Starting /dee2/code/volunteer_pipeline.sh SRR8846496 current disk space = 1500451807232 free memory = 1362355328 SRR8846496 SRAfilesize 87e73e9695f72d44edb27d94f5eb7deb SRR8846496.sra SRR8846496.sra file validated SRR8846496 is single end SRR8846496 is conventional basespace SRR8846496 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8846496_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 48 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.04725 33.0 33.0 34.0 18.0 34.0 2 32.65425 34.0 33.0 34.0 28.0 34.0 3 32.85225 34.0 33.0 34.0 31.0 34.0 4 33.087 34.0 33.0 34.0 32.0 34.0 5 33.13075 34.0 33.0 34.0 32.0 34.0 6 36.828 38.0 37.0 38.0 35.0 38.0 7 37.20125 38.0 38.0 38.0 36.0 38.0 8 37.3775 38.0 38.0 38.0 37.0 38.0 9 37.43125 38.0 38.0 38.0 37.0 38.0 10-11 37.49125 38.0 38.0 38.0 37.0 38.0 12-13 37.53 38.0 38.0 38.0 37.5 38.0 14-15 37.465375 38.0 38.0 38.0 37.0 38.0 16-17 37.401375 38.0 38.0 38.0 37.0 38.0 18-19 37.49325 38.0 38.0 38.0 37.0 38.0 20-21 37.420625 38.0 38.0 38.0 37.0 38.0 22-23 37.41875 38.0 38.0 38.0 37.0 38.0 24-25 37.450874999999996 38.0 38.0 38.0 37.0 38.0 26-27 37.560625 38.0 38.0 38.0 37.5 38.0 28-29 37.376374999999996 38.0 38.0 38.0 37.5 38.0 30-31 37.309875 38.0 38.0 38.0 36.5 38.0 32-33 37.26625 38.0 38.0 38.0 37.0 38.0 34-35 37.00975 38.0 38.0 38.0 36.0 38.0 36-37 36.834625 38.0 38.0 38.0 35.5 38.0 38-39 36.636750000000006 38.0 38.0 38.0 34.0 38.0 40-41 36.755250000000004 38.0 38.0 38.0 35.0 38.0 42-43 36.538124999999994 38.0 38.0 38.0 34.0 38.0 44-45 36.76875 38.0 38.0 38.0 35.0 38.0 46-47 36.707125 38.0 38.0 38.0 34.5 38.0 48-49 36.731624999999994 38.0 38.0 38.0 35.0 38.0 50-51 36.817 38.0 38.0 38.0 35.0 38.0 52-53 36.867000000000004 38.0 38.0 38.0 35.0 38.0 54-55 36.749 38.0 38.0 38.0 34.5 38.0 56-57 36.406000000000006 38.0 37.5 38.0 33.5 38.0 58-59 36.256375000000006 38.0 37.0 38.0 33.5 38.0 60-61 36.095124999999996 38.0 37.0 38.0 32.0 38.0 62-63 35.605625 38.0 37.0 38.0 29.0 38.0 64-65 35.637 38.0 37.0 38.0 29.5 38.0 66-67 34.969625 38.0 36.0 38.0 27.0 38.0 68-69 34.878375 38.0 36.0 38.0 27.0 38.0 70-71 34.506125 38.0 35.5 38.0 26.0 38.0 72-73 34.188125 38.0 34.5 38.0 25.0 38.0 74-75 33.697 38.0 34.0 38.0 20.0 38.0 76-77 33.18325 37.5 33.5 38.0 15.5 38.0 78-79 33.300125 37.0 33.0 38.0 16.0 38.0 80-81 32.597624999999994 37.0 31.0 38.0 15.0 38.0 82-83 32.405 37.0 31.0 38.0 15.0 38.0 84-85 32.200500000000005 37.0 29.0 38.0 15.0 38.0 86-87 32.324749999999995 37.0 30.0 38.0 15.0 38.0 88-89 32.420375 37.0 31.0 38.0 15.0 38.0 90-91 32.542249999999996 37.0 32.0 38.0 15.0 38.0 92-93 32.686125000000004 37.0 33.0 38.0 15.0 38.0 94-95 32.611999999999995 38.0 33.0 38.0 15.0 38.0 96-97 31.180875 37.0 30.0 38.0 8.5 38.0 98-99 30.054375 37.0 28.5 38.0 2.0 38.0 100-101 28.781625 37.0 25.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 10 1.0 11 0.0 12 0.0 13 1.0 14 0.0 15 0.0 16 1.0 17 2.0 18 0.0 19 5.0 20 5.0 21 6.0 22 9.0 23 14.0 24 16.0 25 35.0 26 28.0 27 35.0 28 36.0 29 54.0 30 74.0 31 83.0 32 152.0 33 218.0 34 375.0 35 676.0 36 1283.0 37 891.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 36.247571468220926 23.31390507910075 19.594782126006105 20.84374132667222 2 28.925 26.075 17.125 27.875 3 30.049999999999997 18.65 17.474999999999998 33.825 4 24.349999999999998 38.025 17.575 20.05 5 27.125 23.799999999999997 25.8 23.275000000000002 6 26.150000000000002 24.275 29.349999999999998 20.225 7 39.800000000000004 26.55 16.5 17.150000000000002 8 19.875 22.2 38.65 19.275000000000002 9 23.799999999999997 39.45 19.975 16.775000000000002 10-11 32.1625 22.112499999999997 26.875 18.85 12-13 21.325 21.7 23.549999999999997 33.425 14-15 22.6 41.475 19.900000000000002 16.025 16-17 22.075 25.4375 33.5625 18.925 18-19 35.8375 22.0625 20.45 21.65 20-21 19.6125 29.212500000000002 27.1375 24.0375 22-23 28.487499999999997 30.612499999999997 25.575 15.325 24-25 29.312500000000004 28.3125 21.7875 20.5875 26-27 28.462500000000002 28.549999999999997 21.2375 21.75 28-29 23.6625 24.9375 23.400000000000002 28.000000000000004 30-31 27.5125 20.549999999999997 30.675 21.2625 32-33 21.95 16.7375 35.449999999999996 25.8625 34-35 30.725 16.275000000000002 30.45 22.55 36-37 33.2125 19.75 30.025000000000002 17.0125 38-39 31.612499999999997 20.9375 29.8375 17.6125 40-41 27.175 18.85 28.6875 25.2875 42-43 30.325000000000003 19.175 25.637500000000003 24.8625 44-45 40.225 18.8875 17.4625 23.425 46-47 35.949999999999996 23.599999999999998 17.7625 22.6875 48-49 29.599999999999998 21.9625 18.6625 29.775000000000002 50-51 24.575 25.387500000000003 15.987499999999999 34.050000000000004 52-53 27.9125 30.4375 11.375 30.275000000000002 54-55 25.112499999999997 31.112499999999997 14.787500000000001 28.9875 56-57 22.287499999999998 28.762500000000003 15.174999999999999 33.775 58-59 16.475 27.625 16.0 39.900000000000006 60-61 17.8625 28.8625 17.5375 35.7375 62-63 20.525 25.474999999999998 18.512500000000003 35.4875 64-65 17.549999999999997 28.0625 20.9875 33.4 66-67 16.225 22.2 23.1875 38.3875 68-69 19.825 22.237499999999997 23.8375 34.1 70-71 21.8125 22.2625 26.400000000000002 29.525000000000002 72-73 21.65 22.175 28.3875 27.787499999999998 74-75 19.787499999999998 16.0 29.212500000000002 35.0 76-77 20.7 13.625000000000002 35.199999999999996 30.475 78-79 19.75 12.25 37.1 30.9 80-81 21.775 12.9125 36.3 29.012500000000003 82-83 20.8875 11.3 38.487500000000004 29.325000000000003 84-85 22.3125 9.6125 36.925000000000004 31.15 86-87 19.9625 13.575000000000001 37.4625 28.999999999999996 88-89 16.1 24.2875 37.8875 21.725 90-91 14.575 31.4375 33.675 20.3125 92-93 14.875 39.637499999999996 26.575 18.912499999999998 94-95 13.475000000000001 48.762499999999996 25.424999999999997 12.3375 96-97 10.0 61.775000000000006 20.05 8.175 98-99 7.7 74.7 12.45 5.1499999999999995 100-101 4.9 84.2375 7.2875 3.5749999999999997 >>END_MODULE >>Per sequence GC content fail #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 1.0 33 1.0 34 4.0 35 12.5 36 16.5 37 18.5 38 18.0 39 20.0 40 35.5 41 50.0 42 101.5 43 152.5 44 177.0 45 240.5 46 291.5 47 322.0 48 344.0 49 313.5 50 309.0 51 390.5 52 353.5 53 206.5 54 130.5 55 120.5 56 178.5 57 130.0 58 23.0 59 13.5 60 10.0 61 6.0 62 5.0 63 1.0 64 1.0 65 1.0 66 0.5 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 9.925 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 52.7 #Duplication Level Percentage of deduplicated Percentage of total 1 83.68121442125236 44.1 2 6.59392789373814 6.950000000000001 3 2.846299810246679 4.5 4 1.6603415559772294 3.5000000000000004 5 0.5692599620493358 1.5 6 1.0910815939278937 3.45 7 0.6166982922201139 2.275 8 0.5692599620493358 2.4 9 0.2846299810246679 1.35 >10 1.8975332068311195 19.675 >50 0.09487666034155598 3.5249999999999995 >100 0.09487666034155598 6.775 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences fail #Sequence Count Percentage Possible Source GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 136 3.4000000000000004 No Hit TCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 135 3.375 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 90 2.25 No Hit AGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 51 1.275 No Hit TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 50 1.25 RNA PCR Primer, Index 1 (100% over 29bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 46 1.15 No Hit GGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 44 1.0999999999999999 RNA PCR Primer, Index 1 (100% over 22bp) CTCTGATGATGATCAAACTAATACTTTCGTTCTTCTGGAATTCTCGGGTG 44 1.0999999999999999 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTTGGAATTCT 35 0.8750000000000001 No Hit GACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 35 0.8750000000000001 RNA PCR Primer, Index 1 (100% over 23bp) GACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAAC 30 0.75 RNA PCR Primer, Index 1 (100% over 24bp) GACACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACT 28 0.7000000000000001 RNA PCR Primer, Index 1 (100% over 25bp) CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTC 27 0.675 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 26 0.65 No Hit CTCGGGTGCCAAGGAACTCCAGTCACCGTACGATCTCGTATGCCGTCTTC 23 0.575 RNA PCR Primer, Index 22 (100% over 50bp) ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGC 21 0.525 No Hit CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGG 19 0.475 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 18 0.44999999999999996 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGGAATTCTCGGGTGCCA 17 0.42500000000000004 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 17 0.42500000000000004 Illumina Small RNA Adapter 2 (100% over 21bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTGGAATTCTCGGGTGCCA 17 0.42500000000000004 No Hit NCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 16 0.4 No Hit TTCGGACCAGGCTTCATTCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 16 0.4 RNA PCR Primer, Index 1 (100% over 29bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTTGGAATTCTCGGGTGCCA 16 0.4 No Hit AATTCTCGGGTGCCAAGGAACTCCAGTCACCGTACGATCTCGTATGCCGT 16 0.4 RNA PCR Primer, Index 22 (100% over 50bp) NGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 15 0.375 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 14 0.35000000000000003 Illumina Small RNA Adapter 2 (100% over 21bp) CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGG 14 0.35000000000000003 No Hit TCTCGGGTGCCAAGGAACTCCAGTCACCGTACGATCTCGTATGCCGTCTT 14 0.35000000000000003 RNA PCR Primer, Index 22 (100% over 50bp) GCCCACCCCAAGATGAGTGCTCTCTCTGGAATTCTCGGGTGCCAAGGAAC 14 0.35000000000000003 RNA PCR Primer, Index 1 (100% over 24bp) CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 13 0.325 RNA PCR Primer, Index 1 (100% over 28bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCGTGGAATT 13 0.325 No Hit GCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCC 12 0.3 No Hit AAGGGTGCTGAGAATACTTTGAATCTGACACTGGAATTCTCGGGTGCCAA 12 0.3 No Hit AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 12 0.3 Illumina Small RNA Adapter 2 (100% over 21bp) NGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 11 0.27499999999999997 No Hit TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 11 0.27499999999999997 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTTGGAATTCTCGGGTGC 11 0.27499999999999997 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATATGGAATTCTCGGGTGCCAAGGAA 10 0.25 RNA PCR Primer, Index 1 (100% over 23bp) ATATATTTCAAGTTATTTCGGATCTTGGAATTCTCGGGTGCCAAGGAACT 10 0.25 RNA PCR Primer, Index 1 (100% over 25bp) CCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTG 10 0.25 No Hit CAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTG 10 0.25 No Hit ACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCC 10 0.25 No Hit AGGGCTATAGCTCAGTTCGGTAGAGCAACTCGTTTACACCGAGATGGAAT 10 0.25 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 9 0.22499999999999998 No Hit AGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGT 9 0.22499999999999998 No Hit TCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCG 9 0.22499999999999998 No Hit NTCTGATGATGATCAAACTAATACTTTCGTTCTTCTGGAATTCTCGGGTG 9 0.22499999999999998 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 9 0.22499999999999998 Illumina Small RNA Adapter 2 (100% over 21bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTCATGGAATTCTCGGGTG 9 0.22499999999999998 No Hit NGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 8 0.2 RNA PCR Primer, Index 1 (100% over 22bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGGTGGAATTC 8 0.2 No Hit TCCTGTGGATGAGAAGGCATTTATATTCTGATGATATGGAATTCTCGGGT 8 0.2 No Hit GCACCAGTGGTCTAGTGGTAGAATAGTACCTGGAATTCTCGGGTGCCAAG 8 0.2 No Hit ATTCTCGGGTGCCAAGGAACTCCAGTCACCGTACGATCTCGTATGCCGTC 8 0.2 RNA PCR Primer, Index 22 (100% over 50bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTTGGAATTCTCGGGTGCC 8 0.2 No Hit ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGGTGC 8 0.2 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGATGGAATTCTC 8 0.2 No Hit ATAACCGTAGTAATTCTAGAGCTAATATGGAATTCTCGGGTGCCAAGGAA 8 0.2 RNA PCR Primer, Index 1 (100% over 23bp) GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTAATCCTGGAATTC 8 0.2 No Hit GGGGATATAGCTCAGTTGGTAGATGGAATTCTCGGGTGCCAAGGAACTCC 8 0.2 RNA PCR Primer, Index 1 (100% over 27bp) CACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGC 8 0.2 No Hit CATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit AAGTATGAACTAATTTGAACTGTGAAACTTGGAATTCTCGGGTGCCAAGG 7 0.17500000000000002 Illumina Small RNA Adapter 2 (100% over 21bp) TTCTCGGGTGCCAAGGAACTCCAGTCACCGTACGATCTCGTATGCCGTCT 7 0.17500000000000002 RNA PCR Primer, Index 22 (100% over 50bp) ATAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAACT 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 25bp) CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGG 7 0.17500000000000002 No Hit GGGGATGTAGCTCAGATGGTAGATGGAATTCTCGGGTGCCAAGGAACTCC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 27bp) GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 7 0.17500000000000002 No Hit CACGACTCTCGGCAACGGATATCTCGTGGAATTCTCGGGTGCCAAGGAAC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 24bp) GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGATGGAATTCTCGGGTG 7 0.17500000000000002 No Hit NGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 7 0.17500000000000002 No Hit CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGG 7 0.17500000000000002 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGATGGAATTCTCGGGTGCCAA 7 0.17500000000000002 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGGAATTCTCGGGTGCCAA 7 0.17500000000000002 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAATGGAATTCTCGGGTGCCA 6 0.15 No Hit CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCTGGAATTCTCGGG 6 0.15 No Hit GAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTGC 6 0.15 No Hit ATAACCGTAGTAATTCTAGAGCTAATTGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) TCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTG 6 0.15 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGAGTGGAATTCT 6 0.15 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTGGAATTCTCGGGTGCCAAG 6 0.15 No Hit AGAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTG 6 0.15 No Hit ATAACCGTAGTAATTCTAGAGCTAATACTGGAATTCTCGGGTGCCAAGGA 6 0.15 RNA PCR Primer, Index 1 (100% over 22bp) NATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 6 0.15 No Hit GATAACCGTAGTAATTCTAGAGCTAATACTGGAATTCTCGGGTGCCAAGG 6 0.15 Illumina Small RNA Adapter 2 (100% over 21bp) CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 6 0.15 RNA PCR Primer, Index 1 (100% over 23bp) GTCAGGATAGCTCAGTTGGTAGAGCAGAGGATGGAATTCTCGGGTGCCAA 6 0.15 No Hit AGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGGT 6 0.15 No Hit GAAGTCCTCGTGTTGCATTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA 6 0.15 RNA PCR Primer, Index 1 (100% over 28bp) TGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAA 6 0.15 No Hit GACACGACTCTCGGCAACGGATATCTCGTGGAATTCTCGGGTGCCAAGGA 6 0.15 RNA PCR Primer, Index 1 (100% over 22bp) NACACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACT 6 0.15 RNA PCR Primer, Index 1 (100% over 25bp) ATCAGCTGACACGAGCAAATCTGAACCCTGGAATTCTCGGGTGCCAAGGA 6 0.15 RNA PCR Primer, Index 1 (100% over 22bp) ACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTCT 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTATGGAATTCTCGGGTGCCAA 6 0.15 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTGGAATTCTC 6 0.15 No Hit CACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) CGACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) CGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTCTC 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAAATGGAATTCTCGGGTGCC 5 0.125 No Hit GCGACCCCAGGTCAGGCGGGACTACCCGCTGATGGAATTCTCGGGTGCCA 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAAAAATGGAATTCTCGGGTG 5 0.125 No Hit ATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGCCA 5 0.125 No Hit ACCGTAGTAATTCTAGAGCTAATATGGAATTCTCGGGTGCCAAGGAACTC 5 0.125 RNA PCR Primer, Index 1 (100% over 26bp) NACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) GACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGTGGAATTCTC 5 0.125 No Hit ATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) CTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCA 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.05 0.0 0.0 0.0 2 0.0 0.05 0.0 0.0 0.0 3 0.0 0.05 0.0 0.0 0.0 4 0.0 0.05 0.0 0.0 0.0 5 0.0 0.05 0.0 0.0 0.0 6 0.0 0.05 0.0 0.0 0.0 7 0.0 0.075 0.0 0.0 0.0 8 0.0 0.075 0.0 0.0 0.0 9 0.0 0.15 0.0 0.0 0.0 10-11 0.0 0.2375 0.0 0.0 0.0 12-13 0.0 0.275 0.0 0.0 0.0 14-15 0.0 0.4125 0.0 0.0 0.0 16-17 0.0 0.8374999999999999 0.0 0.0 0.0 18-19 0.0 1.6125 0.0 0.0 0.0 20-21 0.0 2.9375 0.0 0.0 0.0 22-23 0.0 7.7 0.0 0.0 0.0 24-25 0.0 15.149999999999999 0.0 0.0 0.0 26-27 0.0 24.575 0.0 0.0 0.0 28-29 0.0 32.725 0.0 0.0 0.0 30-31 0.0 41.425 0.0 0.0 0.0 32-33 0.0 51.75 0.0 0.0 0.0 34-35 0.0 65.3875 0.0 0.0 0.0 36-37 0.0 76.575 0.0 0.0 0.0 38-39 0.0 82.725 0.0 0.0 0.0 40-41 0.0 86.0 0.0 0.0 0.0 42-43 0.0 90.1125 0.0 0.0 0.0 44-45 0.0 92.4125 0.0 0.0 0.0 46-47 0.0 93.1875 0.0 0.0 0.0 48-49 0.0 93.3625 0.0 0.0 0.0 50-51 0.0 93.5375 0.0 0.0 0.0 52-53 0.0 93.5625 0.0 0.0 0.0 54-55 0.0 93.575 0.0 0.0 0.0 56-57 0.0 93.575 0.0 0.0 0.0 58-59 0.0 93.575 0.0 0.0 0.0 60-61 0.0 93.575 0.0 0.0 0.0 62-63 0.0 93.575 0.0 0.0 0.0 64-65 0.0 93.575 0.0 0.0 0.0 66-67 0.0 93.575 0.0 0.0 0.0 68-69 0.0 93.575 0.0 0.0 0.0 70-71 0.0 93.575 0.0 0.0 0.0 72-73 0.0 93.575 0.0 0.0 0.0 74-75 0.0 93.575 0.0 0.0 0.0 76-77 0.0 93.575 0.0 0.0 0.0 78-79 0.0 93.575 0.0 0.0 0.0 80-81 0.0 93.575 0.0 0.0 0.0 82-83 0.0 93.575 0.0 0.0 0.0 84-85 0.0 93.575 0.0 0.0 0.0 86-87 0.0 93.5875 0.0 0.0 0.0 88-89 0.0 93.6 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GCCTTGA 15 3.5908425E-4 108.42857 1 GGGATTG 40 1.8189894E-12 108.428566 1 CATCGAG 25 1.69337E-7 108.428566 1 GTAGACC 25 3.8591315E-7 94.875 7 TTGTAGT 50 0.0 94.875 5 AGTAGAC 25 3.8591315E-7 94.875 6 GGATTGT 50 0.0 94.875 2 GATTGTA 50 0.0 94.875 3 TAGTTCA 55 0.0 94.875 8 GAGTAGA 25 3.8591315E-7 94.875 5 ATTGTAG 50 0.0 94.875 4 CGAGTAG 25 3.8591315E-7 94.875 4 AGACCTT 25 3.8591315E-7 94.875 9 ATCGAGT 25 3.8591315E-7 94.875 2 TCGAGTA 25 3.8591315E-7 94.875 3 AGTTCAA 55 0.0 94.875 9 GTAGTTC 55 0.0 94.875 7 TAGACCT 25 3.8591315E-7 94.875 8 TGATGGT 20 1.5493324E-5 94.87499 5 GGTGAAA 20 1.5493324E-5 94.87499 9 >>END_MODULE Rejected 1311885 READS because READLEN < 1 Read 1311885 spots for SRR8846496.sra Written 1311885 spots for SRR8846496.sra Rejected 1311885 READS because READLEN < 1 Read 1311885 spots for SRR8846496.sra Written 1311885 spots for SRR8846496.sra Rejected 1311885 READS because READLEN < 1 Read 1311885 spots for SRR8846496.sra Written 1311885 spots for SRR8846496.sra Rejected 1311885 READS because READLEN < 1 Read 1311885 spots for SRR8846496.sra Written 1311885 spots for SRR8846496.sra Rejected 1311885 READS because READLEN < 1 Read 1311885 spots for SRR8846496.sra Written 1311885 spots for SRR8846496.sra Rejected 1311885 READS because READLEN < 1 Read 1311885 spots for SRR8846496.sra Written 1311885 spots for SRR8846496.sra Rejected 1311885 READS because READLEN < 1 Read 1311885 spots for SRR8846496.sra Written 1311885 spots for SRR8846496.sra Rejected 1311885 READS because READLEN < 1 Read 1311885 spots for SRR8846496.sra Written 1311885 spots for SRR8846496.sra Rejected 1311885 READS because READLEN < 1 Read 1311885 spots for SRR8846496.sra Written 1311885 spots for SRR8846496.sra Rejected 1311885 READS because READLEN < 1 Read 1311885 spots for SRR8846496.sra Written 1311885 spots for SRR8846496.sra Rejected 1311885 READS because READLEN < 1 Read 1311885 spots for SRR8846496.sra Written 1311885 spots for SRR8846496.sra Rejected 1311885 READS because READLEN < 1 Read 1311885 spots for SRR8846496.sra Written 1311885 spots for SRR8846496.sra Rejected 1311885 READS because READLEN < 1 Read 1311885 spots for SRR8846496.sra Written 1311885 spots for SRR8846496.sra Rejected 1311885 READS because READLEN < 1 Read 1311885 spots for SRR8846496.sra Written 1311885 spots for SRR8846496.sra Rejected 1311885 READS because READLEN < 1 Read 1311885 spots for SRR8846496.sra Written 1311885 spots for SRR8846496.sra Rejected 1311885 READS because READLEN < 1 Read 1311885 spots for SRR8846496.sra Written 1311885 spots for SRR8846496.sra Rejected 1311885 READS because READLEN < 1 Read 1311885 spots for SRR8846496.sra Written 1311885 spots for SRR8846496.sra Rejected 1311885 READS because READLEN < 1 Read 1311885 spots for SRR8846496.sra Written 1311885 spots for SRR8846496.sra Rejected 1311885 READS because READLEN < 1 Read 1311885 spots for SRR8846496.sra Written 1311885 spots for SRR8846496.sra Rejected 1311885 READS because READLEN < 1 Read 1311885 spots for SRR8846496.sra Written 1311885 spots for SRR8846496.sra SRR ids: ['SRR8846496.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_4pp79f9t SRR8846496.sra spots: 26237700 blocks: [[1, 1311885], [1311886, 2623770], [2623771, 3935655], [3935656, 5247540], [5247541, 6559425], [6559426, 7871310], [7871311, 9183195], [9183196, 10495080], [10495081, 11806965], [11806966, 13118850], [13118851, 14430735], [14430736, 15742620], [15742621, 17054505], [17054506, 18366390], [18366391, 19678275], [19678276, 20990160], [20990161, 22302045], [22302046, 23613930], [23613931, 24925815], [24925816, 26237700]] SRR8846496 file size 6307119 SRR8846496 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 SRR8846496 SRR8846496_1.fastq Input file: SRR8846496_1.fastq trimmed: SRR8846496-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- minimum overlap length for adapter detection (-k): inf -- number of concurrent threads (-t): 20 Sun Dec 8 22:42:58 2024 >> started Sun Dec 8 22:44:07 2024 >> done (69.326s) 26237700 reads processed; of these: 503 ( 0.00%) short reads filtered out after trimming by size control 47 ( 0.00%) empty reads filtered out after trimming by size control 26237150 (100.00%) reads available; of these: 4222639 (16.09%) trimmed reads available after processing 22014511 (83.91%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 97 0.00% 19 85 0.00% 20 104 0.00% 21 124 0.00% 22 114 0.00% 23 124 0.00% 24 177 0.00% 25 259 0.00% 26 433 0.00% 27 566 0.00% 28 631 0.00% 29 780 0.00% 30 669 0.00% 31 644 0.00% 32 865 0.00% 33 623 0.00% 34 659 0.00% 35 522 0.00% 36 497 0.00% 37 406 0.00% 38 438 0.00% 39 482 0.00% 40 457 0.00% 41 500 0.00% 42 688 0.00% 43 662 0.00% 44 820 0.00% 45 951 0.00% 46 850 0.00% 47 855 0.00% 48 678 0.00% 49 709 0.00% 50 717 0.00% 51 764 0.00% 52 712 0.00% 53 888 0.00% 54 928 0.00% 55 1037 0.00% 56 1167 0.00% 57 1269 0.00% 58 1538 0.01% 59 2020 0.01% 60 2387 0.01% 61 3468 0.01% 62 4290 0.02% 63 5231 0.02% 64 6977 0.03% 65 10534 0.04% 66 24379 0.09% 67 78756 0.30% 68 98094 0.37% 69 69220 0.26% 70 53280 0.20% 71 53035 0.20% 72 26667 0.10% 73 11834 0.05% 74 12565 0.05% 75 11011 0.04% 76 10007 0.04% 77 9023 0.03% 78 10186 0.04% 79 9708 0.04% 80 10462 0.04% 81 11725 0.04% 82 15734 0.06% 83 14945 0.06% 84 15685 0.06% 85 17252 0.07% 86 20688 0.08% 87 25580 0.10% 88 34023 0.13% 89 49883 0.19% 90 59660 0.23% 91 65694 0.25% 92 94885 0.36% 93 123790 0.47% 94 170943 0.65% 95 349170 1.33% 96 425215 1.62% 97 474961 1.81% 98 579667 2.21% 99 644164 2.46% 100 480352 1.83% 101 22014511 83.91% 26237150 reads passed initial QC criterion=sequence-density sequence-density=93.94 sequence-density-rank=1 fanout-score=33.02 fanout-score-rank=1 prefix-density=94.41 prefix-fanout=32.9 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGTACGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA criterion=fanout-score sequence-density=93.94 sequence-density-rank=1 fanout-score=33.02 fanout-score-rank=1 prefix-density=94.41 prefix-fanout=32.9 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGTACGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGTACGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA -o SRR8846496 - Input file: STDIN trimmed: SRR8846496-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGTACGATCTCGTATGCCGTCTTCTGCTTGA -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- minimum overlap length for adapter detection (-k): 3 -- number of concurrent threads (-t): 20 Sun Dec 8 22:48:24 2024 >> started Sun Dec 8 22:50:29 2024 >> done (125.782s) 25678913 reads processed; of these: 364313 ( 1.42%) short reads filtered out after trimming by size control 10505 ( 0.04%) empty reads filtered out after trimming by size control 25304095 (98.54%) reads available; of these: 24459258 (96.66%) trimmed reads available after processing 844837 ( 3.34%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 114704 0.45% 19 206561 0.82% 20 244230 0.97% 21 906764 3.58% 22 519925 2.05% 23 731713 2.89% 24 1824446 7.21% 25 938829 3.71% 26 1144959 4.52% 27 1114743 4.41% 28 1138469 4.50% 29 1053752 4.16% 30 1273220 5.03% 31 961653 3.80% 32 2164371 8.55% 33 1741829 6.88% 34 1517631 6.00% 35 1321094 5.22% 36 1569383 6.20% 37 617066 2.44% 38 512340 2.02% 39 464478 1.84% 40 500021 1.98% 41 664262 2.63% 42 528346 2.09% 43 244564 0.97% 44 223581 0.88% 45 95546 0.38% 46 44203 0.17% 47 24603 0.10% 48 20843 0.08% 49 11217 0.04% 50 7122 0.03% 51 6047 0.02% 52 4236 0.02% 53 3177 0.01% 54 3048 0.01% 55 1309 0.01% 56 1476 0.01% 57 1003 0.00% 58 934 0.00% 59 1283 0.01% 60 1362 0.01% 61 2299 0.01% 62 3034 0.01% 63 3989 0.02% 64 5441 0.02% 65 8838 0.03% 66 22093 0.09% 67 75242 0.30% 68 93736 0.37% 69 65129 0.26% 70 49276 0.19% 71 48892 0.19% 72 21584 0.09% 73 6920 0.03% 74 5633 0.02% 75 5287 0.02% 76 4622 0.02% 77 4744 0.02% 78 4600 0.02% 79 3833 0.02% 80 4183 0.02% 81 3751 0.01% 82 3223 0.01% 83 3251 0.01% 84 2493 0.01% 85 2469 0.01% 86 2430 0.01% 87 2273 0.01% 88 2043 0.01% 89 1830 0.01% 90 1848 0.01% 91 1856 0.01% 92 2254 0.01% 93 2645 0.01% 94 3330 0.01% 95 4561 0.02% 96 5639 0.02% 97 6995 0.03% 98 9861 0.04% 99 13103 0.05% 100 15712 0.06% 101 302810 1.20% criterion=sequence-density sequence-density=5.27 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=0.28 sequence-density-rank=16 fanout-score=16.53 fanout-score-rank=1 prefix-density=4.66 prefix-fanout=1.0 sequence=TTGTGAGAATTAAAAA Started job on | Dec 08 22:53:14 Started mapping on | Dec 08 22:53:15 Finished on | Dec 08 23:02:45 Mapping speed, Million of reads per hour | 163.34 Number of input reads | 25862332 Average input read length | 34 UNIQUE READS: Uniquely mapped reads number | 3320287 Uniquely mapped reads % | 12.84% Average mapped length | 28.64 Number of splices: Total | 52948 Number of splices: Annotated (sjdb) | 36550 Number of splices: GT/AG | 49213 Number of splices: GC/AG | 2695 Number of splices: AT/AC | 29 Number of splices: Non-canonical | 1011 Mismatch rate per base, % | 0.15% Deletion rate per base | 0.00% Deletion average length | 1.36 Insertion rate per base | 0.00% Insertion average length | 1.03 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 10642563 % of reads mapped to multiple loci | 41.15% Number of reads mapped to too many loci | 10160849 % of reads mapped to too many loci | 39.29% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 6.35% % of reads unmapped: other | 0.37% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 11899482 11899482 11899482 N_multimapping 10642563 10642563 10642563 N_noFeature 1638345 1921133 3015707 N_ambiguous 62003 39788 626 UnstrandedReadsAssigned:1619939 PositiveStrandReadsAssigned:1359366 NegativeStrandReadsAssigned:303954 Dataset is classified unstranded MeadianReadLen=32 20thPercentileLength=25 echo kmer=21 SRR8846496 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=21 [quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20 [index] k-mer length: 21 [index] number of targets: 52,972 [index] number of k-mers: 65,978,135 [index] number of equivalence classes: 190,841 [quant] running in single-end mode [quant] will process file 1: SRR8846496-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 25,862,332 reads, 6,659,778 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 965 rounds 52973 SRR8846496.ke.tsv 35125 SRR8846496.se.tsv 88098 total ==> SRR8846496.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 2 0.328656 PNS24247 1044 945 0 0 PNS24249 1928 1829 0 0 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 0 0 PNS24243 293 194 0 0 KQK14069 1603 1504 101.795 9.30927 KQK14071 474 375 24.2371 8.88968 ==> SRR8846496.se.tsv <== BRADI_1g14170v3 288 BRADI_1g53295v3 2 BRADI_1g59795v3 10 BRADI_1g07683v3 0 BRADI_1g00485v3 4 BRADI_1g20270v3 61 BRADI_1g74790v3 54 BRADI_1g09890v3 0 BRADI_1g77505v3 11 BRADI_1g48960v3 0 SRR8846496 completed mapping pipeline successfully