Starting /dee2/code/volunteer_pipeline.sh SRR8846551 current disk space = 1528573595648 free memory = 1357870024 SRR8846551 SRAfilesize 0af173474c9780f2df45e06a86d6009a SRR8846551.sra SRR8846551.sra file validated SRR8846551 is single end SRR8846551 is conventional basespace SRR8846551 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8846551_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 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.368 34.0 33.0 34.0 25.0 34.0 2 32.69025 34.0 33.0 34.0 28.0 34.0 3 32.90575 34.0 33.0 34.0 31.0 34.0 4 32.98875 34.0 33.0 34.0 32.0 34.0 5 33.017 34.0 33.0 34.0 32.0 34.0 6 36.8065 38.0 37.0 38.0 35.0 38.0 7 37.18575 38.0 38.0 38.0 36.0 38.0 8 37.339 38.0 38.0 38.0 37.0 38.0 9 37.445 38.0 38.0 38.0 37.0 38.0 10-11 37.478625 38.0 38.0 38.0 37.0 38.0 12-13 37.506 38.0 38.0 38.0 37.0 38.0 14-15 37.46975 38.0 38.0 38.0 37.0 38.0 16-17 37.394125 38.0 38.0 38.0 37.0 38.0 18-19 37.479124999999996 38.0 38.0 38.0 37.0 38.0 20-21 37.447375 38.0 38.0 38.0 37.0 38.0 22-23 37.436125000000004 38.0 38.0 38.0 37.0 38.0 24-25 37.394875 38.0 38.0 38.0 37.0 38.0 26-27 37.525125 38.0 38.0 38.0 38.0 38.0 28-29 37.401375 38.0 38.0 38.0 37.5 38.0 30-31 37.3805 38.0 38.0 38.0 37.0 38.0 32-33 37.380875 38.0 38.0 38.0 37.0 38.0 34-35 37.156375 38.0 38.0 38.0 36.5 38.0 36-37 37.038 38.0 38.0 38.0 36.0 38.0 38-39 36.8575 38.0 38.0 38.0 35.5 38.0 40-41 36.918375 38.0 38.0 38.0 35.5 38.0 42-43 36.7665 38.0 38.0 38.0 35.0 38.0 44-45 36.89625 38.0 38.0 38.0 35.5 38.0 46-47 36.859875 38.0 38.0 38.0 35.0 38.0 48-49 36.814625 38.0 38.0 38.0 35.0 38.0 50-51 36.964749999999995 38.0 38.0 38.0 35.5 38.0 52-53 36.983625 38.0 38.0 38.0 36.0 38.0 54-55 36.85425 38.0 38.0 38.0 35.5 38.0 56-57 36.633 38.0 38.0 38.0 34.5 38.0 58-59 36.502375 38.0 38.0 38.0 33.5 38.0 60-61 36.4795 38.0 38.0 38.0 34.0 38.0 62-63 36.255875 38.0 38.0 38.0 33.0 38.0 64-65 36.4725 38.0 38.0 38.0 33.5 38.0 66-67 36.217375000000004 38.0 37.5 38.0 33.0 38.0 68-69 35.754374999999996 38.0 37.0 38.0 31.0 38.0 70-71 35.27875 38.0 37.0 38.0 29.0 38.0 72-73 35.090875 38.0 37.0 38.0 28.0 38.0 74-75 34.907375 38.0 37.0 38.0 28.0 38.0 76-77 34.56225 38.0 36.0 38.0 26.0 38.0 78-79 34.623625 38.0 36.0 38.0 27.0 38.0 80-81 34.312250000000006 38.0 35.5 38.0 25.5 38.0 82-83 34.091625 38.0 35.0 38.0 24.0 38.0 84-85 33.99225 38.0 35.0 38.0 23.0 38.0 86-87 34.00375 38.0 35.0 38.0 23.5 38.0 88-89 34.1655 38.0 35.5 38.0 24.0 38.0 90-91 34.183875 38.0 35.5 38.0 23.0 38.0 92-93 34.283875 38.0 36.0 38.0 25.5 38.0 94-95 33.97175 38.0 35.5 38.0 20.0 38.0 96-97 32.864625000000004 38.0 34.0 38.0 15.0 38.0 98-99 32.103125000000006 38.0 33.5 38.0 8.5 38.0 100-101 31.085250000000002 38.0 31.5 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 14 1.0 15 0.0 16 2.0 17 1.0 18 3.0 19 0.0 20 2.0 21 2.0 22 6.0 23 14.0 24 22.0 25 60.0 26 28.0 27 34.0 28 29.0 29 42.0 30 70.0 31 65.0 32 94.0 33 127.0 34 192.0 35 345.0 36 879.0 37 1982.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 36.679431072210065 21.088621444201312 18.681619256017505 23.550328227571114 2 29.849999999999998 26.174999999999997 14.2 29.775000000000002 3 28.975 17.4 17.9 35.725 4 25.05 34.599999999999994 19.325 21.025 5 29.225 21.6 25.25 23.925 6 25.324999999999996 24.9 28.975 20.8 7 40.1 26.3 18.4 15.2 8 19.675 20.349999999999998 40.25 19.725 9 25.224999999999998 37.275000000000006 20.125 17.375 10-11 32.824999999999996 21.987499999999997 25.837500000000002 19.35 12-13 22.2125 21.2625 20.8875 35.6375 14-15 23.200000000000003 45.0 17.837500000000002 13.9625 16-17 25.0625 23.5875 32.1375 19.2125 18-19 36.7 23.05 20.2625 19.9875 20-21 19.0625 30.112499999999997 27.900000000000002 22.925 22-23 27.875 32.3125 23.7375 16.075 24-25 28.4 28.8625 19.7375 23.0 26-27 28.599999999999998 27.5875 19.175 24.637500000000003 28-29 24.375 22.3 24.1375 29.1875 30-31 29.7875 20.7 26.700000000000003 22.8125 32-33 22.037499999999998 18.7625 33.2375 25.9625 34-35 26.887499999999996 19.787499999999998 29.812499999999996 23.5125 36-37 25.45 24.825 31.337500000000002 18.387500000000003 38-39 29.349999999999998 24.762500000000003 29.5 16.3875 40-41 26.987499999999997 20.25 31.4375 21.325 42-43 31.225 15.8875 31.25 21.637500000000003 44-45 38.675 18.1125 21.5 21.712500000000002 46-47 35.35 21.475 22.2625 20.9125 48-49 30.837500000000002 19.1 23.724999999999998 26.337500000000002 50-51 26.5375 22.225 21.1125 30.125 52-53 33.074999999999996 24.95 13.237499999999999 28.7375 54-55 32.4375 28.325 15.6375 23.599999999999998 56-57 29.512500000000003 25.074999999999996 15.55 29.862499999999997 58-59 20.0375 29.275000000000002 15.6125 35.075 60-61 23.4625 29.2375 14.85 32.45 62-63 25.6125 27.2625 15.45 31.674999999999997 64-65 22.8 29.099999999999998 17.25 30.85 66-67 21.525 20.4375 22.2 35.8375 68-69 25.2875 20.1 20.0875 34.525 70-71 28.075 16.8 23.25 31.874999999999996 72-73 23.9 18.8 22.85 34.449999999999996 74-75 19.75 15.525 26.700000000000003 38.025 76-77 24.15 13.487499999999999 32.5625 29.799999999999997 78-79 25.7 10.9625 31.0625 32.275 80-81 22.5 13.65 31.175000000000004 32.675 82-83 19.3125 12.562499999999998 35.9625 32.1625 84-85 22.037499999999998 8.3625 36.225 33.375 86-87 20.474999999999998 9.825000000000001 37.4625 32.237500000000004 88-89 18.65 15.812499999999998 41.349999999999994 24.1875 90-91 18.7375 17.599999999999998 37.1125 26.55 92-93 19.037499999999998 22.662499999999998 31.724999999999998 26.575 94-95 17.3375 30.062499999999996 33.6 19.0 96-97 12.4375 42.2375 29.975 15.35 98-99 11.450000000000001 54.1625 22.3625 12.025 100-101 9.55 64.7625 15.987499999999999 9.700000000000001 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 0.0 27 0.0 28 0.0 29 0.0 30 0.0 31 0.0 32 0.0 33 0.0 34 1.0 35 2.0 36 4.5 37 7.5 38 11.0 39 13.5 40 19.0 41 28.0 42 33.0 43 57.5 44 86.0 45 98.0 46 173.0 47 237.0 48 249.5 49 292.5 50 300.5 51 324.0 52 408.0 53 407.0 54 265.0 55 169.0 56 213.5 57 274.5 58 188.5 59 55.5 60 25.5 61 20.0 62 12.0 63 7.5 64 5.0 65 4.5 66 4.0 67 2.0 68 1.0 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 8.6 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 fail #Total Deduplicated Percentage 49.375 #Duplication Level Percentage of deduplicated Percentage of total 1 81.56962025316456 40.275 2 8.354430379746836 8.25 3 2.6835443037974684 3.975 4 1.7721518987341773 3.5000000000000004 5 0.8101265822784811 2.0 6 0.9113924050632912 2.7 7 0.5063291139240507 1.7500000000000002 8 0.40506329113924056 1.6 9 0.35443037974683544 1.575 >10 2.329113924050633 20.3 >50 0.20253164556962028 7.6499999999999995 >100 0.10126582278481014 6.425 >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 137 3.4250000000000003 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 120 3.0 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 83 2.075 No Hit AGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 82 2.0500000000000003 No Hit CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTC 78 1.95 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTTGGAATTCT 63 1.575 No Hit GGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 41 1.0250000000000001 RNA PCR Primer, Index 1 (100% over 22bp) CTCGGGTGCCAAGGAACTCCAGTCACGTGGCCATCTCGTATGCCGTCTTC 31 0.775 RNA PCR Primer, Index 20 (100% over 50bp) CTCTGATGATGATCAAACTAATACTTTCGTTCTTCTGGAATTCTCGGGTG 29 0.7250000000000001 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCGTGGAATT 29 0.7250000000000001 No Hit TCTCGGGTGCCAAGGAACTCCAGTCACGTGGCCATCTCGTATGCCGTCTT 28 0.7000000000000001 RNA PCR Primer, Index 20 (100% over 50bp) TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 26 0.65 RNA PCR Primer, Index 1 (100% over 29bp) AGGGCTATAGCTCAGTTCGGTAGAGCAACTCGTTTACACCGAGATGGAAT 25 0.625 No Hit GACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAAC 24 0.6 RNA PCR Primer, Index 1 (100% over 24bp) AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 24 0.6 Illumina Small RNA Adapter 2 (100% over 21bp) ACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTCT 24 0.6 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTGGAATTCTC 23 0.575 No Hit CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGG 22 0.5499999999999999 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 21 0.525 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 20 0.5 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGAGTGGAATTCT 20 0.5 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 20 0.5 No Hit AATTCTCGGGTGCCAAGGAACTCCAGTCACGTGGCCATCTCGTATGCCGT 20 0.5 RNA PCR Primer, Index 20 (100% over 50bp) GCACCAGTGGTCTAGTGGTAGAATAGTACCTGGAATTCTCGGGTGCCAAG 19 0.475 No Hit CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGGAATTCTCG 18 0.44999999999999996 No Hit GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 17 0.42500000000000004 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGATGGAATTCTC 17 0.42500000000000004 No Hit TTCTCGGGTGCCAAGGAACTCCAGTCACGTGGCCATCTCGTATGCCGTCT 17 0.42500000000000004 RNA PCR Primer, Index 20 (100% over 50bp) NCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 16 0.4 No Hit TCCTGTGGATGAGAAGGCATTTATATTCTGATGATATGGAATTCTCGGGT 16 0.4 No Hit TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 16 0.4 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTAATCCTGGAATTC 16 0.4 No Hit CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGG 15 0.375 No Hit GCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCC 15 0.375 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAAT 14 0.35000000000000003 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCATGGAATTCTCGGGTG 14 0.35000000000000003 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTTGGAATTCTCGGGTGCCA 13 0.325 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 12 0.3 Illumina Small RNA Adapter 2 (100% over 21bp) NCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTTGGAATTCT 12 0.3 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGTGGAATTCTC 12 0.3 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 11 0.27499999999999997 Illumina Small RNA Adapter 2 (100% over 21bp) GACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGTGGA 11 0.27499999999999997 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGGAATTCTCGGGTGCCA 11 0.27499999999999997 No Hit GACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 23bp) NGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 11 0.27499999999999997 No Hit TCGTGCTGAAGAGCGTGGAGGTTCGAGTCCTCTTCAAGGCACCATGGAAT 11 0.27499999999999997 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTAATCTGGAATTCT 10 0.25 No Hit GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTG 10 0.25 No Hit GCACCAGTAGTCTAGTGGTAGAATAGTACCTGGAATTCTCGGGTGCCAAG 10 0.25 No Hit ATTCTCGGGTGCCAAGGAACTCCAGTCACGTGGCCATCTCGTATGCCGTC 10 0.25 RNA PCR Primer, Index 20 (100% over 50bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTTGGAATTCTCGGGTGCC 10 0.25 No Hit GACACGACTCTCGGCAACGGATATCTCGTGGAATTCTCGGGTGCCAAGGA 10 0.25 RNA PCR Primer, Index 1 (100% over 22bp) AGGGCTATAGCTCAGTTCGGTAGAGCAACTCGTTTACACTGGAATTCTCG 9 0.22499999999999998 No Hit CAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTG 9 0.22499999999999998 No Hit CACGACTCTCGGCAACGGATATCTCGTGGAATTCTCGGGTGCCAAGGAAC 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 24bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGTGGAATTCTCGGGTGCC 9 0.22499999999999998 No Hit CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGG 9 0.22499999999999998 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCTGGAATTC 9 0.22499999999999998 No Hit CTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCA 9 0.22499999999999998 No Hit GCACCAGTGGTCTAGTGGTAGAATAGTATGGAATTCTCGGGTGCCAAGGA 8 0.2 RNA PCR Primer, Index 1 (100% over 22bp) CATCGAGTAGACCTTGTTATTGTGAGAATAAATGGAATTCTCGGGTGCCA 8 0.2 No Hit CGACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAA 8 0.2 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGGTGGAATTC 8 0.2 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTCTCGCTGGAATTCTCGGGT 8 0.2 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATTTGGAATTCTCGGG 8 0.2 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTGAATCTGGAATTC 8 0.2 No Hit ACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCC 8 0.2 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAAATGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit AGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGT 7 0.17500000000000002 No Hit AGGGCTATAGCTCAGTTCGGTAGAGCAACTCGTTTACACCGAGTGGAATT 7 0.17500000000000002 No Hit ACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGGAATTCTCGGGTG 7 0.17500000000000002 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 7 0.17500000000000002 Illumina Small RNA Adapter 2 (100% over 21bp) GAAGTCCTCGTGTTGCATTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 28bp) GCCCACCCCAAGATGAGTGCTCTCTCTGGAATTCTCGGGTGCCAAGGAAC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 24bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTGAATCCTGGAATT 7 0.17500000000000002 No Hit ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGC 7 0.17500000000000002 No Hit NGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 6 0.15 RNA PCR Primer, Index 1 (100% over 22bp) TATTCTGGTGTCCTAGGCGTAGAGGAACCACACCAATCCATCCCGATGGA 6 0.15 No Hit CGGATAACCGTAGTAATTCTAGAGCTAATACGTGGAATTCTCGGGTGCCA 6 0.15 No Hit CTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGGAATTCTCGGGTGC 6 0.15 No Hit CATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGCC 6 0.15 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTCTCGTGGAATTCTCGGGTG 6 0.15 No Hit TCGGATAACCGTAGTAATTCTAGAGCTAATACGTGGAATTCTCGGGTGCC 6 0.15 No Hit GCAGTGATGTATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTG 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATTGGAATTCTCGGGT 6 0.15 No Hit TGTATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCT 6 0.15 No Hit CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGG 6 0.15 No Hit TCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCG 6 0.15 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGGAATTCT 6 0.15 No Hit GACACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACT 6 0.15 RNA PCR Primer, Index 1 (100% over 25bp) ACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATT 6 0.15 No Hit NGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 6 0.15 No Hit TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTGGAATTCTCGGGTGC 6 0.15 No Hit TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGG 6 0.15 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCTGGAATTCTCG 5 0.125 No Hit CGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTCTC 5 0.125 No Hit ACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGGAATTCTC 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATGGAATTCTCGGGTGCCAAGGA 5 0.125 RNA PCR Primer, Index 1 (100% over 22bp) CACCATGCGCGGGTTCAATTCCCGTCGTTCGCCCCATGGAATTCTCGGGT 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAAATGGAATTCTCGGGT 5 0.125 No Hit CATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTATGGAATTC 5 0.125 No Hit TCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTATG 5 0.125 No Hit GCTCTGTGATTGTGCCTGTGGAGTTTTAACTGTTGGAATTCTCGGGTGCC 5 0.125 No Hit CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 5 0.125 RNA PCR Primer, Index 1 (100% over 28bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCGGTGGAAT 5 0.125 No Hit GGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCT 5 0.125 No Hit GCCTACTTAACTCAGTGGTTAGAGTATTGCTTTCATACGGCTGGAATTCT 5 0.125 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTGGAATTCTCGGGTGCCA 5 0.125 No Hit AGCTGAGGCATCCTAACGAACGAACGATTTGAATGGAATTCTCGGGTGCC 5 0.125 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTTGGAATTCTCGGGTGC 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 0.025 0.0 0.0 0.0 3 0.0 0.05 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 0.075 0.0 0.0 0.0 8 0.0 0.1 0.0 0.0 0.0 9 0.0 0.225 0.0 0.0 0.0 10-11 0.0 0.25 0.0 0.0 0.0 12-13 0.0 0.2625 0.0 0.0 0.0 14-15 0.0 0.3375 0.0 0.0 0.0 16-17 0.0 0.48750000000000004 0.0 0.0 0.0 18-19 0.0 0.675 0.0 0.0 0.0 20-21 0.0 1.45 0.0 0.0 0.0 22-23 0.0 3.5375 0.0 0.0 0.0 24-25 0.0 6.45 0.0 0.0 0.0 26-27 0.0 11.1875 0.0 0.0 0.0 28-29 0.0 16.4625 0.0 0.0 0.0 30-31 0.0 23.6125 0.0 0.0 0.0 32-33 0.0 32.975 0.0 0.0 0.0 34-35 0.0 46.1375 0.0 0.0 0.0 36-37 0.0 57.587500000000006 0.0 0.0 0.0 38-39 0.0 65.4125 0.0 0.0 0.0 40-41 0.0 71.4875 0.0 0.0 0.0 42-43 0.0 81.475 0.0 0.0 0.0 44-45 0.0 87.7875 0.0 0.0 0.0 46-47 0.0 90.65 0.0 0.0 0.0 48-49 0.0 91.875 0.0 0.0 0.0 50-51 0.0 92.475 0.0 0.0 0.0 52-53 0.0 92.825 0.0 0.0 0.0 54-55 0.0 93.0625 0.0 0.0 0.0 56-57 0.0 93.1125 0.0 0.0 0.0 58-59 0.0 93.125 0.0 0.0 0.0 60-61 0.0 93.125 0.0 0.0 0.0 62-63 0.0 93.15 0.0 0.0 0.0 64-65 0.0 93.15 0.0 0.0 0.0 66-67 0.0 93.15 0.0 0.0 0.0 68-69 0.0 93.15 0.0 0.0 0.0 70-71 0.0 93.15 0.0 0.0 0.0 72-73 0.0 93.15 0.0 0.0 0.0 74-75 0.0 93.15 0.0 0.0 0.0 76-77 0.0 93.15 0.0 0.0 0.0 78-79 0.0 93.15 0.0 0.0 0.0 80-81 0.0 93.15 0.0 0.0 0.0 82-83 0.0 93.15 0.0 0.0 0.0 84-85 0.0 93.15 0.0 0.0 0.0 86-87 0.0 93.15 0.0 0.0 0.0 88-89 0.0 93.15 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GCCTTGA 20 1.1111353E-5 101.26667 1 TCCACTG 25 2.583074E-7 101.26667 1 GGGATTG 40 3.6379788E-12 101.26667 1 GCGAGCG 15 4.7401295E-4 101.26666 1 CATCGAG 30 5.9571903E-9 101.26666 1 CTGAGAT 25 3.8440157E-7 94.93751 5 CACTGAG 25 3.8440157E-7 94.93751 3 CCACTGA 25 3.8440157E-7 94.93751 2 GAGCGTA 15 6.1582687E-4 94.9375 3 GTAGACC 30 9.502401E-9 94.9375 7 GGTGAAA 20 1.5442722E-5 94.9375 9 AGCTCAG 15 6.1582687E-4 94.9375 9 TTGTAGT 40 5.456968E-12 94.9375 5 AGTAGAC 30 9.502401E-9 94.9375 6 TAGCTCA 15 6.1582687E-4 94.9375 8 ATGGTGA 20 1.5442722E-5 94.9375 7 GGATTGT 40 5.456968E-12 94.9375 2 CCTTGAT 20 1.5442722E-5 94.9375 2 GATTGTA 40 5.456968E-12 94.9375 3 TAGTTCA 55 0.0 94.9375 8 >>END_MODULE Rejected 1004033 READS because READLEN < 1 Read 1004033 spots for SRR8846551.sra Written 1004033 spots for SRR8846551.sra Rejected 1004033 READS because READLEN < 1 Read 1004033 spots for SRR8846551.sra Written 1004033 spots for SRR8846551.sra Rejected 1004033 READS because READLEN < 1 Read 1004033 spots for SRR8846551.sra Written 1004033 spots for SRR8846551.sra Rejected 1004033 READS because READLEN < 1 Read 1004033 spots for SRR8846551.sra Written 1004033 spots for SRR8846551.sra Rejected 1004033 READS because READLEN < 1 Read 1004033 spots for SRR8846551.sra Written 1004033 spots for SRR8846551.sra Rejected 1004033 READS because READLEN < 1 Read 1004033 spots for SRR8846551.sra Written 1004033 spots for SRR8846551.sra Rejected 1004033 READS because READLEN < 1 Read 1004033 spots for SRR8846551.sra Written 1004033 spots for SRR8846551.sra Rejected 1004033 READS because READLEN < 1 Read 1004033 spots for SRR8846551.sra Written 1004033 spots for SRR8846551.sra Rejected 1004033 READS because READLEN < 1 Read 1004033 spots for SRR8846551.sra Written 1004033 spots for SRR8846551.sra Rejected 1004033 READS because READLEN < 1 Read 1004033 spots for SRR8846551.sra Written 1004033 spots for SRR8846551.sra Rejected 1004033 READS because READLEN < 1 Read 1004033 spots for SRR8846551.sra Written 1004033 spots for SRR8846551.sra Rejected 1004033 READS because READLEN < 1 Read 1004033 spots for SRR8846551.sra Written 1004033 spots for SRR8846551.sra Rejected 1004033 READS because READLEN < 1 Read 1004033 spots for SRR8846551.sra Written 1004033 spots for SRR8846551.sra Rejected 1004033 READS because READLEN < 1 Read 1004033 spots for SRR8846551.sra Written 1004033 spots for SRR8846551.sra Rejected 1004033 READS because READLEN < 1 Read 1004033 spots for SRR8846551.sra Written 1004033 spots for SRR8846551.sra Rejected 1004033 READS because READLEN < 1 Read 1004033 spots for SRR8846551.sra Written 1004033 spots for SRR8846551.sra Rejected 1004033 READS because READLEN < 1 Read 1004033 spots for SRR8846551.sra Written 1004033 spots for SRR8846551.sra Rejected 1004045 READS because READLEN < 1 Read 1004045 spots for SRR8846551.sra Written 1004045 spots for SRR8846551.sra Rejected 1004033 READS because READLEN < 1 Read 1004033 spots for SRR8846551.sra Written 1004033 spots for SRR8846551.sra Rejected 1004033 READS because READLEN < 1 Read 1004033 spots for SRR8846551.sra Written 1004033 spots for SRR8846551.sra SRR ids: ['SRR8846551.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_na1gjdue SRR8846551.sra spots: 20080672 blocks: [[1, 1004033], [1004034, 2008066], [2008067, 3012099], [3012100, 4016132], [4016133, 5020165], [5020166, 6024198], [6024199, 7028231], [7028232, 8032264], [8032265, 9036297], [9036298, 10040330], [10040331, 11044363], [11044364, 12048396], [12048397, 13052429], [13052430, 14056462], [14056463, 15060495], [15060496, 16064528], [16064529, 17068561], [17068562, 18072594], [18072595, 19076627], [19076628, 20080672]] SRR8846551 file size 4821977 SRR8846551 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 SRR8846551 SRR8846551_1.fastq Input file: SRR8846551_1.fastq trimmed: SRR8846551-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- minimum overlap length for adapter detection (-k): inf -- number of concurrent threads (-t): 20 Mon Dec 9 10:11:09 2024 >> started Mon Dec 9 10:11:57 2024 >> done (48.240s) 20080672 reads processed; of these: 510 ( 0.00%) short reads filtered out after trimming by size control 65 ( 0.00%) empty reads filtered out after trimming by size control 20080097 (100.00%) reads available; of these: 2407012 (11.99%) trimmed reads available after processing 17673085 (88.01%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 67 0.00% 19 62 0.00% 20 70 0.00% 21 77 0.00% 22 92 0.00% 23 100 0.00% 24 143 0.00% 25 192 0.00% 26 334 0.00% 27 408 0.00% 28 555 0.00% 29 697 0.00% 30 673 0.00% 31 590 0.00% 32 709 0.00% 33 522 0.00% 34 506 0.00% 35 469 0.00% 36 510 0.00% 37 600 0.00% 38 631 0.00% 39 668 0.00% 40 584 0.00% 41 676 0.00% 42 619 0.00% 43 694 0.00% 44 720 0.00% 45 807 0.00% 46 588 0.00% 47 613 0.00% 48 562 0.00% 49 581 0.00% 50 581 0.00% 51 652 0.00% 52 663 0.00% 53 762 0.00% 54 685 0.00% 55 687 0.00% 56 925 0.00% 57 877 0.00% 58 995 0.00% 59 1547 0.01% 60 2056 0.01% 61 3198 0.02% 62 4257 0.02% 63 5381 0.03% 64 7412 0.04% 65 11516 0.06% 66 26985 0.13% 67 103635 0.52% 68 125393 0.62% 69 89218 0.44% 70 70123 0.35% 71 81695 0.41% 72 33508 0.17% 73 9681 0.05% 74 10815 0.05% 75 8162 0.04% 76 6817 0.03% 77 6750 0.03% 78 7725 0.04% 79 7439 0.04% 80 7835 0.04% 81 8982 0.04% 82 13232 0.07% 83 12210 0.06% 84 11295 0.06% 85 12056 0.06% 86 13522 0.07% 87 15852 0.08% 88 20625 0.10% 89 26720 0.13% 90 30145 0.15% 91 31611 0.16% 92 42229 0.21% 93 55029 0.27% 94 73701 0.37% 95 147595 0.74% 96 171378 0.85% 97 202856 1.01% 98 309354 1.54% 99 313076 1.56% 100 242450 1.21% 101 17673085 88.01% 20080097 reads passed initial QC criterion=sequence-density sequence-density=92.81 sequence-density-rank=1 fanout-score=31.92 fanout-score-rank=1 prefix-density=93.29 prefix-fanout=31.8 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGGCCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA criterion=fanout-score sequence-density=92.81 sequence-density-rank=1 fanout-score=31.92 fanout-score-rank=1 prefix-density=93.29 prefix-fanout=31.8 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGGCCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGGCCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA -o SRR8846551 - Input file: STDIN trimmed: SRR8846551-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGGCCATCTCGTATGCCGTCTTCTGCTTGA -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- minimum overlap length for adapter detection (-k): 3 -- number of concurrent threads (-t): 20 Mon Dec 9 10:14:39 2024 >> started Mon Dec 9 10:16:12 2024 >> done (93.320s) 19648267 reads processed; of these: 145750 ( 0.74%) short reads filtered out after trimming by size control 13861 ( 0.07%) empty reads filtered out after trimming by size control 19488656 (99.19%) reads available; of these: 18641583 (95.65%) trimmed reads available after processing 847073 ( 4.35%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 27488 0.14% 19 50618 0.26% 20 60689 0.31% 21 242188 1.24% 22 155264 0.80% 23 222700 1.14% 24 716592 3.68% 25 355646 1.82% 26 551464 2.83% 27 449809 2.31% 28 743455 3.81% 29 688185 3.53% 30 856239 4.39% 31 641013 3.29% 32 1344221 6.90% 33 1296861 6.65% 34 1306457 6.70% 35 1074181 5.51% 36 1424232 7.31% 37 618530 3.17% 38 568662 2.92% 39 637421 3.27% 40 716651 3.68% 41 1043541 5.35% 42 1006732 5.17% 43 504670 2.59% 44 506650 2.60% 45 272905 1.40% 46 165164 0.85% 47 100337 0.51% 48 94115 0.48% 49 60335 0.31% 50 40332 0.21% 51 37041 0.19% 52 21596 0.11% 53 14880 0.08% 54 16657 0.09% 55 4701 0.02% 56 3707 0.02% 57 2558 0.01% 58 1917 0.01% 59 2051 0.01% 60 2156 0.01% 61 3289 0.02% 62 3878 0.02% 63 4839 0.02% 64 6701 0.03% 65 10673 0.05% 66 25699 0.13% 67 100729 0.52% 68 121743 0.62% 69 86056 0.44% 70 67405 0.35% 71 78510 0.40% 72 29601 0.15% 73 6455 0.03% 74 4860 0.02% 75 4450 0.02% 76 3895 0.02% 77 4482 0.02% 78 4379 0.02% 79 3675 0.02% 80 3856 0.02% 81 3486 0.02% 82 2957 0.02% 83 3090 0.02% 84 2241 0.01% 85 2124 0.01% 86 2015 0.01% 87 1778 0.01% 88 1633 0.01% 89 1723 0.01% 90 1551 0.01% 91 1505 0.01% 92 1646 0.01% 93 1785 0.01% 94 2135 0.01% 95 2803 0.01% 96 3610 0.02% 97 4676 0.02% 98 6385 0.03% 99 8671 0.04% 100 10628 0.05% 101 196428 1.01% criterion=sequence-density sequence-density=4.78 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=12 prefix-density=0.00 prefix-fanout=1.0 sequence=CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATTCAAGAGTT criterion=fanout-score sequence-density=0.25 sequence-density-rank=16 fanout-score=17.93 fanout-score-rank=1 prefix-density=4.47 prefix-fanout=1.0 sequence=TTGTGAGAATTAAAAA Started job on | Dec 09 10:18:54 Started mapping on | Dec 09 10:18:54 Finished on | Dec 09 10:23:36 Mapping speed, Million of reads per hour | 254.30 Number of input reads | 19920486 Average input read length | 37 UNIQUE READS: Uniquely mapped reads number | 2123902 Uniquely mapped reads % | 10.66% Average mapped length | 32.40 Number of splices: Total | 38351 Number of splices: Annotated (sjdb) | 28614 Number of splices: GT/AG | 35207 Number of splices: GC/AG | 1924 Number of splices: AT/AC | 33 Number of splices: Non-canonical | 1187 Mismatch rate per base, % | 0.16% Deletion rate per base | 0.01% Deletion average length | 1.25 Insertion rate per base | 0.00% Insertion average length | 1.02 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 8099414 % of reads mapped to multiple loci | 40.66% Number of reads mapped to too many loci | 8161169 % of reads mapped to too many loci | 40.97% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 7.38% % of reads unmapped: other | 0.33% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 9697170 9697170 9697170 N_multimapping 8099414 8099414 8099414 N_noFeature 873529 1161257 1822009 N_ambiguous 50153 35906 275 UnstrandedReadsAssigned:1200220 PositiveStrandReadsAssigned:926739 NegativeStrandReadsAssigned:301618 Dataset is classified unstranded MeadianReadLen=35 20thPercentileLength=29 echo kmer=25 SRR8846551 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=25 [quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20 [index] k-mer length: 25 [index] number of targets: 52,972 [index] number of k-mers: 66,414,955 [index] number of equivalence classes: 135,654 [quant] running in single-end mode [quant] will process file 1: SRR8846551-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 19,920,486 reads, 3,841,919 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,032 rounds 52973 SRR8846551.ke.tsv 35125 SRR8846551.se.tsv 88098 total ==> SRR8846551.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 1 0.20182 PNS24249 1928 1829 2 0.208551 PNS24246 1044 945 1 0.20182 PNS24248 1044 945 1 0.20182 PNS24244 1471 1372 4 0.556035 PNS24243 293 194 0 0 KQK14069 1603 1504 137.34 17.4159 KQK14071 474 375 0 0 ==> SRR8846551.se.tsv <== BRADI_1g14170v3 143 BRADI_1g53295v3 2 BRADI_1g59795v3 5 BRADI_1g07683v3 0 BRADI_1g00485v3 3 BRADI_1g20270v3 32 BRADI_1g74790v3 12 BRADI_1g09890v3 1 BRADI_1g77505v3 5 BRADI_1g48960v3 0 SRR8846551 completed mapping pipeline successfully