Starting /dee2/code/volunteer_pipeline.sh SRR8846483 current disk space = 1505283002368 free memory = 1379981396 SRR8846483 SRAfilesize 517e78cee8511a787c1bc50d931f067c SRR8846483.sra SRR8846483.sra file validated SRR8846483 is single end SRR8846483 is conventional basespace SRR8846483 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8846483_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 warn #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.701 34.0 33.0 34.0 27.0 34.0 2 32.6275 34.0 33.0 34.0 28.0 34.0 3 32.99375 34.0 33.0 34.0 32.0 34.0 4 33.222 34.0 33.0 34.0 32.0 34.0 5 33.27075 34.0 33.0 34.0 33.0 34.0 6 37.007 38.0 37.0 38.0 36.0 38.0 7 37.3545 38.0 38.0 38.0 36.0 38.0 8 37.449 38.0 38.0 38.0 37.0 38.0 9 37.513 38.0 38.0 38.0 37.0 38.0 10-11 37.592375000000004 38.0 38.0 38.0 38.0 38.0 12-13 37.636624999999995 38.0 38.0 38.0 38.0 38.0 14-15 37.569375 38.0 38.0 38.0 38.0 38.0 16-17 37.494375000000005 38.0 38.0 38.0 37.5 38.0 18-19 37.48325 38.0 38.0 38.0 38.0 38.0 20-21 37.523375 38.0 38.0 38.0 38.0 38.0 22-23 37.590625 38.0 38.0 38.0 38.0 38.0 24-25 37.6265 38.0 38.0 38.0 38.0 38.0 26-27 37.5845 38.0 38.0 38.0 38.0 38.0 28-29 37.565875000000005 38.0 38.0 38.0 38.0 38.0 30-31 37.5 38.0 38.0 38.0 38.0 38.0 32-33 37.455625 38.0 38.0 38.0 37.0 38.0 34-35 37.287125 38.0 38.0 38.0 37.0 38.0 36-37 37.1725 38.0 38.0 38.0 37.0 38.0 38-39 37.01675 38.0 38.0 38.0 36.0 38.0 40-41 37.1055 38.0 38.0 38.0 37.0 38.0 42-43 37.114875 38.0 38.0 38.0 36.5 38.0 44-45 37.201625 38.0 38.0 38.0 37.0 38.0 46-47 37.134875 38.0 38.0 38.0 36.5 38.0 48-49 37.214124999999996 38.0 38.0 38.0 36.5 38.0 50-51 37.2505 38.0 38.0 38.0 37.0 38.0 52-53 37.376875 38.0 38.0 38.0 37.0 38.0 54-55 37.332625 38.0 38.0 38.0 37.0 38.0 56-57 37.16125 38.0 38.0 38.0 36.5 38.0 58-59 37.121375 38.0 38.0 38.0 36.5 38.0 60-61 37.070750000000004 38.0 38.0 38.0 36.5 38.0 62-63 36.445625 38.0 38.0 38.0 34.0 38.0 64-65 36.03575 38.0 37.5 38.0 31.0 38.0 66-67 35.877875 38.0 37.0 38.0 30.5 38.0 68-69 36.010125 38.0 37.0 38.0 32.0 38.0 70-71 35.734625 38.0 37.0 38.0 30.0 38.0 72-73 35.69825 38.0 37.0 38.0 31.0 38.0 74-75 35.4995 38.0 37.0 38.0 29.5 38.0 76-77 35.25925 38.0 37.0 38.0 28.5 38.0 78-79 35.24725 38.0 37.0 38.0 28.5 38.0 80-81 35.544875000000005 38.0 37.0 38.0 30.0 38.0 82-83 35.1 38.0 37.0 38.0 28.0 38.0 84-85 35.392125 38.0 37.0 38.0 29.0 38.0 86-87 35.384625 38.0 37.0 38.0 30.0 38.0 88-89 35.472375 38.0 37.0 38.0 31.0 38.0 90-91 35.3815 38.0 37.0 38.0 32.0 38.0 92-93 35.30025 38.0 38.0 38.0 31.0 38.0 94-95 34.716499999999996 38.0 37.5 38.0 29.0 38.0 96-97 32.882999999999996 38.0 35.0 38.0 8.5 38.0 98-99 30.376625 38.0 29.5 38.0 2.0 38.0 100-101 26.753875 37.5 8.5 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 0.0 14 1.0 15 1.0 16 0.0 17 1.0 18 1.0 19 0.0 20 1.0 21 3.0 22 3.0 23 6.0 24 16.0 25 35.0 26 30.0 27 24.0 28 19.0 29 29.0 30 49.0 31 60.0 32 88.0 33 121.0 34 181.0 35 380.0 36 880.0 37 2070.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 26.85838307107976 28.567552902875747 22.544763971785134 22.02930005425936 2 23.35 31.424999999999997 17.974999999999998 27.250000000000004 3 23.925 20.25 21.175 34.65 4 28.025 30.25 18.075 23.65 5 30.5 25.45 18.875 25.174999999999997 6 24.325 27.6 25.074999999999996 23.0 7 37.4 23.375 19.2 20.025000000000002 8 22.425 23.7 32.275 21.6 9 25.2 32.25 22.675 19.875 10-11 29.125 26.224999999999998 23.6375 21.0125 12-13 22.725 22.4375 21.1625 33.675 14-15 22.825 35.425000000000004 23.799999999999997 17.95 16-17 24.224999999999998 28.762500000000003 26.887499999999996 20.125 18-19 28.449999999999996 25.087500000000002 21.987499999999997 24.474999999999998 20-21 21.3125 28.487499999999997 27.425 22.775000000000002 22-23 27.900000000000002 27.675 29.45 14.975 24-25 26.75 24.55 27.6625 21.0375 26-27 34.3125 27.3 21.925 16.4625 28-29 21.15 31.6875 26.575 20.5875 30-31 23.7875 20.549999999999997 37.875 17.7875 32-33 23.125 20.1875 34.725 21.9625 34-35 29.475 16.7125 29.925 23.8875 36-37 38.7 13.0125 30.587500000000002 17.7 38-39 36.05 17.9 26.237500000000004 19.8125 40-41 28.95 19.3375 22.5125 29.2 42-43 30.349999999999998 26.5125 22.675 20.4625 44-45 39.324999999999996 19.725 15.6 25.35 46-47 30.15 32.0625 13.3875 24.4 48-49 28.3875 23.6375 19.1875 28.787499999999998 50-51 23.2625 23.375 15.625 37.737500000000004 52-53 22.900000000000002 33.2375 12.4125 31.45 54-55 18.987499999999997 27.462500000000002 17.875 35.675000000000004 56-57 18.075 35.4125 11.4875 35.025 58-59 9.049999999999999 36.65 15.312500000000002 38.987500000000004 60-61 7.324999999999999 37.487500000000004 15.5 39.6875 62-63 8.0375 38.2125 20.625 33.125 64-65 7.675 37.55 24.3 30.475 66-67 6.275 29.525000000000002 27.950000000000003 36.25 68-69 11.3125 31.4375 24.0625 33.1875 70-71 10.875 31.974999999999998 29.925 27.224999999999998 72-73 18.0625 23.5 30.7875 27.650000000000002 74-75 13.5875 21.212500000000002 29.525000000000002 35.675000000000004 76-77 19.325 15.9125 38.987500000000004 25.775 78-79 16.412499999999998 10.15 38.2 35.2375 80-81 18.675 11.25 37.737500000000004 32.337500000000006 82-83 21.65 10.6 43.65 24.099999999999998 84-85 19.2375 9.7375 38.5625 32.4625 86-87 22.4625 16.125 36.9 24.5125 88-89 15.625 34.0125 33.037499999999994 17.325 90-91 12.7 42.15 28.050000000000004 17.1 92-93 12.375 52.5625 21.8125 13.25 94-95 10.424999999999999 62.612500000000004 17.837500000000002 9.125 96-97 7.449999999999999 70.2625 15.712499999999999 6.575 98-99 6.65 79.5125 10.025 3.8125 100-101 3.5749999999999997 87.41250000000001 5.325 3.6875 >>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 1.0 31 3.0 32 5.0 33 11.0 34 17.5 35 18.0 36 13.5 37 16.0 38 50.0 39 72.5 40 114.0 41 188.5 42 242.0 43 337.0 44 381.0 45 421.5 46 403.5 47 324.5 48 303.5 49 243.5 50 181.0 51 124.5 52 87.0 53 94.0 54 163.0 55 124.0 56 23.0 57 14.5 58 9.0 59 4.5 60 4.0 61 1.5 62 2.0 63 1.5 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 warn #Base N-Count 1 7.85 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-11 0.0 12-13 0.0 14-15 0.0 16-17 0.0 18-19 0.0 20-21 0.0 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.0 30-31 0.0 32-33 0.0 34-35 0.0 36-37 0.0 38-39 0.0 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0 54-55 0.0 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0 66-67 0.0 68-69 0.0 70-71 0.0 72-73 0.0 74-75 0.0 76-77 0.0 78-79 0.0 80-81 0.0 82-83 0.0 84-85 0.0 86-87 0.0 88-89 0.0 90-91 0.0 92-93 0.0 94-95 0.0 96-97 0.0 98-99 0.0 100-101 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 101 4000.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 56.474999999999994 #Duplication Level Percentage of deduplicated Percentage of total 1 83.88667552014165 47.375 2 7.791057990261177 8.799999999999999 3 3.054448871181939 5.175 4 0.9738822487826472 2.1999999999999997 5 0.8853474988933155 2.5 6 0.7082779991146525 2.4 7 0.35413899955732625 1.4000000000000001 8 0.3098716246126605 1.4000000000000001 9 0.17706949977866313 0.8999999999999999 >10 1.6378928729526339 16.175 >50 0.17706949977866313 8.05 >100 0.04426737494466578 3.6249999999999996 >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 145 3.6249999999999996 No Hit GGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 87 2.175 RNA PCR Primer, Index 1 (100% over 22bp) TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 81 2.025 RNA PCR Primer, Index 1 (100% over 29bp) AGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 78 1.95 No Hit GACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 76 1.9 RNA PCR Primer, Index 1 (100% over 23bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 36 0.8999999999999999 No Hit CTCTGATGATGATCAAACTAATACTTTCGTTCTTCTGGAATTCTCGGGTG 35 0.8750000000000001 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 28 0.7000000000000001 Illumina Small RNA Adapter 2 (100% over 21bp) CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 27 0.675 No Hit CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTC 27 0.675 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 26 0.65 No Hit ATATATTTCAAGTTATTTCGGATCTTGGAATTCTCGGGTGCCAAGGAACT 25 0.625 RNA PCR Primer, Index 1 (100% over 25bp) AAGGGTGCTGAGAATACTTTGAATCTGACACTGGAATTCTCGGGTGCCAA 25 0.625 No Hit GACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAAC 23 0.575 RNA PCR Primer, Index 1 (100% over 24bp) TCTCGGGTGCCAAGGAACTCCAGTCACCAACTAATCTCGTATGCCGTCTT 23 0.575 RNA PCR Primer, Index 29 (100% over 50bp) GACACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACT 22 0.5499999999999999 RNA PCR Primer, Index 1 (100% over 25bp) CTCGGGTGCCAAGGAACTCCAGTCACCAACTAATCTCGTATGCCGTCTTC 22 0.5499999999999999 RNA PCR Primer, Index 29 (100% over 50bp) AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 19 0.475 Illumina Small RNA Adapter 2 (100% over 21bp) GCCCACCCCAAGATGAGTGCTCTCTCTGGAATTCTCGGGTGCCAAGGAAC 18 0.44999999999999996 RNA PCR Primer, Index 1 (100% over 24bp) AATTCTCGGGTGCCAAGGAACTCCAGTCACCAACTAATCTCGTATGCCGT 18 0.44999999999999996 RNA PCR Primer, Index 29 (100% over 50bp) TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 16 0.4 No Hit GCACCAGTGGTCTAGTGGTAGAATAGTACCTGGAATTCTCGGGTGCCAAG 15 0.375 No Hit CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGG 15 0.375 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCATGGAATTCTCGGGTG 15 0.375 No Hit NGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 14 0.35000000000000003 RNA PCR Primer, Index 1 (100% over 22bp) TCCTGTGGATGAGAAGGCATTTATATTCTGATGATATGGAATTCTCGGGT 14 0.35000000000000003 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 14 0.35000000000000003 Illumina Small RNA Adapter 2 (100% over 21bp) ATTCTCGGGTGCCAAGGAACTCCAGTCACCAACTAATCTCGTATGCCGTC 14 0.35000000000000003 RNA PCR Primer, Index 29 (100% over 50bp) GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 14 0.35000000000000003 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 13 0.325 No Hit CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 13 0.325 RNA PCR Primer, Index 1 (100% over 28bp) CATCGAGTAGACCTTGTTATTGTGAGAATAAATGGAATTCTCGGGTGCCA 12 0.3 No Hit AAGGGTGCTGAGAATACTTTGAATCTGACATGGAATTCTCGGGTGCCAAG 12 0.3 No Hit TATTCTGGTGTCCTAGGCGTAGAGGATGGAATTCTCGGGTGCCAAGGAAC 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 24bp) ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGC 11 0.27499999999999997 No Hit CACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAACT 10 0.25 RNA PCR Primer, Index 1 (100% over 25bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 10 0.25 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATACTCTGGAATTCTCGGGTGCCAAG 10 0.25 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 10 0.25 Illumina Small RNA Adapter 2 (100% over 21bp) CATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGCC 10 0.25 No Hit ATATATTTCAAGTTATTTCGGATCTGGAATTCTCGGGTGCCAAGGAACTC 10 0.25 RNA PCR Primer, Index 1 (100% over 26bp) TTCTCGGGTGCCAAGGAACTCCAGTCACCAACTAATCTCGTATGCCGTCT 10 0.25 RNA PCR Primer, Index 29 (100% over 50bp) NCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 9 0.22499999999999998 No Hit CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGG 9 0.22499999999999998 No Hit CAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTG 9 0.22499999999999998 No Hit TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTGGAATTCTCGGGTGC 9 0.22499999999999998 No Hit TCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTC 8 0.2 RNA PCR Primer, Index 1 (100% over 26bp) CATCGAGTAGACCTTGTTATTGTGAGAATGGAATTCTCGGGTGCCAAGGA 8 0.2 RNA PCR Primer, Index 1 (100% over 22bp) TCCGTCGTAGTCTAGGTGGTTAGGATATGGAATTCTCGGGTGCCAAGGAA 8 0.2 RNA PCR Primer, Index 1 (100% over 23bp) ATAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAACT 8 0.2 RNA PCR Primer, Index 1 (100% over 25bp) CCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTG 8 0.2 No Hit ACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCC 8 0.2 No Hit CAGGGTTCGTTTCCCTGGATGCGCACCATGGAATTCTCGGGTGCCAAGGA 8 0.2 RNA PCR Primer, Index 1 (100% over 22bp) GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit TTCGGACCAGGCTTCATTCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 29bp) TCTCGGACCAGGCTTCATTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 29bp) GGGGATGTAGCTCAGATGGTAGATGGAATTCTCGGGTGCCAAGGAACTCC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 27bp) TGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAA 7 0.17500000000000002 No Hit CACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACTCC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 27bp) GCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit CGGATAACCGTAGTAATTCTAGAGCTAATACTGGAATTCTCGGGTGCCAA 7 0.17500000000000002 No Hit CGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTCTC 6 0.15 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTAATCTGGAATTCT 6 0.15 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTGGAATTCTCGGGTGCCAAG 6 0.15 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTTGGAATTCT 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAAAATGGAATTCTCGGGTGC 6 0.15 No Hit ATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGCCA 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 6 0.15 RNA PCR Primer, Index 1 (100% over 23bp) NCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 6 0.15 RNA PCR Primer, Index 1 (100% over 29bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTGAATCTGGAATTC 6 0.15 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTTGGAATTCTCGGGTGCC 6 0.15 No Hit CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGTGGAATTCTCGG 6 0.15 No Hit GACACGACTCTCGGCAACGGATATCTCGTGGAATTCTCGGGTGCCAAGGA 6 0.15 RNA PCR Primer, Index 1 (100% over 22bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTGGAATTCTCGGGT 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATGGAATTCTCGGGTG 6 0.15 No Hit ATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAA 6 0.15 RNA PCR Primer, Index 1 (100% over 23bp) CTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCA 6 0.15 No Hit GATAACCGTAGTAATTCTAGAGCTAATTGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAAATGGAATTCTCGGGT 5 0.125 No Hit GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTG 5 0.125 No Hit ACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) TGTATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCT 5 0.125 No Hit TCGGGTGCCAAGGAACTCCAGTCACCAACTAATCTCGTATGCCGTCTTCT 5 0.125 RNA PCR Primer, Index 29 (100% over 50bp) GAAGTCCTCGTGTTGCATTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA 5 0.125 RNA PCR Primer, Index 1 (100% over 28bp) CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGGAATTCTCG 5 0.125 No Hit ACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATT 5 0.125 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTTGGAATTCTCGGGTG 5 0.125 No Hit ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGGTGC 5 0.125 No Hit CACGACTCTCGGCAACGGATATCTCGTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) NCCTTGATGGTGAAATGGTAGACACGCGAGACTCATGGAATTCTCGGGTG 5 0.125 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTGGAATTCTCGGGTGCCAAGG 5 0.125 Illumina Small RNA Adapter 2 (100% over 21bp) ACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 5 0.125 RNA PCR Primer, Index 1 (100% over 31bp) AACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAACTCC 5 0.125 RNA PCR Primer, Index 1 (100% over 27bp) GGGGATATAGCTCAGTTGGTAGATGGAATTCTCGGGTGCCAAGGAACTCC 5 0.125 RNA PCR Primer, Index 1 (100% over 27bp) AGCTGAGGCATCCTAACGAACGAACGATTTGAATGGAATTCTCGGGTGCC 5 0.125 No Hit NACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 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 0.025 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 0.1 0.0 0.0 0.0 8 0.0 0.125 0.0 0.0 0.0 9 0.0 0.175 0.0 0.0 0.0 10-11 0.0 0.2125 0.0 0.0 0.0 12-13 0.0 0.3125 0.0 0.0 0.0 14-15 0.0 0.5125 0.0 0.0 0.0 16-17 0.0 1.0875 0.0 0.0 0.0 18-19 0.0 1.775 0.0 0.0 0.0 20-21 0.0 3.5375 0.0 0.0 0.0 22-23 0.0 10.4875 0.0 0.0 0.0 24-25 0.0 22.2625 0.0 0.0 0.0 26-27 0.0 35.8625 0.0 0.0 0.0 28-29 0.0 45.8 0.0 0.0 0.0 30-31 0.0 55.7875 0.0 0.0 0.0 32-33 0.0 64.36250000000001 0.0 0.0 0.0 34-35 0.0 73.225 0.0 0.0 0.0 36-37 0.0 83.025 0.0 0.0 0.0 38-39 0.0 88.3375 0.0 0.0 0.0 40-41 0.0 90.5625 0.0 0.0 0.0 42-43 0.0 93.23750000000001 0.0 0.0 0.0 44-45 0.0 94.575 0.0 0.0 0.0 46-47 0.0 94.9375 0.0 0.0 0.0 48-49 0.0 94.975 0.0 0.0 0.0 50-51 0.0 94.975 0.0 0.0 0.0 52-53 0.0 94.975 0.0 0.0 0.0 54-55 0.0 94.975 0.0 0.0 0.0 56-57 0.0 94.975 0.0 0.0 0.0 58-59 0.0 94.975 0.0 0.0 0.0 60-61 0.0 94.975 0.0 0.0 0.0 62-63 0.0 94.975 0.0 0.0 0.0 64-65 0.0 94.975 0.0 0.0 0.0 66-67 0.0 94.975 0.0 0.0 0.0 68-69 0.0 94.975 0.0 0.0 0.0 70-71 0.0 94.975 0.0 0.0 0.0 72-73 0.0 94.975 0.0 0.0 0.0 74-75 0.0 94.975 0.0 0.0 0.0 76-77 0.0 94.9875 0.0 0.0 0.0 78-79 0.0 95.0 0.0 0.0 0.0 80-81 0.0 95.0 0.0 0.0 0.0 82-83 0.0 95.0125 0.0 0.0 0.0 84-85 0.0 95.025 0.0 0.0 0.0 86-87 0.0 95.025 0.0 0.0 0.0 88-89 0.0 95.025 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGATTG 20 9.691041E-6 104.013695 1 GTAGACC 20 1.5462934E-5 94.912506 7 AGCTCAG 20 1.5462934E-5 94.912506 9 AGTAGAC 20 1.5462934E-5 94.912506 6 TAGCTCA 20 1.5462934E-5 94.912506 8 GGATTGT 20 1.5462934E-5 94.912506 2 GATTGTA 20 1.5462934E-5 94.912506 3 TAGTTCA 25 3.8500548E-7 94.912506 8 GAGTAGA 20 1.5462934E-5 94.912506 5 ATTGTAG 20 1.5462934E-5 94.912506 4 TGTAGTT 20 1.5462934E-5 94.912506 6 CGAGTAG 20 1.5462934E-5 94.912506 4 AGACCTT 20 1.5462934E-5 94.912506 9 TCGAGTA 20 1.5462934E-5 94.912506 3 AGTTCAA 25 3.8500548E-7 94.912506 9 GTAGTTC 25 3.8500548E-7 94.912506 7 TAGACCT 20 1.5462934E-5 94.912506 8 GTCGTAG 15 6.164719E-4 94.9125 4 CGTAGTC 15 6.164719E-4 94.9125 6 CCGTCGT 15 6.164719E-4 94.9125 2 >>END_MODULE Rejected 901629 READS because READLEN < 1 Read 901629 spots for SRR8846483.sra Written 901629 spots for SRR8846483.sra Rejected 901629 READS because READLEN < 1 Read 901629 spots for SRR8846483.sra Written 901629 spots for SRR8846483.sra Rejected 901629 READS because READLEN < 1 Read 901629 spots for SRR8846483.sra Written 901629 spots for SRR8846483.sra Rejected 901629 READS because READLEN < 1 Read 901629 spots for SRR8846483.sra Written 901629 spots for SRR8846483.sra Rejected 901629 READS because READLEN < 1 Read 901629 spots for SRR8846483.sra Written 901629 spots for SRR8846483.sra Rejected 901629 READS because READLEN < 1 Read 901629 spots for SRR8846483.sra Written 901629 spots for SRR8846483.sra Rejected 901629 READS because READLEN < 1 Read 901629 spots for SRR8846483.sra Written 901629 spots for SRR8846483.sra Rejected 901629 READS because READLEN < 1 Read 901629 spots for SRR8846483.sra Written 901629 spots for SRR8846483.sra Rejected 901640 READS because READLEN < 1 Read 901640 spots for SRR8846483.sra Written 901640 spots for SRR8846483.sra Rejected 901629 READS because READLEN < 1 Read 901629 spots for SRR8846483.sra Written 901629 spots for SRR8846483.sra Rejected 901629 READS because READLEN < 1 Read 901629 spots for SRR8846483.sra Written 901629 spots for SRR8846483.sra Rejected 901629 READS because READLEN < 1 Read 901629 spots for SRR8846483.sra Written 901629 spots for SRR8846483.sra Rejected 901629 READS because READLEN < 1 Read 901629 spots for SRR8846483.sra Written 901629 spots for SRR8846483.sra Rejected 901629 READS because READLEN < 1 Read 901629 spots for SRR8846483.sra Written 901629 spots for SRR8846483.sra Rejected 901629 READS because READLEN < 1 Read 901629 spots for SRR8846483.sra Written 901629 spots for SRR8846483.sra Rejected 901629 READS because READLEN < 1 Read 901629 spots for SRR8846483.sra Written 901629 spots for SRR8846483.sra Rejected 901629 READS because READLEN < 1 Read 901629 spots for SRR8846483.sra Written 901629 spots for SRR8846483.sra Rejected 901629 READS because READLEN < 1 Read 901629 spots for SRR8846483.sra Written 901629 spots for SRR8846483.sra Rejected 901629 READS because READLEN < 1 Read 901629 spots for SRR8846483.sra Written 901629 spots for SRR8846483.sra Rejected 901629 READS because READLEN < 1 Read 901629 spots for SRR8846483.sra Written 901629 spots for SRR8846483.sra SRR ids: ['SRR8846483.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_318g52_d SRR8846483.sra spots: 18032591 blocks: [[1, 901629], [901630, 1803258], [1803259, 2704887], [2704888, 3606516], [3606517, 4508145], [4508146, 5409774], [5409775, 6311403], [6311404, 7213032], [7213033, 8114661], [8114662, 9016290], [9016291, 9917919], [9917920, 10819548], [10819549, 11721177], [11721178, 12622806], [12622807, 13524435], [13524436, 14426064], [14426065, 15327693], [15327694, 16229322], [16229323, 17130951], [17130952, 18032591]] SRR8846483 file size 4327957 SRR8846483 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 SRR8846483 SRR8846483_1.fastq Input file: SRR8846483_1.fastq trimmed: SRR8846483-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 17:22:32 2024 >> started Sun Dec 8 17:23:19 2024 >> done (47.177s) 18032591 reads processed; of these: 291 ( 0.00%) short reads filtered out after trimming by size control 50 ( 0.00%) empty reads filtered out after trimming by size control 18032250 (100.00%) reads available; of these: 3844902 (21.32%) trimmed reads available after processing 14187348 (78.68%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 38 0.00% 19 31 0.00% 20 38 0.00% 21 40 0.00% 22 39 0.00% 23 40 0.00% 24 58 0.00% 25 60 0.00% 26 93 0.00% 27 117 0.00% 28 144 0.00% 29 164 0.00% 30 164 0.00% 31 154 0.00% 32 184 0.00% 33 250 0.00% 34 241 0.00% 35 229 0.00% 36 278 0.00% 37 266 0.00% 38 243 0.00% 39 309 0.00% 40 298 0.00% 41 322 0.00% 42 318 0.00% 43 323 0.00% 44 289 0.00% 45 231 0.00% 46 190 0.00% 47 210 0.00% 48 263 0.00% 49 289 0.00% 50 337 0.00% 51 350 0.00% 52 304 0.00% 53 338 0.00% 54 266 0.00% 55 207 0.00% 56 309 0.00% 57 289 0.00% 58 350 0.00% 59 395 0.00% 60 557 0.00% 61 903 0.01% 62 1591 0.01% 63 1844 0.01% 64 3589 0.02% 65 4711 0.03% 66 13100 0.07% 67 68059 0.38% 68 75958 0.42% 69 47696 0.26% 70 37523 0.21% 71 43330 0.24% 72 19445 0.11% 73 6711 0.04% 74 6558 0.04% 75 4981 0.03% 76 4576 0.03% 77 4027 0.02% 78 4834 0.03% 79 5051 0.03% 80 5725 0.03% 81 6401 0.04% 82 10180 0.06% 83 10491 0.06% 84 10344 0.06% 85 11835 0.07% 86 13331 0.07% 87 15751 0.09% 88 24901 0.14% 89 35927 0.20% 90 58770 0.33% 91 58129 0.32% 92 73622 0.41% 93 116145 0.64% 94 153963 0.85% 95 346725 1.92% 96 399988 2.22% 97 418613 2.32% 98 629307 3.49% 99 717321 3.98% 100 363331 2.01% 101 14187348 78.68% 18032250 reads passed initial QC criterion=sequence-density sequence-density=94.11 sequence-density-rank=1 fanout-score=33.51 fanout-score-rank=1 prefix-density=94.49 prefix-fanout=33.4 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAACTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA criterion=fanout-score sequence-density=94.11 sequence-density-rank=1 fanout-score=33.51 fanout-score-rank=1 prefix-density=94.49 prefix-fanout=33.4 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAACTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAACTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA -o SRR8846483 - Input file: STDIN trimmed: SRR8846483-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAACTAATCTCGTATGCCGTCTTCTGCTTGA -- 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 17:26:25 2024 >> started Sun Dec 8 17:27:50 2024 >> done (84.859s) 17652624 reads processed; of these: 305703 ( 1.73%) short reads filtered out after trimming by size control 8179 ( 0.05%) empty reads filtered out after trimming by size control 17338742 (98.22%) reads available; of these: 16741306 (96.55%) trimmed reads available after processing 597436 ( 3.45%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 93689 0.54% 19 161189 0.93% 20 207256 1.20% 21 822474 4.74% 22 430252 2.48% 23 660781 3.81% 24 2354824 13.58% 25 852947 4.92% 26 814280 4.70% 27 894989 5.16% 28 950905 5.48% 29 825363 4.76% 30 1021468 5.89% 31 660161 3.81% 32 630504 3.64% 33 827673 4.77% 34 888010 5.12% 35 785787 4.53% 36 1036294 5.98% 37 384519 2.22% 38 305407 1.76% 39 241385 1.39% 40 206459 1.19% 41 235862 1.36% 42 228394 1.32% 43 72259 0.42% 44 69466 0.40% 45 30531 0.18% 46 15663 0.09% 47 7717 0.04% 48 6151 0.04% 49 3273 0.02% 50 2308 0.01% 51 2078 0.01% 52 1042 0.01% 53 776 0.00% 54 977 0.01% 55 336 0.00% 56 632 0.00% 57 294 0.00% 58 330 0.00% 59 357 0.00% 60 483 0.00% 61 865 0.00% 62 1435 0.01% 63 1694 0.01% 64 3327 0.02% 65 4436 0.03% 66 12685 0.07% 67 66343 0.38% 68 74033 0.43% 69 46377 0.27% 70 36271 0.21% 71 41890 0.24% 72 17595 0.10% 73 4883 0.03% 74 3541 0.02% 75 2672 0.02% 76 2893 0.02% 77 3572 0.02% 78 2901 0.02% 79 2895 0.02% 80 4242 0.02% 81 3239 0.02% 82 2773 0.02% 83 3108 0.02% 84 1842 0.01% 85 1795 0.01% 86 1651 0.01% 87 1542 0.01% 88 1315 0.01% 89 1378 0.01% 90 1216 0.01% 91 1248 0.01% 92 1295 0.01% 93 1611 0.01% 94 1799 0.01% 95 2379 0.01% 96 3637 0.02% 97 4967 0.03% 98 7003 0.04% 99 8211 0.05% 100 10037 0.06% 101 206601 1.19% criterion=sequence-density sequence-density=6.07 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=11 prefix-density=0.00 prefix-fanout=1.0 sequence=CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAA criterion=fanout-score sequence-density=0.26 sequence-density-rank=16 fanout-score=21.13 fanout-score-rank=1 prefix-density=5.54 prefix-fanout=1.0 sequence=TTGTGAGAATTAAAAA Started job on | Dec 08 17:30:19 Started mapping on | Dec 08 17:30:20 Finished on | Dec 08 17:39:28 Mapping speed, Million of reads per hour | 116.40 Number of input reads | 17718368 Average input read length | 32 UNIQUE READS: Uniquely mapped reads number | 3332376 Uniquely mapped reads % | 18.81% Average mapped length | 26.71 Number of splices: Total | 30149 Number of splices: Annotated (sjdb) | 17461 Number of splices: GT/AG | 27934 Number of splices: GC/AG | 1540 Number of splices: AT/AC | 21 Number of splices: Non-canonical | 654 Mismatch rate per base, % | 0.13% Deletion rate per base | 0.00% Deletion average length | 1.36 Insertion rate per base | 0.00% Insertion average length | 1.02 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 5895247 % of reads mapped to multiple loci | 33.27% Number of reads mapped to too many loci | 7237136 % of reads mapped to too many loci | 40.85% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 6.39% % of reads unmapped: other | 0.69% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 8490745 8490745 8490745 N_multimapping 5895247 5895247 5895247 N_noFeature 2077633 2275256 3118898 N_ambiguous 57038 40622 747 UnstrandedReadsAssigned:1197705 PositiveStrandReadsAssigned:1016498 NegativeStrandReadsAssigned:212731 Dataset is classified unstranded MeadianReadLen=29 20thPercentileLength=24 echo kmer=19 SRR8846483 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: SRR8846483-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 17,718,368 reads, 5,276,998 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,098 rounds 52973 SRR8846483.ke.tsv 35125 SRR8846483.se.tsv 88098 total ==> SRR8846483.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 2.43551 0.552872 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 0.355145 PNS24243 293 194 0 0 KQK14069 1603 1504 141.726 17.9045 KQK14071 474 375 0 0 ==> SRR8846483.se.tsv <== BRADI_1g14170v3 262 BRADI_1g53295v3 0 BRADI_1g59795v3 18 BRADI_1g07683v3 0 BRADI_1g00485v3 2 BRADI_1g20270v3 44 BRADI_1g74790v3 39 BRADI_1g09890v3 0 BRADI_1g77505v3 1 BRADI_1g48960v3 0 SRR8846483 completed mapping pipeline successfully