Starting /dee2/code/volunteer_pipeline.sh SRR8846493 current disk space = 1501311905792 free memory = 1349353552 SRR8846493 SRAfilesize c1a9866e494921b848a0b1acbacdf54e SRR8846493.sra SRR8846493.sra file validated SRR8846493 is single end SRR8846493 is conventional basespace SRR8846493 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8846493_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 30.92025 34.0 33.0 34.0 28.0 34.0 2 32.8575 34.0 33.0 34.0 30.0 34.0 3 33.03425 34.0 33.0 34.0 32.0 34.0 4 33.066 34.0 33.0 34.0 32.0 34.0 5 33.115 34.0 33.0 34.0 32.0 34.0 6 36.901 38.0 37.0 38.0 36.0 38.0 7 37.30975 38.0 38.0 38.0 36.0 38.0 8 37.4595 38.0 38.0 38.0 37.0 38.0 9 37.455 38.0 38.0 38.0 37.0 38.0 10-11 37.583375000000004 38.0 38.0 38.0 37.5 38.0 12-13 37.577124999999995 38.0 38.0 38.0 38.0 38.0 14-15 37.435375 38.0 38.0 38.0 37.0 38.0 16-17 37.431625 38.0 38.0 38.0 37.0 38.0 18-19 37.497749999999996 38.0 38.0 38.0 37.0 38.0 20-21 37.44262500000001 38.0 38.0 38.0 37.5 38.0 22-23 37.455375000000004 38.0 38.0 38.0 37.0 38.0 24-25 37.387375 38.0 38.0 38.0 37.0 38.0 26-27 37.484125000000006 38.0 38.0 38.0 37.0 38.0 28-29 37.363375000000005 38.0 38.0 38.0 37.0 38.0 30-31 37.26475 38.0 38.0 38.0 36.5 38.0 32-33 37.3455 38.0 38.0 38.0 37.0 38.0 34-35 37.073125 38.0 38.0 38.0 36.5 38.0 36-37 36.933125000000004 38.0 38.0 38.0 35.5 38.0 38-39 36.775375 38.0 38.0 38.0 35.0 38.0 40-41 36.939875 38.0 38.0 38.0 36.0 38.0 42-43 36.87675 38.0 38.0 38.0 35.5 38.0 44-45 36.92825 38.0 38.0 38.0 35.5 38.0 46-47 36.879375 38.0 38.0 38.0 35.5 38.0 48-49 36.8635 38.0 38.0 38.0 35.0 38.0 50-51 36.979124999999996 38.0 38.0 38.0 36.0 38.0 52-53 36.998999999999995 38.0 38.0 38.0 36.0 38.0 54-55 36.8935 38.0 38.0 38.0 35.5 38.0 56-57 36.691125 38.0 38.0 38.0 34.5 38.0 58-59 36.654125 38.0 38.0 38.0 34.5 38.0 60-61 36.51675 38.0 38.0 38.0 34.0 38.0 62-63 36.249375 38.0 38.0 38.0 33.0 38.0 64-65 36.249624999999995 38.0 37.5 38.0 32.5 38.0 66-67 36.011 38.0 37.0 38.0 32.0 38.0 68-69 35.5535 38.0 37.0 38.0 29.0 38.0 70-71 34.901375 38.0 37.0 38.0 27.5 38.0 72-73 34.533500000000004 38.0 36.5 38.0 27.0 38.0 74-75 34.30875 38.0 36.0 38.0 26.0 38.0 76-77 34.144 38.0 36.0 38.0 25.0 38.0 78-79 34.33825 38.0 36.0 38.0 25.0 38.0 80-81 34.136375 38.0 36.0 38.0 24.5 38.0 82-83 33.711124999999996 38.0 35.0 38.0 19.0 38.0 84-85 33.768625 38.0 35.5 38.0 19.5 38.0 86-87 33.821375 38.0 36.0 38.0 19.5 38.0 88-89 34.04275 38.0 36.0 38.0 24.5 38.0 90-91 33.918625 38.0 36.0 38.0 23.0 38.0 92-93 33.93275 38.0 36.0 38.0 23.5 38.0 94-95 33.71875 38.0 35.5 38.0 19.5 38.0 96-97 32.48375 38.0 34.5 38.0 8.5 38.0 98-99 31.283375 38.0 33.0 38.0 2.0 38.0 100-101 29.641125 38.0 27.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 9 1.0 10 0.0 11 1.0 12 0.0 13 0.0 14 0.0 15 1.0 16 1.0 17 1.0 18 1.0 19 4.0 20 2.0 21 3.0 22 9.0 23 10.0 24 33.0 25 73.0 26 61.0 27 30.0 28 38.0 29 38.0 30 49.0 31 62.0 32 72.0 33 131.0 34 185.0 35 378.0 36 822.0 37 1994.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 39.32221624529317 21.032813340505648 16.729424421732116 22.91554599246907 2 31.724999999999998 27.05 14.95 26.275 3 27.625 15.975 20.974999999999998 35.425000000000004 4 23.525 34.25 19.125 23.1 5 32.125 21.175 27.075 19.625 6 27.025 26.424999999999997 27.725 18.825 7 43.925 24.775 16.575 14.725 8 20.3 16.2 45.925 17.575 9 23.925 40.775 18.875 16.425 10-11 34.7625 22.375 25.25 17.6125 12-13 21.087500000000002 20.875 21.4875 36.55 14-15 20.4625 44.8875 21.125 13.525 16-17 25.474999999999998 24.5125 34.275 15.737499999999999 18-19 36.85 23.275000000000002 22.5875 17.2875 20-21 18.2375 28.3625 30.475 22.925 22-23 28.0625 32.4 24.325 15.2125 24-25 28.762500000000003 30.862499999999997 19.075 21.3 26-27 29.525000000000002 28.525 18.075 23.875 28-29 22.375 25.3 24.712500000000002 27.6125 30-31 28.1625 21.3125 29.7125 20.8125 32-33 20.5625 21.4125 33.287499999999994 24.7375 34-35 27.025 22.7 28.8875 21.3875 36-37 28.787499999999998 25.362499999999997 28.787499999999998 17.0625 38-39 28.349999999999998 24.45 30.4375 16.7625 40-41 26.275 18.675 31.125000000000004 23.925 42-43 31.825 18.125 28.1875 21.8625 44-45 40.8125 18.45 18.4875 22.25 46-47 33.650000000000006 23.825 20.8875 21.637500000000003 48-49 28.6375 19.075 23.925 28.3625 50-51 24.775 22.412499999999998 19.287499999999998 33.525 52-53 32.1 27.650000000000002 12.6375 27.6125 54-55 30.0875 27.224999999999998 17.4125 25.275 56-57 26.125 27.5625 15.9125 30.4 58-59 19.025 31.612499999999997 17.0875 32.275 60-61 21.3625 36.6125 13.8 28.225 62-63 22.05 36.925000000000004 15.862499999999999 25.162499999999998 64-65 17.175 37.85 19.9125 25.0625 66-67 17.0 31.85 22.9625 28.1875 68-69 20.674999999999997 34.4625 20.2625 24.6 70-71 20.599999999999998 36.7875 24.625 17.9875 72-73 17.712500000000002 36.9625 24.2875 21.0375 74-75 16.575 28.262500000000003 27.212500000000002 27.950000000000003 76-77 20.962500000000002 21.025 34.55 23.4625 78-79 19.400000000000002 22.8375 32.1 25.662499999999998 80-81 19.287499999999998 22.775000000000002 32.775 25.162499999999998 82-83 18.9625 14.575 38.5125 27.950000000000003 84-85 20.9 9.7875 37.425000000000004 31.887500000000003 86-87 21.349999999999998 11.875 37.95 28.825 88-89 16.7875 21.224999999999998 39.725 22.2625 90-91 17.6125 23.375 35.6 23.4125 92-93 18.0125 30.2625 28.525 23.200000000000003 94-95 15.024999999999999 38.837500000000006 30.125 16.0125 96-97 10.8875 51.1 26.3125 11.700000000000001 98-99 9.2625 63.224999999999994 18.087500000000002 9.425 100-101 8.1125 71.98750000000001 12.6 7.3 >>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 1.0 31 3.0 32 6.5 33 12.5 34 20.0 35 24.5 36 27.0 37 31.0 38 41.0 39 49.5 40 72.5 41 112.5 42 143.5 43 253.5 44 304.0 45 272.0 46 301.0 47 294.5 48 300.0 49 393.5 50 405.0 51 257.5 52 146.5 53 149.0 54 184.0 55 125.5 56 35.0 57 12.0 58 8.0 59 6.5 60 3.5 61 2.0 62 1.5 63 1.0 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 warn #Base N-Count 1 7.049999999999999 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 fail #Total Deduplicated Percentage 46.45 #Duplication Level Percentage of deduplicated Percentage of total 1 79.70936490850377 37.025000000000006 2 8.988159311087191 8.35 3 3.1754574811625407 4.425 4 2.2604951560818085 4.2 5 0.7534983853606028 1.7500000000000002 6 1.0764262648008611 3.0 7 0.5382131324004306 1.7500000000000002 8 0.3767491926803014 1.4000000000000001 9 0.4305705059203444 1.7999999999999998 >10 2.4219590958019377 23.275000000000002 >50 0.1076426264800861 4.15 >100 0.16146393972012918 8.875 >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 GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 129 3.225 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTTGGAATTCT 114 2.85 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 112 2.8000000000000003 No Hit AGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 93 2.325 No Hit TCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 73 1.825 No Hit GGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 50 1.25 RNA PCR Primer, Index 1 (100% over 22bp) CTCGGGTGCCAAGGAACTCCAGTCACGTGAAAATCTCGTATGCCGTCTTC 47 1.175 RNA PCR Primer, Index 19 (100% over 50bp) TCTCGGGTGCCAAGGAACTCCAGTCACGTGAAAATCTCGTATGCCGTCTT 38 0.95 RNA PCR Primer, Index 19 (100% over 50bp) CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 38 0.95 No Hit GACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 37 0.9249999999999999 RNA PCR Primer, Index 1 (100% over 23bp) CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTC 36 0.8999999999999999 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 34 0.8500000000000001 No Hit TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 34 0.8500000000000001 RNA PCR Primer, Index 1 (100% over 29bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTGGAATTCTC 31 0.775 No Hit TTCTCGGGTGCCAAGGAACTCCAGTCACGTGAAAATCTCGTATGCCGTCT 30 0.75 RNA PCR Primer, Index 19 (100% over 50bp) CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 28 0.7000000000000001 No Hit CTCTGATGATGATCAAACTAATACTTTCGTTCTTCTGGAATTCTCGGGTG 28 0.7000000000000001 No Hit AATTCTCGGGTGCCAAGGAACTCCAGTCACGTGAAAATCTCGTATGCCGT 28 0.7000000000000001 RNA PCR Primer, Index 19 (100% over 50bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCGTGGAATT 26 0.65 No Hit GCACCAGTGGTCTAGTGGTAGAATAGTACCTGGAATTCTCGGGTGCCAAG 21 0.525 No Hit GACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAAC 21 0.525 RNA PCR Primer, Index 1 (100% over 24bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTTGGAATTCTCGGGTGCCA 21 0.525 No Hit ATTCTCGGGTGCCAAGGAACTCCAGTCACGTGAAAATCTCGTATGCCGTC 20 0.5 RNA PCR Primer, Index 19 (100% over 50bp) GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 20 0.5 Illumina Small RNA Adapter 2 (100% over 21bp) TCCTGTGGATGAGAAGGCATTTATATTCTGATGATATGGAATTCTCGGGT 19 0.475 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAATGGAATTCTCGGGTGCCA 17 0.42500000000000004 No Hit AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 17 0.42500000000000004 Illumina Small RNA Adapter 2 (100% over 21bp) AGGGCTATAGCTCAGTTCGGTAGAGCAACTCGTTTACACCGAGATGGAAT 16 0.4 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTGAATCTGGAATTC 15 0.375 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCATGGAATTCTCGGGTG 15 0.375 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 14 0.35000000000000003 Illumina Small RNA Adapter 2 (100% over 21bp) GACACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACT 14 0.35000000000000003 RNA PCR Primer, Index 1 (100% over 25bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGATGGAATTCTC 14 0.35000000000000003 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTAATCCTGGAATTC 14 0.35000000000000003 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 13 0.325 Illumina Small RNA Adapter 2 (100% over 21bp) CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 13 0.325 RNA PCR Primer, Index 1 (100% over 23bp) GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 13 0.325 No Hit GCCCACCCCAAGATGAGTGCTCTCTCTGGAATTCTCGGGTGCCAAGGAAC 13 0.325 RNA PCR Primer, Index 1 (100% over 24bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCTGGAATTC 13 0.325 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATGGAATTCTCGGGTG 13 0.325 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTATGGAATTCTCGGGTGCCAA 13 0.325 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAAATGGAATTCTCGGGT 12 0.3 No Hit CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGGAATTCTCG 12 0.3 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 11 0.27499999999999997 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTAATCTGGAATTCT 11 0.27499999999999997 No Hit CAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTG 11 0.27499999999999997 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGGAATTCTCGGGTGCCA 10 0.25 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAAAATGGAATTCTCGGGTGC 10 0.25 No Hit NGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 10 0.25 No Hit TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGG 10 0.25 No Hit AGGGCTATAGCTCAGTTCGGTAGAGCAACTCGTTTACACTGGAATTCTCG 9 0.22499999999999998 No Hit NGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 9 0.22499999999999998 No Hit GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTG 9 0.22499999999999998 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTTGGAATTCTCGGGTGC 9 0.22499999999999998 No Hit TCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCG 9 0.22499999999999998 No Hit GCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCC 9 0.22499999999999998 No Hit TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 9 0.22499999999999998 No Hit NGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 9 0.22499999999999998 No Hit NCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 8 0.2 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATTGGAATTCTCG 8 0.2 No Hit CGGATAACCGTAGTAATTCTAGAGCTAATACGTGGAATTCTCGGGTGCCA 8 0.2 No Hit TTCGGACCAGGCTTCATTCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 8 0.2 RNA PCR Primer, Index 1 (100% over 29bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGGTGGAATTC 8 0.2 No Hit AGAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTG 8 0.2 No Hit CACGACTCTCGGCAACGGATATCTCGTGGAATTCTCGGGTGCCAAGGAAC 8 0.2 RNA PCR Primer, Index 1 (100% over 24bp) CGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTCTC 7 0.17500000000000002 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGAGTGGAATTCT 7 0.17500000000000002 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTGGAATTCTCGGGTGCCAAG 7 0.17500000000000002 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAAAAATGGAATTCTCGGGTG 7 0.17500000000000002 No Hit CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 28bp) CATCGAGTAGACCTTGTTATTGTGAGAATAAAAAAATGGAATTCTCGGGT 7 0.17500000000000002 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTAAAATGGAATTCTCGGGT 7 0.17500000000000002 No Hit ACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTCT 7 0.17500000000000002 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGTGGAATTCTC 7 0.17500000000000002 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTTGGAATTCTCGGGTGC 7 0.17500000000000002 No Hit CACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAACT 6 0.15 RNA PCR Primer, Index 1 (100% over 25bp) NGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 6 0.15 RNA PCR Primer, Index 1 (100% over 22bp) GACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAAT 6 0.15 No Hit CGACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAA 6 0.15 No Hit TCGGATAACCGTAGTAATTCTAGAGCTAATACGTGGAATTCTCGGGTGCC 6 0.15 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTGGAATTCTCGGGTG 6 0.15 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATATGGAATTCTCGGGTGCCAAGGAA 6 0.15 RNA PCR Primer, Index 1 (100% over 23bp) ATAACCGTAGTAATTCTAGAGCTAATACTGGAATTCTCGGGTGCCAAGGA 6 0.15 RNA PCR Primer, Index 1 (100% over 22bp) NTCGGGTGCCAAGGAACTCCAGTCACGTGAAAATCTCGTATGCCGTCTTC 6 0.15 RNA PCR Primer, Index 19 (98% over 50bp) GATAACCGTAGTAATTCTAGAGCTAATACTGGAATTCTCGGGTGCCAAGG 6 0.15 Illumina Small RNA Adapter 2 (100% over 21bp) GACACGACTCTCGGCAACGGATATCTCGGCTCTCGCTGGAATTCTCGGGT 6 0.15 No Hit TCTCGGACCAGGCTTCATTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 6 0.15 RNA PCR Primer, Index 1 (100% over 29bp) AGCAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTATGTGGAATTCT 6 0.15 No Hit ACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATT 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAAAAAAATGGAATTCTCGGG 6 0.15 No Hit CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGG 6 0.15 No Hit TGCCACGATCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAAT 6 0.15 No Hit CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGG 6 0.15 No Hit NACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 6 0.15 RNA PCR Primer, Index 1 (100% over 23bp) TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTGGAATTCTCGGGTGC 6 0.15 No Hit ATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGG 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAAATGGAATTCTCGGGTGCC 5 0.125 No Hit CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGG 5 0.125 No Hit GAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTGC 5 0.125 No Hit CATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTATGGAATTC 5 0.125 No Hit TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGAAAATCTCGTATGC 5 0.125 RNA PCR Primer, Index 19 (100% over 50bp) TCCGTCGTAGTCTAGGTGGTTAGGATACTCGTGGAATTCTCGGGTGCCAA 5 0.125 No Hit GCAAGTATGAACTAATTTGAACTGTGAAACTTGGAATTCTCGGGTGCCAA 5 0.125 No Hit ATGCAGTTACTAATTCATGATCTGGCTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) TGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAA 5 0.125 No Hit NCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTTGGAATTCT 5 0.125 No Hit ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGC 5 0.125 No Hit CGGATAACCGTAGTAATTCTAGAGCTAATACTGGAATTCTCGGGTGCCAA 5 0.125 No Hit CTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCA 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 0.15 0.0 0.0 0.0 2 0.0 0.15 0.0 0.0 0.0 3 0.0 0.15 0.0 0.0 0.0 4 0.0 0.15 0.0 0.0 0.0 5 0.0 0.15 0.0 0.0 0.0 6 0.0 0.15 0.0 0.0 0.0 7 0.0 0.175 0.0 0.0 0.0 8 0.0 0.175 0.0 0.0 0.0 9 0.0 0.3 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 0.5125 0.0 0.0 0.0 16-17 0.0 0.7250000000000001 0.0 0.0 0.0 18-19 0.0 0.95 0.0 0.0 0.0 20-21 0.0 1.725 0.0 0.0 0.0 22-23 0.0 5.25 0.0 0.0 0.0 24-25 0.0 10.5125 0.0 0.0 0.0 26-27 0.0 16.95 0.0 0.0 0.0 28-29 0.0 23.1125 0.0 0.0 0.0 30-31 0.0 31.237499999999997 0.0 0.0 0.0 32-33 0.0 40.45 0.0 0.0 0.0 34-35 0.0 53.3625 0.0 0.0 0.0 36-37 0.0 64.3125 0.0 0.0 0.0 38-39 0.0 70.75 0.0 0.0 0.0 40-41 0.0 75.8625 0.0 0.0 0.0 42-43 0.0 84.7875 0.0 0.0 0.0 44-45 0.0 89.26249999999999 0.0 0.0 0.0 46-47 0.0 90.9125 0.0 0.0 0.0 48-49 0.0 91.5125 0.0 0.0 0.0 50-51 0.0 91.775 0.0 0.0 0.0 52-53 0.0 91.9 0.0 0.0 0.0 54-55 0.0 91.9375 0.0 0.0 0.0 56-57 0.0 91.95 0.0 0.0 0.0 58-59 0.0 91.95 0.0 0.0 0.0 60-61 0.0 91.95 0.0 0.0 0.0 62-63 0.0 91.95 0.0 0.0 0.0 64-65 0.0 91.95 0.0 0.0 0.0 66-67 0.0 91.95 0.0 0.0 0.0 68-69 0.0 91.95 0.0 0.0 0.0 70-71 0.0 91.95 0.0 0.0 0.0 72-73 0.0 91.95 0.0 0.0 0.0 74-75 0.0 91.95 0.0 0.0 0.0 76-77 0.0 91.95 0.0 0.0 0.0 78-79 0.0 91.95 0.0 0.0 0.0 80-81 0.0 91.98750000000001 0.0 0.0 0.0 82-83 0.0 92.05000000000001 0.0 0.0 0.0 84-85 0.0 92.075 0.0 0.0 0.0 86-87 0.0 92.075 0.0 0.0 0.0 88-89 0.0 92.0875 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AGCTGAG 15 5.548922E-4 97.410255 1 GGGATTG 50 0.0 97.41025 1 TTGTAGT 50 0.0 94.975 5 GATTGTA 50 0.0 94.975 3 TAGTTCA 55 0.0 94.975 8 ATTGTAG 50 0.0 94.975 4 AGTTCAA 55 0.0 94.975 9 GTAGTTC 55 0.0 94.975 7 GTAGACC 15 6.148606E-4 94.97499 7 AGTAGAC 15 6.148606E-4 94.97499 6 GAGTAGA 15 6.148606E-4 94.97499 5 GCTGAGG 15 6.148606E-4 94.97499 2 CGAGTAG 15 6.148606E-4 94.97499 4 AGACCTT 15 6.148606E-4 94.97499 9 TCGAGTA 15 6.148606E-4 94.97499 3 TAGACCT 15 6.148606E-4 94.97499 8 GGATTGT 55 0.0 86.34091 2 TGTAGTT 55 0.0 86.34091 6 GACACGA 30 9.719679E-7 81.17522 1 CATCGAG 20 0.0017401327 73.05769 1 >>END_MODULE Rejected 824960 READS because READLEN < 1 Read 824960 spots for SRR8846493.sra Written 824960 spots for SRR8846493.sra Rejected 824960 READS because READLEN < 1 Read 824960 spots for SRR8846493.sra Written 824960 spots for SRR8846493.sra Rejected 824960 READS because READLEN < 1 Read 824960 spots for SRR8846493.sra Written 824960 spots for SRR8846493.sra Rejected 824960 READS because READLEN < 1 Read 824960 spots for SRR8846493.sra Written 824960 spots for SRR8846493.sra Rejected 824960 READS because READLEN < 1 Read 824960 spots for SRR8846493.sra Written 824960 spots for SRR8846493.sra Rejected 824960 READS because READLEN < 1 Read 824960 spots for SRR8846493.sra Written 824960 spots for SRR8846493.sra Rejected 824960 READS because READLEN < 1 Read 824960 spots for SRR8846493.sra Written 824960 spots for SRR8846493.sra Rejected 824960 READS because READLEN < 1 Read 824960 spots for SRR8846493.sra Written 824960 spots for SRR8846493.sra Rejected 824960 READS because READLEN < 1 Read 824960 spots for SRR8846493.sra Written 824960 spots for SRR8846493.sra Rejected 824973 READS because READLEN < 1 Read 824973 spots for SRR8846493.sra Written 824973 spots for SRR8846493.sra Rejected 824960 READS because READLEN < 1 Read 824960 spots for SRR8846493.sra Written 824960 spots for SRR8846493.sra Rejected 824960 READS because READLEN < 1 Read 824960 spots for SRR8846493.sra Written 824960 spots for SRR8846493.sra Rejected 824960 READS because READLEN < 1 Read 824960 spots for SRR8846493.sra Written 824960 spots for SRR8846493.sra Rejected 824960 READS because READLEN < 1 Read 824960 spots for SRR8846493.sra Written 824960 spots for SRR8846493.sra Rejected 824960 READS because READLEN < 1 Read 824960 spots for SRR8846493.sra Written 824960 spots for SRR8846493.sra Rejected 824960 READS because READLEN < 1 Read 824960 spots for SRR8846493.sra Written 824960 spots for SRR8846493.sra Rejected 824960 READS because READLEN < 1 Read 824960 spots for SRR8846493.sra Written 824960 spots for SRR8846493.sra Rejected 824960 READS because READLEN < 1 Read 824960 spots for SRR8846493.sra Written 824960 spots for SRR8846493.sra Rejected 824960 READS because READLEN < 1 Read 824960 spots for SRR8846493.sra Written 824960 spots for SRR8846493.sra Rejected 824960 READS because READLEN < 1 Read 824960 spots for SRR8846493.sra Written 824960 spots for SRR8846493.sra SRR ids: ['SRR8846493.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_fsqb1xhl SRR8846493.sra spots: 16499213 blocks: [[1, 824960], [824961, 1649920], [1649921, 2474880], [2474881, 3299840], [3299841, 4124800], [4124801, 4949760], [4949761, 5774720], [5774721, 6599680], [6599681, 7424640], [7424641, 8249600], [8249601, 9074560], [9074561, 9899520], [9899521, 10724480], [10724481, 11549440], [11549441, 12374400], [12374401, 13199360], [13199361, 14024320], [14024321, 14849280], [14849281, 15674240], [15674241, 16499213]] SRR8846493 file size 3958090 SRR8846493 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 SRR8846493 SRR8846493_1.fastq Input file: SRR8846493_1.fastq trimmed: SRR8846493-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 Sun Dec 8 21:41:17 2024 >> started Sun Dec 8 21:42:01 2024 >> done (44.205s) 16499213 reads processed; of these: 312 ( 0.00%) short reads filtered out after trimming by size control 36 ( 0.00%) empty reads filtered out after trimming by size control 16498865 (100.00%) reads available; of these: 2470359 (14.97%) trimmed reads available after processing 14028506 (85.03%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 37 0.00% 19 32 0.00% 20 53 0.00% 21 52 0.00% 22 53 0.00% 23 53 0.00% 24 84 0.00% 25 117 0.00% 26 223 0.00% 27 322 0.00% 28 307 0.00% 29 400 0.00% 30 319 0.00% 31 253 0.00% 32 307 0.00% 33 235 0.00% 34 216 0.00% 35 188 0.00% 36 228 0.00% 37 221 0.00% 38 235 0.00% 39 276 0.00% 40 325 0.00% 41 344 0.00% 42 442 0.00% 43 464 0.00% 44 475 0.00% 45 582 0.00% 46 410 0.00% 47 405 0.00% 48 376 0.00% 49 392 0.00% 50 453 0.00% 51 492 0.00% 52 474 0.00% 53 608 0.00% 54 473 0.00% 55 471 0.00% 56 571 0.00% 57 493 0.00% 58 599 0.00% 59 934 0.01% 60 1126 0.01% 61 1812 0.01% 62 2202 0.01% 63 3031 0.02% 64 4806 0.03% 65 8708 0.05% 66 25742 0.16% 67 132205 0.80% 68 149186 0.90% 69 113717 0.69% 70 85545 0.52% 71 91310 0.55% 72 42155 0.26% 73 13398 0.08% 74 20734 0.13% 75 13837 0.08% 76 8879 0.05% 77 8131 0.05% 78 8750 0.05% 79 8083 0.05% 80 8753 0.05% 81 10219 0.06% 82 15936 0.10% 83 13864 0.08% 84 10444 0.06% 85 10162 0.06% 86 10571 0.06% 87 12176 0.07% 88 15554 0.09% 89 20557 0.12% 90 26036 0.16% 91 28503 0.17% 92 38515 0.23% 93 53011 0.32% 94 74065 0.45% 95 161358 0.98% 96 191976 1.16% 97 218193 1.32% 98 304607 1.85% 99 302668 1.83% 100 185840 1.13% 101 14028506 85.03% 16498865 reads passed initial QC criterion=sequence-density sequence-density=91.22 sequence-density-rank=1 fanout-score=32.07 fanout-score-rank=1 prefix-density=91.47 prefix-fanout=32.0 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGAAAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA criterion=fanout-score sequence-density=91.22 sequence-density-rank=1 fanout-score=32.07 fanout-score-rank=1 prefix-density=91.47 prefix-fanout=32.0 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGAAAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGAAAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA -o SRR8846493 - Input file: STDIN trimmed: SRR8846493-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGAAAATCTCGTATGCCGTCTTCTGCTTGA -- 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 Sun Dec 8 21:44:50 2024 >> started Sun Dec 8 21:46:08 2024 >> done (78.444s) 16140194 reads processed; of these: 141756 ( 0.88%) short reads filtered out after trimming by size control 36384 ( 0.23%) empty reads filtered out after trimming by size control 15962054 (98.90%) reads available; of these: 14910467 (93.41%) trimmed reads available after processing 1051587 ( 6.59%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 32583 0.20% 19 63081 0.40% 20 79636 0.50% 21 311336 1.95% 22 189392 1.19% 23 275554 1.73% 24 855889 5.36% 25 385595 2.42% 26 500025 3.13% 27 509931 3.19% 28 633767 3.97% 29 640752 4.01% 30 821421 5.15% 31 525352 3.29% 32 1277568 8.00% 33 1160892 7.27% 34 1040441 6.52% 35 786415 4.93% 36 822569 5.15% 37 422623 2.65% 38 357526 2.24% 39 403624 2.53% 40 521182 3.27% 41 806001 5.05% 42 600060 3.76% 43 273511 1.71% 44 248295 1.56% 45 131983 0.83% 46 71073 0.45% 47 40955 0.26% 48 37637 0.24% 49 22961 0.14% 50 15108 0.09% 51 12880 0.08% 52 8063 0.05% 53 5867 0.04% 54 5674 0.04% 55 1759 0.01% 56 1924 0.01% 57 1108 0.01% 58 969 0.01% 59 1161 0.01% 60 1227 0.01% 61 1866 0.01% 62 2104 0.01% 63 2870 0.02% 64 4596 0.03% 65 8289 0.05% 66 24955 0.16% 67 129204 0.81% 68 145606 0.91% 69 110796 0.69% 70 83213 0.52% 71 88548 0.55% 72 38601 0.24% 73 9641 0.06% 74 6485 0.04% 75 6193 0.04% 76 5830 0.04% 77 7527 0.05% 78 6373 0.04% 79 5471 0.03% 80 6593 0.04% 81 5935 0.04% 82 4624 0.03% 83 5632 0.04% 84 3351 0.02% 85 3185 0.02% 86 2780 0.02% 87 2505 0.02% 88 2081 0.01% 89 2055 0.01% 90 1833 0.01% 91 1891 0.01% 92 2042 0.01% 93 2205 0.01% 94 2626 0.02% 95 3699 0.02% 96 4590 0.03% 97 6055 0.04% 98 8316 0.05% 99 11203 0.07% 100 13641 0.09% 101 271674 1.70% criterion=sequence-density sequence-density=4.42 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=12 prefix-density=0.00 prefix-fanout=1.0 sequence=GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCT criterion=fanout-score sequence-density=0.38 sequence-density-rank=13 fanout-score=19.65 fanout-score-rank=1 prefix-density=7.49 prefix-fanout=1.0 sequence=TTGTGAGAATTAAAAA Started job on | Dec 08 21:48:27 Started mapping on | Dec 08 21:48:28 Finished on | Dec 08 21:56:00 Mapping speed, Million of reads per hour | 129.99 Number of input reads | 16320725 Average input read length | 37 UNIQUE READS: Uniquely mapped reads number | 1893386 Uniquely mapped reads % | 11.60% Average mapped length | 30.55 Number of splices: Total | 26399 Number of splices: Annotated (sjdb) | 16820 Number of splices: GT/AG | 23562 Number of splices: GC/AG | 1782 Number of splices: AT/AC | 19 Number of splices: Non-canonical | 1036 Mismatch rate per base, % | 0.15% Deletion rate per base | 0.00% Deletion average length | 1.29 Insertion rate per base | 0.00% Insertion average length | 1.03 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 7607781 % of reads mapped to multiple loci | 46.61% Number of reads mapped to too many loci | 5232092 % of reads mapped to too many loci | 32.06% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 9.41% % of reads unmapped: other | 0.32% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 6819558 6819558 6819558 N_multimapping 7607781 7607781 7607781 N_noFeature 907478 1157308 1632389 N_ambiguous 40354 29023 298 UnstrandedReadsAssigned:945554 PositiveStrandReadsAssigned:707055 NegativeStrandReadsAssigned:260699 Dataset is classified unstranded MeadianReadLen=33 20thPercentileLength=27 echo kmer=23 SRR8846493 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=23 [quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20 [index] k-mer length: 23 [index] number of targets: 52,972 [index] number of k-mers: 66,237,239 [index] number of equivalence classes: 154,277 [quant] running in single-end mode [quant] will process file 1: SRR8846493-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 16,320,725 reads, 4,107,796 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 894 rounds 52973 SRR8846493.ke.tsv 35125 SRR8846493.se.tsv 88098 total ==> SRR8846493.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 4 0.554466 PNS24243 293 194 0 0 KQK14069 1603 1504 137.845 17.4306 KQK14071 474 375 0 0 ==> SRR8846493.se.tsv <== BRADI_1g14170v3 151 BRADI_1g53295v3 0 BRADI_1g59795v3 3 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 31 BRADI_1g74790v3 18 BRADI_1g09890v3 0 BRADI_1g77505v3 2 BRADI_1g48960v3 0 SRR8846493 completed mapping pipeline successfully