Starting /dee2/code/volunteer_pipeline.sh SRR8846508 current disk space = 1506930139136 free memory = 1364855392 SRR8846508 SRAfilesize 06a0e5fe8e41b4cf633e583453d4e550 SRR8846508.sra SRR8846508.sra file validated SRR8846508 is single end SRR8846508 is conventional basespace SRR8846508 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8846508_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 101 %GC 46 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.222 34.0 33.0 34.0 30.0 34.0 2 32.63425 34.0 33.0 34.0 28.0 34.0 3 32.982 34.0 33.0 34.0 32.0 34.0 4 33.162 34.0 33.0 34.0 32.0 34.0 5 33.24875 34.0 33.0 34.0 33.0 34.0 6 36.9775 38.0 37.0 38.0 36.0 38.0 7 37.30475 38.0 38.0 38.0 36.0 38.0 8 37.488 38.0 38.0 38.0 37.0 38.0 9 37.53525 38.0 38.0 38.0 37.0 38.0 10-11 37.56925 38.0 38.0 38.0 38.0 38.0 12-13 37.594 38.0 38.0 38.0 38.0 38.0 14-15 37.514250000000004 38.0 38.0 38.0 38.0 38.0 16-17 37.496624999999995 38.0 38.0 38.0 37.5 38.0 18-19 37.506375000000006 38.0 38.0 38.0 38.0 38.0 20-21 37.466125 38.0 38.0 38.0 38.0 38.0 22-23 37.494125 38.0 38.0 38.0 38.0 38.0 24-25 37.612 38.0 38.0 38.0 38.0 38.0 26-27 37.541 38.0 38.0 38.0 38.0 38.0 28-29 37.574 38.0 38.0 38.0 38.0 38.0 30-31 37.543875 38.0 38.0 38.0 38.0 38.0 32-33 37.497375000000005 38.0 38.0 38.0 38.0 38.0 34-35 37.383250000000004 38.0 38.0 38.0 37.5 38.0 36-37 37.210875 38.0 38.0 38.0 37.0 38.0 38-39 37.144 38.0 38.0 38.0 37.0 38.0 40-41 37.210125000000005 38.0 38.0 38.0 37.0 38.0 42-43 37.230875 38.0 38.0 38.0 37.0 38.0 44-45 37.277125 38.0 38.0 38.0 37.0 38.0 46-47 37.307625 38.0 38.0 38.0 37.0 38.0 48-49 37.27825 38.0 38.0 38.0 37.0 38.0 50-51 37.28475 38.0 38.0 38.0 37.0 38.0 52-53 37.357375 38.0 38.0 38.0 37.0 38.0 54-55 37.320750000000004 38.0 38.0 38.0 37.0 38.0 56-57 37.241 38.0 38.0 38.0 37.0 38.0 58-59 37.0675 38.0 38.0 38.0 36.5 38.0 60-61 37.142375 38.0 38.0 38.0 36.0 38.0 62-63 36.612 38.0 38.0 38.0 34.0 38.0 64-65 36.485375 38.0 38.0 38.0 33.5 38.0 66-67 36.356875 38.0 37.0 38.0 34.0 38.0 68-69 36.163 38.0 37.0 38.0 33.5 38.0 70-71 36.06175 38.0 37.0 38.0 33.0 38.0 72-73 36.05475 38.0 38.0 38.0 33.0 38.0 74-75 35.919124999999994 38.0 37.0 38.0 33.0 38.0 76-77 35.714124999999996 38.0 37.0 38.0 31.0 38.0 78-79 35.627625 38.0 37.0 38.0 31.0 38.0 80-81 35.726375000000004 38.0 37.0 38.0 32.0 38.0 82-83 35.381875 38.0 37.0 38.0 29.0 38.0 84-85 35.428375 38.0 37.0 38.0 29.5 38.0 86-87 35.448125 38.0 37.0 38.0 31.0 38.0 88-89 35.549875 38.0 37.0 38.0 32.0 38.0 90-91 35.345375000000004 38.0 37.0 38.0 31.0 38.0 92-93 34.928875 38.0 37.0 38.0 28.5 38.0 94-95 34.126875 38.0 36.5 38.0 21.0 38.0 96-97 32.08525 38.0 34.0 38.0 2.0 38.0 98-99 30.0185 38.0 28.5 38.0 2.0 38.0 100-101 27.372125 37.5 19.5 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 15 1.0 16 3.0 17 1.0 18 1.0 19 1.0 20 2.0 21 1.0 22 4.0 23 3.0 24 14.0 25 30.0 26 24.0 27 17.0 28 20.0 29 26.0 30 43.0 31 54.0 32 81.0 33 144.0 34 247.0 35 392.0 36 740.0 37 2151.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 33.28004263256062 22.968292033040235 22.56861177724487 21.183053557154278 2 26.075 29.125 17.8 27.0 3 25.775 20.625 19.0 34.599999999999994 4 25.7 35.449999999999996 15.75 23.1 5 26.575 24.925 23.075000000000003 25.424999999999997 6 27.175 25.05 26.55 21.224999999999998 7 36.275 28.299999999999997 17.349999999999998 18.075 8 20.65 23.625 34.0 21.725 9 23.974999999999998 34.225 22.775000000000002 19.025 10-11 29.4375 23.8125 26.387500000000003 20.3625 12-13 22.75 21.6625 22.75 32.8375 14-15 24.875 36.15 20.8 18.175 16-17 23.150000000000002 28.3375 29.5 19.0125 18-19 33.287499999999994 22.725 21.375 22.6125 20-21 23.400000000000002 27.762500000000003 26.700000000000003 22.1375 22-23 27.8375 30.0875 27.825 14.249999999999998 24-25 27.737499999999997 27.0625 26.025 19.175 26-27 28.549999999999997 27.737499999999997 23.7875 19.925 28-29 24.0 26.400000000000002 25.4375 24.1625 30-31 27.8875 20.424999999999997 31.8125 19.875 32-33 23.9125 18.5 34.6875 22.900000000000002 34-35 30.2375 14.975 31.162499999999998 23.625 36-37 35.2875 16.175 28.7375 19.8 38-39 35.55 18.375 26.400000000000002 19.675 40-41 30.2875 19.5875 24.675 25.45 42-43 30.887500000000003 22.4375 21.587500000000002 25.087500000000002 44-45 36.725 22.6125 14.774999999999999 25.887500000000003 46-47 32.237500000000004 28.175 16.1 23.4875 48-49 27.625 25.35 17.5375 29.4875 50-51 22.3 26.637499999999996 15.625 35.4375 52-53 23.5 30.099999999999998 12.8875 33.5125 54-55 20.7125 29.7375 15.475 34.075 56-57 18.5625 31.1 14.2625 36.075 58-59 13.7125 32.875 14.424999999999999 38.987500000000004 60-61 14.887500000000001 29.75 15.6 39.7625 62-63 14.000000000000002 30.925000000000004 20.7375 34.3375 64-65 13.6875 32.237500000000004 23.775 30.3 66-67 12.675 25.624999999999996 26.700000000000003 35.0 68-69 14.762500000000001 25.412499999999998 25.337500000000002 34.4875 70-71 17.4125 24.8625 28.962500000000002 28.762500000000003 72-73 20.9125 20.7375 31.9625 26.387500000000003 74-75 16.1375 18.15 33.7125 32.0 76-77 19.8 13.1625 36.8125 30.225 78-79 19.7125 9.950000000000001 37.7875 32.550000000000004 80-81 19.7125 11.2375 38.800000000000004 30.25 82-83 19.475 11.774999999999999 42.175000000000004 26.575 84-85 21.224999999999998 12.425 37.3 29.049999999999997 86-87 19.8625 19.1 34.849999999999994 26.187500000000004 88-89 15.987499999999999 31.5625 34.7125 17.7375 90-91 13.337499999999999 41.875 28.775000000000002 16.0125 92-93 12.837499999999999 52.1125 20.75 14.299999999999999 94-95 10.725 60.35 19.7 9.225 96-97 8.35 69.7625 14.875 7.012500000000001 98-99 6.625 78.85 10.1125 4.4125 100-101 3.8875 85.1625 6.775 4.175 >>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 3.0 33 6.0 34 9.5 35 13.0 36 10.5 37 6.5 38 12.5 39 35.5 40 65.5 41 131.5 42 195.5 43 216.0 44 282.5 45 337.5 46 369.0 47 392.0 48 367.0 49 313.0 50 296.5 51 270.0 52 171.5 53 109.0 54 96.0 55 130.0 56 96.0 57 25.0 58 14.0 59 5.0 60 6.0 61 7.5 62 3.5 63 1.0 64 0.5 65 1.0 66 1.0 67 0.5 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 6.175 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 56.775 #Duplication Level Percentage of deduplicated Percentage of total 1 82.82694848084545 47.025 2 8.234258036107441 9.35 3 3.126376045794804 5.325 4 1.4971378247468077 3.4000000000000004 5 0.9687362395420519 2.75 6 0.7045354469396742 2.4 7 0.3522677234698371 1.4000000000000001 8 0.3522677234698371 1.6 9 0.22016732716864817 1.125 >10 1.4090708938793484 12.925 >50 0.26420079260237783 10.100000000000001 >100 0.044033465433729636 2.6 >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 TCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 104 2.6 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 93 2.325 No Hit GACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 84 2.1 RNA PCR Primer, Index 1 (100% over 23bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 63 1.575 No Hit TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 59 1.4749999999999999 RNA PCR Primer, Index 1 (100% over 29bp) GGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 54 1.35 RNA PCR Primer, Index 1 (100% over 22bp) GACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAAC 51 1.275 RNA PCR Primer, Index 1 (100% over 24bp) AGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 43 1.075 No Hit GACACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACT 30 0.75 RNA PCR Primer, Index 1 (100% over 25bp) AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 26 0.65 Illumina Small RNA Adapter 2 (100% over 21bp) CTCTGATGATGATCAAACTAATACTTTCGTTCTTCTGGAATTCTCGGGTG 22 0.5499999999999999 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 21 0.525 No Hit GCACCAGTGGTCTAGTGGTAGAATAGTACCTGGAATTCTCGGGTGCCAAG 21 0.525 No Hit CTCGGGTGCCAAGGAACTCCAGTCACCACGATATCTCGTATGCCGTCTTC 21 0.525 RNA PCR Primer, Index 31 (100% over 50bp) CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 20 0.5 RNA PCR Primer, Index 1 (100% over 28bp) CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 18 0.44999999999999996 No Hit TCTCGGGTGCCAAGGAACTCCAGTCACCACGATATCTCGTATGCCGTCTT 17 0.42500000000000004 RNA PCR Primer, Index 31 (100% over 50bp) GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 16 0.4 Illumina Small RNA Adapter 2 (100% over 21bp) GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 16 0.4 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCATGGAATTCTCGGGTG 16 0.4 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 15 0.375 Illumina Small RNA Adapter 2 (100% over 21bp) TTCGGACCAGGCTTCATTCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 15 0.375 RNA PCR Primer, Index 1 (100% over 29bp) GCCCACCCCAAGATGAGTGCTCTCTCTGGAATTCTCGGGTGCCAAGGAAC 15 0.375 RNA PCR Primer, Index 1 (100% over 24bp) GCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCC 14 0.35000000000000003 No Hit CACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAACT 13 0.325 RNA PCR Primer, Index 1 (100% over 25bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 13 0.325 No Hit CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTC 13 0.325 No Hit GCACCAGTGGTCTAGTGGTAGAATAGTATGGAATTCTCGGGTGCCAAGGA 12 0.3 RNA PCR Primer, Index 1 (100% over 22bp) CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 12 0.3 RNA PCR Primer, Index 1 (100% over 23bp) TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 12 0.3 No Hit ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGC 12 0.3 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTGGAATTCTCGGGTGCCAAG 11 0.27499999999999997 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATATGGAATTCTCGGGTGCCAAGGAA 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 23bp) TTCTCGGGTGCCAAGGAACTCCAGTCACCACGATATCTCGTATGCCGTCT 11 0.27499999999999997 RNA PCR Primer, Index 31 (100% over 50bp) ACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCC 11 0.27499999999999997 No Hit GCACCAGTAGTCTAGTGGTAGAATAGTACCTGGAATTCTCGGGTGCCAAG 10 0.25 No Hit CGACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGA 10 0.25 RNA PCR Primer, Index 1 (100% over 22bp) CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 10 0.25 Illumina Small RNA Adapter 2 (100% over 21bp) CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGG 10 0.25 No Hit CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGG 9 0.22499999999999998 No Hit TCGGATAACCGTAGTAATTCTAGAGCTAATACGTGGAATTCTCGGGTGCC 9 0.22499999999999998 No Hit ATATATTTCAAGTTATTTCGGATCTTGGAATTCTCGGGTGCCAAGGAACT 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 25bp) CAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTG 9 0.22499999999999998 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTTGGAATTCTCGGGTGC 9 0.22499999999999998 No Hit CGACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAA 8 0.2 RNA PCR Primer, Index 1 (100% over 23bp) TCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTC 8 0.2 RNA PCR Primer, Index 1 (100% over 26bp) GATAACCGTAGTAATTCTAGAGCTAATTGGAATTCTCGGGTGCCAAGGAA 8 0.2 RNA PCR Primer, Index 1 (100% over 23bp) ATAACCGTAGTAATTCTAGAGCTAATTGGAATTCTCGGGTGCCAAGGAAC 8 0.2 RNA PCR Primer, Index 1 (100% over 24bp) ATAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAACT 8 0.2 RNA PCR Primer, Index 1 (100% over 25bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCGTGGAATT 8 0.2 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTGGAATTCTCGGGTGCCA 8 0.2 No Hit TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTGGAATTCTCGGGTGC 8 0.2 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATACTCTGGAATTCTCGGGTGCCAAG 7 0.17500000000000002 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGGTGGAATTC 7 0.17500000000000002 No Hit CCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTG 7 0.17500000000000002 No Hit GATAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAAC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 24bp) CACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACTCC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 27bp) TAACCGTAGTAATTCTAGAGCTAATATGGAATTCTCGGGTGCCAAGGAAC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 24bp) ATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 23bp) ATTCTCGGGTGCCAAGGAACTCCAGTCACCACGATATCTCGTATGCCGTC 7 0.17500000000000002 RNA PCR Primer, Index 31 (100% over 50bp) CGGATAACCGTAGTAATTCTAGAGCTAATACGTGGAATTCTCGGGTGCCA 6 0.15 No Hit CATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGCC 6 0.15 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTCTCGTGGAATTCTCGGGTG 6 0.15 No Hit GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTG 6 0.15 No Hit GACACGACTCTCGGCAACGTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 6 0.15 RNA PCR Primer, Index 1 (100% over 31bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTTGGAATTCT 6 0.15 No Hit ACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAACT 6 0.15 RNA PCR Primer, Index 1 (100% over 25bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTTGGAATTCTCGGGTG 6 0.15 No Hit AAGGGTGCTGAGAATACTTTGAATCTGACACTGGAATTCTCGGGTGCCAA 6 0.15 No Hit CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGG 6 0.15 No Hit NGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATGGAATTCTCGGGTG 6 0.15 No Hit GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGGTG 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTATGGAATTCTCGGGTGCCAA 6 0.15 No Hit TAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAACTC 6 0.15 RNA PCR Primer, Index 1 (100% over 26bp) TCGCTTGGTGCAGATCGGGACTGGAATTCTCGGGTGCCAAGGAACTCCAG 6 0.15 RNA PCR Primer, Index 1 (100% over 29bp) GACACGACTCTCGGCAACGGATATGGAATTCTCGGGTGCCAAGGAACTCC 5 0.125 RNA PCR Primer, Index 1 (100% over 27bp) ACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAACTCCA 5 0.125 RNA PCR Primer, Index 1 (100% over 28bp) TAATTCATGATCTGGCATGTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 5 0.125 RNA PCR Primer, Index 1 (100% over 31bp) CGACACGACTCTCGGCAACGGATGGAATTCTCGGGTGCCAAGGAACTCCA 5 0.125 RNA PCR Primer, Index 1 (100% over 28bp) CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGG 5 0.125 No Hit AACCGTAGTAATTCTAGAGCTAATTGGAATTCTCGGGTGCCAAGGAACTC 5 0.125 RNA PCR Primer, Index 1 (100% over 26bp) TCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCG 5 0.125 No Hit TGCAAGTATGAACTAATTTGAACTGTGAAACTTGGAATTCTCGGGTGCCA 5 0.125 No Hit CATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) ATGCAGTTACTAATTCATGATCTGGCTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) TGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAA 5 0.125 No Hit CACGACTCTCGGCAACGGATATCTCGTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) GCCTTGATGGTGAAATGGTAGACACGCGAGATGGAATTCTCGGGTGCCAA 5 0.125 No Hit NACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) TCTCTGATGATGATCAAACTAATACTTTCGTTCTTCTGGAATTCTCGGGT 5 0.125 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGTGGAATTCTC 5 0.125 No Hit CAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTC 5 0.125 RNA PCR Primer, Index 1 (100% over 26bp) CGGATAACCGTAGTAATTCTAGAGCTAATACTGGAATTCTCGGGTGCCAA 5 0.125 No Hit AGGGCTATAGCTCAGTTCGGTAGAGCAACTCGTTTACACCGAGATGGAAT 5 0.125 No Hit AATTCTCGGGTGCCAAGGAACTCCAGTCACCACGATATCTCGTATGCCGT 5 0.125 RNA PCR Primer, Index 31 (100% over 50bp) CACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGC 5 0.125 No Hit CAGGGTTCGTTTCCCTGGATGCGCACCATGGAATTCTCGGGTGCCAAGGA 5 0.125 RNA PCR Primer, Index 1 (100% over 22bp) >>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 0.025 0.0 0.0 0.0 2 0.0 0.05 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 0.1 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 0.225 0.0 0.0 0.0 10-11 0.0 0.4125 0.0 0.0 0.0 12-13 0.0 0.4625 0.0 0.0 0.0 14-15 0.0 0.6375 0.0 0.0 0.0 16-17 0.0 1.4375 0.0 0.0 0.0 18-19 0.0 3.075 0.0 0.0 0.0 20-21 0.0 5.762499999999999 0.0 0.0 0.0 22-23 0.0 12.825 0.0 0.0 0.0 24-25 0.0 22.425 0.0 0.0 0.0 26-27 0.0 34.025000000000006 0.0 0.0 0.0 28-29 0.0 45.474999999999994 0.0 0.0 0.0 30-31 0.0 55.075 0.0 0.0 0.0 32-33 0.0 63.137499999999996 0.0 0.0 0.0 34-35 0.0 73.55000000000001 0.0 0.0 0.0 36-37 0.0 81.8875 0.0 0.0 0.0 38-39 0.0 86.4375 0.0 0.0 0.0 40-41 0.0 89.0625 0.0 0.0 0.0 42-43 0.0 91.425 0.0 0.0 0.0 44-45 0.0 93.05 0.0 0.0 0.0 46-47 0.0 93.7625 0.0 0.0 0.0 48-49 0.0 93.85 0.0 0.0 0.0 50-51 0.0 93.875 0.0 0.0 0.0 52-53 0.0 93.92500000000001 0.0 0.0 0.0 54-55 0.0 93.9625 0.0 0.0 0.0 56-57 0.0 93.975 0.0 0.0 0.0 58-59 0.0 93.975 0.0 0.0 0.0 60-61 0.0 93.975 0.0 0.0 0.0 62-63 0.0 93.975 0.0 0.0 0.0 64-65 0.0 93.9875 0.0 0.0 0.0 66-67 0.0 94.0 0.0 0.0 0.0 68-69 0.0 94.0 0.0 0.0 0.0 70-71 0.0 94.0125 0.0 0.0 0.0 72-73 0.0 94.025 0.0 0.0 0.0 74-75 0.0 94.0625 0.0 0.0 0.0 76-77 0.0 94.075 0.0 0.0 0.0 78-79 0.0 94.125 0.0 0.0 0.0 80-81 0.0 94.1875 0.0 0.0 0.0 82-83 0.0 94.2875 0.0 0.0 0.0 84-85 0.0 94.4875 0.0 0.0 0.0 86-87 0.0 94.5875 0.0 0.0 0.0 88-89 0.0 94.6125 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGATTG 25 2.583074E-7 101.26667 1 CTCTGAT 15 4.7401295E-4 101.26666 1 CATCGAG 30 5.9571903E-9 101.26666 1 GGATTGT 25 3.8440157E-7 94.93751 2 GATTGTA 25 3.8440157E-7 94.93751 3 TAGTTCA 25 3.8440157E-7 94.93751 8 ATTGTAG 25 3.8440157E-7 94.93751 4 AGTTCAA 25 3.8440157E-7 94.93751 9 GTAGACC 30 9.502401E-9 94.9375 7 TTGTAGT 30 9.502401E-9 94.9375 5 AGTAGAC 30 9.502401E-9 94.9375 6 ATGATCA 15 6.1582687E-4 94.9375 9 GATGATC 15 6.1582687E-4 94.9375 8 GAGTAGA 30 9.502401E-9 94.9375 5 CGAGTAG 30 9.502401E-9 94.9375 4 AGACCTT 30 9.502401E-9 94.9375 9 ATCGAGT 30 9.502401E-9 94.9375 2 TCGAGTA 30 9.502401E-9 94.9375 3 TAGACCT 30 9.502401E-9 94.9375 8 TGTAGTT 30 1.1382763E-6 79.11458 6 >>END_MODULE Rejected 842975 READS because READLEN < 1 Read 842975 spots for SRR8846508.sra Written 842975 spots for SRR8846508.sra Rejected 842975 READS because READLEN < 1 Read 842975 spots for SRR8846508.sra Written 842975 spots for SRR8846508.sra Rejected 842975 READS because READLEN < 1 Read 842975 spots for SRR8846508.sra Written 842975 spots for SRR8846508.sra Rejected 842975 READS because READLEN < 1 Read 842975 spots for SRR8846508.sra Written 842975 spots for SRR8846508.sra Rejected 842975 READS because READLEN < 1 Read 842975 spots for SRR8846508.sra Written 842975 spots for SRR8846508.sra Rejected 842975 READS because READLEN < 1 Read 842975 spots for SRR8846508.sra Written 842975 spots for SRR8846508.sra Rejected 842975 READS because READLEN < 1 Read 842975 spots for SRR8846508.sra Written 842975 spots for SRR8846508.sra Rejected 842975 READS because READLEN < 1 Read 842975 spots for SRR8846508.sra Written 842975 spots for SRR8846508.sra Rejected 842975 READS because READLEN < 1 Read 842975 spots for SRR8846508.sra Written 842975 spots for SRR8846508.sra Rejected 842975 READS because READLEN < 1 Read 842975 spots for SRR8846508.sra Written 842975 spots for SRR8846508.sra Rejected 842975 READS because READLEN < 1 Read 842975 spots for SRR8846508.sra Written 842975 spots for SRR8846508.sra Rejected 842975 READS because READLEN < 1 Read 842975 spots for SRR8846508.sra Written 842975 spots for SRR8846508.sra Rejected 842975 READS because READLEN < 1 Read 842975 spots for SRR8846508.sra Written 842975 spots for SRR8846508.sra Rejected 842994 READS because READLEN < 1 Read 842994 spots for SRR8846508.sra Written 842994 spots for SRR8846508.sra Rejected 842975 READS because READLEN < 1 Read 842975 spots for SRR8846508.sra Written 842975 spots for SRR8846508.sra Rejected 842975 READS because READLEN < 1 Read 842975 spots for SRR8846508.sra Written 842975 spots for SRR8846508.sra Rejected 842975 READS because READLEN < 1 Read 842975 spots for SRR8846508.sra Written 842975 spots for SRR8846508.sra Rejected 842975 READS because READLEN < 1 Read 842975 spots for SRR8846508.sra Written 842975 spots for SRR8846508.sra Rejected 842975 READS because READLEN < 1 Read 842975 spots for SRR8846508.sra Written 842975 spots for SRR8846508.sra Rejected 842975 READS because READLEN < 1 Read 842975 spots for SRR8846508.sra Written 842975 spots for SRR8846508.sra SRR ids: ['SRR8846508.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_8oygw8wb SRR8846508.sra spots: 16859519 blocks: [[1, 842975], [842976, 1685950], [1685951, 2528925], [2528926, 3371900], [3371901, 4214875], [4214876, 5057850], [5057851, 5900825], [5900826, 6743800], [6743801, 7586775], [7586776, 8429750], [8429751, 9272725], [9272726, 10115700], [10115701, 10958675], [10958676, 11801650], [11801651, 12644625], [12644626, 13487600], [13487601, 14330575], [14330576, 15173550], [15173551, 16016525], [16016526, 16859519]] SRR8846508 file size 4045000 SRR8846508 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 SRR8846508 SRR8846508_1.fastq Input file: SRR8846508_1.fastq trimmed: SRR8846508-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 03:45:54 2024 >> started Mon Dec 9 03:46:34 2024 >> done (40.664s) 16859519 reads processed; of these: 308 ( 0.00%) short reads filtered out after trimming by size control 35 ( 0.00%) empty reads filtered out after trimming by size control 16859176 (100.00%) reads available; of these: 3643433 (21.61%) trimmed reads available after processing 13215743 (78.39%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 49 0.00% 19 43 0.00% 20 42 0.00% 21 44 0.00% 22 43 0.00% 23 52 0.00% 24 82 0.00% 25 106 0.00% 26 135 0.00% 27 180 0.00% 28 265 0.00% 29 296 0.00% 30 290 0.00% 31 335 0.00% 32 292 0.00% 33 244 0.00% 34 280 0.00% 35 224 0.00% 36 230 0.00% 37 200 0.00% 38 148 0.00% 39 186 0.00% 40 182 0.00% 41 186 0.00% 42 188 0.00% 43 221 0.00% 44 227 0.00% 45 289 0.00% 46 244 0.00% 47 236 0.00% 48 257 0.00% 49 283 0.00% 50 241 0.00% 51 282 0.00% 52 279 0.00% 53 308 0.00% 54 323 0.00% 55 361 0.00% 56 409 0.00% 57 461 0.00% 58 518 0.00% 59 614 0.00% 60 679 0.00% 61 1110 0.01% 62 1501 0.01% 63 1837 0.01% 64 3180 0.02% 65 4054 0.02% 66 10453 0.06% 67 48800 0.29% 68 56273 0.33% 69 39015 0.23% 70 34089 0.20% 71 38475 0.23% 72 17175 0.10% 73 5996 0.04% 74 7298 0.04% 75 5074 0.03% 76 4532 0.03% 77 4171 0.02% 78 5476 0.03% 79 5610 0.03% 80 7304 0.04% 81 9107 0.05% 82 18189 0.11% 83 16469 0.10% 84 14107 0.08% 85 15580 0.09% 86 20059 0.12% 87 23368 0.14% 88 38353 0.23% 89 54357 0.32% 90 77079 0.46% 91 82227 0.49% 92 109572 0.65% 93 174281 1.03% 94 203620 1.21% 95 375627 2.23% 96 410936 2.44% 97 407315 2.42% 98 459457 2.73% 99 502451 2.98% 100 319302 1.89% 101 13215743 78.39% 16859176 reads passed initial QC criterion=sequence-density sequence-density=94.28 sequence-density-rank=1 fanout-score=34.28 fanout-score-rank=1 prefix-density=94.64 prefix-fanout=34.1 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACGATATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA criterion=fanout-score sequence-density=94.28 sequence-density-rank=1 fanout-score=34.28 fanout-score-rank=1 prefix-density=94.64 prefix-fanout=34.1 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACGATATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACGATATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA -o SRR8846508 - Input file: STDIN trimmed: SRR8846508-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACGATATCTCGTATGCCGTCTTCTGCTTGA -- 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 03:49:08 2024 >> started Mon Dec 9 03:50:26 2024 >> done (77.947s) 16504246 reads processed; of these: 477752 ( 2.89%) short reads filtered out after trimming by size control 10945 ( 0.07%) empty reads filtered out after trimming by size control 16015549 (97.04%) reads available; of these: 15464859 (96.56%) trimmed reads available after processing 550690 ( 3.44%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 147126 0.92% 19 269159 1.68% 20 271604 1.70% 21 829907 5.18% 22 484606 3.03% 23 604278 3.77% 24 1344171 8.39% 25 786130 4.91% 26 845560 5.28% 27 1004466 6.27% 28 834347 5.21% 29 716817 4.48% 30 857588 5.35% 31 576145 3.60% 32 937725 5.86% 33 873164 5.45% 34 782791 4.89% 35 693205 4.33% 36 823946 5.14% 37 321441 2.01% 38 257647 1.61% 39 218270 1.36% 40 198332 1.24% 41 192554 1.20% 42 221054 1.38% 43 106203 0.66% 44 86515 0.54% 45 40625 0.25% 46 17723 0.11% 47 9924 0.06% 48 8066 0.05% 49 4336 0.03% 50 2975 0.02% 51 2992 0.02% 52 1906 0.01% 53 1528 0.01% 54 1869 0.01% 55 788 0.00% 56 1170 0.01% 57 705 0.00% 58 690 0.00% 59 720 0.00% 60 809 0.01% 61 1231 0.01% 62 1470 0.01% 63 1764 0.01% 64 3042 0.02% 65 3812 0.02% 66 10167 0.06% 67 47611 0.30% 68 54989 0.34% 69 37892 0.24% 70 33350 0.21% 71 37304 0.23% 72 15369 0.10% 73 4723 0.03% 74 3497 0.02% 75 2635 0.02% 76 4099 0.03% 77 8498 0.05% 78 3484 0.02% 79 4253 0.03% 80 13503 0.08% 81 11179 0.07% 82 8922 0.06% 83 18949 0.12% 84 5314 0.03% 85 4536 0.03% 86 3882 0.02% 87 3336 0.02% 88 2016 0.01% 89 2903 0.02% 90 2096 0.01% 91 1942 0.01% 92 2462 0.02% 93 2928 0.02% 94 2098 0.01% 95 3131 0.02% 96 3808 0.02% 97 5143 0.03% 98 6953 0.04% 99 7349 0.05% 100 8754 0.05% 101 233578 1.46% criterion=sequence-density sequence-density=4.36 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=12 prefix-density=0.00 prefix-fanout=1.0 sequence=CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATTCAAGAGTTGTAAGGAGGGACTTA criterion=fanout-score sequence-density=0.01 sequence-density-rank=43 fanout-score=147.92 fanout-score-rank=1 prefix-density=0.77 prefix-fanout=1.0 sequence=TAGCCAAGTGCGGAGAGGATAACTGCTGAAAGCATATAAGTAGTAAGCCCACCCCAAGATGAGTGCTCTCTCCTCCGACTTCC Started job on | Dec 09 03:52:19 Started mapping on | Dec 09 03:52:20 Finished on | Dec 09 03:58:18 Mapping speed, Million of reads per hour | 164.62 Number of input reads | 16370479 Average input read length | 33 UNIQUE READS: Uniquely mapped reads number | 2222622 Uniquely mapped reads % | 13.58% Average mapped length | 29.25 Number of splices: Total | 32047 Number of splices: Annotated (sjdb) | 20296 Number of splices: GT/AG | 29513 Number of splices: GC/AG | 1966 Number of splices: AT/AC | 22 Number of splices: Non-canonical | 546 Mismatch rate per base, % | 0.16% Deletion rate per base | 0.00% Deletion average length | 1.41 Insertion rate per base | 0.00% Insertion average length | 1.11 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 6014834 % of reads mapped to multiple loci | 36.74% Number of reads mapped to too many loci | 7065400 % of reads mapped to too many loci | 43.16% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 6.09% % of reads unmapped: other | 0.43% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 8133023 8133023 8133023 N_multimapping 6014834 6014834 6014834 N_noFeature 1162089 1292705 2075238 N_ambiguous 52675 35648 388 UnstrandedReadsAssigned:1007858 PositiveStrandReadsAssigned:894269 NegativeStrandReadsAssigned:146996 Dataset is classified positive stranded MeadianReadLen=29 20thPercentileLength=24 echo kmer=19 SRR8846508 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: SRR8846508-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 16,370,479 reads, 2,636,423 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 985 rounds 52973 SRR8846508.ke.tsv 35125 SRR8846508.se.tsv 88098 total ==> SRR8846508.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 3 1.0363 PNS24243 293 194 0 0 KQK14069 1603 1504 144.055 45.394 KQK14071 474 375 0 0 ==> SRR8846508.se.tsv <== BRADI_1g14170v3 198 BRADI_1g53295v3 3 BRADI_1g59795v3 6 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 26 BRADI_1g74790v3 15 BRADI_1g09890v3 1 BRADI_1g77505v3 5 BRADI_1g48960v3 0 SRR8846508 completed mapping pipeline successfully