Starting /dee2/code/volunteer_pipeline.sh SRR8846484 current disk space = 1505032617984 free memory = 1350631568 SRR8846484 SRAfilesize ec1d27907995fe047c13db87e6878557 SRR8846484.sra SRR8846484.sra file validated SRR8846484 is single end SRR8846484 is conventional basespace SRR8846484 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8846484_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 45 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.0345 33.0 33.0 34.0 28.0 34.0 2 32.79425 34.0 33.0 34.0 30.0 34.0 3 32.9785 34.0 33.0 34.0 32.0 34.0 4 33.112 34.0 33.0 34.0 32.0 34.0 5 33.1195 34.0 33.0 34.0 32.0 34.0 6 36.82225 38.0 37.0 38.0 36.0 38.0 7 37.2645 38.0 38.0 38.0 36.0 38.0 8 37.444 38.0 38.0 38.0 37.0 38.0 9 37.3735 38.0 38.0 38.0 37.0 38.0 10-11 37.422 38.0 38.0 38.0 37.0 38.0 12-13 37.5 38.0 38.0 38.0 38.0 38.0 14-15 37.422625 38.0 38.0 38.0 37.0 38.0 16-17 37.3895 38.0 38.0 38.0 37.0 38.0 18-19 37.477374999999995 38.0 38.0 38.0 37.5 38.0 20-21 37.419624999999996 38.0 38.0 38.0 37.0 38.0 22-23 37.424875 38.0 38.0 38.0 37.0 38.0 24-25 37.49025 38.0 38.0 38.0 37.5 38.0 26-27 37.3665 38.0 38.0 38.0 37.0 38.0 28-29 37.364875 38.0 38.0 38.0 37.0 38.0 30-31 37.390625 38.0 38.0 38.0 37.0 38.0 32-33 37.286375 38.0 38.0 38.0 37.0 38.0 34-35 37.172 38.0 38.0 38.0 36.5 38.0 36-37 37.014250000000004 38.0 38.0 38.0 35.5 38.0 38-39 36.943 38.0 38.0 38.0 36.0 38.0 40-41 37.0245 38.0 38.0 38.0 36.0 38.0 42-43 36.89175 38.0 38.0 38.0 35.5 38.0 44-45 36.989625000000004 38.0 38.0 38.0 35.5 38.0 46-47 37.067625 38.0 38.0 38.0 36.0 38.0 48-49 37.067125000000004 38.0 38.0 38.0 36.0 38.0 50-51 36.92975 38.0 38.0 38.0 35.5 38.0 52-53 36.931375 38.0 38.0 38.0 36.0 38.0 54-55 36.8905 38.0 38.0 38.0 35.5 38.0 56-57 36.772375 38.0 38.0 38.0 35.0 38.0 58-59 36.479875 38.0 38.0 38.0 34.0 38.0 60-61 36.115624999999994 38.0 37.0 38.0 31.5 38.0 62-63 35.988875 38.0 37.0 38.0 31.0 38.0 64-65 35.72975 38.0 36.5 38.0 30.0 38.0 66-67 35.469 38.0 36.5 38.0 28.5 38.0 68-69 35.393249999999995 38.0 36.5 38.0 28.5 38.0 70-71 35.34725 38.0 37.0 38.0 28.5 38.0 72-73 35.188625 38.0 37.0 38.0 29.0 38.0 74-75 34.868125000000006 38.0 36.5 38.0 27.5 38.0 76-77 34.661125 38.0 36.0 38.0 27.0 38.0 78-79 34.12625 38.0 35.0 38.0 24.5 38.0 80-81 34.065875 38.0 35.0 38.0 24.5 38.0 82-83 33.804500000000004 38.0 34.5 38.0 19.5 38.0 84-85 33.598749999999995 38.0 34.0 38.0 15.0 38.0 86-87 33.729875 38.0 34.5 38.0 19.5 38.0 88-89 33.9885 38.0 35.5 38.0 20.0 38.0 90-91 33.370625000000004 38.0 34.0 38.0 15.0 38.0 92-93 33.112875 38.0 34.5 38.0 15.0 38.0 94-95 31.849625 38.0 33.5 38.0 8.0 38.0 96-97 29.798125 38.0 28.5 38.0 2.0 38.0 98-99 26.602 36.5 8.5 38.0 2.0 38.0 100-101 22.4825 31.5 2.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 3 1.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 1.0 11 1.0 12 0.0 13 0.0 14 1.0 15 0.0 16 1.0 17 1.0 18 1.0 19 2.0 20 2.0 21 6.0 22 9.0 23 10.0 24 27.0 25 40.0 26 55.0 27 22.0 28 32.0 29 46.0 30 75.0 31 96.0 32 135.0 33 220.0 34 334.0 35 556.0 36 933.0 37 1393.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 25.679999999999996 30.64 21.52 22.16 2 22.95 32.05 20.325 24.675 3 25.624999999999996 21.75 23.9 28.725 4 29.175 28.849999999999998 18.7 23.275000000000002 5 30.125 27.875 19.25 22.75 6 25.1 27.224999999999998 24.325 23.35 7 33.275 25.75 20.325 20.65 8 22.85 21.75 31.2 24.2 9 24.275 31.324999999999996 23.549999999999997 20.849999999999998 10-11 29.4 26.387500000000003 23.275000000000002 20.9375 12-13 23.962500000000002 23.2875 22.5625 30.1875 14-15 22.662499999999998 34.4 24.087500000000002 18.85 16-17 25.2625 27.1625 28.712500000000002 18.862499999999997 18-19 28.4375 26.525 23.7 21.337500000000002 20-21 23.5875 27.1375 27.375 21.9 22-23 29.025000000000002 27.3125 27.762500000000003 15.9 24-25 26.2875 26.1125 28.787499999999998 18.8125 26-27 34.949999999999996 25.974999999999998 24.7375 14.3375 28-29 21.725 31.55 26.9625 19.7625 30-31 22.9375 18.55 39.65 18.862499999999997 32-33 26.437500000000004 17.5375 32.025 24.0 34-35 31.424999999999997 16.775000000000002 28.9125 22.8875 36-37 40.475 13.625000000000002 26.650000000000002 19.25 38-39 33.475 17.5 27.0875 21.9375 40-41 30.099999999999998 19.5125 19.6875 30.7 42-43 30.825000000000003 29.65 18.175 21.349999999999998 44-45 38.8625 22.975 13.825000000000001 24.337500000000002 46-47 26.825 32.1125 14.625 26.437500000000004 48-49 23.75 25.6125 18.325 32.3125 50-51 23.05 23.075000000000003 15.4 38.475 52-53 22.912499999999998 33.3625 12.562499999999998 31.162499999999998 54-55 20.5375 24.3125 19.412499999999998 35.7375 56-57 17.299999999999997 29.875 11.575000000000001 41.25 58-59 19.2375 29.212500000000002 13.9875 37.5625 60-61 11.1625 33.95 16.85 38.0375 62-63 11.5875 34.1 23.7 30.612499999999997 64-65 11.0 30.925000000000004 27.437499999999996 30.6375 66-67 12.625 24.775 28.775000000000002 33.825 68-69 17.1875 24.825 26.5125 31.474999999999998 70-71 15.575 26.0375 31.3125 27.075 72-73 20.175 20.025000000000002 32.35 27.450000000000003 74-75 17.1625 15.162500000000001 30.7625 36.9125 76-77 20.3 11.9625 40.9125 26.825 78-79 16.5125 9.125 40.6875 33.675 80-81 18.637500000000003 9.6125 39.425 32.324999999999996 82-83 21.55 10.7625 43.1375 24.55 84-85 19.2625 14.3125 37.8 28.625 86-87 20.724999999999998 23.1125 35.5875 20.575 88-89 14.5875 42.575 27.1375 15.7 90-91 10.5625 51.31250000000001 25.112499999999997 13.0125 92-93 10.8125 60.68750000000001 18.275 10.225 94-95 8.137500000000001 69.825 14.674999999999999 7.3625 96-97 6.0 76.9625 12.3125 4.725 98-99 5.1625 82.4125 8.799999999999999 3.6249999999999996 100-101 3.65 85.8875 6.3625 4.1000000000000005 >>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 1.5 33 3.0 34 7.5 35 11.0 36 14.0 37 17.5 38 29.5 39 80.5 40 104.0 41 133.0 42 212.5 43 299.5 44 384.0 45 395.0 46 433.0 47 427.5 48 336.0 49 291.0 50 251.0 51 177.5 52 107.0 53 75.5 54 60.0 55 66.5 56 43.5 57 10.5 58 7.5 59 5.5 60 4.5 61 4.0 62 3.0 63 1.5 64 1.5 65 1.0 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 6.25 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 61.85000000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 85.56992724333064 52.925 2 7.235246564268391 8.95 3 2.263540824575586 4.2 4 1.0509296685529508 2.6 5 0.8084074373484237 2.5 6 0.5658852061438965 2.1 7 0.3637833468067906 1.575 8 0.3637833468067906 1.7999999999999998 9 0.16168148746968472 0.8999999999999999 >10 1.5359741309620047 18.875 >50 0.08084074373484236 3.5749999999999997 >100 0.0 0.0 >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 TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 83 2.075 RNA PCR Primer, Index 1 (100% over 29bp) AGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 60 1.5 No Hit GGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 42 1.05 RNA PCR Primer, Index 1 (100% over 22bp) GACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAAC 40 1.0 RNA PCR Primer, Index 1 (100% over 24bp) CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 36 0.8999999999999999 No Hit ATATATTTCAAGTTATTTCGGATCTTGGAATTCTCGGGTGCCAAGGAACT 35 0.8750000000000001 RNA PCR Primer, Index 1 (100% over 25bp) AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 33 0.8250000000000001 Illumina Small RNA Adapter 2 (100% over 21bp) AATTCTCGGGTGCCAAGGAACTCCAGTCACGCCAATATCTCGTATGCCGT 32 0.8 RNA PCR Primer, Index 6 (100% over 50bp) TCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 31 0.775 No Hit TCTCGGGTGCCAAGGAACTCCAGTCACGCCAATATCTCGTATGCCGTCTT 30 0.75 RNA PCR Primer, Index 6 (100% over 50bp) GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 28 0.7000000000000001 Illumina Small RNA Adapter 2 (100% over 21bp) GACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 28 0.7000000000000001 RNA PCR Primer, Index 1 (100% over 23bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 25 0.625 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 24 0.6 No Hit CTCTGATGATGATCAAACTAATACTTTCGTTCTTCTGGAATTCTCGGGTG 23 0.575 No Hit CTCGGGTGCCAAGGAACTCCAGTCACGCCAATATCTCGTATGCCGTCTTC 22 0.5499999999999999 RNA PCR Primer, Index 6 (100% over 50bp) ATTCTCGGGTGCCAAGGAACTCCAGTCACGCCAATATCTCGTATGCCGTC 20 0.5 RNA PCR Primer, Index 6 (100% over 50bp) GACACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACT 19 0.475 RNA PCR Primer, Index 1 (100% over 25bp) TTCGGACCAGGCTTCATTCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 18 0.44999999999999996 RNA PCR Primer, Index 1 (100% over 29bp) ATAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAACT 16 0.4 RNA PCR Primer, Index 1 (100% over 25bp) CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 16 0.4 RNA PCR Primer, Index 1 (100% over 28bp) GGGGATGTAGCTCAGATGGTAGATGGAATTCTCGGGTGCCAAGGAACTCC 15 0.375 RNA PCR Primer, Index 1 (100% over 27bp) CACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACTCC 15 0.375 RNA PCR Primer, Index 1 (100% over 27bp) GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 14 0.35000000000000003 No Hit AAGGGTGCTGAGAATACTTTGAATCTGACACTGGAATTCTCGGGTGCCAA 14 0.35000000000000003 No Hit CAGGGTTCGTTTCCCTGGATGCGCACCATGGAATTCTCGGGTGCCAAGGA 14 0.35000000000000003 RNA PCR Primer, Index 1 (100% over 22bp) TCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTC 13 0.325 RNA PCR Primer, Index 1 (100% over 26bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 13 0.325 Illumina Small RNA Adapter 2 (100% over 21bp) CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 13 0.325 RNA PCR Primer, Index 1 (100% over 23bp) GCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCC 13 0.325 No Hit TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 13 0.325 No Hit ACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCC 13 0.325 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 12 0.3 No Hit CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTC 12 0.3 No Hit CACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAACT 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 25bp) AAGGGTGCTGAGAATACTTTGAATCTGACATGGAATTCTCGGGTGCCAAG 11 0.27499999999999997 No Hit ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGC 11 0.27499999999999997 No Hit CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGG 10 0.25 No Hit ATATATTTCAAGTTATTTCGGATCTGGAATTCTCGGGTGCCAAGGAACTC 10 0.25 RNA PCR Primer, Index 1 (100% over 26bp) TGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAA 10 0.25 No Hit AGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGT 9 0.22499999999999998 No Hit GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTG 9 0.22499999999999998 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGAATTCTCGGGTGCCAAGGAACTCCA 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 28bp) ATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACT 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 25bp) CGGATAACCGTAGTAATTCTAGAGCTAATACGTGGAATTCTCGGGTGCCA 8 0.2 No Hit AGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCC 8 0.2 RNA PCR Primer, Index 1 (100% over 27bp) GACACGACTCTCGGCAACGGATATCTCGGCTGGAATTCTCGGGTGCCAAG 8 0.2 No Hit GCACCAGTGGTCTAGTGGTAGAATAGTACCTGGAATTCTCGGGTGCCAAG 8 0.2 No Hit TTCTCGGGTGCCAAGGAACTCCAGTCACGCCAATATCTCGTATGCCGTCT 8 0.2 RNA PCR Primer, Index 6 (100% over 50bp) CAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTG 8 0.2 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 8 0.2 Illumina Small RNA Adapter 2 (100% over 21bp) CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGG 8 0.2 No Hit CACGACTCTCGGCAACGGATATCTCGTGGAATTCTCGGGTGCCAAGGAAC 8 0.2 RNA PCR Primer, Index 1 (100% over 24bp) CATCGAGTAGACCTTGTTATTGTGAGAATGGAATTCTCGGGTGCCAAGGA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 22bp) TAATTCATGATCTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACG 7 0.17500000000000002 RNA PCR Primer, Index 6 (100% over 34bp) CACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAACTC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 26bp) TCCACAGGCTTTCTTGAACTGTGGAATTCTCGGGTGCCAAGGAACTCCAG 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 29bp) ATAACCGTAGTAATTCTAGAGCTAATACTGGAATTCTCGGGTGCCAAGGA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 22bp) CGTTTCCCGGCTGGTGCACCATGGAATTCTCGGGTGCCAAGGAACTCCAG 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 29bp) GGGGATATGGCGAAATCGGTAGACGCTACGGACTTTGGAATTCTCGGGTG 7 0.17500000000000002 No Hit TCTCGGACCAGGCTTCATTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 29bp) CTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCA 7 0.17500000000000002 No Hit GACACGACTCTCGGCAACGGATATGGAATTCTCGGGTGCCAAGGAACTCC 6 0.15 RNA PCR Primer, Index 1 (100% over 27bp) CATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGCC 6 0.15 No Hit TAATTCATGATCTGGCATGTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 6 0.15 RNA PCR Primer, Index 1 (100% over 31bp) TCCTGTGGATGAGAAGGCATTTATATTCTGATGATATGGAATTCTCGGGT 6 0.15 No Hit AGTTACTAATTCATGATCTGGCTGGAATTCTCGGGTGCCAAGGAACTCCA 6 0.15 RNA PCR Primer, Index 1 (100% over 28bp) GATAACCGTAGTAATTCTAGAGCTAATATGGAATTCTCGGGTGCCAAGGA 6 0.15 RNA PCR Primer, Index 1 (100% over 22bp) CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGGAATTCTCG 6 0.15 No Hit GCCCACCCCAAGATGAGTGCTCTCTCTGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTCATGGAATTCTCGGGTG 6 0.15 No Hit ATAACCGTAGTAATTCTAGAGCTAATATGGAATTCTCGGGTGCCAAGGAA 6 0.15 RNA PCR Primer, Index 1 (100% over 23bp) GGGGATATAGCTCAGTTGGTAGATGGAATTCTCGGGTGCCAAGGAACTCC 6 0.15 RNA PCR Primer, Index 1 (100% over 27bp) GCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAA 6 0.15 RNA PCR Primer, Index 1 (100% over 23bp) GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGGTG 6 0.15 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTGGAATTCTC 6 0.15 No Hit GCACCAGTGGTCTAGTGGTAGAATAGTATGGAATTCTCGGGTGCCAAGGA 5 0.125 RNA PCR Primer, Index 1 (100% over 22bp) ATAACCGTAGTAATTCTAGAGCTAATTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) GAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAG 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGGAATTCTCGGGTGCCAAGGAACTCCA 5 0.125 RNA PCR Primer, Index 1 (100% over 28bp) TCGGATAACCGTAGTAATTCTAGAGCTAATACGTGGAATTCTCGGGTGCC 5 0.125 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTTGGAATTCT 5 0.125 No Hit ACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) TAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAG 5 0.125 RNA PCR Primer, Index 1 (100% over 29bp) GATAACCGTAGTAATTCTAGAGCTAATACTGGAATTCTCGGGTGCCAAGG 5 0.125 Illumina Small RNA Adapter 2 (100% over 21bp) GACACGACTCTCGGCAACGGATATCTCGGCTCTCGCTGGAATTCTCGGGT 5 0.125 No Hit TAACCGTAGTAATTCTAGAGCTAATTGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) GATAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) CATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) AGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGGT 5 0.125 No Hit GAAGTCCTCGTGTTGCATTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA 5 0.125 RNA PCR Primer, Index 1 (100% over 28bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATGGAATTCTCGGGTG 5 0.125 No Hit CGGATAACCGTAGTAATTCTAGAGCTAATACTGGAATTCTCGGGTGCCAA 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTATGGAATTCTCGGGTGCCAA 5 0.125 No Hit ATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) TAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAACTC 5 0.125 RNA PCR Primer, Index 1 (100% over 26bp) >>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 0.1 0.0 0.0 0.0 7 0.0 0.125 0.0 0.0 0.0 8 0.0 0.125 0.0 0.0 0.0 9 0.0 0.15 0.0 0.0 0.0 10-11 0.0 0.3 0.0 0.0 0.0 12-13 0.0 0.48750000000000004 0.0 0.0 0.0 14-15 0.0 0.8625 0.0 0.0 0.0 16-17 0.0 1.9625000000000001 0.0 0.0 0.0 18-19 0.0 3.9000000000000004 0.0 0.0 0.0 20-21 0.0 6.925000000000001 0.0 0.0 0.0 22-23 0.0 16.700000000000003 0.0 0.0 0.0 24-25 0.0 30.1 0.0 0.0 0.0 26-27 0.0 45.25 0.0 0.0 0.0 28-29 0.0 54.0 0.0 0.0 0.0 30-31 0.0 63.987500000000004 0.0 0.0 0.0 32-33 0.0 71.5875 0.0 0.0 0.0 34-35 0.0 78.9125 0.0 0.0 0.0 36-37 0.0 85.45 0.0 0.0 0.0 38-39 0.0 89.07499999999999 0.0 0.0 0.0 40-41 0.0 90.8375 0.0 0.0 0.0 42-43 0.0 92.3625 0.0 0.0 0.0 44-45 0.0 93.075 0.0 0.0 0.0 46-47 0.0 93.2625 0.0 0.0 0.0 48-49 0.0 93.3375 0.0 0.0 0.0 50-51 0.0 93.3625 0.0 0.0 0.0 52-53 0.0 93.375 0.0 0.0 0.0 54-55 0.0 93.375 0.0 0.0 0.0 56-57 0.0 93.375 0.0 0.0 0.0 58-59 0.0 93.375 0.0 0.0 0.0 60-61 0.0 93.375 0.0 0.0 0.0 62-63 0.0 93.375 0.0 0.0 0.0 64-65 0.0 93.375 0.0 0.0 0.0 66-67 0.0 93.375 0.0 0.0 0.0 68-69 0.0 93.375 0.0 0.0 0.0 70-71 0.0 93.375 0.0 0.0 0.0 72-73 0.0 93.375 0.0 0.0 0.0 74-75 0.0 93.375 0.0 0.0 0.0 76-77 0.0 93.375 0.0 0.0 0.0 78-79 0.0 93.375 0.0 0.0 0.0 80-81 0.0 93.4 0.0 0.0 0.0 82-83 0.0 93.4 0.0 0.0 0.0 84-85 0.0 93.4 0.0 0.0 0.0 86-87 0.0 93.4 0.0 0.0 0.0 88-89 0.0 93.4 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AGCTGAG 20 1.1111353E-5 101.26667 1 GATAACC 15 4.7401295E-4 101.26666 1 CATCGAG 15 4.7401295E-4 101.26666 1 GTAGACC 15 6.1582687E-4 94.9375 7 AGTAGAC 15 6.1582687E-4 94.9375 6 ATAACCG 15 6.1582687E-4 94.9375 2 TAACCGT 15 6.1582687E-4 94.9375 3 GAGTAGA 15 6.1582687E-4 94.9375 5 CGAGTAG 15 6.1582687E-4 94.9375 4 AGACCTT 15 6.1582687E-4 94.9375 9 ATCGAGT 15 6.1582687E-4 94.9375 2 TCGAGTA 15 6.1582687E-4 94.9375 3 TAGACCT 15 6.1582687E-4 94.9375 8 CTGAGGC 25 4.6741432E-5 75.950005 3 GCTGAGG 25 4.6741432E-5 75.950005 2 TGAGGCA 25 4.6741432E-5 75.950005 4 CACGACT 35 1.9148938E-6 72.333336 1 AACCGTA 20 0.0019308104 71.203125 4 AGCTCAG 20 0.0019308104 71.203125 9 TCGGCAA 40 7.000381E-8 71.203125 9 >>END_MODULE Rejected 719506 READS because READLEN < 1 Read 719506 spots for SRR8846484.sra Written 719506 spots for SRR8846484.sra Rejected 719506 READS because READLEN < 1 Read 719506 spots for SRR8846484.sra Written 719506 spots for SRR8846484.sra Rejected 719506 READS because READLEN < 1 Read 719506 spots for SRR8846484.sra Written 719506 spots for SRR8846484.sra Rejected 719506 READS because READLEN < 1 Read 719506 spots for SRR8846484.sra Written 719506 spots for SRR8846484.sra Rejected 719506 READS because READLEN < 1 Read 719506 spots for SRR8846484.sra Written 719506 spots for SRR8846484.sra Rejected 719506 READS because READLEN < 1 Read 719506 spots for SRR8846484.sra Written 719506 spots for SRR8846484.sra Rejected 719506 READS because READLEN < 1 Read 719506 spots for SRR8846484.sra Written 719506 spots for SRR8846484.sra Rejected 719506 READS because READLEN < 1 Read 719506 spots for SRR8846484.sra Written 719506 spots for SRR8846484.sra Rejected 719506 READS because READLEN < 1 Read 719506 spots for SRR8846484.sra Written 719506 spots for SRR8846484.sra Rejected 719506 READS because READLEN < 1 Read 719506 spots for SRR8846484.sra Written 719506 spots for SRR8846484.sra Rejected 719515 READS because READLEN < 1 Read 719515 spots for SRR8846484.sra Written 719515 spots for SRR8846484.sra Rejected 719506 READS because READLEN < 1 Read 719506 spots for SRR8846484.sra Written 719506 spots for SRR8846484.sra Rejected 719506 READS because READLEN < 1 Read 719506 spots for SRR8846484.sra Written 719506 spots for SRR8846484.sra Rejected 719506 READS because READLEN < 1 Read 719506 spots for SRR8846484.sra Written 719506 spots for SRR8846484.sra Rejected 719506 READS because READLEN < 1 Read 719506 spots for SRR8846484.sra Written 719506 spots for SRR8846484.sra Rejected 719506 READS because READLEN < 1 Read 719506 spots for SRR8846484.sra Written 719506 spots for SRR8846484.sra Rejected 719506 READS because READLEN < 1 Read 719506 spots for SRR8846484.sra Written 719506 spots for SRR8846484.sra Rejected 719506 READS because READLEN < 1 Read 719506 spots for SRR8846484.sra Written 719506 spots for SRR8846484.sra Rejected 719506 READS because READLEN < 1 Read 719506 spots for SRR8846484.sra Written 719506 spots for SRR8846484.sra Rejected 719506 READS because READLEN < 1 Read 719506 spots for SRR8846484.sra Written 719506 spots for SRR8846484.sra SRR ids: ['SRR8846484.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_rvh99l0e SRR8846484.sra spots: 14390129 blocks: [[1, 719506], [719507, 1439012], [1439013, 2158518], [2158519, 2878024], [2878025, 3597530], [3597531, 4317036], [4317037, 5036542], [5036543, 5756048], [5756049, 6475554], [6475555, 7195060], [7195061, 7914566], [7914567, 8634072], [8634073, 9353578], [9353579, 10073084], [10073085, 10792590], [10792591, 11512096], [11512097, 12231602], [12231603, 12951108], [12951109, 13670614], [13670615, 14390129]] SRR8846484 file size 3449356 SRR8846484 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 SRR8846484 SRR8846484_1.fastq Input file: SRR8846484_1.fastq trimmed: SRR8846484-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 17:48:20 2024 >> started Sun Dec 8 17:48:57 2024 >> done (37.653s) 14390129 reads processed; of these: 304 ( 0.00%) short reads filtered out after trimming by size control 42 ( 0.00%) empty reads filtered out after trimming by size control 14389783 (100.00%) reads available; of these: 4058176 (28.20%) trimmed reads available after processing 10331607 (71.80%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 40 0.00% 19 38 0.00% 20 30 0.00% 21 36 0.00% 22 48 0.00% 23 52 0.00% 24 68 0.00% 25 92 0.00% 26 104 0.00% 27 111 0.00% 28 122 0.00% 29 123 0.00% 30 124 0.00% 31 135 0.00% 32 115 0.00% 33 156 0.00% 34 184 0.00% 35 165 0.00% 36 190 0.00% 37 163 0.00% 38 140 0.00% 39 128 0.00% 40 137 0.00% 41 131 0.00% 42 153 0.00% 43 175 0.00% 44 168 0.00% 45 181 0.00% 46 164 0.00% 47 184 0.00% 48 160 0.00% 49 151 0.00% 50 181 0.00% 51 174 0.00% 52 197 0.00% 53 208 0.00% 54 215 0.00% 55 180 0.00% 56 301 0.00% 57 316 0.00% 58 365 0.00% 59 474 0.00% 60 758 0.01% 61 1003 0.01% 62 1276 0.01% 63 1506 0.01% 64 3064 0.02% 65 4378 0.03% 66 9812 0.07% 67 49079 0.34% 68 58704 0.41% 69 40677 0.28% 70 35369 0.25% 71 48299 0.34% 72 21365 0.15% 73 6395 0.04% 74 7790 0.05% 75 5148 0.04% 76 3526 0.02% 77 3556 0.02% 78 4266 0.03% 79 4612 0.03% 80 5345 0.04% 81 6218 0.04% 82 8497 0.06% 83 9956 0.07% 84 10698 0.07% 85 13581 0.09% 86 15400 0.11% 87 21269 0.15% 88 35466 0.25% 89 55423 0.39% 90 79630 0.55% 91 92313 0.64% 92 105478 0.73% 93 161738 1.12% 94 199988 1.39% 95 395298 2.75% 96 472940 3.29% 97 459970 3.20% 98 609094 4.23% 99 631534 4.39% 100 351178 2.44% 101 10331607 71.80% 14389783 reads passed initial QC criterion=sequence-density sequence-density=93.51 sequence-density-rank=1 fanout-score=37.10 fanout-score-rank=1 prefix-density=93.88 prefix-fanout=37.0 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGCCAATATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA criterion=fanout-score sequence-density=93.51 sequence-density-rank=1 fanout-score=37.10 fanout-score-rank=1 prefix-density=93.88 prefix-fanout=37.0 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGCCAATATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGCCAATATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA -o SRR8846484 - Input file: STDIN trimmed: SRR8846484-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGCCAATATCTCGTATGCCGTCTTCTGCTTGA -- 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 17:51:32 2024 >> started Sun Dec 8 17:52:41 2024 >> done (69.873s) 14083618 reads processed; of these: 444451 ( 3.16%) short reads filtered out after trimming by size control 12407 ( 0.09%) empty reads filtered out after trimming by size control 13626760 (96.76%) reads available; of these: 13088988 (96.05%) trimmed reads available after processing 537772 ( 3.95%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 147996 1.09% 19 248979 1.83% 20 267571 1.96% 21 893771 6.56% 22 512673 3.76% 23 647649 4.75% 24 1955626 14.35% 25 785555 5.76% 26 688251 5.05% 27 632952 4.64% 28 618297 4.54% 29 676621 4.97% 30 791031 5.80% 31 514129 3.77% 32 500214 3.67% 33 578240 4.24% 34 607393 4.46% 35 511488 3.75% 36 445938 3.27% 37 248041 1.82% 38 197158 1.45% 39 148026 1.09% 40 119959 0.88% 41 111828 0.82% 42 100309 0.74% 43 42334 0.31% 44 43953 0.32% 45 18997 0.14% 46 9864 0.07% 47 5807 0.04% 48 4911 0.04% 49 2409 0.02% 50 1590 0.01% 51 1476 0.01% 52 738 0.01% 53 656 0.00% 54 810 0.01% 55 264 0.00% 56 365 0.00% 57 291 0.00% 58 310 0.00% 59 378 0.00% 60 650 0.00% 61 872 0.01% 62 1094 0.01% 63 1344 0.01% 64 2826 0.02% 65 4069 0.03% 66 9362 0.07% 67 47787 0.35% 68 57079 0.42% 69 39354 0.29% 70 34251 0.25% 71 46746 0.34% 72 19126 0.14% 73 4459 0.03% 74 3189 0.02% 75 2142 0.02% 76 1831 0.01% 77 2412 0.02% 78 2019 0.01% 79 1876 0.01% 80 2563 0.02% 81 1973 0.01% 82 1858 0.01% 83 2314 0.02% 84 1358 0.01% 85 1290 0.01% 86 1168 0.01% 87 1081 0.01% 88 954 0.01% 89 1026 0.01% 90 1030 0.01% 91 1220 0.01% 92 1083 0.01% 93 1300 0.01% 94 1375 0.01% 95 2058 0.02% 96 2881 0.02% 97 4017 0.03% 98 6036 0.04% 99 6810 0.05% 100 8875 0.07% 101 207154 1.52% criterion=sequence-density sequence-density=5.12 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=17 prefix-density=0.00 prefix-fanout=1.0 sequence=CATCGAGTAGACCTTGTTATTGTGAGAAT criterion=fanout-score sequence-density=0.51 sequence-density-rank=8 fanout-score=8.73 fanout-score-rank=1 prefix-density=4.46 prefix-fanout=1.0 sequence=ATTGTGAGAATAAAAA Started job on | Dec 08 17:54:59 Started mapping on | Dec 08 17:54:59 Finished on | Dec 08 18:01:50 Mapping speed, Million of reads per hour | 122.04 Number of input reads | 13932925 Average input read length | 31 UNIQUE READS: Uniquely mapped reads number | 2492201 Uniquely mapped reads % | 17.89% Average mapped length | 25.96 Number of splices: Total | 32198 Number of splices: Annotated (sjdb) | 20758 Number of splices: GT/AG | 30626 Number of splices: GC/AG | 1159 Number of splices: AT/AC | 9 Number of splices: Non-canonical | 404 Mismatch rate per base, % | 0.14% Deletion rate per base | 0.00% Deletion average length | 1.36 Insertion rate per base | 0.00% Insertion average length | 1.02 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 4816512 % of reads mapped to multiple loci | 34.57% Number of reads mapped to too many loci | 5549814 % of reads mapped to too many loci | 39.83% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 7.03% % of reads unmapped: other | 0.68% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 6624212 6624212 6624212 N_multimapping 4816512 4816512 4816512 N_noFeature 1565039 1711604 2333063 N_ambiguous 33991 20889 661 UnstrandedReadsAssigned:893171 PositiveStrandReadsAssigned:759708 NegativeStrandReadsAssigned:158477 Dataset is classified unstranded MeadianReadLen=28 20thPercentileLength=24 echo kmer=19 SRR8846484 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: SRR8846484-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 13,932,925 reads, 4,172,741 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,078 rounds 52973 SRR8846484.ke.tsv 35125 SRR8846484.se.tsv 88098 total ==> SRR8846484.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 2 0.25887 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 0 0 PNS24243 293 194 0 0 KQK14069 1603 1504 166.122 26.1484 KQK14071 474 375 0 0 ==> SRR8846484.se.tsv <== BRADI_1g14170v3 167 BRADI_1g53295v3 3 BRADI_1g59795v3 9 BRADI_1g07683v3 0 BRADI_1g00485v3 1 BRADI_1g20270v3 34 BRADI_1g74790v3 24 BRADI_1g09890v3 1 BRADI_1g77505v3 7 BRADI_1g48960v3 0 SRR8846484 completed mapping pipeline successfully