Starting /dee2/code/volunteer_pipeline.sh SRR8846486 current disk space = 1503888490496 free memory = 1349404180 SRR8846486 SRAfilesize 3d10f7be85d0eff974ceda0385a65aa0 SRR8846486.sra SRR8846486.sra file validated SRR8846486 is single end SRR8846486 is conventional basespace SRR8846486 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8846486_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 101 %GC 46 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 29.92625 34.0 33.0 34.0 2.0 34.0 2 32.64675 34.0 33.0 34.0 28.0 34.0 3 32.831 34.0 33.0 34.0 31.0 34.0 4 33.13225 34.0 33.0 34.0 32.0 34.0 5 33.17325 34.0 33.0 34.0 32.0 34.0 6 36.83025 38.0 37.0 38.0 35.0 38.0 7 37.216 38.0 38.0 38.0 36.0 38.0 8 37.3345 38.0 38.0 38.0 37.0 38.0 9 37.4195 38.0 38.0 38.0 37.0 38.0 10-11 37.457375 38.0 38.0 38.0 37.0 38.0 12-13 37.462 38.0 38.0 38.0 37.0 38.0 14-15 37.453125 38.0 38.0 38.0 37.5 38.0 16-17 37.431375 38.0 38.0 38.0 37.0 38.0 18-19 37.427625 38.0 38.0 38.0 37.0 38.0 20-21 37.355375 38.0 38.0 38.0 37.0 38.0 22-23 37.440124999999995 38.0 38.0 38.0 37.0 38.0 24-25 37.444374999999994 38.0 38.0 38.0 37.5 38.0 26-27 37.491125 38.0 38.0 38.0 37.0 38.0 28-29 37.283500000000004 38.0 38.0 38.0 36.5 38.0 30-31 37.311375 38.0 38.0 38.0 37.0 38.0 32-33 37.304874999999996 38.0 38.0 38.0 37.0 38.0 34-35 37.125125 38.0 38.0 38.0 36.5 38.0 36-37 37.024375 38.0 38.0 38.0 36.0 38.0 38-39 36.958375000000004 38.0 38.0 38.0 36.0 38.0 40-41 36.67875 38.0 38.0 38.0 35.0 38.0 42-43 36.837 38.0 38.0 38.0 35.5 38.0 44-45 36.887875 38.0 38.0 38.0 35.5 38.0 46-47 36.761750000000006 38.0 38.0 38.0 35.0 38.0 48-49 36.777875 38.0 38.0 38.0 34.5 38.0 50-51 36.818375 38.0 38.0 38.0 35.0 38.0 52-53 36.879125 38.0 38.0 38.0 35.0 38.0 54-55 36.797250000000005 38.0 38.0 38.0 35.5 38.0 56-57 36.280249999999995 38.0 38.0 38.0 33.0 38.0 58-59 36.34125 38.0 37.5 38.0 33.5 38.0 60-61 36.27575 38.0 37.5 38.0 33.0 38.0 62-63 35.966375 38.0 37.0 38.0 30.0 38.0 64-65 35.545125 38.0 36.5 38.0 28.5 38.0 66-67 35.187250000000006 38.0 36.0 38.0 27.5 38.0 68-69 35.741875 38.0 37.0 38.0 29.5 38.0 70-71 35.269000000000005 38.0 37.0 38.0 28.0 38.0 72-73 35.473 38.0 37.0 38.0 28.5 38.0 74-75 35.056 38.0 36.5 38.0 28.0 38.0 76-77 34.908500000000004 38.0 36.0 38.0 27.5 38.0 78-79 34.004374999999996 38.0 34.0 38.0 20.5 38.0 80-81 34.458875 38.0 35.5 38.0 26.0 38.0 82-83 34.1775 38.0 35.0 38.0 24.5 38.0 84-85 34.460375 38.0 35.5 38.0 26.0 38.0 86-87 34.711625 38.0 36.0 38.0 27.0 38.0 88-89 34.465374999999995 38.0 35.5 38.0 27.0 38.0 90-91 34.1495 38.0 35.0 38.0 24.0 38.0 92-93 33.706125 38.0 34.5 38.0 19.5 38.0 94-95 33.323125 38.0 34.5 38.0 15.0 38.0 96-97 31.851125000000003 38.0 34.0 38.0 8.0 38.0 98-99 29.32125 38.0 27.5 38.0 2.0 38.0 100-101 26.22175 36.5 2.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 0.0 14 0.0 15 0.0 16 1.0 17 0.0 18 2.0 19 0.0 20 3.0 21 4.0 22 2.0 23 13.0 24 24.0 25 29.0 26 33.0 27 35.0 28 38.0 29 42.0 30 59.0 31 83.0 32 132.0 33 163.0 34 278.0 35 523.0 36 1080.0 37 1455.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 29.239766081871345 28.32080200501253 20.439988861041492 21.99944305207463 2 27.075 27.224999999999998 19.650000000000002 26.05 3 26.55 22.1 20.175 31.175000000000004 4 27.325 30.525000000000002 19.375 22.775000000000002 5 28.325 26.825 22.175 22.675 6 23.825 27.525 26.450000000000003 22.2 7 34.4 26.3 19.8 19.5 8 22.225 22.575 33.050000000000004 22.15 9 25.75 32.6 20.9 20.75 10-11 29.8875 25.3 23.825 20.9875 12-13 24.575 23.6125 21.224999999999998 30.587500000000002 14-15 23.200000000000003 36.125 21.987499999999997 18.6875 16-17 23.962500000000002 27.3375 28.95 19.75 18-19 31.0125 24.462500000000002 22.725 21.8 20-21 22.3 29.062500000000004 25.662499999999998 22.975 22-23 27.950000000000003 29.15 25.85 17.05 24-25 27.450000000000003 25.4875 26.5875 20.474999999999998 26-27 35.2625 26.125 21.462500000000002 17.150000000000002 28-29 23.625 31.6 23.962500000000002 20.8125 30-31 24.462500000000002 20.6375 36.1875 18.712500000000002 32-33 23.1875 17.5375 34.7125 24.5625 34-35 31.574999999999996 16.6 28.725 23.1 36-37 37.3125 15.950000000000001 29.212500000000002 17.525 38-39 33.4875 18.1375 29.2375 19.1375 40-41 28.549999999999997 18.6 23.799999999999997 29.049999999999997 42-43 30.099999999999998 25.924999999999997 22.925 21.05 44-45 40.2125 20.549999999999997 17.0375 22.2 46-47 30.425 29.95 16.1 23.525 48-49 27.462500000000002 22.6 19.875 30.062499999999996 50-51 24.7 23.2125 16.2125 35.875 52-53 27.400000000000002 30.4875 12.3875 29.725 54-55 23.6625 27.925 17.65 30.7625 56-57 21.8125 31.337500000000002 13.9875 32.8625 58-59 20.4875 33.7875 14.924999999999999 30.8 60-61 17.0875 29.95 19.925 33.037499999999994 62-63 21.987499999999997 32.2875 16.6125 29.1125 64-65 17.299999999999997 32.824999999999996 23.4375 26.437500000000004 66-67 16.125 24.3625 26.875 32.6375 68-69 20.875 25.924999999999997 23.25 29.95 70-71 19.6875 28.050000000000004 28.999999999999996 23.2625 72-73 22.7 21.1875 29.475 26.637499999999996 74-75 21.15 17.75 26.4125 34.6875 76-77 21.5625 15.137500000000001 36.95 26.35 78-79 17.724999999999998 10.9 38.65 32.725 80-81 20.599999999999998 11.0125 37.1375 31.25 82-83 22.05 10.012500000000001 40.775 27.1625 84-85 20.8625 9.45 39.225 30.4625 86-87 21.975 14.75 37.5875 25.687500000000004 88-89 16.575 31.2125 33.074999999999996 19.1375 90-91 13.5875 38.525 29.912499999999998 17.974999999999998 92-93 13.100000000000001 46.8375 23.5625 16.5 94-95 12.1625 55.93749999999999 21.075 10.825 96-97 8.3 64.6875 18.4125 8.6 98-99 7.8125 73.2 13.0125 5.975 100-101 5.5875 79.9125 9.7875 4.7125 >>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 0.0 32 0.0 33 2.5 34 5.0 35 5.0 36 6.5 37 11.0 38 15.0 39 51.0 40 80.5 41 98.0 42 161.5 43 219.0 44 277.5 45 330.5 46 373.0 47 381.5 48 310.0 49 291.0 50 320.5 51 274.5 52 180.5 53 129.5 54 123.5 55 150.0 56 114.0 57 36.0 58 20.0 59 12.5 60 8.0 61 4.5 62 2.0 63 2.0 64 2.0 65 1.5 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 10.225 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 63.24999999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 86.7588932806324 54.87499999999999 2 5.8102766798418966 7.35 3 2.292490118577075 4.35 4 1.4229249011857708 3.5999999999999996 5 0.7509881422924901 2.375 6 0.6324110671936759 2.4 7 0.47430830039525695 2.1 8 0.3557312252964427 1.7999999999999998 9 0.15810276679841898 0.8999999999999999 >10 1.225296442687747 15.45 >50 0.11857707509881424 4.8 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences fail #Sequence Count Percentage Possible Source TCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 88 2.1999999999999997 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 53 1.325 No Hit GGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 51 1.275 RNA PCR Primer, Index 1 (100% over 22bp) AGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 50 1.25 No Hit TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 44 1.0999999999999999 RNA PCR Primer, Index 1 (100% over 29bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 43 1.075 No Hit GACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAAC 36 0.8999999999999999 RNA PCR Primer, Index 1 (100% over 24bp) ATATATTTCAAGTTATTTCGGATCTTGGAATTCTCGGGTGCCAAGGAACT 29 0.7250000000000001 RNA PCR Primer, Index 1 (100% over 25bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTTGGAATTCT 28 0.7000000000000001 No Hit CTCTGATGATGATCAAACTAATACTTTCGTTCTTCTGGAATTCTCGGGTG 27 0.675 No Hit AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 23 0.575 Illumina Small RNA Adapter 2 (100% over 21bp) TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 22 0.5499999999999999 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 21 0.525 Illumina Small RNA Adapter 2 (100% over 21bp) CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 21 0.525 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 19 0.475 No Hit CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGG 19 0.475 No Hit CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTC 19 0.475 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTGGAATTCTC 18 0.44999999999999996 No Hit AATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCGTATGCCGT 17 0.42500000000000004 RNA PCR Primer, Index 9 (100% over 50bp) GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 15 0.375 No Hit ACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCC 15 0.375 No Hit GCACCAGTGGTCTAGTGGTAGAATAGTACCTGGAATTCTCGGGTGCCAAG 13 0.325 No Hit CAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTG 13 0.325 No Hit GCCCACCCCAAGATGAGTGCTCTCTCTGGAATTCTCGGGTGCCAAGGAAC 13 0.325 RNA PCR Primer, Index 1 (100% over 24bp) GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTG 12 0.3 No Hit CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 12 0.3 RNA PCR Primer, Index 1 (100% over 28bp) GACACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACT 12 0.3 RNA PCR Primer, Index 1 (100% over 25bp) TCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCGTATGCCGTCTT 12 0.3 RNA PCR Primer, Index 9 (100% over 50bp) ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGC 12 0.3 No Hit NCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 11 0.27499999999999997 No Hit GACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 23bp) CTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCGTATGCCGTCTTC 11 0.27499999999999997 RNA PCR Primer, Index 9 (100% over 50bp) CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGG 10 0.25 No Hit CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGGAATTCTCG 10 0.25 No Hit CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGG 9 0.22499999999999998 No Hit CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 23bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTCATGGAATTCTCGGGTG 9 0.22499999999999998 No Hit CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGG 9 0.22499999999999998 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTAATCTGGAATTCT 8 0.2 No Hit AGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGT 8 0.2 No Hit ATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCGTATGCCGTC 8 0.2 RNA PCR Primer, Index 9 (100% over 50bp) TCGGATAACCGTAGTAATTCTAGAGCTAATACGTGGAATTCTCGGGTGCC 8 0.2 No Hit CGGTCGAGGGCACGCCTGCCTGGGCGTCACGCTGGAATTCTCGGGTGCCA 8 0.2 No Hit TCTCGGACCAGGCTTCATTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 8 0.2 RNA PCR Primer, Index 1 (100% over 29bp) NCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 8 0.2 RNA PCR Primer, Index 1 (100% over 29bp) NGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 8 0.2 No Hit CGGATAACCGTAGTAATTCTAGAGCTAATACTGGAATTCTCGGGTGCCAA 8 0.2 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit CGGATAACCGTAGTAATTCTAGAGCTAATACGTGGAATTCTCGGGTGCCA 7 0.17500000000000002 No Hit TTCGGACCAGGCTTCATTCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 29bp) TCCTGTGGATGAGAAGGCATTTATATTCTGATGATATGGAATTCTCGGGT 7 0.17500000000000002 No Hit GGGGATGTAGCTCAGATGGTAGATGGAATTCTCGGGTGCCAAGGAACTCC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 27bp) ACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATT 7 0.17500000000000002 No Hit TGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAA 7 0.17500000000000002 No Hit ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGGTGC 7 0.17500000000000002 No Hit GCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit GACACGACTCTCGGCAACGGATATCTCGTGGAATTCTCGGGTGCCAAGGA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 22bp) GACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGTGGAATTCTC 7 0.17500000000000002 No Hit CTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCA 7 0.17500000000000002 No Hit TCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTC 6 0.15 RNA PCR Primer, Index 1 (100% over 26bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 6 0.15 Illumina Small RNA Adapter 2 (100% over 21bp) AAGGGTGCTGAGAATACTTTGAATCTGACATGGAATTCTCGGGTGCCAAG 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAAAAATGGAATTCTCGGGTG 6 0.15 No Hit CCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTG 6 0.15 No Hit GATAACCGTAGTAATTCTAGAGCTAATACTGGAATTCTCGGGTGCCAAGG 6 0.15 Illumina Small RNA Adapter 2 (100% over 21bp) TGCAAGTATGAACTAATTTGAACTGTGAAACTTGGAATTCTCGGGTGCCA 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 6 0.15 Illumina Small RNA Adapter 2 (100% over 21bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTGAATCTGGAATTC 6 0.15 No Hit CACGACTCTCGGCAACGGATATCTCGTGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) AAGGGTGCTGAGAATACTTTGAATCTGACACTGGAATTCTCGGGTGCCAA 6 0.15 No Hit TTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCGTATGCCGTCT 6 0.15 RNA PCR Primer, Index 9 (100% over 50bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCTGGAATTC 6 0.15 No Hit GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGGTG 6 0.15 No Hit TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGG 6 0.15 No Hit CAGGGTTCGTTTCCCTGGATGCGCACCATGGAATTCTCGGGTGCCAAGGA 6 0.15 RNA PCR Primer, Index 1 (100% over 22bp) TCCGTCGTAGTCTAGGTGGTTAGGATACTCTGGAATTCTCGGGTGCCAAG 5 0.125 No Hit CACCATGCGCGGGTTCAATTCCCGTCGTTCGCCCCATGGAATTCTCGGGT 5 0.125 No Hit CATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGCC 5 0.125 No Hit NGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 5 0.125 Illumina Small RNA Adapter 2 (100% over 21bp) AAGTATGAACTAATTTGAACTGTGAAACTTGGAATTCTCGGGTGCCAAGG 5 0.125 Illumina Small RNA Adapter 2 (100% over 21bp) ATTGTATCCTTAACCATTTCTTTTTTGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) GATAACCGTAGTAATTCTAGAGCTAATATGGAATTCTCGGGTGCCAAGGA 5 0.125 RNA PCR Primer, Index 1 (100% over 22bp) TCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCG 5 0.125 No Hit CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTCGGGT 5 0.125 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGAATTCTCGGGTGCCAAGGAACTCCA 5 0.125 RNA PCR Primer, Index 1 (100% over 28bp) GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTAATCCTGGAATTC 5 0.125 No Hit GGGGATATAGCTCAGTTGGTAGATGGAATTCTCGGGTGCCAAGGAACTCC 5 0.125 RNA PCR Primer, Index 1 (100% over 27bp) NACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) CAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTC 5 0.125 RNA PCR Primer, Index 1 (100% over 26bp) CATCGAGTAGACCTTGTTATTGTGAGAATTATGGAATTCTCGGGTGCCAA 5 0.125 No Hit ATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) NGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 5 0.125 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTTGGAATTCTCGGGTGC 5 0.125 No Hit CACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGC 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 0.05 0.0 0.0 0.0 7 0.0 0.05 0.0 0.0 0.0 8 0.0 0.05 0.0 0.0 0.0 9 0.0 0.125 0.0 0.0 0.0 10-11 0.0 0.16249999999999998 0.0 0.0 0.0 12-13 0.0 0.25 0.0 0.0 0.0 14-15 0.0 0.375 0.0 0.0 0.0 16-17 0.0 0.9 0.0 0.0 0.0 18-19 0.0 1.5 0.0 0.0 0.0 20-21 0.0 2.9749999999999996 0.0 0.0 0.0 22-23 0.0 8.675 0.0 0.0 0.0 24-25 0.0 19.825 0.0 0.0 0.0 26-27 0.0 32.7375 0.0 0.0 0.0 28-29 0.0 40.8 0.0 0.0 0.0 30-31 0.0 50.025000000000006 0.0 0.0 0.0 32-33 0.0 58.7375 0.0 0.0 0.0 34-35 0.0 68.1 0.0 0.0 0.0 36-37 0.0 77.35 0.0 0.0 0.0 38-39 0.0 83.05000000000001 0.0 0.0 0.0 40-41 0.0 86.4375 0.0 0.0 0.0 42-43 0.0 90.625 0.0 0.0 0.0 44-45 0.0 92.8125 0.0 0.0 0.0 46-47 0.0 93.5875 0.0 0.0 0.0 48-49 0.0 93.9125 0.0 0.0 0.0 50-51 0.0 94.0625 0.0 0.0 0.0 52-53 0.0 94.15 0.0 0.0 0.0 54-55 0.0 94.1625 0.0 0.0 0.0 56-57 0.0 94.2 0.0 0.0 0.0 58-59 0.0 94.2 0.0 0.0 0.0 60-61 0.0 94.2 0.0 0.0 0.0 62-63 0.0 94.2 0.0 0.0 0.0 64-65 0.0 94.2 0.0 0.0 0.0 66-67 0.0 94.2 0.0 0.0 0.0 68-69 0.0 94.2 0.0 0.0 0.0 70-71 0.0 94.2 0.0 0.0 0.0 72-73 0.0 94.2 0.0 0.0 0.0 74-75 0.0 94.2 0.0 0.0 0.0 76-77 0.0 94.2 0.0 0.0 0.0 78-79 0.0 94.2 0.0 0.0 0.0 80-81 0.0 94.2 0.0 0.0 0.0 82-83 0.0 94.2 0.0 0.0 0.0 84-85 0.0 94.2 0.0 0.0 0.0 86-87 0.0 94.2 0.0 0.0 0.0 88-89 0.0 94.2 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GACACGA 15 4.4910912E-4 102.62162 1 TCCACTG 15 4.4910912E-4 102.62162 1 GGGATTG 15 4.4910912E-4 102.62162 1 CATCGAG 20 1.038194E-5 102.62161 1 GTAGACC 25 3.8470353E-7 94.924995 7 ACACGAC 15 6.1614934E-4 94.924995 2 TTGTAGT 15 6.1614934E-4 94.924995 5 AGTAGAC 25 3.8470353E-7 94.924995 6 CACTGAG 15 6.1614934E-4 94.924995 3 GATTGTA 15 6.1614934E-4 94.924995 3 TAGTTCA 15 6.1614934E-4 94.924995 8 CCACTGA 15 6.1614934E-4 94.924995 2 GAGTAGA 25 3.8470353E-7 94.924995 5 ATTGTAG 15 6.1614934E-4 94.924995 4 TGTAGTT 15 6.1614934E-4 94.924995 6 CGAGTAG 25 3.8470353E-7 94.924995 4 AGACCTT 25 3.8470353E-7 94.924995 9 ATCGAGT 25 3.8470353E-7 94.924995 2 TCGAGTA 25 3.8470353E-7 94.924995 3 AGTTCAA 15 6.1614934E-4 94.924995 9 >>END_MODULE Rejected 1219724 READS because READLEN < 1 Read 1219724 spots for SRR8846486.sra Written 1219724 spots for SRR8846486.sra Rejected 1219724 READS because READLEN < 1 Read 1219724 spots for SRR8846486.sra Written 1219724 spots for SRR8846486.sra Rejected 1219724 READS because READLEN < 1 Read 1219724 spots for SRR8846486.sra Written 1219724 spots for SRR8846486.sra Rejected 1219724 READS because READLEN < 1 Read 1219724 spots for SRR8846486.sra Written 1219724 spots for SRR8846486.sra Rejected 1219724 READS because READLEN < 1 Read 1219724 spots for SRR8846486.sra Written 1219724 spots for SRR8846486.sra Rejected 1219724 READS because READLEN < 1 Read 1219724 spots for SRR8846486.sra Written 1219724 spots for SRR8846486.sra Rejected 1219724 READS because READLEN < 1 Read 1219724 spots for SRR8846486.sra Written 1219724 spots for SRR8846486.sra Rejected 1219724 READS because READLEN < 1 Read 1219724 spots for SRR8846486.sra Written 1219724 spots for SRR8846486.sra Rejected 1219724 READS because READLEN < 1 Read 1219724 spots for SRR8846486.sra Written 1219724 spots for SRR8846486.sra Rejected 1219724 READS because READLEN < 1 Read 1219724 spots for SRR8846486.sra Written 1219724 spots for SRR8846486.sra Rejected 1219724 READS because READLEN < 1 Read 1219724 spots for SRR8846486.sra Written 1219724 spots for SRR8846486.sra Rejected 1219724 READS because READLEN < 1 Read 1219724 spots for SRR8846486.sra Written 1219724 spots for SRR8846486.sra Rejected 1219724 READS because READLEN < 1 Read 1219724 spots for SRR8846486.sra Written 1219724 spots for SRR8846486.sra Rejected 1219724 READS because READLEN < 1 Read 1219724 spots for SRR8846486.sra Written 1219724 spots for SRR8846486.sra Rejected 1219731 READS because READLEN < 1 Read 1219731 spots for SRR8846486.sra Written 1219731 spots for SRR8846486.sra Rejected 1219724 READS because READLEN < 1 Read 1219724 spots for SRR8846486.sra Written 1219724 spots for SRR8846486.sra Rejected 1219724 READS because READLEN < 1 Read 1219724 spots for SRR8846486.sra Written 1219724 spots for SRR8846486.sra Rejected 1219724 READS because READLEN < 1 Read 1219724 spots for SRR8846486.sra Written 1219724 spots for SRR8846486.sra Rejected 1219724 READS because READLEN < 1 Read 1219724 spots for SRR8846486.sra Written 1219724 spots for SRR8846486.sra Rejected 1219724 READS because READLEN < 1 Read 1219724 spots for SRR8846486.sra Written 1219724 spots for SRR8846486.sra SRR ids: ['SRR8846486.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_9udo27r0 SRR8846486.sra spots: 24394487 blocks: [[1, 1219724], [1219725, 2439448], [2439449, 3659172], [3659173, 4878896], [4878897, 6098620], [6098621, 7318344], [7318345, 8538068], [8538069, 9757792], [9757793, 10977516], [10977517, 12197240], [12197241, 13416964], [13416965, 14636688], [14636689, 15856412], [15856413, 17076136], [17076137, 18295860], [18295861, 19515584], [19515585, 20735308], [20735309, 21955032], [21955033, 23174756], [23174757, 24394487]] SRR8846486 file size 5862516 SRR8846486 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 SRR8846486 SRR8846486_1.fastq Input file: SRR8846486_1.fastq trimmed: SRR8846486-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 18:38:40 2024 >> started Sun Dec 8 18:39:43 2024 >> done (62.487s) 24394487 reads processed; of these: 485 ( 0.00%) short reads filtered out after trimming by size control 75 ( 0.00%) empty reads filtered out after trimming by size control 24393927 (100.00%) reads available; of these: 4640633 (19.02%) trimmed reads available after processing 19753294 (80.98%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 65 0.00% 19 49 0.00% 20 56 0.00% 21 53 0.00% 22 64 0.00% 23 92 0.00% 24 97 0.00% 25 138 0.00% 26 162 0.00% 27 205 0.00% 28 249 0.00% 29 269 0.00% 30 238 0.00% 31 239 0.00% 32 239 0.00% 33 212 0.00% 34 247 0.00% 35 223 0.00% 36 220 0.00% 37 231 0.00% 38 247 0.00% 39 254 0.00% 40 265 0.00% 41 285 0.00% 42 317 0.00% 43 337 0.00% 44 335 0.00% 45 408 0.00% 46 405 0.00% 47 351 0.00% 48 376 0.00% 49 392 0.00% 50 357 0.00% 51 335 0.00% 52 378 0.00% 53 390 0.00% 54 407 0.00% 55 325 0.00% 56 406 0.00% 57 458 0.00% 58 481 0.00% 59 592 0.00% 60 752 0.00% 61 1029 0.00% 62 1556 0.01% 63 1700 0.01% 64 2851 0.01% 65 4014 0.02% 66 9230 0.04% 67 44088 0.18% 68 56209 0.23% 69 44711 0.18% 70 37268 0.15% 71 48646 0.20% 72 20603 0.08% 73 6231 0.03% 74 7075 0.03% 75 4555 0.02% 76 3861 0.02% 77 3821 0.02% 78 4290 0.02% 79 4564 0.02% 80 4848 0.02% 81 5918 0.02% 82 9245 0.04% 83 9621 0.04% 84 10324 0.04% 85 11625 0.05% 86 14073 0.06% 87 19264 0.08% 88 26153 0.11% 89 39724 0.16% 90 58557 0.24% 91 69712 0.29% 92 91805 0.38% 93 153412 0.63% 94 198313 0.81% 95 447459 1.83% 96 536475 2.20% 97 560520 2.30% 98 807604 3.31% 99 837156 3.43% 100 410322 1.68% 101 19753294 80.98% 24393927 reads passed initial QC criterion=sequence-density sequence-density=94.53 sequence-density-rank=1 fanout-score=35.58 fanout-score-rank=2 prefix-density=94.88 prefix-fanout=35.5 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA criterion=fanout-score sequence-density=1.92 sequence-density-rank=4 fanout-score=51.88 fanout-score-rank=1 prefix-density=98.88 prefix-fanout=1.0 sequence=CACGATCAGATATCGTATGCCGT 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA -o SRR8846486 - Input file: STDIN trimmed: SRR8846486-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCGTATGCCGTCTTCTGCTTGA -- 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 18:43:44 2024 >> started Sun Dec 8 18:45:43 2024 >> done (118.380s) 23880371 reads processed; of these: 296253 ( 1.24%) short reads filtered out after trimming by size control 12751 ( 0.05%) empty reads filtered out after trimming by size control 23571367 (98.71%) reads available; of these: 23028510 (97.70%) trimmed reads available after processing 542857 ( 2.30%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 114038 0.48% 19 213376 0.91% 20 258348 1.10% 21 992527 4.21% 22 599280 2.54% 23 844476 3.58% 24 2790280 11.84% 25 1114165 4.73% 26 1050821 4.46% 27 956634 4.06% 28 1058031 4.49% 29 1135218 4.82% 30 1176856 4.99% 31 929443 3.94% 32 1177886 5.00% 33 1226984 5.21% 34 1232670 5.23% 35 1136977 4.82% 36 1199053 5.09% 37 648445 2.75% 38 554913 2.35% 39 485719 2.06% 40 472293 2.00% 41 530387 2.25% 42 500850 2.12% 43 207923 0.88% 44 208747 0.89% 45 88657 0.38% 46 42881 0.18% 47 25306 0.11% 48 20083 0.09% 49 10424 0.04% 50 6189 0.03% 51 5705 0.02% 52 2945 0.01% 53 2176 0.01% 54 2435 0.01% 55 930 0.00% 56 864 0.00% 57 505 0.00% 58 463 0.00% 59 473 0.00% 60 551 0.00% 61 823 0.00% 62 1189 0.01% 63 1373 0.01% 64 2429 0.01% 65 3596 0.02% 66 8655 0.04% 67 42716 0.18% 68 54438 0.23% 69 43104 0.18% 70 35882 0.15% 71 46903 0.20% 72 18073 0.08% 73 4049 0.02% 74 1991 0.01% 75 1479 0.01% 76 1879 0.01% 77 2845 0.01% 78 2113 0.01% 79 1999 0.01% 80 2440 0.01% 81 1942 0.01% 82 1860 0.01% 83 2169 0.01% 84 1388 0.01% 85 1234 0.01% 86 1224 0.01% 87 1098 0.00% 88 996 0.00% 89 1052 0.00% 90 1088 0.00% 91 1196 0.01% 92 1232 0.01% 93 1462 0.01% 94 1454 0.01% 95 2076 0.01% 96 3015 0.01% 97 3928 0.02% 98 5916 0.03% 99 7263 0.03% 100 9273 0.04% 101 215598 0.91% criterion=sequence-density sequence-density=3.52 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=11 prefix-density=0.00 prefix-fanout=1.0 sequence=CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATTCAAGAG criterion=fanout-score sequence-density=0.01 sequence-density-rank=38 fanout-score=106.54 fanout-score-rank=1 prefix-density=0.65 prefix-fanout=1.0 sequence=GTAGCCAAGTGCGGAGAGGATAACTGCTGAAAGCATATAAGTAGTAAGCCCACCCCAAGATGAGTGCTCTCTCCT Started job on | Dec 08 18:48:24 Started mapping on | Dec 08 18:48:24 Finished on | Dec 08 18:58:32 Mapping speed, Million of reads per hour | 142.61 Number of input reads | 24084923 Average input read length | 32 UNIQUE READS: Uniquely mapped reads number | 3903263 Uniquely mapped reads % | 16.21% Average mapped length | 27.36 Number of splices: Total | 57210 Number of splices: Annotated (sjdb) | 40450 Number of splices: GT/AG | 53848 Number of splices: GC/AG | 2288 Number of splices: AT/AC | 36 Number of splices: Non-canonical | 1038 Mismatch rate per base, % | 0.12% Deletion rate per base | 0.00% Deletion average length | 1.32 Insertion rate per base | 0.00% Insertion average length | 1.03 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 8700920 % of reads mapped to multiple loci | 36.13% Number of reads mapped to too many loci | 10102401 % of reads mapped to too many loci | 41.94% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 5.15% % of reads unmapped: other | 0.57% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 11480740 11480740 11480740 N_multimapping 8700920 8700920 8700920 N_noFeature 2236739 2563769 3556842 N_ambiguous 56537 36485 898 UnstrandedReadsAssigned:1609987 PositiveStrandReadsAssigned:1303009 NegativeStrandReadsAssigned:345523 Dataset is classified unstranded MeadianReadLen=30 20thPercentileLength=24 echo kmer=19 SRR8846486 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: SRR8846486-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 24,084,923 reads, 6,495,647 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,117 rounds 52973 SRR8846486.ke.tsv 35125 SRR8846486.se.tsv 88098 total ==> SRR8846486.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 1.72969 0.263773 PNS24249 1928 1829 1.94417 0.153184 PNS24246 1044 945 1.72969 0.263773 PNS24248 1044 945 1.72969 0.263773 PNS24244 1471 1372 0 0 PNS24243 293 194 2 1.48567 KQK14069 1603 1504 33.4044 3.20073 KQK14071 474 375 0 0 ==> SRR8846486.se.tsv <== BRADI_1g14170v3 50 BRADI_1g53295v3 3 BRADI_1g59795v3 13 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 44 BRADI_1g74790v3 41 BRADI_1g09890v3 2 BRADI_1g77505v3 5 BRADI_1g48960v3 0 SRR8846486 completed mapping pipeline successfully