Starting /dee2/code/volunteer_pipeline.sh SRR8846555 current disk space = 1527829299200 free memory = 1530828540 SRR8846555 SRAfilesize 0f748358166592736a1a3a4fa2b7953d SRR8846555.sra SRR8846555.sra file validated SRR8846555 is single end SRR8846555 is conventional basespace SRR8846555 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8846555_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 31.2855 34.0 33.0 34.0 30.0 34.0 2 32.90325 34.0 33.0 34.0 31.0 34.0 3 33.08 34.0 33.0 34.0 32.0 34.0 4 33.2065 34.0 33.0 34.0 32.0 34.0 5 33.2755 34.0 33.0 34.0 33.0 34.0 6 36.939 38.0 37.0 38.0 36.0 38.0 7 37.27925 38.0 38.0 38.0 36.0 38.0 8 37.42325 38.0 38.0 38.0 37.0 38.0 9 37.49575 38.0 38.0 38.0 37.0 38.0 10-11 37.46425 38.0 38.0 38.0 37.0 38.0 12-13 37.475375 38.0 38.0 38.0 38.0 38.0 14-15 37.568375 38.0 38.0 38.0 37.5 38.0 16-17 37.4795 38.0 38.0 38.0 37.5 38.0 18-19 37.473875 38.0 38.0 38.0 37.5 38.0 20-21 37.492999999999995 38.0 38.0 38.0 38.0 38.0 22-23 37.425124999999994 38.0 38.0 38.0 37.0 38.0 24-25 37.52225 38.0 38.0 38.0 37.5 38.0 26-27 37.437875 38.0 38.0 38.0 37.5 38.0 28-29 37.443625 38.0 38.0 38.0 37.0 38.0 30-31 37.40675 38.0 38.0 38.0 37.0 38.0 32-33 37.3655 38.0 38.0 38.0 37.0 38.0 34-35 37.167125 38.0 38.0 38.0 37.0 38.0 36-37 37.076625 38.0 38.0 38.0 36.0 38.0 38-39 36.95675 38.0 38.0 38.0 35.5 38.0 40-41 37.019375 38.0 38.0 38.0 36.0 38.0 42-43 36.955875 38.0 38.0 38.0 36.0 38.0 44-45 37.086375000000004 38.0 38.0 38.0 36.0 38.0 46-47 37.084875 38.0 38.0 38.0 36.0 38.0 48-49 37.1015 38.0 38.0 38.0 36.0 38.0 50-51 37.054874999999996 38.0 38.0 38.0 36.0 38.0 52-53 37.082375 38.0 38.0 38.0 36.0 38.0 54-55 36.97125 38.0 38.0 38.0 36.0 38.0 56-57 36.905625 38.0 38.0 38.0 35.5 38.0 58-59 36.64 38.0 38.0 38.0 34.0 38.0 60-61 36.21225 38.0 37.0 38.0 33.0 38.0 62-63 35.863375 38.0 37.0 38.0 29.0 38.0 64-65 35.6365 38.0 36.5 38.0 29.0 38.0 66-67 35.176375 38.0 36.0 38.0 28.0 38.0 68-69 35.115125 38.0 36.5 38.0 28.0 38.0 70-71 34.727625 38.0 36.5 38.0 26.5 38.0 72-73 34.360875 38.0 36.5 38.0 25.0 38.0 74-75 34.09675 38.0 36.0 38.0 20.5 38.0 76-77 33.878625 38.0 36.0 38.0 20.0 38.0 78-79 33.546625000000006 38.0 35.0 38.0 16.0 38.0 80-81 33.4935 38.0 35.0 38.0 15.5 38.0 82-83 33.416624999999996 38.0 34.5 38.0 15.0 38.0 84-85 33.341125000000005 38.0 34.0 38.0 15.0 38.0 86-87 33.342875 38.0 34.5 38.0 15.0 38.0 88-89 33.718875 38.0 36.0 38.0 15.0 38.0 90-91 33.287875 38.0 35.0 38.0 15.0 38.0 92-93 32.920875 38.0 34.5 38.0 14.5 38.0 94-95 31.649875 38.0 34.0 38.0 2.0 38.0 96-97 29.298000000000002 38.0 26.5 38.0 2.0 38.0 98-99 26.325 37.0 8.5 38.0 2.0 38.0 100-101 22.666125 31.5 2.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 4 1.0 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 1.0 16 1.0 17 0.0 18 0.0 19 5.0 20 5.0 21 3.0 22 8.0 23 12.0 24 31.0 25 79.0 26 62.0 27 34.0 28 36.0 29 43.0 30 59.0 31 94.0 32 134.0 33 185.0 34 323.0 35 566.0 36 922.0 37 1396.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 23.72746553552492 31.627783669141042 23.515376458112407 21.12937433722163 2 22.175 29.7 22.7 25.424999999999997 3 26.025 21.4 25.0 27.575 4 30.3 25.55 20.025000000000002 24.125 5 31.424999999999997 27.800000000000004 18.125 22.650000000000002 6 24.275 28.299999999999997 26.150000000000002 21.275 7 34.4 24.224999999999998 19.6 21.775 8 24.5 22.425 31.924999999999997 21.15 9 25.974999999999998 30.575000000000003 21.525 21.925 10-11 30.062499999999996 26.437500000000004 22.225 21.275 12-13 23.825 22.787499999999998 22.975 30.412499999999998 14-15 23.4125 34.675 23.825 18.087500000000002 16-17 25.45 26.525 30.0875 17.9375 18-19 28.799999999999997 24.7875 24.825 21.587500000000002 20-21 22.6875 25.587500000000002 27.900000000000002 23.825 22-23 28.575 26.5375 28.6375 16.25 24-25 26.825 25.9875 28.287499999999998 18.9 26-27 34.637499999999996 25.75 23.849999999999998 15.7625 28-29 19.9875 33.575 26.150000000000002 20.2875 30-31 22.412499999999998 19.950000000000003 39.1625 18.475 32-33 28.787499999999998 18.25 30.1875 22.775000000000002 34-35 32.425 17.025000000000002 28.499999999999996 22.05 36-37 41.275 14.3625 25.637500000000003 18.725 38-39 32.5 17.2125 28.0625 22.225 40-41 29.525000000000002 19.375 20.200000000000003 30.9 42-43 31.2 29.862499999999997 18.775 20.1625 44-45 38.975 21.912499999999998 14.7375 24.375 46-47 26.650000000000002 31.162499999999998 14.7375 27.450000000000003 48-49 23.474999999999998 25.55 19.2625 31.7125 50-51 22.8 22.112499999999997 16.775000000000002 38.3125 52-53 22.3625 34.6875 13.25 29.7 54-55 17.549999999999997 26.650000000000002 21.05 34.75 56-57 15.8875 34.575 12.6375 36.9 58-59 17.3375 34.2125 17.3375 31.112499999999997 60-61 21.4125 35.612500000000004 15.3375 27.6375 62-63 21.0 29.349999999999998 23.7625 25.887500000000003 64-65 15.2 33.85 25.4 25.55 66-67 18.087500000000002 25.55 28.287499999999998 28.075 68-69 21.675 26.7625 24.525 27.037499999999998 70-71 20.3125 27.125 30.1375 22.425 72-73 25.674999999999997 18.337500000000002 31.7875 24.2 74-75 20.0 14.524999999999999 30.0 35.475 76-77 21.8625 13.4125 40.475 24.25 78-79 18.375 9.7375 39.137499999999996 32.75 80-81 19.287499999999998 10.25 37.6125 32.85 82-83 22.7375 11.0 43.05 23.2125 84-85 18.9625 14.5875 37.425000000000004 29.025000000000002 86-87 20.075000000000003 22.900000000000002 36.5375 20.4875 88-89 15.3625 41.475 27.6875 15.475 90-91 10.65 49.8125 25.3 14.2375 92-93 11.862499999999999 58.475 19.9125 9.75 94-95 8.2125 69.0375 15.375 7.375 96-97 6.612500000000001 76.1625 12.0625 5.1625 98-99 5.325 82.0375 8.737499999999999 3.9 100-101 3.925 85.46249999999999 6.575 4.0375000000000005 >>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 0.0 31 0.5 32 1.0 33 9.0 34 16.0 35 21.5 36 32.5 37 34.0 38 34.0 39 83.5 40 112.5 41 144.0 42 228.5 43 286.0 44 375.0 45 391.5 46 393.0 47 405.0 48 317.5 49 267.5 50 222.5 51 166.0 52 130.5 53 93.0 54 68.5 55 68.5 56 50.5 57 16.5 58 10.0 59 7.5 60 6.0 61 5.0 62 1.5 63 0.5 64 0.0 65 0.0 66 0.0 67 0.0 68 0.0 69 0.0 70 0.0 71 0.0 72 0.0 73 0.0 74 0.0 75 0.0 76 0.5 77 0.5 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 5.7 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 59.95 #Duplication Level Percentage of deduplicated Percentage of total 1 84.57047539616347 50.7 2 7.9649708090075055 9.55 3 2.5020850708924103 4.5 4 1.292743953294412 3.1 5 0.79232693911593 2.375 6 0.45871559633027525 1.6500000000000001 7 0.4170141784820684 1.7500000000000002 8 0.2919099249374479 1.4000000000000001 9 0.2085070892410342 1.125 >10 1.3344453711426187 17.025000000000002 >50 0.12510425354462051 4.3 >100 0.041701417848206836 2.5250000000000004 >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 101 2.5250000000000004 RNA PCR Primer, Index 1 (100% over 29bp) AATTCTCGGGTGCCAAGGAACTCCAGTCACACAGTGATCTCGTATGCCGT 63 1.575 RNA PCR Primer, Index 5 (100% over 50bp) ATATATTTCAAGTTATTTCGGATCTTGGAATTCTCGGGTGCCAAGGAACT 56 1.4000000000000001 RNA PCR Primer, Index 1 (100% over 25bp) AGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 53 1.325 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 45 1.125 No Hit TCTCGGGTGCCAAGGAACTCCAGTCACACAGTGATCTCGTATGCCGTCTT 41 1.0250000000000001 RNA PCR Primer, Index 5 (100% over 50bp) CTCGGGTGCCAAGGAACTCCAGTCACACAGTGATCTCGTATGCCGTCTTC 37 0.9249999999999999 RNA PCR Primer, Index 5 (100% over 50bp) GGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 34 0.8500000000000001 RNA PCR Primer, Index 1 (100% over 22bp) GACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 32 0.8 RNA PCR Primer, Index 1 (100% over 23bp) TTCTCGGGTGCCAAGGAACTCCAGTCACACAGTGATCTCGTATGCCGTCT 31 0.775 RNA PCR Primer, Index 5 (100% over 50bp) CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 30 0.75 RNA PCR Primer, Index 1 (100% over 28bp) TCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 29 0.7250000000000001 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 27 0.675 No Hit TTCGGACCAGGCTTCATTCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 26 0.65 RNA PCR Primer, Index 1 (100% over 29bp) CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 25 0.625 Illumina Small RNA Adapter 2 (100% over 21bp) GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 24 0.6 Illumina Small RNA Adapter 2 (100% over 21bp) AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 23 0.575 Illumina Small RNA Adapter 2 (100% over 21bp) CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 22 0.5499999999999999 No Hit ATTCTCGGGTGCCAAGGAACTCCAGTCACACAGTGATCTCGTATGCCGTC 21 0.525 RNA PCR Primer, Index 5 (100% over 50bp) GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 21 0.525 No Hit TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 18 0.44999999999999996 No Hit GACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAAC 17 0.42500000000000004 RNA PCR Primer, Index 1 (100% over 24bp) GACACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACT 17 0.42500000000000004 RNA PCR Primer, Index 1 (100% over 25bp) AAGGGTGCTGAGAATACTTTGAATCTGACATGGAATTCTCGGGTGCCAAG 15 0.375 No Hit TAATTCATGATCTGGCATGTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 15 0.375 RNA PCR Primer, Index 1 (100% over 31bp) TCCTGTGGATGAGAAGGCATTTATATTCTGATGATATGGAATTCTCGGGT 15 0.375 No Hit AAGGGTGCTGAGAATACTTTGAATCTGACACTGGAATTCTCGGGTGCCAA 15 0.375 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 13 0.325 No Hit ACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCC 13 0.325 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 12 0.3 Illumina Small RNA Adapter 2 (100% over 21bp) ATATATTTCAAGTTATTTCGGATCTGGAATTCTCGGGTGCCAAGGAACTC 12 0.3 RNA PCR Primer, Index 1 (100% over 26bp) GCCCACCCCAAGATGAGTGCTCTCTCTGGAATTCTCGGGTGCCAAGGAAC 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 24bp) CATCGAGTAGACCTTGTTATTGTGAGAATAAATGGAATTCTCGGGTGCCA 10 0.25 No Hit GCACCAGTGGTCTAGTGGTAGAATAGTACCTGGAATTCTCGGGTGCCAAG 10 0.25 No Hit NCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 10 0.25 RNA PCR Primer, Index 1 (100% over 29bp) CATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAAC 10 0.25 RNA PCR Primer, Index 1 (100% over 24bp) CACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAACT 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 25bp) TCCACAGGCTTTCTTGAACTGTGGAATTCTCGGGTGCCAAGGAACTCCAG 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 29bp) TGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAA 9 0.22499999999999998 No Hit CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTC 9 0.22499999999999998 No Hit CCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACT 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 25bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 8 0.2 No Hit TCGGATAACCGTAGTAATTCTAGAGCTAATACGTGGAATTCTCGGGTGCC 8 0.2 No Hit CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 8 0.2 RNA PCR Primer, Index 1 (100% over 23bp) TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACAGTGATCTCGTATGC 8 0.2 RNA PCR Primer, Index 5 (100% over 50bp) CACGACTCTCGGCAACGGATATCTCGTGGAATTCTCGGGTGCCAAGGAAC 8 0.2 RNA PCR Primer, Index 1 (100% over 24bp) GCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCC 8 0.2 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTATGGAATTCTCGGGTGCCAA 8 0.2 No Hit TCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 26bp) TAATTCATGATCTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 34bp) GACACGACTCTCGGCAACGGATATCTCGGCTGGAATTCTCGGGTGCCAAG 7 0.17500000000000002 No Hit ATTGTATCCTTAACCATTTCTTTTTTGGAATTCTCGGGTGCCAAGGAACT 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 25bp) CCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTG 7 0.17500000000000002 No Hit CTCTGATGATGATCAAACTAATACTTTCGTTCTTCTGGAATTCTCGGGTG 7 0.17500000000000002 No Hit CACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACTCC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 27bp) CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGG 7 0.17500000000000002 No Hit GCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 23bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTGGAATTCTC 7 0.17500000000000002 No Hit CGGATAACCGTAGTAATTCTAGAGCTAATACGTGGAATTCTCGGGTGCCA 6 0.15 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATACTCTGGAATTCTCGGGTGCCAAG 6 0.15 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTTGGAATTCT 6 0.15 No Hit NTCGGGTGCCAAGGAACTCCAGTCACACAGTGATCTCGTATGCCGTCTTC 6 0.15 RNA PCR Primer, Index 5 (98% over 50bp) GATAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) TCTCGGACCAGGCTTCATTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 6 0.15 RNA PCR Primer, Index 1 (100% over 29bp) CAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTG 6 0.15 No Hit AACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGT 6 0.15 RNA PCR Primer, Index 1 (100% over 30bp) CAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTC 6 0.15 RNA PCR Primer, Index 1 (100% over 26bp) TCGCTTGGTGCAGATCGGGACTGGAATTCTCGGGTGCCAAGGAACTCCAG 6 0.15 RNA PCR Primer, Index 1 (100% over 29bp) CACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGC 6 0.15 No Hit GATAACCGTAGTAATTCTAGAGCTAATTGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) ATAACCGTAGTAATTCTAGAGCTAATTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) CATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGCC 5 0.125 No Hit TCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) AGTTACTAATTCATGATCTGGCTGGAATTCTCGGGTGCCAAGGAACTCCA 5 0.125 RNA PCR Primer, Index 1 (100% over 28bp) GCACCAGTAGTCTAGTGGTAGAATAGTATGGAATTCTCGGGTGCCAAGGA 5 0.125 RNA PCR Primer, Index 1 (100% over 22bp) TCGTGACCCTGACCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACA 5 0.125 RNA PCR Primer, Index 5 (100% over 36bp) TCCCGTGCTGTAAAATAACTGATTTGCCTATCTGATCTGGAATTCTCGGG 5 0.125 No Hit CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGGAATTCTCG 5 0.125 No Hit CACGACTCTCGGCAACGGATGGAATTCTCGGGTGCCAAGGAACTCCAGTC 5 0.125 RNA PCR Primer, Index 1 (100% over 31bp) ACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACTCCA 5 0.125 RNA PCR Primer, Index 1 (100% over 28bp) ATATTGGGTAGGTTGTGGTATTTCATTGCTGGAATTCTCGGGTGCCAAGG 5 0.125 Illumina Small RNA Adapter 2 (100% over 21bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGTGGAATTCTCGGGTGCC 5 0.125 No Hit TGTCGTGCCAATTCAACATAAACCCCTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) TCAAAAGAGGAAAGGCTTGCGGTGGAATTCTCGGGTGCCAAGGAACTCCA 5 0.125 RNA PCR Primer, Index 1 (100% over 28bp) ATTGTATCCTTAACCATTTCTTTTTGGAATTCTCGGGTGCCAAGGAACTC 5 0.125 RNA PCR Primer, Index 1 (100% over 26bp) CATCGAGTAGACCTTGTTATTGTGAGAATTAAAAATGGAATTCTCGGGTG 5 0.125 No Hit CGGATAACCGTAGTAATTCTAGAGCTAATACTGGAATTCTCGGGTGCCAA 5 0.125 No Hit ATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) >>END_MODULE >>Adapter Content fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.3 0.0 0.0 0.0 2 0.0 0.35 0.0 0.0 0.0 3 0.0 0.375 0.0 0.0 0.0 4 0.0 0.4 0.0 0.0 0.0 5 0.0 0.45 0.0 0.0 0.0 6 0.0 0.45 0.0 0.0 0.0 7 0.0 0.45 0.0 0.0 0.0 8 0.0 0.45 0.0 0.0 0.0 9 0.0 0.625 0.0 0.0 0.0 10-11 0.0 0.8 0.0 0.0 0.0 12-13 0.0 0.925 0.0 0.0 0.0 14-15 0.0 1.3624999999999998 0.0 0.0 0.0 16-17 0.0 2.2375 0.0 0.0 0.0 18-19 0.0 3.8125 0.0 0.0 0.0 20-21 0.0 6.9375 0.0 0.0 0.0 22-23 0.0 16.575 0.0 0.0 0.0 24-25 0.0 29.0375 0.0 0.0 0.0 26-27 0.0 43.8 0.0 0.0 0.0 28-29 0.0 51.6375 0.0 0.0 0.0 30-31 0.0 61.5 0.0 0.0 0.0 32-33 0.0 69.4125 0.0 0.0 0.0 34-35 0.0 76.86250000000001 0.0 0.0 0.0 36-37 0.0 83.35 0.0 0.0 0.0 38-39 0.0 87.2125 0.0 0.0 0.0 40-41 0.0 89.1125 0.0 0.0 0.0 42-43 0.0 90.6625 0.0 0.0 0.0 44-45 0.0 91.48750000000001 0.0 0.0 0.0 46-47 0.0 91.7125 0.0 0.0 0.0 48-49 0.0 91.8375 0.0 0.0 0.0 50-51 0.0 91.8875 0.0 0.0 0.0 52-53 0.0 91.9125 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 92.025 0.0 0.0 0.0 84-85 0.0 92.125 0.0 0.0 0.0 86-87 0.0 92.125 0.0 0.0 0.0 88-89 0.0 92.125 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GTAGACC 25 3.8440157E-7 94.93751 7 AGTAGAC 25 3.8440157E-7 94.93751 6 GAGTAGA 25 3.8440157E-7 94.93751 5 CGAGTAG 25 3.8440157E-7 94.93751 4 AGACCTT 25 3.8440157E-7 94.93751 9 TCGAGTA 25 3.8440157E-7 94.93751 3 TAGACCT 25 3.8440157E-7 94.93751 8 CATCGAG 30 7.653234E-7 84.388885 1 ATCGAGT 30 1.1382763E-6 79.11458 2 TGAGAAT 25 2.5915197E-5 47.468754 22-23 TGTGAGA 25 2.5915197E-5 47.468754 20-21 TTGTTAT 25 2.5915197E-5 47.468754 14-15 TTATTGT 25 2.5915197E-5 47.468754 16-17 CCTTGTT 25 2.5915197E-5 47.468754 12-13 TATTGTG 25 2.5915197E-5 47.468754 18-19 TGTTATT 25 2.5915197E-5 47.468754 14-15 GTGAGAA 25 2.5915197E-5 47.468754 22-23 ATTGTGA 25 2.5915197E-5 47.468754 18-19 CTTGTTA 25 2.5915197E-5 47.468754 12-13 ACCTTGT 25 2.5915197E-5 47.468754 10-11 >>END_MODULE Rejected 692287 READS because READLEN < 1 Read 692287 spots for SRR8846555.sra Written 692287 spots for SRR8846555.sra Rejected 692287 READS because READLEN < 1 Read 692287 spots for SRR8846555.sra Written 692287 spots for SRR8846555.sra Rejected 692287 READS because READLEN < 1 Read 692287 spots for SRR8846555.sra Written 692287 spots for SRR8846555.sra Rejected 692287 READS because READLEN < 1 Read 692287 spots for SRR8846555.sra Written 692287 spots for SRR8846555.sra Rejected 692287 READS because READLEN < 1 Read 692287 spots for SRR8846555.sra Written 692287 spots for SRR8846555.sra Rejected 692287 READS because READLEN < 1 Read 692287 spots for SRR8846555.sra Written 692287 spots for SRR8846555.sra Rejected 692287 READS because READLEN < 1 Read 692287 spots for SRR8846555.sra Written 692287 spots for SRR8846555.sra Rejected 692287 READS because READLEN < 1 Read 692287 spots for SRR8846555.sra Written 692287 spots for SRR8846555.sra Rejected 692287 READS because READLEN < 1 Read 692287 spots for SRR8846555.sra Written 692287 spots for SRR8846555.sra Rejected 692287 READS because READLEN < 1 Read 692287 spots for SRR8846555.sra Written 692287 spots for SRR8846555.sra Rejected 692287 READS because READLEN < 1 Read 692287 spots for SRR8846555.sra Written 692287 spots for SRR8846555.sra Rejected 692287 READS because READLEN < 1 Read 692287 spots for SRR8846555.sra Written 692287 spots for SRR8846555.sra Rejected 692287 READS because READLEN < 1 Read 692287 spots for SRR8846555.sra Written 692287 spots for SRR8846555.sra Rejected 692287 READS because READLEN < 1 Read 692287 spots for SRR8846555.sra Written 692287 spots for SRR8846555.sra Rejected 692287 READS because READLEN < 1 Read 692287 spots for SRR8846555.sra Written 692287 spots for SRR8846555.sra Rejected 692287 READS because READLEN < 1 Read 692287 spots for SRR8846555.sra Written 692287 spots for SRR8846555.sra Rejected 692287 READS because READLEN < 1 Read 692287 spots for SRR8846555.sra Written 692287 spots for SRR8846555.sra Rejected 692292 READS because READLEN < 1 Read 692292 spots for SRR8846555.sra Written 692292 spots for SRR8846555.sra Rejected 692287 READS because READLEN < 1 Read 692287 spots for SRR8846555.sra Written 692287 spots for SRR8846555.sra Rejected 692287 READS because READLEN < 1 Read 692287 spots for SRR8846555.sra Written 692287 spots for SRR8846555.sra SRR ids: ['SRR8846555.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_ezzf1bjc SRR8846555.sra spots: 13845745 blocks: [[1, 692287], [692288, 1384574], [1384575, 2076861], [2076862, 2769148], [2769149, 3461435], [3461436, 4153722], [4153723, 4846009], [4846010, 5538296], [5538297, 6230583], [6230584, 6922870], [6922871, 7615157], [7615158, 8307444], [8307445, 8999731], [8999732, 9692018], [9692019, 10384305], [10384306, 11076592], [11076593, 11768879], [11768880, 12461166], [12461167, 13153453], [13153454, 13845745]] SRR8846555 file size 3318044 SRR8846555 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 SRR8846555 SRR8846555_1.fastq Input file: SRR8846555_1.fastq trimmed: SRR8846555-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 Mon Dec 9 11:10:17 2024 >> started Mon Dec 9 11:10:28 2024 >> done (10.899s) 13845745 reads processed; of these: 258 ( 0.00%) short reads filtered out after trimming by size control 43 ( 0.00%) empty reads filtered out after trimming by size control 13845444 (100.00%) reads available; of these: 3916430 (28.29%) trimmed reads available after processing 9929014 (71.71%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 28 0.00% 19 19 0.00% 20 22 0.00% 21 38 0.00% 22 37 0.00% 23 41 0.00% 24 53 0.00% 25 60 0.00% 26 59 0.00% 27 75 0.00% 28 89 0.00% 29 105 0.00% 30 104 0.00% 31 83 0.00% 32 86 0.00% 33 103 0.00% 34 147 0.00% 35 117 0.00% 36 101 0.00% 37 123 0.00% 38 125 0.00% 39 107 0.00% 40 134 0.00% 41 113 0.00% 42 151 0.00% 43 149 0.00% 44 153 0.00% 45 201 0.00% 46 170 0.00% 47 189 0.00% 48 165 0.00% 49 162 0.00% 50 161 0.00% 51 139 0.00% 52 135 0.00% 53 176 0.00% 54 152 0.00% 55 169 0.00% 56 221 0.00% 57 218 0.00% 58 298 0.00% 59 402 0.00% 60 649 0.00% 61 939 0.01% 62 1522 0.01% 63 2081 0.02% 64 4252 0.03% 65 5700 0.04% 66 13350 0.10% 67 75374 0.54% 68 85614 0.62% 69 67030 0.48% 70 70639 0.51% 71 119440 0.86% 72 47894 0.35% 73 12635 0.09% 74 25965 0.19% 75 13567 0.10% 76 6195 0.04% 77 5516 0.04% 78 6356 0.05% 79 6749 0.05% 80 7321 0.05% 81 8050 0.06% 82 10602 0.08% 83 11691 0.08% 84 11761 0.08% 85 13465 0.10% 86 14572 0.11% 87 19117 0.14% 88 30986 0.22% 89 43445 0.31% 90 70468 0.51% 91 80005 0.58% 92 89385 0.65% 93 141207 1.02% 94 175330 1.27% 95 400566 2.89% 96 441295 3.19% 97 395836 2.86% 98 554261 4.00% 99 547790 3.96% 100 272430 1.97% 101 9929014 71.71% 13845444 reads passed initial QC criterion=sequence-density sequence-density=91.43 sequence-density-rank=1 fanout-score=38.22 fanout-score-rank=2 prefix-density=91.47 prefix-fanout=38.2 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACAGTGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA criterion=fanout-score sequence-density=1.91 sequence-density-rank=3 fanout-score=52.24 fanout-score-rank=1 prefix-density=98.56 prefix-fanout=1.0 sequence=CACACAGTGATATCGTATGCCGT 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACAGTGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA -o SRR8846555 - Input file: STDIN trimmed: SRR8846555-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACAGTGATCTCGTATGCCGTCTTCTGCTTGA -- 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 Mon Dec 9 11:12:15 2024 >> started Mon Dec 9 11:12:28 2024 >> done (12.798s) 13544456 reads processed; of these: 382024 ( 2.82%) short reads filtered out after trimming by size control 56036 ( 0.41%) empty reads filtered out after trimming by size control 13106396 (96.77%) reads available; of these: 12218956 (93.23%) trimmed reads available after processing 887440 ( 6.77%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 120099 0.92% 19 207318 1.58% 20 227201 1.73% 21 923416 7.05% 22 437513 3.34% 23 556160 4.24% 24 1964502 14.99% 25 724112 5.52% 26 549623 4.19% 27 527331 4.02% 28 509461 3.89% 29 600153 4.58% 30 755147 5.76% 31 496485 3.79% 32 473875 3.62% 33 565854 4.32% 34 540301 4.12% 35 450938 3.44% 36 486560 3.71% 37 235039 1.79% 38 178293 1.36% 39 147556 1.13% 40 133655 1.02% 41 128237 0.98% 42 112831 0.86% 43 47465 0.36% 44 50849 0.39% 45 22739 0.17% 46 10641 0.08% 47 6597 0.05% 48 5491 0.04% 49 2987 0.02% 50 1938 0.01% 51 1854 0.01% 52 939 0.01% 53 894 0.01% 54 858 0.01% 55 394 0.00% 56 471 0.00% 57 364 0.00% 58 384 0.00% 59 451 0.00% 60 620 0.00% 61 942 0.01% 62 1446 0.01% 63 1982 0.02% 64 4092 0.03% 65 5476 0.04% 66 12886 0.10% 67 73430 0.56% 68 83465 0.64% 69 65142 0.50% 70 68552 0.52% 71 116071 0.89% 72 43420 0.33% 73 7781 0.06% 74 4634 0.04% 75 3215 0.02% 76 3122 0.02% 77 4804 0.04% 78 3839 0.03% 79 3955 0.03% 80 5075 0.04% 81 3988 0.03% 82 3775 0.03% 83 4990 0.04% 84 2717 0.02% 85 2418 0.02% 86 2099 0.02% 87 2022 0.02% 88 1607 0.01% 89 1561 0.01% 90 1527 0.01% 91 1695 0.01% 92 1558 0.01% 93 1637 0.01% 94 1812 0.01% 95 2597 0.02% 96 3719 0.03% 97 5695 0.04% 98 7867 0.06% 99 10521 0.08% 100 14495 0.11% 101 307171 2.34% criterion=sequence-density sequence-density=5.59 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=16 prefix-density=0.00 prefix-fanout=1.0 sequence=CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATTCAAGA criterion=fanout-score sequence-density=0.01 sequence-density-rank=29 fanout-score=237.90 fanout-score-rank=1 prefix-density=2.93 prefix-fanout=1.0 sequence=CTCGGGTGCCATTGTATCCTTAACCATTTCTTTTTTTTGACAC Started job on | Dec 09 11:14:34 Started mapping on | Dec 09 11:14:34 Finished on | Dec 09 11:15:27 Mapping speed, Million of reads per hour | 910.69 Number of input reads | 13407384 Average input read length | 33 UNIQUE READS: Uniquely mapped reads number | 2542408 Uniquely mapped reads % | 18.96% Average mapped length | 26.06 Number of splices: Total | 29359 Number of splices: Annotated (sjdb) | 18312 Number of splices: GT/AG | 27767 Number of splices: GC/AG | 1144 Number of splices: AT/AC | 13 Number of splices: Non-canonical | 435 Mismatch rate per base, % | 0.13% Deletion rate per base | 0.00% Deletion average length | 1.36 Insertion rate per base | 0.00% Insertion average length | 1.01 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 4789793 % of reads mapped to multiple loci | 35.73% Number of reads mapped to too many loci | 4668732 % of reads mapped to too many loci | 34.82% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 9.73% % of reads unmapped: other | 0.76% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 6075183 6075183 6075183 N_multimapping 4789793 4789793 4789793 N_noFeature 1624845 1790679 2364539 N_ambiguous 37361 24898 589 UnstrandedReadsAssigned:880202 PositiveStrandReadsAssigned:726831 NegativeStrandReadsAssigned:177280 Dataset is classified unstranded MeadianReadLen=28 20thPercentileLength=24 echo kmer=19 SRR8846555 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: SRR8846555-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 13,407,384 reads, 4,262,054 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,107 rounds 52973 SRR8846555.ke.tsv 35125 SRR8846555.se.tsv 88098 total ==> SRR8846555.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 1.72524 0.214945 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 2.27476 0.377809 PNS24243 293 194 0 0 KQK14069 1603 1504 170.73 25.8675 KQK14071 474 375 11.9636 7.2698 ==> SRR8846555.se.tsv <== BRADI_1g14170v3 200 BRADI_1g53295v3 0 BRADI_1g59795v3 6 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 27 BRADI_1g74790v3 16 BRADI_1g09890v3 1 BRADI_1g77505v3 1 BRADI_1g48960v3 0 SRR8846555 completed mapping pipeline successfully