Starting /dee2/code/volunteer_pipeline.sh SRR8846494 current disk space = 1501070024704 free memory = 1385000264 SRR8846494 SRAfilesize 0764a8ac8fbd5e48c5c3f5ff6386cd71 SRR8846494.sra SRR8846494.sra file validated SRR8846494 is single end SRR8846494 is conventional basespace SRR8846494 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8846494_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 warn #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.274 34.0 33.0 34.0 31.0 34.0 2 32.901 34.0 33.0 34.0 31.0 34.0 3 32.9675 34.0 33.0 34.0 32.0 34.0 4 33.06 34.0 33.0 34.0 32.0 34.0 5 33.0445 34.0 33.0 34.0 32.0 34.0 6 36.58075 38.0 37.0 38.0 34.0 38.0 7 37.02975 38.0 38.0 38.0 35.0 38.0 8 37.29175 38.0 38.0 38.0 36.0 38.0 9 37.25875 38.0 38.0 38.0 36.0 38.0 10-11 37.3275 38.0 38.0 38.0 37.0 38.0 12-13 37.422625 38.0 38.0 38.0 37.0 38.0 14-15 37.361125 38.0 38.0 38.0 37.0 38.0 16-17 37.309625 38.0 38.0 38.0 37.0 38.0 18-19 37.354124999999996 38.0 38.0 38.0 37.0 38.0 20-21 37.332375 38.0 38.0 38.0 37.0 38.0 22-23 37.30975 38.0 38.0 38.0 37.0 38.0 24-25 37.31625 38.0 38.0 38.0 37.0 38.0 26-27 37.316125 38.0 38.0 38.0 37.0 38.0 28-29 37.275625000000005 38.0 38.0 38.0 37.0 38.0 30-31 37.289 38.0 38.0 38.0 37.0 38.0 32-33 37.141875 38.0 38.0 38.0 36.0 38.0 34-35 36.937125 38.0 38.0 38.0 35.5 38.0 36-37 36.7125 38.0 38.0 38.0 34.5 38.0 38-39 36.650625 38.0 38.0 38.0 34.5 38.0 40-41 36.969375 38.0 38.0 38.0 35.5 38.0 42-43 37.025000000000006 38.0 38.0 38.0 36.0 38.0 44-45 36.893375 38.0 38.0 38.0 35.5 38.0 46-47 36.857375000000005 38.0 38.0 38.0 35.0 38.0 48-49 36.9955 38.0 38.0 38.0 36.0 38.0 50-51 37.053875000000005 38.0 38.0 38.0 36.0 38.0 52-53 37.14125 38.0 38.0 38.0 36.0 38.0 54-55 36.943375 38.0 38.0 38.0 36.0 38.0 56-57 36.867000000000004 38.0 38.0 38.0 35.0 38.0 58-59 36.849875 38.0 38.0 38.0 35.5 38.0 60-61 36.783874999999995 38.0 38.0 38.0 35.0 38.0 62-63 36.334875 38.0 37.5 38.0 33.5 38.0 64-65 36.094375 38.0 37.0 38.0 31.5 38.0 66-67 35.8255 38.0 37.0 38.0 30.0 38.0 68-69 35.810625 38.0 37.0 38.0 29.0 38.0 70-71 35.4965 38.0 37.0 38.0 29.0 38.0 72-73 35.2605 38.0 36.5 38.0 29.0 38.0 74-75 34.70225 38.0 36.0 38.0 26.0 38.0 76-77 34.86775 38.0 36.0 38.0 27.5 38.0 78-79 34.86 38.0 36.0 38.0 27.5 38.0 80-81 34.47925 38.0 35.5 38.0 26.0 38.0 82-83 34.644125 38.0 36.0 38.0 27.0 38.0 84-85 34.6005 38.0 35.5 38.0 27.0 38.0 86-87 34.728875 38.0 36.0 38.0 27.0 38.0 88-89 34.831500000000005 38.0 36.0 38.0 27.5 38.0 90-91 34.29600000000001 38.0 35.5 38.0 26.0 38.0 92-93 34.183499999999995 38.0 35.5 38.0 25.5 38.0 94-95 33.638625000000005 38.0 35.0 38.0 19.5 38.0 96-97 31.99825 38.0 34.0 38.0 8.0 38.0 98-99 29.721625 38.0 28.5 38.0 2.0 38.0 100-101 26.916 36.5 8.5 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 16 1.0 17 1.0 18 0.0 19 0.0 20 4.0 21 1.0 22 4.0 23 8.0 24 17.0 25 37.0 26 26.0 27 21.0 28 32.0 29 32.0 30 57.0 31 81.0 32 137.0 33 169.0 34 258.0 35 520.0 36 993.0 37 1601.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 35.4753053637812 25.27881040892193 20.738183749336166 18.5077004779607 2 28.1 26.325 16.2 29.375 3 29.299999999999997 17.525 19.2 33.975 4 25.8 35.425000000000004 17.7 21.075 5 26.224999999999998 25.124999999999996 26.35 22.3 6 23.486743371685844 24.137068534267133 27.763881940970485 24.61230615307654 7 36.675000000000004 24.375 17.974999999999998 20.974999999999998 8 20.625 19.725 38.725 20.925 9 23.849999999999998 36.95 19.875 19.325 10-11 30.9 23.1 26.075 19.925 12-13 21.8 21.675 24.0375 32.487500000000004 14-15 22.0625 41.6375 19.4375 16.8625 16-17 24.1875 25.412499999999998 32.35 18.05 18-19 34.7125 22.650000000000002 20.7875 21.85 20-21 20.7125 28.5625 27.0875 23.6375 22-23 28.549999999999997 29.275000000000002 27.5125 14.662500000000001 24-25 27.987499999999997 26.6125 25.7375 19.662499999999998 26-27 31.125000000000004 28.462500000000002 21.5375 18.875 28-29 22.3875 27.437499999999996 25.174999999999997 25.0 30-31 27.0 19.4625 33.6625 19.875 32-33 23.1125 18.35 34.2625 24.275 34-35 32.6 16.0625 29.375 21.9625 36-37 36.0875 18.325 26.575 19.0125 38-39 33.300000000000004 18.7625 28.775000000000002 19.162499999999998 40-41 28.762500000000003 17.349999999999998 24.875 29.012500000000003 42-43 30.825000000000003 24.125 21.1625 23.8875 44-45 41.3 20.7875 13.737499999999999 24.175 46-47 31.275 29.212500000000002 16.425 23.0875 48-49 26.400000000000002 24.125 17.875 31.6 50-51 21.6125 27.575 15.3375 35.475 52-53 26.575 31.6 12.1875 29.6375 54-55 20.474999999999998 32.525 16.375 30.625000000000004 56-57 19.5125 30.6875 16.9125 32.887499999999996 58-59 15.925 33.8375 16.037499999999998 34.2 60-61 14.075 34.862500000000004 18.55 32.5125 62-63 14.299999999999999 37.9375 19.8625 27.900000000000002 64-65 11.3125 37.3625 23.724999999999998 27.6 66-67 12.1625 32.574999999999996 25.75 29.512500000000003 68-69 16.6875 29.512500000000003 25.887500000000003 27.9125 70-71 15.187500000000002 32.025 28.1 24.6875 72-73 18.475 26.5875 29.775000000000002 25.162499999999998 74-75 14.662500000000001 21.2625 30.0 34.075 76-77 20.45 13.975000000000001 37.4125 28.1625 78-79 17.95 12.025 38.2125 31.8125 80-81 19.275000000000002 12.875 37.487500000000004 30.362499999999997 82-83 20.7625 10.25 40.75 28.237499999999997 84-85 21.1125 11.262500000000001 37.6 30.025000000000002 86-87 20.225 18.0625 36.525 25.1875 88-89 14.4875 32.775 34.575 18.1625 90-91 13.9875 41.5 28.275 16.2375 92-93 12.4 51.5875 21.1625 14.85 94-95 10.9875 60.5625 20.2125 8.2375 96-97 7.6625 72.52499999999999 13.700000000000001 6.1125 98-99 5.6625000000000005 81.4375 8.6375 4.2625 100-101 3.5749999999999997 86.7875 5.6625000000000005 3.975 >>END_MODULE >>Per sequence GC content warn #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 0.5 31 2.0 32 6.5 33 7.0 34 9.5 35 13.0 36 17.5 37 23.0 38 41.0 39 64.0 40 121.5 41 186.5 42 227.0 43 307.0 44 326.0 45 366.5 46 392.5 47 312.0 48 290.0 49 351.5 50 317.0 51 165.0 52 83.0 53 83.0 54 131.5 55 99.5 56 26.5 57 13.0 58 6.5 59 4.5 60 2.0 61 1.5 62 1.0 63 0.5 64 0.0 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 5.8500000000000005 2 0.0 3 0.0 4 0.0 5 0.0 6 0.05 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 53.574999999999996 #Duplication Level Percentage of deduplicated Percentage of total 1 85.30097993467102 45.7 2 6.299580027998133 6.75 3 2.519832011199253 4.05 4 1.6332244517032197 3.5000000000000004 5 0.6066262249183387 1.625 6 0.5599626691553896 1.7999999999999998 7 0.23331777881474566 0.8750000000000001 8 0.4199720018665422 1.7999999999999998 9 0.18665422305179655 0.8999999999999999 >10 1.959869342043864 18.35 >50 0.18665422305179655 8.375 >100 0.09332711152589827 6.275 >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 148 3.6999999999999997 No Hit GGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 103 2.5749999999999997 RNA PCR Primer, Index 1 (100% over 22bp) TCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 91 2.275 No Hit TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 88 2.1999999999999997 RNA PCR Primer, Index 1 (100% over 29bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 86 2.15 No Hit AGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 70 1.7500000000000002 No Hit GCCCACCCCAAGATGAGTGCTCTCTCTGGAATTCTCGGGTGCCAAGGAAC 40 1.0 RNA PCR Primer, Index 1 (100% over 24bp) GACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 39 0.975 RNA PCR Primer, Index 1 (100% over 23bp) GACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAAC 35 0.8750000000000001 RNA PCR Primer, Index 1 (100% over 24bp) CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTC 30 0.75 No Hit CTCTGATGATGATCAAACTAATACTTTCGTTCTTCTGGAATTCTCGGGTG 28 0.7000000000000001 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 28 0.7000000000000001 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 27 0.675 No Hit AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 27 0.675 Illumina Small RNA Adapter 2 (100% over 21bp) GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 26 0.65 Illumina Small RNA Adapter 2 (100% over 21bp) TCTCGGGTGCCAAGGAACTCCAGTCACAGTCAAATCTCGTATGCCGTCTT 25 0.625 RNA PCR Primer, Index 13 (100% over 50bp) GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 23 0.575 No Hit CACGACTCTCGGCAACGGATATCTCGTGGAATTCTCGGGTGCCAAGGAAC 20 0.5 RNA PCR Primer, Index 1 (100% over 24bp) TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 19 0.475 No Hit CTCGGGTGCCAAGGAACTCCAGTCACAGTCAAATCTCGTATGCCGTCTTC 18 0.44999999999999996 RNA PCR Primer, Index 13 (100% over 50bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTGGAATTCTCGGGTGCCA 17 0.42500000000000004 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTTGGAATTCT 16 0.4 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATATGGAATTCTCGGGTGCCAAGGAA 16 0.4 RNA PCR Primer, Index 1 (100% over 23bp) AATTCTCGGGTGCCAAGGAACTCCAGTCACAGTCAAATCTCGTATGCCGT 15 0.375 RNA PCR Primer, Index 13 (100% over 50bp) GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGGAATTCTCGGGTGCCA 14 0.35000000000000003 No Hit CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 14 0.35000000000000003 RNA PCR Primer, Index 1 (100% over 23bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTTGGAATTCTCGGGTGCC 14 0.35000000000000003 No Hit GGGGATATAGCTCAGTTGGTAGATGGAATTCTCGGGTGCCAAGGAACTCC 14 0.35000000000000003 RNA PCR Primer, Index 1 (100% over 27bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTGGAATTCTC 14 0.35000000000000003 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 13 0.325 No Hit TCCTGTGGATGAGAAGGCATTTATATTCTGATGATATGGAATTCTCGGGT 13 0.325 No Hit GACACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACT 13 0.325 RNA PCR Primer, Index 1 (100% over 25bp) TTCTCGGGTGCCAAGGAACTCCAGTCACAGTCAAATCTCGTATGCCGTCT 13 0.325 RNA PCR Primer, Index 13 (100% over 50bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTCATGGAATTCTCGGGTG 13 0.325 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTTGGAATTCTCGGGTGC 13 0.325 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 12 0.3 Illumina Small RNA Adapter 2 (100% over 21bp) GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 11 0.27499999999999997 No Hit TAATTCATGATCTGGCATGTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 31bp) GCACCAGTGGTCTAGTGGTAGAATAGTACCTGGAATTCTCGGGTGCCAAG 11 0.27499999999999997 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 11 0.27499999999999997 Illumina Small RNA Adapter 2 (100% over 21bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTTGGAATTCTCGGGTGCCA 11 0.27499999999999997 No Hit NGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 10 0.25 RNA PCR Primer, Index 1 (100% over 22bp) GCGACCCCAGGTCAGGCGGGACTACCCGCTGATGGAATTCTCGGGTGCCA 10 0.25 No Hit ATATATTTCAAGTTATTTCGGATCTTGGAATTCTCGGGTGCCAAGGAACT 10 0.25 RNA PCR Primer, Index 1 (100% over 25bp) ATATATTTCAAGTTATTTCGGATCTGGAATTCTCGGGTGCCAAGGAACTC 10 0.25 RNA PCR Primer, Index 1 (100% over 26bp) GCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCC 10 0.25 No Hit GACACGACTCTCGGCAACGGATATCTCGTGGAATTCTCGGGTGCCAAGGA 10 0.25 RNA PCR Primer, Index 1 (100% over 22bp) GCCTTGATGGTGAAATGGTAGACACGCGAGATGGAATTCTCGGGTGCCAA 10 0.25 No Hit CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 28bp) TCTCGGACCAGGCTTCATTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 29bp) ATGCAGTTACTAATTCATGATCTGGCTGGAATTCTCGGGTGCCAAGGAAC 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 24bp) CGGATAACCGTAGTAATTCTAGAGCTAATACTGGAATTCTCGGGTGCCAA 9 0.22499999999999998 No Hit TCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTC 8 0.2 RNA PCR Primer, Index 1 (100% over 26bp) CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGG 8 0.2 No Hit GCACCAGTAGTCTAGTGGTAGAATAGTACCTGGAATTCTCGGGTGCCAAG 8 0.2 No Hit ATAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAACT 8 0.2 RNA PCR Primer, Index 1 (100% over 25bp) CAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTG 8 0.2 No Hit CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGGAATTCTCG 8 0.2 No Hit ACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTCT 8 0.2 No Hit GCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAA 8 0.2 RNA PCR Primer, Index 1 (100% over 23bp) CAGGGTTCGTTTCCCTGGATGCGCACCATGGAATTCTCGGGTGCCAAGGA 8 0.2 RNA PCR Primer, Index 1 (100% over 22bp) NCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 7 0.17500000000000002 No Hit AGAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTG 7 0.17500000000000002 No Hit ATTCTCGGGTGCCAAGGAACTCCAGTCACAGTCAAATCTCGTATGCCGTC 7 0.17500000000000002 RNA PCR Primer, Index 13 (100% over 50bp) CCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTG 7 0.17500000000000002 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGTGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit CACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAACT 6 0.15 RNA PCR Primer, Index 1 (100% over 25bp) NGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 6 0.15 No Hit GCACCAGTGGTCTAGTGGTAGAATAGTATGGAATTCTCGGGTGCCAAGGA 6 0.15 RNA PCR Primer, Index 1 (100% over 22bp) TCCGTCGTAGTCTAGGTGGTTAGGATACTCTGGAATTCTCGGGTGCCAAG 6 0.15 No Hit TTCGGACCAGGCTTCATTCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 6 0.15 RNA PCR Primer, Index 1 (100% over 29bp) AGTTACTAATTCATGATCTGGCTGGAATTCTCGGGTGCCAAGGAACTCCA 6 0.15 RNA PCR Primer, Index 1 (100% over 28bp) GACACGACTCTCGGCAACGTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 6 0.15 RNA PCR Primer, Index 1 (100% over 31bp) TCCACAGGCTTTCTTGAACTGTGGAATTCTCGGGTGCCAAGGAACTCCAG 6 0.15 RNA PCR Primer, Index 1 (100% over 29bp) ACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAACT 6 0.15 RNA PCR Primer, Index 1 (100% over 25bp) ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGC 6 0.15 No Hit ACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCC 6 0.15 No Hit ATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAA 6 0.15 RNA PCR Primer, Index 1 (100% over 23bp) CATCGAGTAGACCTTGTTATTGTGAGAATAAATGGAATTCTCGGGTGCCA 5 0.125 No Hit CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCTGGAATTCTCGGG 5 0.125 No Hit TATTCTGGTGTCCTAGGCGTAGAGGAACCTGGAATTCTCGGGTGCCAAGG 5 0.125 Illumina Small RNA Adapter 2 (100% over 21bp) GGGGATGTAGCTCAGATGGTAGATGGAATTCTCGGGTGCCAAGGAACTCC 5 0.125 RNA PCR Primer, Index 1 (100% over 27bp) GAAGTCCTCGTGTTGCATTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA 5 0.125 RNA PCR Primer, Index 1 (100% over 28bp) TGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAA 5 0.125 No Hit CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGG 5 0.125 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTAATCCTGGAATTC 5 0.125 No Hit AGCTGAGGCATCCTAACGAACGAACGATTTGAATGGAATTCTCGGGTGCC 5 0.125 No Hit TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTGGAATTCTCGGGTGC 5 0.125 No Hit TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGG 5 0.125 No Hit CCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) 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 0.05 0.0 0.0 0.0 2 0.0 0.05 0.0 0.0 0.0 3 0.0 0.05 0.0 0.0 0.0 4 0.0 0.05 0.0 0.0 0.0 5 0.0 0.05 0.0 0.0 0.0 6 0.0 0.075 0.0 0.0 0.0 7 0.0 0.1 0.0 0.0 0.0 8 0.0 0.1 0.0 0.0 0.0 9 0.0 0.15 0.0 0.0 0.0 10-11 0.0 0.2375 0.0 0.0 0.0 12-13 0.0 0.3125 0.0 0.0 0.0 14-15 0.0 0.5125 0.0 0.0 0.0 16-17 0.0 1.35 0.0 0.0 0.0 18-19 0.0 2.375 0.0 0.0 0.0 20-21 0.0 4.4875 0.0 0.0 0.0 22-23 0.0 11.825 0.0 0.0 0.0 24-25 0.0 22.225 0.0 0.0 0.0 26-27 0.0 34.275 0.0 0.0 0.0 28-29 0.0 44.425 0.0 0.0 0.0 30-31 0.0 53.8125 0.0 0.0 0.0 32-33 0.0 63.375 0.0 0.0 0.0 34-35 0.0 75.525 0.0 0.0 0.0 36-37 0.0 83.375 0.0 0.0 0.0 38-39 0.0 87.4875 0.0 0.0 0.0 40-41 0.0 89.8625 0.0 0.0 0.0 42-43 0.0 92.48750000000001 0.0 0.0 0.0 44-45 0.0 93.76249999999999 0.0 0.0 0.0 46-47 0.0 94.15 0.0 0.0 0.0 48-49 0.0 94.2625 0.0 0.0 0.0 50-51 0.0 94.275 0.0 0.0 0.0 52-53 0.0 94.2875 0.0 0.0 0.0 54-55 0.0 94.3125 0.0 0.0 0.0 56-57 0.0 94.325 0.0 0.0 0.0 58-59 0.0 94.325 0.0 0.0 0.0 60-61 0.0 94.325 0.0 0.0 0.0 62-63 0.0 94.325 0.0 0.0 0.0 64-65 0.0 94.325 0.0 0.0 0.0 66-67 0.0 94.325 0.0 0.0 0.0 68-69 0.0 94.325 0.0 0.0 0.0 70-71 0.0 94.325 0.0 0.0 0.0 72-73 0.0 94.325 0.0 0.0 0.0 74-75 0.0 94.325 0.0 0.0 0.0 76-77 0.0 94.3375 0.0 0.0 0.0 78-79 0.0 94.35 0.0 0.0 0.0 80-81 0.0 94.35 0.0 0.0 0.0 82-83 0.0125 94.35 0.0 0.0 0.0 84-85 0.025 94.375 0.0 0.0 0.0 86-87 0.025 94.375 0.0 0.0 0.0 88-89 0.025 94.375 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGATTG 35 1.364242E-10 101.26667 1 TCGGACC 15 4.7401295E-4 101.26666 1 GTAGACC 20 1.5442722E-5 94.9375 7 TTGTAGT 35 2.3283064E-10 94.9375 5 AGTAGAC 20 1.5442722E-5 94.9375 6 GGACCAG 20 1.5442722E-5 94.9375 3 GGATTGT 35 2.3283064E-10 94.9375 2 CGGACCA 20 1.5442722E-5 94.9375 2 GATTGTA 35 2.3283064E-10 94.9375 3 GAGTAGA 20 1.5442722E-5 94.9375 5 ATTGTAG 35 2.3283064E-10 94.9375 4 AGGCTTC 20 1.5442722E-5 94.9375 8 TGTAGTT 35 2.3283064E-10 94.9375 6 GGCTTCA 20 1.5442722E-5 94.9375 9 CGAGTAG 20 1.5442722E-5 94.9375 4 CAGGCTT 20 1.5442722E-5 94.9375 7 AGACCTT 20 1.5442722E-5 94.9375 9 TCGAGTA 20 1.5442722E-5 94.9375 3 GACCAGG 20 1.5442722E-5 94.9375 4 TAGACCT 20 1.5442722E-5 94.9375 8 >>END_MODULE Rejected 765726 READS because READLEN < 1 Read 765726 spots for SRR8846494.sra Written 765726 spots for SRR8846494.sra Rejected 765726 READS because READLEN < 1 Read 765726 spots for SRR8846494.sra Written 765726 spots for SRR8846494.sra Rejected 765726 READS because READLEN < 1 Read 765726 spots for SRR8846494.sra Written 765726 spots for SRR8846494.sra Rejected 765726 READS because READLEN < 1 Read 765726 spots for SRR8846494.sra Written 765726 spots for SRR8846494.sra Rejected 765726 READS because READLEN < 1 Read 765726 spots for SRR8846494.sra Written 765726 spots for SRR8846494.sra Rejected 765726 READS because READLEN < 1 Read 765726 spots for SRR8846494.sra Written 765726 spots for SRR8846494.sra Rejected 765726 READS because READLEN < 1 Read 765726 spots for SRR8846494.sra Written 765726 spots for SRR8846494.sra Rejected 765726 READS because READLEN < 1 Read 765726 spots for SRR8846494.sra Written 765726 spots for SRR8846494.sra Rejected 765726 READS because READLEN < 1 Read 765726 spots for SRR8846494.sra Written 765726 spots for SRR8846494.sra Rejected 765726 READS because READLEN < 1 Read 765726 spots for SRR8846494.sra Written 765726 spots for SRR8846494.sra Rejected 765726 READS because READLEN < 1 Read 765726 spots for SRR8846494.sra Written 765726 spots for SRR8846494.sra Rejected 765726 READS because READLEN < 1 Read 765726 spots for SRR8846494.sra Written 765726 spots for SRR8846494.sra Rejected 765726 READS because READLEN < 1 Read 765726 spots for SRR8846494.sra Written 765726 spots for SRR8846494.sra Rejected 765745 READS because READLEN < 1 Read 765745 spots for SRR8846494.sra Written 765745 spots for SRR8846494.sra Rejected 765726 READS because READLEN < 1 Read 765726 spots for SRR8846494.sra Written 765726 spots for SRR8846494.sra Rejected 765726 READS because READLEN < 1 Read 765726 spots for SRR8846494.sra Written 765726 spots for SRR8846494.sra Rejected 765726 READS because READLEN < 1 Read 765726 spots for SRR8846494.sra Written 765726 spots for SRR8846494.sra Rejected 765726 READS because READLEN < 1 Read 765726 spots for SRR8846494.sra Written 765726 spots for SRR8846494.sra Rejected 765726 READS because READLEN < 1 Read 765726 spots for SRR8846494.sra Written 765726 spots for SRR8846494.sra Rejected 765726 READS because READLEN < 1 Read 765726 spots for SRR8846494.sra Written 765726 spots for SRR8846494.sra SRR ids: ['SRR8846494.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_hu8tq88f SRR8846494.sra spots: 15314539 blocks: [[1, 765726], [765727, 1531452], [1531453, 2297178], [2297179, 3062904], [3062905, 3828630], [3828631, 4594356], [4594357, 5360082], [5360083, 6125808], [6125809, 6891534], [6891535, 7657260], [7657261, 8422986], [8422987, 9188712], [9188713, 9954438], [9954439, 10720164], [10720165, 11485890], [11485891, 12251616], [12251617, 13017342], [13017343, 13783068], [13783069, 14548794], [14548795, 15314539]] SRR8846494 file size 3672333 SRR8846494 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 SRR8846494 SRR8846494_1.fastq Input file: SRR8846494_1.fastq trimmed: SRR8846494-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 22:00:32 2024 >> started Sun Dec 8 22:01:11 2024 >> done (39.407s) 15314539 reads processed; of these: 240 ( 0.00%) short reads filtered out after trimming by size control 43 ( 0.00%) empty reads filtered out after trimming by size control 15314256 (100.00%) reads available; of these: 3225863 (21.06%) trimmed reads available after processing 12088393 (78.94%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 45 0.00% 19 26 0.00% 20 29 0.00% 21 37 0.00% 22 42 0.00% 23 48 0.00% 24 70 0.00% 25 83 0.00% 26 98 0.00% 27 176 0.00% 28 241 0.00% 29 228 0.00% 30 200 0.00% 31 164 0.00% 32 200 0.00% 33 119 0.00% 34 129 0.00% 35 92 0.00% 36 116 0.00% 37 86 0.00% 38 116 0.00% 39 144 0.00% 40 124 0.00% 41 143 0.00% 42 121 0.00% 43 134 0.00% 44 133 0.00% 45 156 0.00% 46 124 0.00% 47 123 0.00% 48 117 0.00% 49 127 0.00% 50 115 0.00% 51 135 0.00% 52 108 0.00% 53 133 0.00% 54 139 0.00% 55 133 0.00% 56 189 0.00% 57 160 0.00% 58 247 0.00% 59 313 0.00% 60 449 0.00% 61 814 0.01% 62 1184 0.01% 63 1316 0.01% 64 1933 0.01% 65 3209 0.02% 66 8437 0.06% 67 44202 0.29% 68 50439 0.33% 69 36746 0.24% 70 29601 0.19% 71 32371 0.21% 72 16652 0.11% 73 6197 0.04% 74 6099 0.04% 75 4070 0.03% 76 3307 0.02% 77 3543 0.02% 78 3751 0.02% 79 4236 0.03% 80 4910 0.03% 81 5775 0.04% 82 7808 0.05% 83 7654 0.05% 84 8133 0.05% 85 9088 0.06% 86 10111 0.07% 87 13779 0.09% 88 26126 0.17% 89 39126 0.26% 90 50663 0.33% 91 56006 0.37% 92 70056 0.46% 93 106648 0.70% 94 148877 0.97% 95 284290 1.86% 96 374863 2.45% 97 378456 2.47% 98 529682 3.46% 99 539668 3.52% 100 290125 1.89% 101 12088393 78.94% 15314256 reads passed initial QC criterion=sequence-density sequence-density=94.51 sequence-density-rank=1 fanout-score=31.24 fanout-score-rank=2 prefix-density=94.96 prefix-fanout=31.1 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTCAAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA criterion=fanout-score sequence-density=1.52 sequence-density-rank=4 fanout-score=65.38 fanout-score-rank=1 prefix-density=98.51 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTCAAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA -o SRR8846494 - Input file: STDIN trimmed: SRR8846494-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 Sun Dec 8 22:03:51 2024 >> started Sun Dec 8 22:05:03 2024 >> done (72.255s) 14991851 reads processed; of these: 306620 ( 2.05%) short reads filtered out after trimming by size control 9166 ( 0.06%) empty reads filtered out after trimming by size control 14676065 (97.89%) reads available; of these: 14195722 (96.73%) trimmed reads available after processing 480343 ( 3.27%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 97947 0.67% 19 190770 1.30% 20 198347 1.35% 21 807729 5.50% 22 448605 3.06% 23 568749 3.88% 24 1773470 12.08% 25 615411 4.19% 26 822077 5.60% 27 675760 4.60% 28 847604 5.78% 29 672426 4.58% 30 677422 4.62% 31 485547 3.31% 32 1090071 7.43% 33 863308 5.88% 34 737557 5.03% 35 580226 3.95% 36 647736 4.41% 37 230332 1.57% 38 185608 1.26% 39 176719 1.20% 40 172249 1.17% 41 231801 1.58% 42 205964 1.40% 43 69963 0.48% 44 61473 0.42% 45 25988 0.18% 46 12342 0.08% 47 5674 0.04% 48 4833 0.03% 49 2870 0.02% 50 1758 0.01% 51 1599 0.01% 52 842 0.01% 53 641 0.00% 54 792 0.01% 55 236 0.00% 56 327 0.00% 57 181 0.00% 58 228 0.00% 59 280 0.00% 60 411 0.00% 61 758 0.01% 62 1073 0.01% 63 1181 0.01% 64 1773 0.01% 65 2988 0.02% 66 8077 0.06% 67 43071 0.29% 68 49194 0.34% 69 35720 0.24% 70 28623 0.20% 71 31240 0.21% 72 15015 0.10% 73 4677 0.03% 74 2957 0.02% 75 1917 0.01% 76 1867 0.01% 77 2725 0.02% 78 2029 0.01% 79 2084 0.01% 80 2545 0.02% 81 1977 0.01% 82 1688 0.01% 83 1864 0.01% 84 1327 0.01% 85 1268 0.01% 86 1038 0.01% 87 878 0.01% 88 843 0.01% 89 864 0.01% 90 796 0.01% 91 847 0.01% 92 954 0.01% 93 1103 0.01% 94 1533 0.01% 95 2310 0.02% 96 2936 0.02% 97 3805 0.03% 98 6160 0.04% 99 6980 0.05% 100 8955 0.06% 101 194552 1.33% criterion=sequence-density sequence-density=3.72 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=7 prefix-density=0.00 prefix-fanout=1.0 sequence=CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATTCAAGA criterion=fanout-score sequence-density=0.03 sequence-density-rank=26 fanout-score=13.11 fanout-score-rank=1 prefix-density=0.31 prefix-fanout=1.1 sequence=GGCGGATTGCTCGAGCTGCTCACGCGGCGAGAGCGGGTCGCCGCGTGCCGGCCGGGGGACGGACCGGGAGTCGCCCCTTCGGGGGCTTTCCCCGAGCGCTGAACAGTCGACTCAGAACTGGTACGGACAAGGGGAATCCGACTGTTTAATTAAAACAAAGCATTGCG Started job on | Dec 08 22:07:19 Started mapping on | Dec 08 22:07:19 Finished on | Dec 08 22:13:49 Mapping speed, Million of reads per hour | 138.45 Number of input reads | 14998470 Average input read length | 32 UNIQUE READS: Uniquely mapped reads number | 2537674 Uniquely mapped reads % | 16.92% Average mapped length | 26.61 Number of splices: Total | 29245 Number of splices: Annotated (sjdb) | 15835 Number of splices: GT/AG | 26462 Number of splices: GC/AG | 2179 Number of splices: AT/AC | 4 Number of splices: Non-canonical | 600 Mismatch rate per base, % | 0.13% Deletion rate per base | 0.00% Deletion average length | 1.34 Insertion rate per base | 0.00% Insertion average length | 1.02 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 6625414 % of reads mapped to multiple loci | 44.17% Number of reads mapped to too many loci | 4824331 % of reads mapped to too many loci | 32.17% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 6.16% % of reads unmapped: other | 0.58% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 5835382 5835382 5835382 N_multimapping 6625414 6625414 6625414 N_noFeature 1583620 1769768 2337839 N_ambiguous 40278 26154 588 UnstrandedReadsAssigned:913776 PositiveStrandReadsAssigned:741752 NegativeStrandReadsAssigned:199247 Dataset is classified unstranded MeadianReadLen=29 20thPercentileLength=24 echo kmer=19 SRR8846494 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: SRR8846494-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 14,998,470 reads, 4,087,616 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,087 rounds 52973 SRR8846494.ke.tsv 35125 SRR8846494.se.tsv 88098 total ==> SRR8846494.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 73.3424 10.8999 KQK14071 474 375 0 0 ==> SRR8846494.se.tsv <== BRADI_1g14170v3 70 BRADI_1g53295v3 1 BRADI_1g59795v3 3 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 27 BRADI_1g74790v3 35 BRADI_1g09890v3 0 BRADI_1g77505v3 4 BRADI_1g48960v3 0 SRR8846494 completed mapping pipeline successfully