejected 257564 READS because READLEN < 1 Read 257564 spots for SRR6941545.sra Written 257564 spots for SRR6941545.sra Rejected 257569 READS because READLEN < 1 Read 257569 spots for SRR6941545.sra Written 257569 spots for SRR6941545.sra Rejected 257564 READS because READLEN < 1 Read 257564 spots for SRR6941545.sra Written 257564 spots for SRR6941545.sra Rejected 257564 READS because READLEN < 1 Read 257564 spots for SRR6941545.sra Written 257564 spots for SRR6941545.sra Rejected 257564 READS because READLEN < 1 Read 257564 spots for SRR6941545.sra Written 257564 spots for SRR6941545.sra Rejected 257564 READS because READLEN < 1 Read 257564 spots for SRR6941545.sra Written 257564 spots for SRR6941545.sra Rejected 257564 READS because READLEN < 1 Read 257564 spots for SRR6941545.sra Written 257564 spots for SRR6941545.sra Rejected 257564 READS because READLEN < 1 Read 257564 spots for SRR6941545.sra Written 257564 spots for SRR6941545.sra Rejected 257564 READS because READLEN < 1 Read 257564 spots for SRR6941545.sra Written 257564 spots for SRR6941545.sra Rejected 257564 READS because READLEN < 1 Read 257564 spots for SRR6941545.sra Written 257564 spots for SRR6941545.sra Rejected 257564 READS because READLEN < 1 Read 257564 spots for SRR6941545.sra Written 257564 spots for SRR6941545.sra Rejected 257564 READS because READLEN < 1 Read 257564 spots for SRR6941545.sra Written 257564 spots for SRR6941545.sra Rejected 257564 READS because READLEN < 1 Read 257564 spots for SRR6941545.sra Written 257564 spots for SRR6941545.sra SRR ids: ['SRR6941545.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_g3xo_hvt SRR6941545.sra spots: 5151285 blocks: [[1, 257564], [257565, 515128], [515129, 772692], [772693, 1030256], [1030257, 1287820], [1287821, 1545384], [1545385, 1802948], [1802949, 2060512], [2060513, 2318076], [2318077, 2575640], [2575641, 2833204], [2833205, 3090768], [3090769, 3348332], [3348333, 3605896], [3605897, 3863460], [3863461, 4121024], [4121025, 4378588], [4378589, 4636152], [4636153, 4893716], [4893717, 5151285]] SRR6941545 file size 1230316 SRR6941545 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 SRR6941545 SRR6941545_1.fastq Input file: SRR6941545_1.fastq trimmed: SRR6941545-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 10:44:13 2024 >> started Fri Dec 6 10:44:17 2024 >> done (3.810s) 5151285 reads processed; of these: 70 ( 0.00%) short reads filtered out after trimming by size control 11 ( 0.00%) empty reads filtered out after trimming by size control 5151204 (100.00%) reads available; of these: 763163 (14.82%) trimmed reads available after processing 4388041 (85.18%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 6 0.00% 19 4 0.00% 20 7 0.00% 21 8 0.00% 22 8 0.00% 23 7 0.00% 24 13 0.00% 25 15 0.00% 26 22 0.00% 27 29 0.00% 28 32 0.00% 29 45 0.00% 30 39 0.00% 31 34 0.00% 32 41 0.00% 33 22 0.00% 34 36 0.00% 35 31 0.00% 36 25 0.00% 37 23 0.00% 38 23 0.00% 39 29 0.00% 40 35 0.00% 41 29 0.00% 42 37 0.00% 43 31 0.00% 44 32 0.00% 45 41 0.00% 46 49 0.00% 47 39 0.00% 48 37 0.00% 49 30 0.00% 50 21 0.00% 51 27 0.00% 52 26 0.00% 53 30 0.00% 54 37 0.00% 55 34 0.00% 56 29 0.00% 57 29 0.00% 58 26 0.00% 59 28 0.00% 60 36 0.00% 61 42 0.00% 62 34 0.00% 63 29 0.00% 64 35 0.00% 65 38 0.00% 66 53 0.00% 67 53 0.00% 68 86 0.00% 69 116 0.00% 70 143 0.00% 71 137 0.00% 72 249 0.00% 73 698 0.01% 74 3974 0.08% 75 3324 0.06% 76 1210 0.02% 77 444 0.01% 78 508 0.01% 79 606 0.01% 80 663 0.01% 81 646 0.01% 82 767 0.01% 83 953 0.02% 84 1405 0.03% 85 1661 0.03% 86 1659 0.03% 87 1800 0.03% 88 2189 0.04% 89 3057 0.06% 90 4326 0.08% 91 6265 0.12% 92 8280 0.16% 93 15067 0.29% 94 27783 0.54% 95 82541 1.60% 96 92232 1.79% 97 94931 1.84% 98 147047 2.85% 99 183729 3.57% 100 73201 1.42% 101 4388041 85.18% 5151204 reads passed initial QC criterion=sequence-density sequence-density=97.34 sequence-density-rank=1 fanout-score=25.49 fanout-score-rank=3 prefix-density=97.55 prefix-fanout=25.4 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTCAAATCTCGTATGCCGTCTTCTGCTTGAAAAAA criterion=fanout-score sequence-density=1.96 sequence-density-rank=6 fanout-score=50.81 fanout-score-rank=1 prefix-density=98.32 prefix-fanout=1.0 sequence=CACAGTCAAATATCGTATGCCGT 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTCAAATCTCGTATGCCGTCTTCTGCTTGAAAAAA -o SRR6941545 - Input file: STDIN trimmed: SRR6941545-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTCAAATCTCGTATGCCGTCTTCTGCTTGA -- 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 10:44:32 2024 >> started Fri Dec 6 10:44:39 2024 >> done (6.525s) 5046078 reads processed; of these: 31077 ( 0.62%) short reads filtered out after trimming by size control 17518 ( 0.35%) empty reads filtered out after trimming by size control 4997483 (99.04%) reads available; of these: 4959238 (99.23%) trimmed reads available after processing 38245 ( 0.77%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 10027 0.20% 19 25212 0.50% 20 34137 0.68% 21 244569 4.89% 22 166340 3.33% 23 128205 2.57% 24 932832 18.67% 25 112069 2.24% 26 88193 1.76% 27 73345 1.47% 28 74857 1.50% 29 284044 5.68% 30 424319 8.49% 31 285709 5.72% 32 373396 7.47% 33 526534 10.54% 34 420895 8.42% 35 326190 6.53% 36 130770 2.62% 37 65808 1.32% 38 30182 0.60% 39 23063 0.46% 40 40835 0.82% 41 56038 1.12% 42 46513 0.93% 43 8034 0.16% 44 14271 0.29% 45 5789 0.12% 46 1672 0.03% 47 1837 0.04% 48 774 0.02% 49 381 0.01% 50 162 0.00% 51 182 0.00% 52 98 0.00% 53 70 0.00% 54 55 0.00% 55 55 0.00% 56 28 0.00% 57 33 0.00% 58 27 0.00% 59 18 0.00% 60 19 0.00% 61 25 0.00% 62 19 0.00% 63 10 0.00% 64 17 0.00% 65 11 0.00% 66 27 0.00% 67 21 0.00% 68 36 0.00% 69 39 0.00% 70 69 0.00% 71 44 0.00% 72 39 0.00% 73 55 0.00% 74 48 0.00% 75 71 0.00% 76 100 0.00% 77 299 0.01% 78 87 0.00% 79 112 0.00% 80 278 0.01% 81 129 0.00% 82 258 0.01% 83 210 0.00% 84 137 0.00% 85 97 0.00% 86 156 0.00% 87 210 0.00% 88 95 0.00% 89 117 0.00% 90 141 0.00% 91 206 0.00% 92 208 0.00% 93 246 0.00% 94 263 0.01% 95 366 0.01% 96 426 0.01% 97 489 0.01% 98 889 0.02% 99 620 0.01% 100 652 0.01% 101 32574 0.65% criterion=sequence-density sequence-density=10.22 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=11 prefix-density=0.00 prefix-fanout=1.0 sequence=GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCG criterion=fanout-score sequence-density=0.27 sequence-density-rank=18 fanout-score=37.90 fanout-score-rank=1 prefix-density=6.57 prefix-fanout=1.6 sequence=GTGAGAATTCTAAAAA Started job on | Dec 06 10:44:57 Started mapping on | Dec 06 10:44:58 Finished on | Dec 06 10:45:13 Mapping speed, Million of reads per hour | 1224.63 Number of input reads | 5102609 Average input read length | 31 UNIQUE READS: Uniquely mapped reads number | 1095938 Uniquely mapped reads % | 21.48% Average mapped length | 26.20 Number of splices: Total | 3556 Number of splices: Annotated (sjdb) | 1261 Number of splices: GT/AG | 3381 Number of splices: GC/AG | 117 Number of splices: AT/AC | 0 Number of splices: Non-canonical | 58 Mismatch rate per base, % | 0.12% Deletion rate per base | 0.00% Deletion average length | 1.49 Insertion rate per base | 0.00% Insertion average length | 1.03 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 3259650 % of reads mapped to multiple loci | 63.88% Number of reads mapped to too many loci | 535258 % of reads mapped to too many loci | 10.49% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.53% % of reads unmapped: other | 0.62% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 747021 747021 747021 N_multimapping 3259650 3259650 3259650 N_noFeature 733557 931478 894713 N_ambiguous 8530 5014 241 UnstrandedReadsAssigned:353851 PositiveStrandReadsAssigned:159446 NegativeStrandReadsAssigned:200984 Dataset is classified unstranded MeadianReadLen=30 20thPercentileLength=24 echo kmer=19 SRR6941545 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: SRR6941545-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 5,102,609 reads, 2,568,167 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 892 rounds 52973 SRR6941545.ke.tsv 35125 SRR6941545.se.tsv 88098 total ==> SRR6941545.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 35.3613 3.37672 KQK14071 474 375 0 0 ==> SRR6941545.se.tsv <== BRADI_1g14170v3 57 BRADI_1g53295v3 1 BRADI_1g59795v3 1 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 2 BRADI_1g74790v3 3 BRADI_1g09890v3 0 BRADI_1g77505v3 0 BRADI_1g48960v3 0 SRR6941545 completed mapping pipeline successfully