Starting /dee2/code/volunteer_pipeline.sh SRR8846487 current disk space = 1503442128896 free memory = 1379360832 SRR8846487 SRAfilesize c1fd79ccf2cdac3947910697034c9a31 SRR8846487.sra SRR8846487.sra file validated SRR8846487 is single end SRR8846487 is conventional basespace SRR8846487 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8846487_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 fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.44075 34.0 33.0 34.0 25.0 34.0 2 32.72325 34.0 33.0 34.0 28.0 34.0 3 32.92625 34.0 33.0 34.0 32.0 34.0 4 33.1625 34.0 33.0 34.0 32.0 34.0 5 33.21875 34.0 33.0 34.0 33.0 34.0 6 36.8415 38.0 37.0 38.0 35.0 38.0 7 37.17025 38.0 38.0 38.0 36.0 38.0 8 37.2685 38.0 38.0 38.0 37.0 38.0 9 37.4235 38.0 38.0 38.0 37.0 38.0 10-11 37.484875 38.0 38.0 38.0 37.0 38.0 12-13 37.450375 38.0 38.0 38.0 37.0 38.0 14-15 37.435 38.0 38.0 38.0 37.0 38.0 16-17 37.45225 38.0 38.0 38.0 37.0 38.0 18-19 37.504 38.0 38.0 38.0 37.5 38.0 20-21 37.3885 38.0 38.0 38.0 37.0 38.0 22-23 37.39325 38.0 38.0 38.0 37.0 38.0 24-25 37.430625 38.0 38.0 38.0 37.0 38.0 26-27 37.465375 38.0 38.0 38.0 37.0 38.0 28-29 37.261624999999995 38.0 38.0 38.0 36.5 38.0 30-31 37.386375 38.0 38.0 38.0 37.0 38.0 32-33 37.342 38.0 38.0 38.0 37.0 38.0 34-35 37.149874999999994 38.0 38.0 38.0 36.5 38.0 36-37 37.009125 38.0 38.0 38.0 36.0 38.0 38-39 37.05675 38.0 38.0 38.0 36.0 38.0 40-41 36.781875 38.0 38.0 38.0 35.0 38.0 42-43 36.926125 38.0 38.0 38.0 35.5 38.0 44-45 37.00375 38.0 38.0 38.0 36.0 38.0 46-47 36.863749999999996 38.0 38.0 38.0 35.0 38.0 48-49 36.9135 38.0 38.0 38.0 35.5 38.0 50-51 36.91974999999999 38.0 38.0 38.0 35.0 38.0 52-53 37.00725 38.0 38.0 38.0 36.0 38.0 54-55 36.900875 38.0 38.0 38.0 35.5 38.0 56-57 36.465125 38.0 38.0 38.0 34.0 38.0 58-59 36.455124999999995 38.0 38.0 38.0 33.5 38.0 60-61 36.272875 38.0 37.5 38.0 33.0 38.0 62-63 35.982749999999996 38.0 37.0 38.0 31.0 38.0 64-65 35.8715 38.0 36.5 38.0 31.0 38.0 66-67 35.4615 38.0 36.5 38.0 28.5 38.0 68-69 35.897375 38.0 37.0 38.0 31.0 38.0 70-71 35.4335 38.0 37.0 38.0 29.0 38.0 72-73 35.60275 38.0 37.0 38.0 30.0 38.0 74-75 35.2615 38.0 37.0 38.0 29.0 38.0 76-77 35.154875000000004 38.0 36.5 38.0 28.5 38.0 78-79 34.272125 38.0 35.0 38.0 24.5 38.0 80-81 34.457375 38.0 35.5 38.0 26.0 38.0 82-83 34.211625 38.0 35.0 38.0 24.5 38.0 84-85 34.224625 38.0 35.0 38.0 25.5 38.0 86-87 34.474000000000004 38.0 35.5 38.0 26.5 38.0 88-89 33.768375 38.0 35.0 38.0 15.5 38.0 90-91 33.325125 38.0 34.0 38.0 15.0 38.0 92-93 32.620125 38.0 34.0 38.0 15.0 38.0 94-95 32.051125 38.0 33.5 38.0 8.0 38.0 96-97 29.731 38.0 28.0 38.0 2.0 38.0 98-99 26.86375 37.0 8.5 38.0 2.0 38.0 100-101 23.141875 33.0 2.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 11 1.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 3.0 18 1.0 19 1.0 20 1.0 21 6.0 22 2.0 23 14.0 24 14.0 25 32.0 26 44.0 27 35.0 28 36.0 29 50.0 30 74.0 31 105.0 32 149.0 33 193.0 34 331.0 35 579.0 36 921.0 37 1408.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 24.910934502603453 30.090435735818033 21.62236229103864 23.376267470539876 2 21.75 29.9 21.9 26.450000000000003 3 25.95 22.525000000000002 21.2 30.325000000000003 4 29.775000000000002 27.625 18.775 23.825 5 31.1 28.249999999999996 18.75 21.9 6 25.650000000000002 29.175 23.125 22.05 7 32.4 24.5 21.925 21.175 8 22.900000000000002 23.200000000000003 30.099999999999998 23.799999999999997 9 24.75 30.25 23.75 21.25 10-11 29.362500000000004 26.237500000000004 22.2625 22.1375 12-13 24.637500000000003 22.55 22.125 30.6875 14-15 23.5 33.45 23.6875 19.3625 16-17 25.162499999999998 27.5125 27.900000000000002 19.425 18-19 28.675 25.637500000000003 23.3125 22.375 20-21 22.5 28.299999999999997 26.700000000000003 22.5 22-23 27.675 27.450000000000003 28.425 16.45 24-25 26.400000000000002 24.9875 28.812500000000004 19.8 26-27 37.2125 24.3 23.2375 15.25 28-29 21.8625 33.7 25.474999999999998 18.9625 30-31 23.3625 19.025 39.725 17.8875 32-33 26.35 17.3625 32.9625 23.325000000000003 34-35 31.724999999999998 16.05 28.712500000000002 23.5125 36-37 40.699999999999996 14.099999999999998 26.674999999999997 18.525 38-39 33.1 18.0625 28.449999999999996 20.3875 40-41 29.4 18.525 20.8875 31.1875 42-43 29.25 30.0375 19.400000000000002 21.3125 44-45 40.9625 20.1125 15.049999999999999 23.875 46-47 27.700000000000003 31.8625 14.475 25.9625 48-49 25.124999999999996 24.425 18.912499999999998 31.5375 50-51 23.25 23.5875 14.787500000000001 38.375 52-53 23.65 34.4875 11.875 29.9875 54-55 18.0625 26.2875 19.2 36.449999999999996 56-57 17.7 34.599999999999994 12.025 35.675000000000004 58-59 14.000000000000002 33.375 16.3375 36.2875 60-61 17.05 34.4875 15.5 32.9625 62-63 11.774999999999999 26.450000000000003 24.3125 37.4625 64-65 11.924999999999999 32.0375 25.387500000000003 30.65 66-67 12.6 24.025 28.525 34.849999999999994 68-69 17.5625 24.337500000000002 24.349999999999998 33.75 70-71 15.85 26.525 31.175000000000004 26.450000000000003 72-73 21.45 18.15 32.5125 27.8875 74-75 16.4375 13.850000000000001 30.125 39.5875 76-77 20.1875 12.5 40.150000000000006 27.1625 78-79 17.675 9.1625 39.375 33.7875 80-81 18.637500000000003 9.950000000000001 38.6 32.8125 82-83 22.575 10.212499999999999 42.262499999999996 24.95 84-85 19.3375 13.700000000000001 37.6 29.362500000000004 86-87 20.7625 20.5375 36.4625 22.237499999999997 88-89 14.912500000000001 39.137499999999996 28.6375 17.3125 90-91 10.8125 47.3125 27.3875 14.4875 92-93 11.7875 55.8125 20.3875 12.0125 94-95 8.987499999999999 65.3 17.6125 8.1 96-97 7.6875 72.52499999999999 13.900000000000002 5.887499999999999 98-99 5.800000000000001 80.0375 9.8125 4.35 100-101 3.9875000000000003 83.0875 8.924999999999999 4.0 >>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 0.5 27 0.5 28 0.0 29 0.0 30 0.0 31 0.5 32 0.5 33 2.0 34 4.0 35 7.0 36 13.5 37 20.0 38 23.5 39 64.0 40 93.5 41 117.5 42 194.0 43 274.5 44 364.5 45 368.5 46 383.0 47 413.0 48 334.5 49 286.0 50 270.5 51 207.5 52 136.0 53 103.0 54 90.0 55 104.0 56 72.0 57 15.0 58 9.0 59 9.5 60 8.0 61 5.5 62 1.5 63 1.5 64 1.0 65 0.5 66 0.5 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 8.774999999999999 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 64.3 #Duplication Level Percentage of deduplicated Percentage of total 1 86.54743390357699 55.65 2 6.60964230171073 8.5 3 2.3716951788491447 4.575 4 1.2830482115085537 3.3000000000000003 5 0.583203732503888 1.875 6 0.38880248833592534 1.5 7 0.5443234836702955 2.45 8 0.11664074650077762 0.6 9 0.19440124416796267 1.125 >10 1.244167962674961 15.6 >50 0.11664074650077762 4.825 >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 78 1.95 RNA PCR Primer, Index 1 (100% over 29bp) AGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 58 1.4500000000000002 No Hit TCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 57 1.425 No Hit ATATATTTCAAGTTATTTCGGATCTTGGAATTCTCGGGTGCCAAGGAACT 35 0.8750000000000001 RNA PCR Primer, Index 1 (100% over 25bp) AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 34 0.8500000000000001 Illumina Small RNA Adapter 2 (100% over 21bp) GGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 33 0.8250000000000001 RNA PCR Primer, Index 1 (100% over 22bp) CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 31 0.775 No Hit GACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 29 0.7250000000000001 RNA PCR Primer, Index 1 (100% over 23bp) CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 28 0.7000000000000001 Illumina Small RNA Adapter 2 (100% over 21bp) GACACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACT 28 0.7000000000000001 RNA PCR Primer, Index 1 (100% over 25bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 26 0.65 Illumina Small RNA Adapter 2 (100% over 21bp) GACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAAC 26 0.65 RNA PCR Primer, Index 1 (100% over 24bp) CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 25 0.625 No Hit GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 24 0.6 No Hit CTCGGGTGCCAAGGAACTCCAGTCACCAGATCATCTCGTATGCCGTCTTC 22 0.5499999999999999 RNA PCR Primer, Index 7 (100% over 50bp) CTCTGATGATGATCAAACTAATACTTTCGTTCTTCTGGAATTCTCGGGTG 21 0.525 No Hit AATTCTCGGGTGCCAAGGAACTCCAGTCACCAGATCATCTCGTATGCCGT 20 0.5 RNA PCR Primer, Index 7 (100% over 50bp) TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 19 0.475 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 18 0.44999999999999996 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 17 0.42500000000000004 No Hit TTCGGACCAGGCTTCATTCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 15 0.375 RNA PCR Primer, Index 1 (100% over 29bp) ACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCC 15 0.375 No Hit TCTCGGGTGCCAAGGAACTCCAGTCACCAGATCATCTCGTATGCCGTCTT 15 0.375 RNA PCR Primer, Index 7 (100% over 50bp) CAGGGTTCGTTTCCCTGGATGCGCACCATGGAATTCTCGGGTGCCAAGGA 15 0.375 RNA PCR Primer, Index 1 (100% over 22bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTCATGGAATTCTCGGGTG 14 0.35000000000000003 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAATGGAATTCTCGGGTGCCA 13 0.325 No Hit CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGG 13 0.325 No Hit CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 13 0.325 RNA PCR Primer, Index 1 (100% over 28bp) AAGGGTGCTGAGAATACTTTGAATCTGACACTGGAATTCTCGGGTGCCAA 13 0.325 No Hit ATTCTCGGGTGCCAAGGAACTCCAGTCACCAGATCATCTCGTATGCCGTC 11 0.27499999999999997 RNA PCR Primer, Index 7 (100% over 50bp) CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 23bp) TCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTC 10 0.25 RNA PCR Primer, Index 1 (100% over 26bp) GCACCAGTGGTCTAGTGGTAGAATAGTACCTGGAATTCTCGGGTGCCAAG 10 0.25 No Hit CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTC 10 0.25 No Hit CTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCA 10 0.25 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 9 0.22499999999999998 No Hit TCGGATAACCGTAGTAATTCTAGAGCTAATACGTGGAATTCTCGGGTGCC 9 0.22499999999999998 No Hit TGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAA 9 0.22499999999999998 No Hit ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGC 9 0.22499999999999998 No Hit CACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGC 9 0.22499999999999998 No Hit AGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGT 8 0.2 No Hit CACGACTCTCGGCAACGGATATCTCGTGGAATTCTCGGGTGCCAAGGAAC 8 0.2 RNA PCR Primer, Index 1 (100% over 24bp) GCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCC 8 0.2 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 7 0.17500000000000002 No Hit TTCTCGGGTGCCAAGGAACTCCAGTCACCAGATCATCTCGTATGCCGTCT 7 0.17500000000000002 RNA PCR Primer, Index 7 (100% over 50bp) GCACCAGTGGTCTAGTGGTAGAATAGTATGGAATTCTCGGGTGCCAAGGA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 22bp) TCCGTCGTAGTCTAGGTGGTTAGGATACTCTGGAATTCTCGGGTGCCAAG 7 0.17500000000000002 No Hit GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTG 7 0.17500000000000002 No Hit TCCTGTGGATGAGAAGGCATTTATATTCTGATGATATGGAATTCTCGGGT 7 0.17500000000000002 No Hit ACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAAC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 24bp) TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGATCATCTCGTATGC 7 0.17500000000000002 RNA PCR Primer, Index 7 (100% over 50bp) CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGG 7 0.17500000000000002 No Hit ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGGTGC 7 0.17500000000000002 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTGGAATTCTCGGGTGCCAAGG 7 0.17500000000000002 Illumina Small RNA Adapter 2 (100% over 21bp) GCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 23bp) GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGGTG 7 0.17500000000000002 No Hit ATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 23bp) CACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAACT 6 0.15 RNA PCR Primer, Index 1 (100% over 25bp) GATCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGG 6 0.15 No Hit TCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) GACACGACTCTCGGCAACGGATATCTCGGCTGGAATTCTCGGGTGCCAAG 6 0.15 No Hit CCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTG 6 0.15 No Hit CAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTG 6 0.15 No Hit ATGCAGTTACTAATTCATGATCTGGCTGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) ATCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGG 6 0.15 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTTGGAATTCTCGGGTGCCA 6 0.15 No Hit CTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCA 6 0.15 No Hit GGGGATGTAGCTCAAATGGTAGATGGAATTCTCGGGTGCCAAGGAACTCC 5 0.125 RNA PCR Primer, Index 1 (100% over 27bp) GACACGACTCTCGGCAACGGATATGGAATTCTCGGGTGCCAAGGAACTCC 5 0.125 RNA PCR Primer, Index 1 (100% over 27bp) AAGGGTGCTGAGAATACTTTGAATCTGACATGGAATTCTCGGGTGCCAAG 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGGAATTCTCGGGTGCCAAGGAACTCCA 5 0.125 RNA PCR Primer, Index 1 (100% over 28bp) TCCACAGGCTTTCTTGAACTGTGGAATTCTCGGGTGCCAAGGAACTCCAG 5 0.125 RNA PCR Primer, Index 1 (100% over 29bp) ATATATTTCAAGTTATTTCGGATCTGGAATTCTCGGGTGCCAAGGAACTC 5 0.125 RNA PCR Primer, Index 1 (100% over 26bp) GATAACCGTAGTAATTCTAGAGCTAATACTGGAATTCTCGGGTGCCAAGG 5 0.125 Illumina Small RNA Adapter 2 (100% over 21bp) TGCAAGTATGAACTAATTTGAACTGTGAAACTTGGAATTCTCGGGTGCCA 5 0.125 No Hit NCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 5 0.125 RNA PCR Primer, Index 1 (100% over 29bp) NTCGGGTGCCAAGGAACTCCAGTCACCAGATCATCTCGTATGCCGTCTTC 5 0.125 RNA PCR Primer, Index 7 (98% over 50bp) CACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACTCC 5 0.125 RNA PCR Primer, Index 1 (100% over 27bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGATGGAATTCTC 5 0.125 No Hit NGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 5 0.125 No Hit ATAACCGTAGTAATTCTAGAGCTAATATGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) TCGTGACCCTGACCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAG 5 0.125 RNA PCR Primer, Index 7 (100% over 36bp) >>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 0.2 0.0 0.0 0.0 2 0.0 0.2 0.0 0.0 0.0 3 0.0 0.2 0.0 0.0 0.0 4 0.0 0.2 0.0 0.0 0.0 5 0.0 0.2 0.0 0.0 0.0 6 0.0 0.225 0.0 0.0 0.0 7 0.0 0.25 0.0 0.0 0.0 8 0.0 0.325 0.0 0.0 0.0 9 0.0 0.425 0.0 0.0 0.0 10-11 0.0 0.6000000000000001 0.0 0.0 0.0 12-13 0.0 0.75 0.0 0.0 0.0 14-15 0.0 1.175 0.0 0.0 0.0 16-17 0.0 2.325 0.0 0.0 0.0 18-19 0.0 3.7874999999999996 0.0 0.0 0.0 20-21 0.0 6.625 0.0 0.0 0.0 22-23 0.0 15.0 0.0 0.0 0.0 24-25 0.0 27.575000000000003 0.0 0.0 0.0 26-27 0.0 42.0375 0.0 0.0 0.0 28-29 0.0 50.1375 0.0 0.0 0.0 30-31 0.0 60.087500000000006 0.0 0.0 0.0 32-33 0.0 68.275 0.0 0.0 0.0 34-35 0.0 76.9375 0.0 0.0 0.0 36-37 0.0 84.6 0.0 0.0 0.0 38-39 0.0 88.975 0.0 0.0 0.0 40-41 0.0 91.26249999999999 0.0 0.0 0.0 42-43 0.0 92.6875 0.0 0.0 0.0 44-45 0.0 93.625 0.0 0.0 0.0 46-47 0.0 93.925 0.0 0.0 0.0 48-49 0.0 94.11250000000001 0.0 0.0 0.0 50-51 0.0 94.1625 0.0 0.0 0.0 52-53 0.0 94.2 0.0 0.0 0.0 54-55 0.0 94.2125 0.0 0.0 0.0 56-57 0.0 94.225 0.0 0.0 0.0 58-59 0.0 94.225 0.0 0.0 0.0 60-61 0.0 94.225 0.0 0.0 0.0 62-63 0.0 94.225 0.0 0.0 0.0 64-65 0.0 94.225 0.0 0.0 0.0 66-67 0.0 94.225 0.0 0.0 0.0 68-69 0.0 94.225 0.0 0.0 0.0 70-71 0.0 94.225 0.0 0.0 0.0 72-73 0.0 94.225 0.0 0.0 0.0 74-75 0.0 94.225 0.0 0.0 0.0 76-77 0.0 94.225 0.0 0.0 0.0 78-79 0.0 94.225 0.0 0.0 0.0 80-81 0.0 94.225 0.0 0.0 0.0 82-83 0.0 94.225 0.0 0.0 0.0 84-85 0.0 94.225 0.0 0.0 0.0 86-87 0.0 94.225 0.0 0.0 0.0 88-89 0.0 94.225 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CACGACT 30 5.9643753E-7 87.87037 1 TCGGCAA 35 2.8531358E-6 67.78571 9 CTCTCGG 35 2.8531358E-6 67.78571 6 ACTCTCG 35 2.8531358E-6 67.78571 5 CTCGGCA 35 2.8531358E-6 67.78571 8 ACGACTC 35 2.8531358E-6 67.78571 2 GACTCTC 35 2.8531358E-6 67.78571 4 CGACTCT 35 2.8531358E-6 67.78571 3 ATCTCGG 20 5.098269E-4 47.45 20-21 TATCTCG 25 2.5975807E-5 47.45 20-21 ATATCTC 25 2.5975807E-5 47.45 18-19 TCGGCTC 15 0.009998714 47.449997 24-25 CTCTCGC 15 0.009998714 47.449997 28-29 GGCTCTC 15 0.009998714 47.449997 26-27 CGGCTCT 15 0.009998714 47.449997 24-25 GCTCTCG 15 0.009998714 47.449997 26-27 TCTCGGC 55 4.15513E-5 43.136364 7 GGCAACG 35 3.825222E-6 40.671425 10-11 GGATATC 35 3.825222E-6 40.671425 16-17 ACGGATA 40 9.570871E-6 35.5875 14-15 >>END_MODULE Rejected 1093559 READS because READLEN < 1 Read 1093559 spots for SRR8846487.sra Written 1093559 spots for SRR8846487.sra Rejected 1093559 READS because READLEN < 1 Read 1093559 spots for SRR8846487.sra Written 1093559 spots for SRR8846487.sra Rejected 1093559 READS because READLEN < 1 Read 1093559 spots for SRR8846487.sra Written 1093559 spots for SRR8846487.sra Rejected 1093559 READS because READLEN < 1 Read 1093559 spots for SRR8846487.sra Written 1093559 spots for SRR8846487.sra Rejected 1093559 READS because READLEN < 1 Read 1093559 spots for SRR8846487.sra Written 1093559 spots for SRR8846487.sra Rejected 1093559 READS because READLEN < 1 Read 1093559 spots for SRR8846487.sra Written 1093559 spots for SRR8846487.sra Rejected 1093559 READS because READLEN < 1 Read 1093559 spots for SRR8846487.sra Written 1093559 spots for SRR8846487.sra Rejected 1093559 READS because READLEN < 1 Read 1093559 spots for SRR8846487.sra Written 1093559 spots for SRR8846487.sra Rejected 1093559 READS because READLEN < 1 Read 1093559 spots for SRR8846487.sra Written 1093559 spots for SRR8846487.sra Rejected 1093559 READS because READLEN < 1 Read 1093559 spots for SRR8846487.sra Written 1093559 spots for SRR8846487.sra Rejected 1093559 READS because READLEN < 1 Read 1093559 spots for SRR8846487.sra Written 1093559 spots for SRR8846487.sra Rejected 1093559 READS because READLEN < 1 Read 1093559 spots for SRR8846487.sra Written 1093559 spots for SRR8846487.sra Rejected 1093559 READS because READLEN < 1 Read 1093559 spots for SRR8846487.sra Written 1093559 spots for SRR8846487.sra Rejected 1093559 READS because READLEN < 1 Read 1093559 spots for SRR8846487.sra Written 1093559 spots for SRR8846487.sra Rejected 1093559 READS because READLEN < 1 Read 1093559 spots for SRR8846487.sra Written 1093559 spots for SRR8846487.sra Rejected 1093559 READS because READLEN < 1 Read 1093559 spots for SRR8846487.sra Written 1093559 spots for SRR8846487.sra Rejected 1093574 READS because READLEN < 1 Read 1093574 spots for SRR8846487.sra Written 1093574 spots for SRR8846487.sra Rejected 1093559 READS because READLEN < 1 Read 1093559 spots for SRR8846487.sra Written 1093559 spots for SRR8846487.sra Rejected 1093559 READS because READLEN < 1 Read 1093559 spots for SRR8846487.sra Written 1093559 spots for SRR8846487.sra Rejected 1093559 READS because READLEN < 1 Read 1093559 spots for SRR8846487.sra Written 1093559 spots for SRR8846487.sra SRR ids: ['SRR8846487.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_96lf3cz1 SRR8846487.sra spots: 21871195 blocks: [[1, 1093559], [1093560, 2187118], [2187119, 3280677], [3280678, 4374236], [4374237, 5467795], [5467796, 6561354], [6561355, 7654913], [7654914, 8748472], [8748473, 9842031], [9842032, 10935590], [10935591, 12029149], [12029150, 13122708], [13122709, 14216267], [14216268, 15309826], [15309827, 16403385], [16403386, 17496944], [17496945, 18590503], [18590504, 19684062], [19684063, 20777621], [20777622, 21871195]] SRR8846487 file size 5253871 SRR8846487 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 SRR8846487 SRR8846487_1.fastq Input file: SRR8846487_1.fastq trimmed: SRR8846487-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 19:04:00 2024 >> started Sun Dec 8 19:04:57 2024 >> done (56.481s) 21871195 reads processed; of these: 372 ( 0.00%) short reads filtered out after trimming by size control 55 ( 0.00%) empty reads filtered out after trimming by size control 21870768 (100.00%) reads available; of these: 5864873 (26.82%) trimmed reads available after processing 16005895 (73.18%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 44 0.00% 19 46 0.00% 20 42 0.00% 21 44 0.00% 22 52 0.00% 23 57 0.00% 24 79 0.00% 25 109 0.00% 26 118 0.00% 27 108 0.00% 28 143 0.00% 29 180 0.00% 30 161 0.00% 31 202 0.00% 32 191 0.00% 33 228 0.00% 34 250 0.00% 35 242 0.00% 36 184 0.00% 37 206 0.00% 38 194 0.00% 39 211 0.00% 40 202 0.00% 41 190 0.00% 42 236 0.00% 43 266 0.00% 44 230 0.00% 45 238 0.00% 46 212 0.00% 47 200 0.00% 48 186 0.00% 49 202 0.00% 50 217 0.00% 51 187 0.00% 52 200 0.00% 53 231 0.00% 54 206 0.00% 55 233 0.00% 56 304 0.00% 57 299 0.00% 58 366 0.00% 59 582 0.00% 60 724 0.00% 61 1137 0.01% 62 1574 0.01% 63 2096 0.01% 64 3685 0.02% 65 5553 0.03% 66 12507 0.06% 67 55878 0.26% 68 69829 0.32% 69 48160 0.22% 70 49197 0.22% 71 71233 0.33% 72 29448 0.13% 73 10422 0.05% 74 19979 0.09% 75 10485 0.05% 76 6164 0.03% 77 5980 0.03% 78 6336 0.03% 79 7140 0.03% 80 8011 0.04% 81 10249 0.05% 82 14059 0.06% 83 15570 0.07% 84 17237 0.08% 85 20276 0.09% 86 24426 0.11% 87 32818 0.15% 88 47063 0.22% 89 70163 0.32% 90 113235 0.52% 91 119931 0.55% 92 141463 0.65% 93 219783 1.00% 94 264989 1.21% 95 562235 2.57% 96 643211 2.94% 97 642838 2.94% 98 952788 4.36% 99 1010415 4.62% 100 508508 2.33% 101 16005895 73.18% 21870768 reads passed initial QC criterion=sequence-density sequence-density=94.37 sequence-density-rank=1 fanout-score=38.16 fanout-score-rank=1 prefix-density=94.62 prefix-fanout=38.1 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGATCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA criterion=fanout-score sequence-density=94.37 sequence-density-rank=1 fanout-score=38.16 fanout-score-rank=1 prefix-density=94.62 prefix-fanout=38.1 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGATCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGATCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA -o SRR8846487 - Input file: STDIN trimmed: SRR8846487-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGATCATCTCGTATGCCGTCTTCTGCTTGA -- 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 19:08:36 2024 >> started Sun Dec 8 19:10:17 2024 >> done (101.752s) 21410331 reads processed; of these: 609509 ( 2.85%) short reads filtered out after trimming by size control 43754 ( 0.20%) empty reads filtered out after trimming by size control 20757068 (96.95%) reads available; of these: 20064462 (96.66%) trimmed reads available after processing 692606 ( 3.34%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 185025 0.89% 19 319404 1.54% 20 337990 1.63% 21 1266443 6.10% 22 661008 3.18% 23 911482 4.39% 24 3145345 15.15% 25 1149471 5.54% 26 934755 4.50% 27 961813 4.63% 28 881553 4.25% 29 1122809 5.41% 30 1223379 5.89% 31 829169 3.99% 32 820383 3.95% 33 933757 4.50% 34 907912 4.37% 35 843995 4.07% 36 771574 3.72% 37 416605 2.01% 38 325278 1.57% 39 245837 1.18% 40 208298 1.00% 41 200809 0.97% 42 180035 0.87% 43 82616 0.40% 44 93523 0.45% 45 39826 0.19% 46 20514 0.10% 47 12751 0.06% 48 10513 0.05% 49 5192 0.03% 50 3491 0.02% 51 3128 0.02% 52 1573 0.01% 53 1434 0.01% 54 1348 0.01% 55 541 0.00% 56 639 0.00% 57 427 0.00% 58 372 0.00% 59 510 0.00% 60 590 0.00% 61 1018 0.00% 62 1415 0.01% 63 1856 0.01% 64 3359 0.02% 65 5172 0.02% 66 11920 0.06% 67 54321 0.26% 68 67780 0.33% 69 46474 0.22% 70 47377 0.23% 71 68554 0.33% 72 25659 0.12% 73 5784 0.03% 74 2915 0.01% 75 2100 0.01% 76 2380 0.01% 77 3513 0.02% 78 2683 0.01% 79 2527 0.01% 80 2799 0.01% 81 2497 0.01% 82 2223 0.01% 83 2510 0.01% 84 1750 0.01% 85 1712 0.01% 86 1755 0.01% 87 1565 0.01% 88 1437 0.01% 89 1554 0.01% 90 1645 0.01% 91 1784 0.01% 92 2289 0.01% 93 2535 0.01% 94 2797 0.01% 95 4276 0.02% 96 5191 0.03% 97 5948 0.03% 98 7858 0.04% 99 9706 0.05% 100 12516 0.06% 101 260797 1.26% criterion=sequence-density sequence-density=5.21 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=16 prefix-density=0.00 prefix-fanout=1.0 sequence=CATCGAGTAGACCTTGTTATTGTGAGAAT criterion=fanout-score sequence-density=0.01 sequence-density-rank=44 fanout-score=219.93 fanout-score-rank=1 prefix-density=1.18 prefix-fanout=1.0 sequence=AGCCAAGTGCGGAGAGGATAACTGCTGAAAGCATATAAGTAGTAAGCCCACCCCAAGATGAGTGCTCTCTCCTCCGACT Started job on | Dec 08 19:12:53 Started mapping on | Dec 08 19:12:54 Finished on | Dec 08 19:23:02 Mapping speed, Million of reads per hour | 125.63 Number of input reads | 21217505 Average input read length | 31 UNIQUE READS: Uniquely mapped reads number | 4020945 Uniquely mapped reads % | 18.95% Average mapped length | 26.03 Number of splices: Total | 49639 Number of splices: Annotated (sjdb) | 32702 Number of splices: GT/AG | 47019 Number of splices: GC/AG | 1843 Number of splices: AT/AC | 29 Number of splices: Non-canonical | 748 Mismatch rate per base, % | 0.11% Deletion rate per base | 0.00% Deletion average length | 1.30 Insertion rate per base | 0.00% Insertion average length | 1.01 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 7571907 % of reads mapped to multiple loci | 35.69% Number of reads mapped to too many loci | 8112460 % of reads mapped to too many loci | 38.23% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 6.44% % of reads unmapped: other | 0.69% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 9624653 9624653 9624653 N_multimapping 7571907 7571907 7571907 N_noFeature 2567605 2822323 3746680 N_ambiguous 52860 32615 955 UnstrandedReadsAssigned:1400480 PositiveStrandReadsAssigned:1166007 NegativeStrandReadsAssigned:273310 Dataset is classified unstranded MeadianReadLen=28 20thPercentileLength=24 echo kmer=19 SRR8846487 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: SRR8846487-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 21,217,505 reads, 6,487,641 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,144 rounds 52973 SRR8846487.ke.tsv 35125 SRR8846487.se.tsv 88098 total ==> SRR8846487.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 3 0.201722 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 0 0 PNS24243 293 194 0 0 KQK14069 1603 1504 243.989 19.9511 KQK14071 474 375 11.9098 3.90586 ==> SRR8846487.se.tsv <== BRADI_1g14170v3 294 BRADI_1g53295v3 0 BRADI_1g59795v3 7 BRADI_1g07683v3 1 BRADI_1g00485v3 2 BRADI_1g20270v3 50 BRADI_1g74790v3 52 BRADI_1g09890v3 0 BRADI_1g77505v3 1 BRADI_1g48960v3 0 SRR8846487 completed mapping pipeline successfully