Starting /dee2/code/volunteer_pipeline.sh SRR8846485 current disk space = 1504602882048 free memory = 1360380604 SRR8846485 SRAfilesize 8288fe3817208809b4fb8f7d59c4cde4 SRR8846485.sra SRR8846485.sra file validated SRR8846485 is single end SRR8846485 is conventional basespace SRR8846485 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8846485_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 pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.55375 34.0 33.0 34.0 31.0 34.0 2 32.88475 34.0 33.0 34.0 31.0 34.0 3 33.00275 34.0 33.0 34.0 32.0 34.0 4 33.12175 34.0 33.0 34.0 32.0 34.0 5 32.8855 34.0 33.0 34.0 32.0 34.0 6 36.643 38.0 37.0 38.0 34.0 38.0 7 37.195 38.0 38.0 38.0 36.0 38.0 8 37.316 38.0 38.0 38.0 37.0 38.0 9 37.30675 38.0 38.0 38.0 37.0 38.0 10-11 37.41075 38.0 38.0 38.0 37.0 38.0 12-13 37.504 38.0 38.0 38.0 37.5 38.0 14-15 37.454875 38.0 38.0 38.0 37.0 38.0 16-17 37.36 38.0 38.0 38.0 37.0 38.0 18-19 37.444500000000005 38.0 38.0 38.0 37.0 38.0 20-21 37.388374999999996 38.0 38.0 38.0 37.0 38.0 22-23 37.43000000000001 38.0 38.0 38.0 37.0 38.0 24-25 37.427875 38.0 38.0 38.0 37.0 38.0 26-27 37.5155 38.0 38.0 38.0 38.0 38.0 28-29 37.47725 38.0 38.0 38.0 37.5 38.0 30-31 37.465875 38.0 38.0 38.0 38.0 38.0 32-33 37.37875 38.0 38.0 38.0 37.0 38.0 34-35 37.167625 38.0 38.0 38.0 36.5 38.0 36-37 37.163875 38.0 38.0 38.0 37.0 38.0 38-39 37.109125 38.0 38.0 38.0 36.5 38.0 40-41 37.160250000000005 38.0 38.0 38.0 36.5 38.0 42-43 37.003875 38.0 38.0 38.0 36.5 38.0 44-45 37.059250000000006 38.0 38.0 38.0 36.0 38.0 46-47 36.973625 38.0 38.0 38.0 36.0 38.0 48-49 37.025625000000005 38.0 38.0 38.0 36.0 38.0 50-51 37.050125 38.0 38.0 38.0 36.0 38.0 52-53 37.157625 38.0 38.0 38.0 36.5 38.0 54-55 37.072125 38.0 38.0 38.0 36.0 38.0 56-57 36.937375 38.0 38.0 38.0 36.0 38.0 58-59 36.877375 38.0 38.0 38.0 35.5 38.0 60-61 36.967749999999995 38.0 38.0 38.0 36.0 38.0 62-63 36.77725 38.0 38.0 38.0 35.0 38.0 64-65 36.662125 38.0 38.0 38.0 34.5 38.0 66-67 36.46 38.0 38.0 38.0 34.0 38.0 68-69 36.316125 38.0 38.0 38.0 34.0 38.0 70-71 35.991749999999996 38.0 37.5 38.0 33.0 38.0 72-73 35.7915 38.0 37.5 38.0 32.0 38.0 74-75 35.586875 38.0 37.0 38.0 30.0 38.0 76-77 35.204625 38.0 37.0 38.0 28.5 38.0 78-79 35.011250000000004 38.0 36.5 38.0 28.0 38.0 80-81 35.08375 38.0 37.0 38.0 28.0 38.0 82-83 34.921125 38.0 36.0 38.0 27.5 38.0 84-85 35.055 38.0 36.5 38.0 28.0 38.0 86-87 35.374375 38.0 37.0 38.0 29.5 38.0 88-89 35.312375 38.0 37.0 38.0 29.0 38.0 90-91 35.21375 38.0 37.0 38.0 29.0 38.0 92-93 34.947125 38.0 37.0 38.0 28.5 38.0 94-95 34.689875 38.0 37.0 38.0 27.5 38.0 96-97 33.634249999999994 38.0 35.5 38.0 19.5 38.0 98-99 32.34675 38.0 34.5 38.0 8.5 38.0 100-101 30.262625 38.0 30.5 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 2.0 16 3.0 17 0.0 18 1.0 19 3.0 20 2.0 21 1.0 22 4.0 23 8.0 24 13.0 25 44.0 26 30.0 27 23.0 28 25.0 29 34.0 30 39.0 31 63.0 32 76.0 33 106.0 34 146.0 35 328.0 36 783.0 37 2265.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 28.886554621848738 26.811974789915965 17.883403361344538 26.418067226890756 2 25.874999999999996 31.624999999999996 17.65 24.85 3 24.75 21.224999999999998 20.849999999999998 33.175 4 26.8 29.825000000000003 19.425 23.95 5 31.3 26.1 20.599999999999998 22.0 6 26.85 29.95 23.025000000000002 20.175 7 35.8 27.175 18.55 18.475 8 23.549999999999997 21.5 33.2 21.75 9 25.15 34.8 21.45 18.6 10-11 30.9625 26.5 23.1375 19.400000000000002 12-13 24.1125 25.85 18.787499999999998 31.25 14-15 22.8125 36.4625 24.1875 16.537499999999998 16-17 25.55 28.712500000000002 27.237499999999997 18.5 18-19 30.7625 27.675 22.3125 19.25 20-21 22.0 30.5375 26.2625 21.2 22-23 26.737499999999997 30.4 26.0125 16.85 24-25 26.2625 28.15 23.3625 22.225 26-27 32.3875 27.187499999999996 21.625 18.8 28-29 24.8625 28.537499999999998 24.675 21.925 30-31 24.887500000000003 22.325 33.35 19.4375 32-33 22.6375 20.474999999999998 35.1625 21.725 34-35 24.087500000000002 20.7 32.4125 22.8 36-37 31.637500000000003 18.6625 31.2625 18.4375 38-39 29.262500000000003 23.1875 29.7 17.849999999999998 40-41 28.6375 17.275 30.75 23.3375 42-43 29.15 20.825 27.762500000000003 22.2625 44-45 36.8625 18.6125 21.3625 23.1625 46-47 34.725 24.15 18.9625 22.162499999999998 48-49 30.25 21.85 22.05 25.85 50-51 26.787499999999998 20.925 18.45 33.8375 52-53 27.737499999999997 29.5375 14.124999999999998 28.599999999999998 54-55 28.000000000000004 25.837500000000002 16.9625 29.2 56-57 22.037499999999998 31.387500000000003 14.975 31.6 58-59 15.137500000000001 30.4 19.275000000000002 35.1875 60-61 12.9 29.575000000000003 24.1875 33.3375 62-63 13.375 29.099999999999998 28.025 29.5 64-65 10.037500000000001 28.9375 31.75 29.275000000000002 66-67 7.000000000000001 24.675 35.125 33.2 68-69 8.6375 24.025 34.825 32.5125 70-71 9.6875 22.9875 42.425000000000004 24.9 72-73 11.5625 19.825 44.8625 23.75 74-75 11.425 18.712500000000002 40.2 29.6625 76-77 13.750000000000002 16.3 42.95 27.0 78-79 15.875 12.2 43.3375 28.5875 80-81 16.55 13.325000000000001 43.125 27.0 82-83 19.5125 11.5625 42.3625 26.5625 84-85 19.4875 10.274999999999999 37.5875 32.65 86-87 22.2125 11.525 38.75 27.5125 88-89 17.95 20.325 37.275000000000006 24.45 90-91 15.825 25.874999999999996 35.975 22.325 92-93 16.75 33.0125 29.7125 20.525 94-95 13.575000000000001 42.075 26.9625 17.3875 96-97 11.924999999999999 51.337500000000006 25.55 11.1875 98-99 9.7125 63.949999999999996 17.5625 8.774999999999999 100-101 7.7 72.5 12.937499999999998 6.862500000000001 >>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 1.0 30 3.0 31 7.0 32 11.5 33 17.0 34 20.5 35 20.0 36 18.0 37 34.0 38 43.0 39 77.5 40 120.0 41 144.5 42 247.5 43 316.0 44 330.5 45 356.5 46 336.5 47 353.0 48 388.5 49 322.5 50 184.0 51 136.0 52 156.0 53 152.5 54 102.5 55 33.5 56 18.5 57 18.0 58 15.0 59 9.5 60 4.0 61 1.0 62 1.0 63 0.5 64 0.0 65 0.0 66 0.0 67 0.0 68 0.0 69 0.0 70 0.0 71 0.0 72 0.0 73 0.0 74 0.0 75 0.0 76 0.0 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 pass #Base N-Count 1 4.8 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 53.900000000000006 #Duplication Level Percentage of deduplicated Percentage of total 1 82.42115027829313 44.425 2 7.421150278293136 8.0 3 3.339517625231911 5.4 4 1.2523191094619666 2.7 5 1.2523191094619666 3.375 6 0.6957328385899815 2.25 7 0.4174397031539889 1.575 8 0.5565862708719851 2.4 9 0.3246753246753247 1.575 >10 2.1799628942486082 22.95 >50 0.0927643784786642 2.75 >100 0.0463821892393321 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 AGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 104 2.6 No Hit GGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 59 1.4749999999999999 RNA PCR Primer, Index 1 (100% over 22bp) CTCTGATGATGATCAAACTAATACTTTCGTTCTTCTGGAATTCTCGGGTG 51 1.275 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 47 1.175 No Hit TCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 47 1.175 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTTGGAATTCT 44 1.0999999999999999 No Hit CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTC 42 1.05 No Hit GACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 33 0.8250000000000001 RNA PCR Primer, Index 1 (100% over 23bp) CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGG 31 0.775 No Hit AATTCTCGGGTGCCAAGGAACTCCAGTCACCATTTTATCTCGTATGCCGT 29 0.7250000000000001 RNA PCR Primer, Index 35 (100% over 50bp) CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 26 0.65 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 26 0.65 No Hit AAGGGTGCTGAGAATACTTTGAATCTGACACTGGAATTCTCGGGTGCCAA 23 0.575 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 21 0.525 No Hit CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGG 21 0.525 No Hit AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 21 0.525 Illumina Small RNA Adapter 2 (100% over 21bp) ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGC 21 0.525 No Hit GACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAAC 20 0.5 RNA PCR Primer, Index 1 (100% over 24bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTCATGGAATTCTCGGGTG 20 0.5 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTAATCTGGAATTCT 19 0.475 No Hit CTCGGGTGCCAAGGAACTCCAGTCACCATTTTATCTCGTATGCCGTCTTC 19 0.475 RNA PCR Primer, Index 35 (100% over 50bp) TCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCG 19 0.475 No Hit GACACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACT 18 0.44999999999999996 RNA PCR Primer, Index 1 (100% over 25bp) CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGG 18 0.44999999999999996 No Hit GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTG 17 0.42500000000000004 No Hit TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 17 0.42500000000000004 RNA PCR Primer, Index 1 (100% over 29bp) GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 17 0.42500000000000004 No Hit CATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGCC 16 0.4 No Hit TCCTGTGGATGAGAAGGCATTTATATTCTGATGATATGGAATTCTCGGGT 16 0.4 No Hit ATATATTTCAAGTTATTTCGGATCTTGGAATTCTCGGGTGCCAAGGAACT 16 0.4 RNA PCR Primer, Index 1 (100% over 25bp) TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 16 0.4 No Hit TCTCGGGTGCCAAGGAACTCCAGTCACCATTTTATCTCGTATGCCGTCTT 15 0.375 RNA PCR Primer, Index 35 (100% over 50bp) GGGGATATGGCGAAATCGGTAGACGCTACGGACTTTGGAATTCTCGGGTG 15 0.375 No Hit GCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCC 15 0.375 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 14 0.35000000000000003 Illumina Small RNA Adapter 2 (100% over 21bp) TTCTCGGGTGCCAAGGAACTCCAGTCACCATTTTATCTCGTATGCCGTCT 14 0.35000000000000003 RNA PCR Primer, Index 35 (100% over 50bp) ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTATGGAATT 14 0.35000000000000003 No Hit ATTCTCGGGTGCCAAGGAACTCCAGTCACCATTTTATCTCGTATGCCGTC 13 0.325 RNA PCR Primer, Index 35 (100% over 50bp) CAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTG 13 0.325 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 13 0.325 Illumina Small RNA Adapter 2 (100% over 21bp) TGCCACGATCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAAT 13 0.325 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 12 0.3 Illumina Small RNA Adapter 2 (100% over 21bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTTGGAATTCTCGGGTGCC 12 0.3 No Hit GTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTC 11 0.27499999999999997 No Hit AGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGT 11 0.27499999999999997 No Hit CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGG 11 0.27499999999999997 No Hit CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGGAATTCTCG 11 0.27499999999999997 No Hit AGGGCTATAGCTCAGTTCGGTAGAGCAACTCGTTTACACCGAGATGGAAT 11 0.27499999999999997 No Hit ATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGCCA 10 0.25 No Hit TAACCGTAGTAATTCTAGAGCTAATATGGAATTCTCGGGTGCCAAGGAAC 10 0.25 RNA PCR Primer, Index 1 (100% over 24bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGGTGGAATTC 9 0.22499999999999998 No Hit TCGGATAACCGTAGTAATTCTAGAGCTAATACGTGGAATTCTCGGGTGCC 9 0.22499999999999998 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTGGAATTCTCGGGTGCCAAG 9 0.22499999999999998 No Hit AGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGGT 9 0.22499999999999998 No Hit ACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCC 9 0.22499999999999998 No Hit CGGATAACCGTAGTAATTCTAGAGCTAATACTGGAATTCTCGGGTGCCAA 9 0.22499999999999998 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTGGAATTCTC 9 0.22499999999999998 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAATGGAATTCTCGGGTGCCA 8 0.2 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTAAAATGGAATTCTCGGGTGC 8 0.2 No Hit TTCGGACCAGGCTTCATTCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 8 0.2 RNA PCR Primer, Index 1 (100% over 29bp) AAGGGTGCTGAGAATACTTTGAATCTGACATGGAATTCTCGGGTGCCAAG 8 0.2 No Hit GCACCAGTGGTCTAGTGGTAGAATAGTACCTGGAATTCTCGGGTGCCAAG 8 0.2 No Hit ATAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAACT 8 0.2 RNA PCR Primer, Index 1 (100% over 25bp) GATAACCGTAGTAATTCTAGAGCTAATACTGGAATTCTCGGGTGCCAAGG 8 0.2 Illumina Small RNA Adapter 2 (100% over 21bp) GATAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAAC 8 0.2 RNA PCR Primer, Index 1 (100% over 24bp) ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGGTGC 8 0.2 No Hit CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTCGGGT 8 0.2 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATGGAATTCTCGGGTG 8 0.2 No Hit CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTCGGG 8 0.2 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATTGGAATTC 7 0.17500000000000002 No Hit CCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTG 7 0.17500000000000002 No Hit CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 23bp) GACACGACTCTCGGCAACGGATATCTCGGCTCTCGCTGGAATTCTCGGGT 7 0.17500000000000002 No Hit GGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCT 7 0.17500000000000002 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGATGGAATTCTC 7 0.17500000000000002 No Hit ATAACCGTAGTAATTCTAGAGCTAATATGGAATTCTCGGGTGCCAAGGAA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 23bp) GACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGTGGAATTCTC 7 0.17500000000000002 No Hit CTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCA 7 0.17500000000000002 No Hit TCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCG 6 0.15 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 6 0.15 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATTGGAATTCTCG 6 0.15 No Hit AGGGCTATAGCTCAGTTCGGTAGAGCAACTCGTTTACACCTGGAATTCTC 6 0.15 No Hit GATAACCGTAGTAATTCTAGAGCTAATTGGAATTCTCGGGTGCCAAGGAA 6 0.15 RNA PCR Primer, Index 1 (100% over 23bp) ATAACCGTAGTAATTCTAGAGCTAATTGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) CGACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAA 6 0.15 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTCTCGTGGAATTCTCGGGTG 6 0.15 No Hit TAAGATGAGCTCAACGAGAACAGAAATCTCGTGTGGAATTCTCGGGTGCC 6 0.15 No Hit GGGATTGTAGTTCAATTGGTCAGAGCTGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) GCAAGTATGAACTAATTTGAACTGTGAAACTTGGAATTCTCGGGTGCCAA 6 0.15 No Hit GGCATCCTAACGAACGAACGATTTGAATGGAATTCTCGGGTGCCAAGGAA 6 0.15 RNA PCR Primer, Index 1 (100% over 23bp) GCCCACCCCAAGATGAGTGCTCTCTCTGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGGTG 6 0.15 No Hit TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGG 6 0.15 No Hit GCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGT 5 0.125 No Hit CGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTCTC 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAAATGGAATTCTCGGGTGCC 5 0.125 No Hit CGGATAACCGTAGTAATTCTAGAGCTAATACGTGGAATTCTCGGGTGCCA 5 0.125 No Hit ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGATTTGGAATTCTC 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAAATGGAATTCTCGGGT 5 0.125 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTTGGAATTCTCGGGTGCCAA 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAAAATGGAATTCTCGGG 5 0.125 No Hit GATAACCGTAGTAATTCTAGAGCTAATATGGAATTCTCGGGTGCCAAGGA 5 0.125 RNA PCR Primer, Index 1 (100% over 22bp) TGTATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCT 5 0.125 No Hit CAGGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATT 5 0.125 No Hit ATATATTTCAAGTTATTTCGGATCTGGAATTCTCGGGTGCCAAGGAACTC 5 0.125 RNA PCR Primer, Index 1 (100% over 26bp) TCCGTCGTAGTCTAGGTGGTTAGGATACTCGTGGAATTCTCGGGTGCCAA 5 0.125 No Hit NTCTGATGATGATCAAACTAATACTTTCGTTCTTCTGGAATTCTCGGGTG 5 0.125 No Hit CGGATAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGA 5 0.125 RNA PCR Primer, Index 1 (100% over 22bp) AGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGCCAAG 5 0.125 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTTGGAATTCTCGGGTG 5 0.125 No Hit CACGACTCTCGGCAACGGATATCTCGTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) NGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 5 0.125 No Hit CAGGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATT 5 0.125 No Hit TCGGATAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGG 5 0.125 Illumina Small RNA Adapter 2 (100% over 21bp) CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTAATTCTCGGG 5 0.125 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCTGGAATTC 5 0.125 No Hit GGGGATATAGCTCAGTTGGTAGATGGAATTCTCGGGTGCCAAGGAACTCC 5 0.125 RNA PCR Primer, Index 1 (100% over 27bp) AGCTGAGGCATCCTAACGAACGAACGATTTGAATGGAATTCTCGGGTGCC 5 0.125 No Hit TAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAACTC 5 0.125 RNA PCR Primer, Index 1 (100% over 26bp) 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 0.075 0.0 0.0 0.0 2 0.0 0.075 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 0.075 0.0 0.0 0.0 6 0.0 0.075 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 0.2 0.0 0.0 0.0 10-11 0.0 0.21250000000000002 0.0 0.0 0.0 12-13 0.0 0.38749999999999996 0.0 0.0 0.0 14-15 0.0 0.5125 0.0 0.0 0.0 16-17 0.0 0.925 0.0 0.0 0.0 18-19 0.0 1.4500000000000002 0.0 0.0 0.0 20-21 0.0 2.2625 0.0 0.0 0.0 22-23 0.0 5.175 0.0 0.0 0.0 24-25 0.0 10.6875 0.0 0.0 0.0 26-27 0.0 19.112499999999997 0.0 0.0 0.0 28-29 0.0 26.1875 0.0 0.0 0.0 30-31 0.0 34.9 0.0 0.0 0.0 32-33 0.0 43.3875 0.0 0.0 0.0 34-35 0.0 54.225 0.0 0.0 0.0 36-37 0.0 65.5875 0.0 0.0 0.0 38-39 0.0 72.0875 0.0 0.0 0.0 40-41 0.0 77.5125 0.0 0.0 0.0 42-43 0.0 83.92500000000001 0.0 0.0 0.0 44-45 0.0 87.7625 0.0 0.0 0.0 46-47 0.0 89.6625 0.0 0.0 0.0 48-49 0.0 90.19999999999999 0.0 0.0 0.0 50-51 0.0 90.5 0.0 0.0 0.0 52-53 0.0 90.6875 0.0 0.0 0.0 54-55 0.0 90.7375 0.0 0.0 0.0 56-57 0.0 90.75 0.0 0.0 0.0 58-59 0.0 90.75 0.0 0.0 0.0 60-61 0.0 90.75 0.0 0.0 0.0 62-63 0.0 90.75 0.0 0.0 0.0 64-65 0.0 90.75 0.0 0.0 0.0 66-67 0.0 90.75 0.0 0.0 0.0 68-69 0.0 90.75 0.0 0.0 0.0 70-71 0.0 90.75 0.0 0.0 0.0 72-73 0.0 90.75 0.0 0.0 0.0 74-75 0.0 90.75 0.0 0.0 0.0 76-77 0.0 90.75 0.0 0.0 0.0 78-79 0.0 90.75 0.0 0.0 0.0 80-81 0.0 90.75 0.0 0.0 0.0 82-83 0.0 90.75 0.0 0.0 0.0 84-85 0.0 90.75 0.0 0.0 0.0 86-87 0.0 90.775 0.0 0.0 0.0 88-89 0.0 90.775 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGATTG 25 2.8007162E-7 99.94737 1 GCCTTGA 15 4.9992715E-4 99.947365 1 GACACGA 15 4.9992715E-4 99.947365 1 TTGTAGT 25 3.8410144E-7 94.950005 5 GGATTGT 25 3.8410144E-7 94.950005 2 GATTGTA 25 3.8410144E-7 94.950005 3 TAGTTCA 25 3.8410144E-7 94.950005 8 ATTGTAG 25 3.8410144E-7 94.950005 4 TGTAGTT 25 3.8410144E-7 94.950005 6 AGTTCAA 25 3.8410144E-7 94.950005 9 GTAGTTC 25 3.8410144E-7 94.950005 7 TGATGGT 15 6.1550457E-4 94.95 5 ACACGAC 15 6.1550457E-4 94.95 2 GGTGAAA 15 6.1550457E-4 94.95 9 ATGGTGA 15 6.1550457E-4 94.95 7 CCTTGAT 15 6.1550457E-4 94.95 2 TTGATGG 15 6.1550457E-4 94.95 4 CTTGATG 15 6.1550457E-4 94.95 3 TGGTGAA 15 6.1550457E-4 94.95 8 GATGGTG 15 6.1550457E-4 94.95 6 >>END_MODULE Rejected 642684 READS because READLEN < 1 Read 642684 spots for SRR8846485.sra Written 642684 spots for SRR8846485.sra Rejected 642684 READS because READLEN < 1 Read 642684 spots for SRR8846485.sra Written 642684 spots for SRR8846485.sra Rejected 642684 READS because READLEN < 1 Read 642684 spots for SRR8846485.sra Written 642684 spots for SRR8846485.sra Rejected 642684 READS because READLEN < 1 Read 642684 spots for SRR8846485.sra Written 642684 spots for SRR8846485.sra Rejected 642689 READS because READLEN < 1 Read 642689 spots for SRR8846485.sra Written 642689 spots for SRR8846485.sra Rejected 642684 READS because READLEN < 1 Read 642684 spots for SRR8846485.sra Written 642684 spots for SRR8846485.sra Rejected 642684 READS because READLEN < 1 Read 642684 spots for SRR8846485.sra Written 642684 spots for SRR8846485.sra Rejected 642684 READS because READLEN < 1 Read 642684 spots for SRR8846485.sra Written 642684 spots for SRR8846485.sra Rejected 642684 READS because READLEN < 1 Read 642684 spots for SRR8846485.sra Written 642684 spots for SRR8846485.sra Rejected 642684 READS because READLEN < 1 Read 642684 spots for SRR8846485.sra Written 642684 spots for SRR8846485.sra Rejected 642684 READS because READLEN < 1 Read 642684 spots for SRR8846485.sra Written 642684 spots for SRR8846485.sra Rejected 642684 READS because READLEN < 1 Read 642684 spots for SRR8846485.sra Written 642684 spots for SRR8846485.sra Rejected 642684 READS because READLEN < 1 Read 642684 spots for SRR8846485.sra Written 642684 spots for SRR8846485.sra Rejected 642684 READS because READLEN < 1 Read 642684 spots for SRR8846485.sra Written 642684 spots for SRR8846485.sra Rejected 642684 READS because READLEN < 1 Read 642684 spots for SRR8846485.sra Written 642684 spots for SRR8846485.sra Rejected 642684 READS because READLEN < 1 Read 642684 spots for SRR8846485.sra Written 642684 spots for SRR8846485.sra Rejected 642684 READS because READLEN < 1 Read 642684 spots for SRR8846485.sra Written 642684 spots for SRR8846485.sra Rejected 642684 READS because READLEN < 1 Read 642684 spots for SRR8846485.sra Written 642684 spots for SRR8846485.sra Rejected 642684 READS because READLEN < 1 Read 642684 spots for SRR8846485.sra Written 642684 spots for SRR8846485.sra Rejected 642684 READS because READLEN < 1 Read 642684 spots for SRR8846485.sra Written 642684 spots for SRR8846485.sra SRR ids: ['SRR8846485.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_eq59rd3f SRR8846485.sra spots: 12853685 blocks: [[1, 642684], [642685, 1285368], [1285369, 1928052], [1928053, 2570736], [2570737, 3213420], [3213421, 3856104], [3856105, 4498788], [4498789, 5141472], [5141473, 5784156], [5784157, 6426840], [6426841, 7069524], [7069525, 7712208], [7712209, 8354892], [8354893, 8997576], [8997577, 9640260], [9640261, 10282944], [10282945, 10925628], [10925629, 11568312], [11568313, 12210996], [12210997, 12853685]] SRR8846485 file size 3078749 SRR8846485 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 SRR8846485 SRR8846485_1.fastq Input file: SRR8846485_1.fastq trimmed: SRR8846485-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 18:09:08 2024 >> started Sun Dec 8 18:09:40 2024 >> done (32.618s) 12853685 reads processed; of these: 303 ( 0.00%) short reads filtered out after trimming by size control 54 ( 0.00%) empty reads filtered out after trimming by size control 12853328 (100.00%) reads available; of these: 1790675 (13.93%) trimmed reads available after processing 11062653 (86.07%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 36 0.00% 19 31 0.00% 20 39 0.00% 21 34 0.00% 22 43 0.00% 23 35 0.00% 24 54 0.00% 25 62 0.00% 26 74 0.00% 27 78 0.00% 28 78 0.00% 29 123 0.00% 30 146 0.00% 31 168 0.00% 32 187 0.00% 33 317 0.00% 34 500 0.00% 35 336 0.00% 36 611 0.00% 37 516 0.00% 38 534 0.00% 39 661 0.01% 40 648 0.01% 41 568 0.00% 42 476 0.00% 43 415 0.00% 44 441 0.00% 45 390 0.00% 46 330 0.00% 47 349 0.00% 48 405 0.00% 49 461 0.00% 50 549 0.00% 51 561 0.00% 52 450 0.00% 53 366 0.00% 54 289 0.00% 55 217 0.00% 56 262 0.00% 57 245 0.00% 58 361 0.00% 59 586 0.00% 60 649 0.01% 61 1311 0.01% 62 1839 0.01% 63 2518 0.02% 64 3926 0.03% 65 4007 0.03% 66 11138 0.09% 67 46256 0.36% 68 49568 0.39% 69 33128 0.26% 70 23741 0.18% 71 29268 0.23% 72 11762 0.09% 73 3653 0.03% 74 4255 0.03% 75 2996 0.02% 76 2661 0.02% 77 2592 0.02% 78 2904 0.02% 79 3166 0.02% 80 3334 0.03% 81 4035 0.03% 82 6179 0.05% 83 6069 0.05% 84 5846 0.05% 85 6304 0.05% 86 7485 0.06% 87 9869 0.08% 88 13523 0.11% 89 18207 0.14% 90 25553 0.20% 91 27459 0.21% 92 35190 0.27% 93 52907 0.41% 94 67511 0.53% 95 129112 1.00% 96 157913 1.23% 97 186482 1.45% 98 304727 2.37% 99 284197 2.21% 100 184403 1.43% 101 11062653 86.07% 12853328 reads passed initial QC criterion=sequence-density sequence-density=90.80 sequence-density-rank=1 fanout-score=30.15 fanout-score-rank=1 prefix-density=91.26 prefix-fanout=30.0 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCATTTTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA criterion=fanout-score sequence-density=90.80 sequence-density-rank=1 fanout-score=30.15 fanout-score-rank=1 prefix-density=91.26 prefix-fanout=30.0 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCATTTTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCATTTTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA -o SRR8846485 - Input file: STDIN trimmed: SRR8846485-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCATTTTATCTCGTATGCCGTCTTCTGCTTGA -- 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 18:12:01 2024 >> started Sun Dec 8 18:13:02 2024 >> done (60.876s) 12570837 reads processed; of these: 124001 ( 0.99%) short reads filtered out after trimming by size control 6436 ( 0.05%) empty reads filtered out after trimming by size control 12440400 (98.96%) reads available; of these: 11961970 (96.15%) trimmed reads available after processing 478430 ( 3.85%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 34114 0.27% 19 58327 0.47% 20 76569 0.62% 21 243701 1.96% 22 161212 1.30% 23 268053 2.15% 24 774019 6.22% 25 395553 3.18% 26 428857 3.45% 27 484039 3.89% 28 570068 4.58% 29 594060 4.78% 30 649364 5.22% 31 518465 4.17% 32 582852 4.69% 33 708819 5.70% 34 841860 6.77% 35 784026 6.30% 36 639320 5.14% 37 496527 3.99% 38 436785 3.51% 39 371668 2.99% 40 329948 2.65% 41 428454 3.44% 42 404822 3.25% 43 192282 1.55% 44 203226 1.63% 45 102108 0.82% 46 59660 0.48% 47 35806 0.29% 48 29929 0.24% 49 16693 0.13% 50 11608 0.09% 51 10142 0.08% 52 5102 0.04% 53 3929 0.03% 54 4689 0.04% 55 1496 0.01% 56 1522 0.01% 57 813 0.01% 58 688 0.01% 59 811 0.01% 60 739 0.01% 61 1440 0.01% 62 1788 0.01% 63 2477 0.02% 64 3781 0.03% 65 3825 0.03% 66 10798 0.09% 67 45059 0.36% 68 48211 0.39% 69 32118 0.26% 70 22868 0.18% 71 28075 0.23% 72 10168 0.08% 73 2390 0.02% 74 1807 0.01% 75 1306 0.01% 76 1361 0.01% 77 1958 0.02% 78 1451 0.01% 79 1528 0.01% 80 2219 0.02% 81 1732 0.01% 82 1440 0.01% 83 2116 0.02% 84 1029 0.01% 85 962 0.01% 86 953 0.01% 87 923 0.01% 88 883 0.01% 89 828 0.01% 90 782 0.01% 91 931 0.01% 92 1053 0.01% 93 1239 0.01% 94 1397 0.01% 95 1835 0.01% 96 2754 0.02% 97 3936 0.03% 98 6410 0.05% 99 6166 0.05% 100 7861 0.06% 101 207817 1.67% criterion=sequence-density sequence-density=2.32 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=13 prefix-density=0.00 prefix-fanout=1.0 sequence=GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCT criterion=fanout-score sequence-density=0.22 sequence-density-rank=15 fanout-score=24.62 fanout-score-rank=1 prefix-density=5.35 prefix-fanout=1.0 sequence=TTGTGAGAATTAAAAA Started job on | Dec 08 18:15:18 Started mapping on | Dec 08 18:15:19 Finished on | Dec 08 18:21:59 Mapping speed, Million of reads per hour | 114.51 Number of input reads | 12722891 Average input read length | 35 UNIQUE READS: Uniquely mapped reads number | 1596833 Uniquely mapped reads % | 12.55% Average mapped length | 30.03 Number of splices: Total | 24462 Number of splices: Annotated (sjdb) | 17650 Number of splices: GT/AG | 22302 Number of splices: GC/AG | 1368 Number of splices: AT/AC | 10 Number of splices: Non-canonical | 782 Mismatch rate per base, % | 0.15% Deletion rate per base | 0.00% Deletion average length | 1.38 Insertion rate per base | 0.00% Insertion average length | 1.02 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 4093074 % of reads mapped to multiple loci | 32.17% Number of reads mapped to too many loci | 6128157 % of reads mapped to too many loci | 48.17% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 6.66% % of reads unmapped: other | 0.45% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 7032984 7032984 7032984 N_multimapping 4093074 4093074 4093074 N_noFeature 691984 813548 1466342 N_ambiguous 34381 25277 247 UnstrandedReadsAssigned:870468 PositiveStrandReadsAssigned:758008 NegativeStrandReadsAssigned:130244 Dataset is classified positive stranded MeadianReadLen=33 20thPercentileLength=27 echo kmer=23 SRR8846485 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=23 [quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20 [index] k-mer length: 23 [index] number of targets: 52,972 [index] number of k-mers: 66,237,239 [index] number of equivalence classes: 154,277 [quant] running in single-end mode [quant] will process file 1: SRR8846485-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 12,722,891 reads, 1,595,545 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 890 rounds 52973 SRR8846485.ke.tsv 35125 SRR8846485.se.tsv 88098 total ==> SRR8846485.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0.435514 0.450044 PNS24247 1044 945 0 0 PNS24249 1928 1829 0 0 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 2.56449 1.61668 PNS24243 293 194 0 0 KQK14069 1603 1504 170.165 97.8591 KQK14071 474 375 6.76317 15.599 ==> SRR8846485.se.tsv <== BRADI_1g14170v3 306 BRADI_1g53295v3 0 BRADI_1g59795v3 21 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 42 BRADI_1g74790v3 5 BRADI_1g09890v3 0 BRADI_1g77505v3 3 BRADI_1g48960v3 0 SRR8846485 completed mapping pipeline successfully