Starting /dee2/code/volunteer_pipeline.sh SRR8846523 current disk space = 1505491628032 free memory = 1365385328 SRR8846523 SRAfilesize 94d4b63aef0ebe69b16794dc05c64ad3 SRR8846523.sra SRR8846523.sra file validated SRR8846523 is single end SRR8846523 is conventional basespace SRR8846523 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8846523_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 30.65025 34.0 33.0 34.0 25.0 34.0 2 32.75675 34.0 33.0 34.0 28.0 34.0 3 32.8715 34.0 33.0 34.0 31.0 34.0 4 33.12975 34.0 33.0 34.0 32.0 34.0 5 33.1345 34.0 33.0 34.0 32.0 34.0 6 36.749 38.0 37.0 38.0 35.0 38.0 7 37.13275 38.0 38.0 38.0 36.0 38.0 8 37.22175 38.0 38.0 38.0 36.0 38.0 9 37.34325 38.0 38.0 38.0 37.0 38.0 10-11 37.438875 38.0 38.0 38.0 37.0 38.0 12-13 37.430625 38.0 38.0 38.0 37.0 38.0 14-15 37.39975 38.0 38.0 38.0 37.0 38.0 16-17 37.376 38.0 38.0 38.0 37.0 38.0 18-19 37.460750000000004 38.0 38.0 38.0 37.0 38.0 20-21 37.366125 38.0 38.0 38.0 37.0 38.0 22-23 37.434 38.0 38.0 38.0 37.0 38.0 24-25 37.464 38.0 38.0 38.0 37.0 38.0 26-27 37.494625 38.0 38.0 38.0 37.0 38.0 28-29 37.316500000000005 38.0 38.0 38.0 36.5 38.0 30-31 37.37375 38.0 38.0 38.0 37.0 38.0 32-33 37.281875 38.0 38.0 38.0 37.0 38.0 34-35 37.117375 38.0 38.0 38.0 36.5 38.0 36-37 37.019125 38.0 38.0 38.0 35.5 38.0 38-39 37.04625 38.0 38.0 38.0 36.0 38.0 40-41 36.799625 38.0 38.0 38.0 35.0 38.0 42-43 36.8975 38.0 38.0 38.0 35.5 38.0 44-45 36.825874999999996 38.0 38.0 38.0 35.0 38.0 46-47 36.70825 38.0 38.0 38.0 34.5 38.0 48-49 36.759 38.0 38.0 38.0 34.5 38.0 50-51 36.8245 38.0 38.0 38.0 35.0 38.0 52-53 36.85075 38.0 38.0 38.0 35.0 38.0 54-55 36.8505 38.0 38.0 38.0 35.0 38.0 56-57 36.47075 38.0 38.0 38.0 34.0 38.0 58-59 36.375125 38.0 37.5 38.0 33.0 38.0 60-61 36.325625 38.0 37.0 38.0 33.0 38.0 62-63 35.951875 38.0 37.0 38.0 31.0 38.0 64-65 35.828500000000005 38.0 37.0 38.0 30.0 38.0 66-67 35.497875 38.0 36.5 38.0 28.5 38.0 68-69 36.030625 38.0 37.0 38.0 32.0 38.0 70-71 35.71 38.0 37.0 38.0 30.0 38.0 72-73 35.8855 38.0 37.0 38.0 32.0 38.0 74-75 35.42275 38.0 37.0 38.0 29.0 38.0 76-77 35.194 38.0 36.0 38.0 28.5 38.0 78-79 34.343625 38.0 35.0 38.0 25.0 38.0 80-81 34.63175 38.0 36.0 38.0 27.0 38.0 82-83 34.200625 38.0 34.5 38.0 24.5 38.0 84-85 34.3765 38.0 35.0 38.0 26.0 38.0 86-87 34.545249999999996 38.0 35.5 38.0 26.5 38.0 88-89 34.048500000000004 38.0 35.0 38.0 24.0 38.0 90-91 33.653125 38.0 34.5 38.0 15.0 38.0 92-93 33.269125 38.0 34.0 38.0 15.0 38.0 94-95 32.494375 38.0 33.5 38.0 15.0 38.0 96-97 30.464624999999998 38.0 30.0 38.0 2.0 38.0 98-99 27.471125 37.0 13.5 38.0 2.0 38.0 100-101 23.467875 33.5 2.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 16 1.0 17 0.0 18 0.0 19 2.0 20 6.0 21 4.0 22 4.0 23 6.0 24 20.0 25 24.0 26 33.0 27 32.0 28 46.0 29 51.0 30 69.0 31 100.0 32 121.0 33 199.0 34 337.0 35 564.0 36 999.0 37 1382.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 27.68897317800054 29.314548902736387 23.32701164995936 19.66946626930371 2 24.575 27.775 19.225 28.425 3 26.525 20.65 19.925 32.9 4 28.275 31.15 19.15 21.425 5 27.0 27.075 22.400000000000002 23.525 6 25.63140785196299 26.231557889472366 25.056264066016503 23.080770192548137 7 33.15 26.525 19.625 20.7 8 21.375 24.825 31.55 22.25 9 28.349999999999998 30.075000000000003 21.15 20.424999999999997 10-11 29.6875 25.25 24.075 20.9875 12-13 23.95 22.625 23.2125 30.2125 14-15 24.6125 35.3875 20.3875 19.6125 16-17 23.8875 25.85 29.7125 20.549999999999997 18-19 30.412499999999998 23.9875 22.4375 23.1625 20-21 23.1375 27.200000000000003 26.174999999999997 23.4875 22-23 28.3625 26.737499999999997 26.950000000000003 17.95 24-25 27.5625 23.35 27.8125 21.275 26-27 36.4875 25.637500000000003 21.3625 16.5125 28-29 22.15 32.475 24.575 20.8 30-31 23.200000000000003 18.375 39.875 18.55 32-33 23.9875 15.0875 35.3875 25.5375 34-35 33.1875 14.5375 27.5875 24.6875 36-37 42.55 14.2375 26.275 16.9375 38-39 34.35 18.6 28.15 18.9 40-41 26.487500000000004 19.6375 21.7 32.175 42-43 28.549999999999997 30.7375 20.5375 20.175 44-45 41.449999999999996 21.4125 15.0 22.1375 46-47 28.487499999999997 32.65 16.075 22.787499999999998 48-49 24.875 21.587500000000002 20.837500000000002 32.7 50-51 22.9625 21.4875 16.125 39.425 52-53 26.2125 32.4125 12.562499999999998 28.812500000000004 54-55 20.0125 25.6125 22.2625 32.1125 56-57 19.55 33.1125 15.35 31.9875 58-59 12.587499999999999 31.087500000000002 26.325 30.0 60-61 19.1375 24.1125 23.325000000000003 33.425 62-63 12.575 22.6 37.675 27.150000000000002 64-65 10.975 28.0625 34.887499999999996 26.075 66-67 12.1375 17.837500000000002 36.7875 33.2375 68-69 17.8625 20.75 31.162499999999998 30.225 70-71 16.6 22.6125 37.925 22.8625 72-73 22.275 14.424999999999999 37.45 25.85 74-75 14.4125 12.687499999999998 34.75 38.15 76-77 21.5625 10.8625 42.3375 25.2375 78-79 15.6125 7.8 42.1875 34.4 80-81 18.2375 9.1625 41.05 31.55 82-83 22.162499999999998 9.3125 44.5 24.025 84-85 20.5 10.674999999999999 37.375 31.45 86-87 22.4625 18.4 36.7875 22.35 88-89 14.725 38.6625 30.0875 16.525000000000002 90-91 11.9125 45.875 25.837500000000002 16.375 92-93 11.637500000000001 53.237500000000004 21.325 13.8 94-95 10.1125 60.5 19.825 9.5625 96-97 7.9 67.7875 17.0 7.3125 98-99 7.1499999999999995 75.53750000000001 12.075 5.2375 100-101 4.95 79.3625 10.875 4.8125 >>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 3.0 33 4.5 34 5.5 35 5.5 36 8.0 37 17.0 38 50.5 39 73.0 40 108.0 41 176.5 42 246.0 43 321.0 44 337.5 45 379.0 46 376.5 47 299.0 48 287.5 49 285.0 50 246.5 51 177.0 52 125.0 53 113.5 54 157.0 55 121.5 56 33.0 57 17.0 58 9.5 59 7.0 60 6.0 61 2.5 62 0.0 63 0.5 64 0.5 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 0.0 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 7.725 2 0.0 3 0.0 4 0.0 5 0.0 6 0.025 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 64.925 #Duplication Level Percentage of deduplicated Percentage of total 1 87.94763188294186 57.099999999999994 2 5.467847516365037 7.1 3 1.809780515979977 3.5249999999999995 4 0.9626492106276472 2.5 5 1.001155179052753 3.25 6 0.7316134000770119 2.85 7 0.3080477474008471 1.4000000000000001 8 0.3080477474008471 1.6 9 0.19252984212552945 1.125 >10 1.1551790527531767 13.3 >50 0.07701193685021178 3.6249999999999996 >100 0.03850596842510589 2.625 >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 105 2.625 No Hit TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 94 2.35 RNA PCR Primer, Index 1 (100% over 29bp) GGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 51 1.275 RNA PCR Primer, Index 1 (100% over 22bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 44 1.0999999999999999 No Hit AGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 44 1.0999999999999999 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 36 0.8999999999999999 No Hit GACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 36 0.8999999999999999 RNA PCR Primer, Index 1 (100% over 23bp) ATATATTTCAAGTTATTTCGGATCTTGGAATTCTCGGGTGCCAAGGAACT 21 0.525 RNA PCR Primer, Index 1 (100% over 25bp) CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTC 20 0.5 No Hit ACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCC 20 0.5 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 18 0.44999999999999996 No Hit TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 18 0.44999999999999996 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTTGGAATTCT 17 0.42500000000000004 No Hit CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 17 0.42500000000000004 RNA PCR Primer, Index 1 (100% over 28bp) GACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAAC 17 0.42500000000000004 RNA PCR Primer, Index 1 (100% over 24bp) CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 16 0.4 RNA PCR Primer, Index 1 (100% over 23bp) CTCTGATGATGATCAAACTAATACTTTCGTTCTTCTGGAATTCTCGGGTG 15 0.375 No Hit GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 15 0.375 No Hit TCTCGGGTGCCAAGGAACTCCAGTCACTAGCTTATCTCGTATGCCGTCTT 14 0.35000000000000003 RNA PCR Primer, Index 10 (100% over 50bp) AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 14 0.35000000000000003 Illumina Small RNA Adapter 2 (100% over 21bp) ATTCTCGGGTGCCAAGGAACTCCAGTCACTAGCTTATCTCGTATGCCGTC 13 0.325 RNA PCR Primer, Index 10 (100% over 50bp) GACACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACT 13 0.325 RNA PCR Primer, Index 1 (100% over 25bp) GCCCACCCCAAGATGAGTGCTCTCTCTGGAATTCTCGGGTGCCAAGGAAC 13 0.325 RNA PCR Primer, Index 1 (100% over 24bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTGGAATTCTC 13 0.325 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 12 0.3 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 12 0.3 Illumina Small RNA Adapter 2 (100% over 21bp) AAGGGTGCTGAGAATACTTTGAATCTGACACTGGAATTCTCGGGTGCCAA 12 0.3 No Hit AATTCTCGGGTGCCAAGGAACTCCAGTCACTAGCTTATCTCGTATGCCGT 11 0.27499999999999997 RNA PCR Primer, Index 10 (100% over 50bp) CACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGC 11 0.27499999999999997 No Hit CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGG 10 0.25 No Hit CAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTG 10 0.25 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGAATTCTCGGGTGCCAAGGAACTCCA 10 0.25 RNA PCR Primer, Index 1 (100% over 28bp) CAGGGTTCGTTTCCCTGGATGCGCACCATGGAATTCTCGGGTGCCAAGGA 10 0.25 RNA PCR Primer, Index 1 (100% over 22bp) NCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 9 0.22499999999999998 No Hit TCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTC 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 26bp) GAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAG 9 0.22499999999999998 No Hit TGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAA 9 0.22499999999999998 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCATGGAATTCTCGGGTG 9 0.22499999999999998 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 8 0.2 No Hit TTCGGACCAGGCTTCATTCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 8 0.2 RNA PCR Primer, Index 1 (100% over 29bp) AGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCC 8 0.2 RNA PCR Primer, Index 1 (100% over 27bp) GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTG 8 0.2 No Hit ATATATTTCAAGTTATTTCGGATCTGGAATTCTCGGGTGCCAAGGAACTC 8 0.2 RNA PCR Primer, Index 1 (100% over 26bp) CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGG 8 0.2 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTAATCCTGGAATTC 8 0.2 No Hit GCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAA 8 0.2 RNA PCR Primer, Index 1 (100% over 23bp) CGGATAACCGTAGTAATTCTAGAGCTAATACGTGGAATTCTCGGGTGCCA 7 0.17500000000000002 No Hit CATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTCTCGTGGAATTCTCGGGTG 7 0.17500000000000002 No Hit TCTCGGACCAGGCTTCATTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 29bp) NCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 29bp) CACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACTCC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 27bp) CAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 26bp) ATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACT 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 25bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 6 0.15 No Hit NGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 6 0.15 RNA PCR Primer, Index 1 (100% over 22bp) TTCTCGGGTGCCAAGGAACTCCAGTCACTAGCTTATCTCGTATGCCGTCT 6 0.15 RNA PCR Primer, Index 10 (100% over 50bp) AGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGT 6 0.15 No Hit AGAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTG 6 0.15 No Hit AGTTACTAATTCATGATCTGGCTGGAATTCTCGGGTGCCAAGGAACTCCA 6 0.15 RNA PCR Primer, Index 1 (100% over 28bp) ACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGGAATTCTCGGGTG 6 0.15 No Hit TCCACAGGCTTTCTTGAACTGTGGAATTCTCGGGTGCCAAGGAACTCCAG 6 0.15 RNA PCR Primer, Index 1 (100% over 29bp) TCCGTCGTAGTCTAGGTGGTTAGGATATGGAATTCTCGGGTGCCAAGGAA 6 0.15 RNA PCR Primer, Index 1 (100% over 23bp) GCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCCA 6 0.15 RNA PCR Primer, Index 1 (100% over 28bp) CCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTG 6 0.15 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTCTCGCTGGAATTCTCGGGT 6 0.15 No Hit CACGACTCTCGGCAACGGATATCTCGTGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) NGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATGGAATTCTCGGGTG 6 0.15 No Hit GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGGTG 6 0.15 No Hit CCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACT 6 0.15 RNA PCR Primer, Index 1 (100% over 25bp) ATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAA 6 0.15 RNA PCR Primer, Index 1 (100% over 23bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTTGGAATTCTCGGGTGC 6 0.15 No Hit CACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTGGAATTCTCGGGT 5 0.125 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTAATCTGGAATTCT 5 0.125 No Hit GAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTGC 5 0.125 No Hit AAGGGTGCTGAGAATACTTTGAATCTGACATGGAATTCTCGGGTGCCAAG 5 0.125 No Hit TAATTCATGATCTGGCATGTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 5 0.125 RNA PCR Primer, Index 1 (100% over 31bp) ATTGTATCCTTAACCATTTCTTTTTTGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) ATAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) TGTCGTGCCAATTCAACATAAACCCTGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 5 0.125 Illumina Small RNA Adapter 2 (100% over 21bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTGAATCTGGAATTC 5 0.125 No Hit GGGGATGTAGCTCAGATGGTAGATGGAATTCTCGGGTGCCAAGGAACTCC 5 0.125 RNA PCR Primer, Index 1 (100% over 27bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTTGGAATTCTCGGGTGCC 5 0.125 No Hit CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGGAATTCTCG 5 0.125 No Hit CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGG 5 0.125 No Hit GCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCC 5 0.125 No Hit CTCGGGTGCCAAGGAACTCCAGTCACTAGCTTATCTCGTATGCCGTCTTC 5 0.125 RNA PCR Primer, Index 10 (100% over 50bp) TGCCACGATCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAAT 5 0.125 No Hit CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGG 5 0.125 No Hit ACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTCT 5 0.125 No Hit ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGC 5 0.125 No Hit TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTGGAATTCTCGGGTGC 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGATGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCATGGAATTCTCGGGTGCC 5 0.125 No Hit TAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAACTC 5 0.125 RNA PCR Primer, Index 1 (100% over 26bp) 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 0.075 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 0.125 0.0 0.0 0.0 7 0.0 0.125 0.0 0.0 0.0 8 0.0 0.15 0.0 0.0 0.0 9 0.0 0.2 0.0 0.0 0.0 10-11 0.0 0.2375 0.0 0.0 0.0 12-13 0.0 0.32499999999999996 0.0 0.0 0.0 14-15 0.0 0.5 0.0 0.0 0.0 16-17 0.0 1.1625 0.0 0.0 0.0 18-19 0.0 2.25 0.0 0.0 0.0 20-21 0.0 4.0875 0.0 0.0 0.0 22-23 0.0 12.3375 0.0 0.0 0.0 24-25 0.0 25.5625 0.0 0.0 0.0 26-27 0.0 40.8625 0.0 0.0 0.0 28-29 0.0 48.8625 0.0 0.0 0.0 30-31 0.0 56.0375 0.0 0.0 0.0 32-33 0.0 63.712500000000006 0.0 0.0 0.0 34-35 0.0 72.65 0.0 0.0 0.0 36-37 0.0 81.23750000000001 0.0 0.0 0.0 38-39 0.0 86.425 0.0 0.0 0.0 40-41 0.0 89.525 0.0 0.0 0.0 42-43 0.0 92.7 0.0 0.0 0.0 44-45 0.0 94.23750000000001 0.0 0.0 0.0 46-47 0.0 94.825 0.0 0.0 0.0 48-49 0.0 94.9875 0.0 0.0 0.0 50-51 0.0 95.025 0.0 0.0 0.0 52-53 0.0 95.025 0.0 0.0 0.0 54-55 0.0 95.025 0.0 0.0 0.0 56-57 0.0 95.025 0.0 0.0 0.0 58-59 0.0 95.025 0.0 0.0 0.0 60-61 0.0 95.025 0.0 0.0 0.0 62-63 0.0 95.025 0.0 0.0 0.0 64-65 0.0 95.025 0.0 0.0 0.0 66-67 0.0 95.025 0.0 0.0 0.0 68-69 0.0 95.025 0.0 0.0 0.0 70-71 0.0 95.025 0.0 0.0 0.0 72-73 0.0 95.025 0.0 0.0 0.0 74-75 0.0 95.025 0.0 0.0 0.0 76-77 0.0 95.025 0.0 0.0 0.0 78-79 0.0 95.05 0.0 0.0 0.0 80-81 0.0 95.05 0.0 0.0 0.0 82-83 0.0 95.05 0.0 0.0 0.0 84-85 0.0 95.05 0.0 0.0 0.0 86-87 0.0 95.05 0.0 0.0 0.0 88-89 0.0 95.05 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GCCTTGA 20 9.691041E-6 104.013695 1 TGATGGT 20 1.5462934E-5 94.912506 5 GGTGAAA 20 1.5462934E-5 94.912506 9 ATGGTGA 20 1.5462934E-5 94.912506 7 CCTTGAT 20 1.5462934E-5 94.912506 2 TTGATGG 20 1.5462934E-5 94.912506 4 CTTGATG 20 1.5462934E-5 94.912506 3 TGGTGAA 20 1.5462934E-5 94.912506 8 GATGGTG 20 1.5462934E-5 94.912506 6 GTAGACA 20 5.094958E-4 47.456253 18-19 ACACGCG 20 5.094958E-4 47.456253 22-23 GAAATGG 20 5.094958E-4 47.456253 12-13 CACGCGA 20 5.094958E-4 47.456253 22-23 ATGGTAG 20 5.094958E-4 47.456253 14-15 GACACGC 20 5.094958E-4 47.456253 20-21 AATGGTA 20 5.094958E-4 47.456253 14-15 CGAGACT 20 5.094958E-4 47.456253 26-27 GTGAAAT 20 5.094958E-4 47.456253 10-11 ACGCGAG 20 5.094958E-4 47.456253 24-25 AGACACG 20 5.094958E-4 47.456253 20-21 >>END_MODULE Rejected 927005 READS because READLEN < 1 Read 927005 spots for SRR8846523.sra Written 927005 spots for SRR8846523.sra Rejected 927005 READS because READLEN < 1 Read 927005 spots for SRR8846523.sra Written 927005 spots for SRR8846523.sra Rejected 927005 READS because READLEN < 1 Read 927005 spots for SRR8846523.sra Written 927005 spots for SRR8846523.sra Rejected 927005 READS because READLEN < 1 Read 927005 spots for SRR8846523.sra Written 927005 spots for SRR8846523.sra Rejected 927005 READS because READLEN < 1 Read 927005 spots for SRR8846523.sra Written 927005 spots for SRR8846523.sra Rejected 927005 READS because READLEN < 1 Read 927005 spots for SRR8846523.sra Written 927005 spots for SRR8846523.sra Rejected 927005 READS because READLEN < 1 Read 927005 spots for SRR8846523.sra Written 927005 spots for SRR8846523.sra Rejected 927005 READS because READLEN < 1 Read 927005 spots for SRR8846523.sra Written 927005 spots for SRR8846523.sra Rejected 927005 READS because READLEN < 1 Read 927005 spots for SRR8846523.sra Written 927005 spots for SRR8846523.sra Rejected 927005 READS because READLEN < 1 Read 927005 spots for SRR8846523.sra Written 927005 spots for SRR8846523.sra Rejected 927005 READS because READLEN < 1 Read 927005 spots for SRR8846523.sra Written 927005 spots for SRR8846523.sra Rejected 927005 READS because READLEN < 1 Read 927005 spots for SRR8846523.sra Written 927005 spots for SRR8846523.sra Rejected 927005 READS because READLEN < 1 Read 927005 spots for SRR8846523.sra Written 927005 spots for SRR8846523.sra Rejected 927005 READS because READLEN < 1 Read 927005 spots for SRR8846523.sra Written 927005 spots for SRR8846523.sra Rejected 927005 READS because READLEN < 1 Read 927005 spots for SRR8846523.sra Written 927005 spots for SRR8846523.sra Rejected 927005 READS because READLEN < 1 Read 927005 spots for SRR8846523.sra Written 927005 spots for SRR8846523.sra Rejected 927008 READS because READLEN < 1 Read 927008 spots for SRR8846523.sra Written 927008 spots for SRR8846523.sra Rejected 927005 READS because READLEN < 1 Read 927005 spots for SRR8846523.sra Written 927005 spots for SRR8846523.sra Rejected 927005 READS because READLEN < 1 Read 927005 spots for SRR8846523.sra Written 927005 spots for SRR8846523.sra Rejected 927005 READS because READLEN < 1 Read 927005 spots for SRR8846523.sra Written 927005 spots for SRR8846523.sra SRR ids: ['SRR8846523.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_qwfsgv35 SRR8846523.sra spots: 18540103 blocks: [[1, 927005], [927006, 1854010], [1854011, 2781015], [2781016, 3708020], [3708021, 4635025], [4635026, 5562030], [5562031, 6489035], [6489036, 7416040], [7416041, 8343045], [8343046, 9270050], [9270051, 10197055], [10197056, 11124060], [11124061, 12051065], [12051066, 12978070], [12978071, 13905075], [13905076, 14832080], [14832081, 15759085], [15759086, 16686090], [16686091, 17613095], [17613096, 18540103]] SRR8846523 file size 4450375 SRR8846523 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 SRR8846523 SRR8846523_1.fastq Input file: SRR8846523_1.fastq trimmed: SRR8846523-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 06:20:04 2024 >> started Mon Dec 9 06:20:49 2024 >> done (45.065s) 18540103 reads processed; of these: 382 ( 0.00%) short reads filtered out after trimming by size control 42 ( 0.00%) empty reads filtered out after trimming by size control 18539679 (100.00%) reads available; of these: 4934654 (26.62%) trimmed reads available after processing 13605025 (73.38%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 51 0.00% 19 41 0.00% 20 55 0.00% 21 46 0.00% 22 61 0.00% 23 49 0.00% 24 88 0.00% 25 92 0.00% 26 113 0.00% 27 172 0.00% 28 221 0.00% 29 249 0.00% 30 252 0.00% 31 224 0.00% 32 184 0.00% 33 162 0.00% 34 241 0.00% 35 177 0.00% 36 186 0.00% 37 162 0.00% 38 199 0.00% 39 176 0.00% 40 180 0.00% 41 207 0.00% 42 209 0.00% 43 224 0.00% 44 222 0.00% 45 230 0.00% 46 203 0.00% 47 193 0.00% 48 190 0.00% 49 201 0.00% 50 172 0.00% 51 158 0.00% 52 171 0.00% 53 191 0.00% 54 176 0.00% 55 158 0.00% 56 206 0.00% 57 248 0.00% 58 299 0.00% 59 420 0.00% 60 520 0.00% 61 813 0.00% 62 1219 0.01% 63 1549 0.01% 64 2469 0.01% 65 3196 0.02% 66 6960 0.04% 67 31038 0.17% 68 39819 0.21% 69 26307 0.14% 70 28571 0.15% 71 41387 0.22% 72 16328 0.09% 73 5237 0.03% 74 8267 0.04% 75 4490 0.02% 76 3429 0.02% 77 3276 0.02% 78 3574 0.02% 79 4123 0.02% 80 4705 0.03% 81 5912 0.03% 82 8676 0.05% 83 9488 0.05% 84 10964 0.06% 85 12609 0.07% 86 15681 0.08% 87 21458 0.12% 88 29961 0.16% 89 44844 0.24% 90 68205 0.37% 91 78647 0.42% 92 104269 0.56% 93 170503 0.92% 94 215283 1.16% 95 506272 2.73% 96 558139 3.01% 97 574606 3.10% 98 930840 5.02% 99 929563 5.01% 100 393998 2.13% 101 13605025 73.38% 18539679 reads passed initial QC criterion=sequence-density sequence-density=95.01 sequence-density-rank=1 fanout-score=35.81 fanout-score-rank=1 prefix-density=95.43 prefix-fanout=35.7 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTAGCTTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAT criterion=fanout-score sequence-density=95.01 sequence-density-rank=1 fanout-score=35.81 fanout-score-rank=1 prefix-density=95.43 prefix-fanout=35.7 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTAGCTTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAT 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTAGCTTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAT -o SRR8846523 - Input file: STDIN trimmed: SRR8846523-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTAGCTTATCTCGTATGCCGTCTTCTGCTTGA -- 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 06:23:59 2024 >> started Mon Dec 9 06:25:21 2024 >> done (82.608s) 18153436 reads processed; of these: 326729 ( 1.80%) short reads filtered out after trimming by size control 16250 ( 0.09%) empty reads filtered out after trimming by size control 17810457 (98.11%) reads available; of these: 17390920 (97.64%) trimmed reads available after processing 419537 ( 2.36%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 122719 0.69% 19 226638 1.27% 20 251033 1.41% 21 1069136 6.00% 22 558087 3.13% 23 784663 4.41% 24 2882896 16.19% 25 887260 4.98% 26 750680 4.21% 27 758289 4.26% 28 738044 4.14% 29 720905 4.05% 30 775544 4.35% 31 622492 3.50% 32 806242 4.53% 33 860249 4.83% 34 792691 4.45% 35 776039 4.36% 36 937932 5.27% 37 395842 2.22% 38 327539 1.84% 39 267791 1.50% 40 246407 1.38% 41 270702 1.52% 42 257128 1.44% 43 96145 0.54% 44 108709 0.61% 45 39088 0.22% 46 18569 0.10% 47 11430 0.06% 48 9772 0.05% 49 5296 0.03% 50 3427 0.02% 51 3159 0.02% 52 1615 0.01% 53 1103 0.01% 54 1262 0.01% 55 477 0.00% 56 620 0.00% 57 325 0.00% 58 329 0.00% 59 366 0.00% 60 425 0.00% 61 725 0.00% 62 1064 0.01% 63 1363 0.01% 64 2201 0.01% 65 2912 0.02% 66 6565 0.04% 67 30081 0.17% 68 38568 0.22% 69 25280 0.14% 70 27349 0.15% 71 39769 0.22% 72 14023 0.08% 73 2866 0.02% 74 1467 0.01% 75 1044 0.01% 76 1259 0.01% 77 1917 0.01% 78 1261 0.01% 79 1223 0.01% 80 1664 0.01% 81 1274 0.01% 82 1298 0.01% 83 1608 0.01% 84 1048 0.01% 85 923 0.01% 86 952 0.01% 87 938 0.01% 88 791 0.00% 89 802 0.00% 90 883 0.00% 91 894 0.01% 92 988 0.01% 93 1190 0.01% 94 1351 0.01% 95 1782 0.01% 96 2720 0.02% 97 3389 0.02% 98 5105 0.03% 99 6081 0.03% 100 7650 0.04% 101 177124 0.99% criterion=sequence-density sequence-density=3.94 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=12 prefix-density=0.00 prefix-fanout=1.0 sequence=GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCGGA criterion=fanout-score sequence-density=0.04 sequence-density-rank=22 fanout-score=11.91 fanout-score-rank=1 prefix-density=0.46 prefix-fanout=1.1 sequence=GGCGGATTGCTCGAGCTGCTCACGCGGCGAGAGCGGGTCGCCGCGTGCCGGCCGGGGGACGGACCGGGAGTCGCCCCTTCGGGGGCTTTCCCCGAGCGCTGAACAGTCGACTCAGAACTGGTACGGACAAGGGGAATCCGACTGTTTAATTAAAACAAAGCATTGCGATGGTCCTCGCGGATGCTGACGCAATGTGATTTCTGCCCAGTGCTCTGAATGTCAAAGTGAAGAAATTCAACCAAGCGC Started job on | Dec 09 06:27:47 Started mapping on | Dec 09 06:27:48 Finished on | Dec 09 06:33:16 Mapping speed, Million of reads per hour | 199.72 Number of input reads | 18196700 Average input read length | 31 UNIQUE READS: Uniquely mapped reads number | 3554715 Uniquely mapped reads % | 19.53% Average mapped length | 26.14 Number of splices: Total | 40665 Number of splices: Annotated (sjdb) | 26245 Number of splices: GT/AG | 37942 Number of splices: GC/AG | 2028 Number of splices: AT/AC | 20 Number of splices: Non-canonical | 675 Mismatch rate per base, % | 0.11% Deletion rate per base | 0.00% Deletion average length | 1.33 Insertion rate per base | 0.00% Insertion average length | 1.01 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 6558723 % of reads mapped to multiple loci | 36.04% Number of reads mapped to too many loci | 6950747 % of reads mapped to too many loci | 38.20% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 5.47% % of reads unmapped: other | 0.75% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 8083262 8083262 8083262 N_multimapping 6558723 6558723 6558723 N_noFeature 2311310 2590324 3259822 N_ambiguous 41909 25333 916 UnstrandedReadsAssigned:1201496 PositiveStrandReadsAssigned:939058 NegativeStrandReadsAssigned:293977 Dataset is classified unstranded MeadianReadLen=28 20thPercentileLength=24 echo kmer=19 SRR8846523 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: SRR8846523-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 18,196,700 reads, 5,037,765 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,131 rounds 52973 SRR8846523.ke.tsv 35125 SRR8846523.se.tsv 88098 total ==> SRR8846523.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 8.00438 0.814283 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 0.995624 0.135021 PNS24243 293 194 0 0 KQK14069 1603 1504 46.3361 5.73236 KQK14071 474 375 0 0 ==> SRR8846523.se.tsv <== BRADI_1g14170v3 44 BRADI_1g53295v3 2 BRADI_1g59795v3 0 BRADI_1g07683v3 0 BRADI_1g00485v3 1 BRADI_1g20270v3 34 BRADI_1g74790v3 59 BRADI_1g09890v3 0 BRADI_1g77505v3 6 BRADI_1g48960v3 0 SRR8846523 completed mapping pipeline successfully