Starting /dee2/code/volunteer_pipeline.sh SRR6941544 current disk space = 1551498694656 free memory = 1599087132 SRR6941544 SRAfilesize a135d765708ed65532e290b04e4e6a62 SRR6941544.sra SRR6941544.sra file validated SRR6941544 is single end SRR6941544 is conventional basespace SRR6941544 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6941544_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 fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.258 34.0 33.0 34.0 32.0 34.0 2 33.32275 34.0 33.0 34.0 33.0 34.0 3 33.06575 34.0 33.0 34.0 31.0 34.0 4 33.22375 34.0 33.0 34.0 32.0 34.0 5 33.201 34.0 33.0 34.0 33.0 34.0 6 37.00175 38.0 37.0 38.0 36.0 38.0 7 37.35675 38.0 38.0 38.0 37.0 38.0 8 37.4985 38.0 38.0 38.0 37.0 38.0 9 37.499 38.0 38.0 38.0 38.0 38.0 10-11 37.524249999999995 38.0 38.0 38.0 37.5 38.0 12-13 37.39175 38.0 38.0 38.0 37.0 38.0 14-15 37.45825 38.0 38.0 38.0 37.0 38.0 16-17 36.035624999999996 38.0 37.0 38.0 27.0 38.0 18-19 36.820499999999996 38.0 37.5 38.0 33.5 38.0 20-21 36.327375 38.0 38.0 38.0 31.5 38.0 22-23 37.342875 38.0 38.0 38.0 36.5 38.0 24-25 37.462875 38.0 38.0 38.0 37.0 38.0 26-27 37.4345 38.0 38.0 38.0 37.0 38.0 28-29 37.439 38.0 38.0 38.0 37.5 38.0 30-31 37.36425 38.0 38.0 38.0 37.5 38.0 32-33 37.2375 38.0 38.0 38.0 37.0 38.0 34-35 37.228375 38.0 38.0 38.0 37.0 38.0 36-37 37.1505 38.0 38.0 38.0 36.5 38.0 38-39 37.168 38.0 38.0 38.0 37.0 38.0 40-41 37.15 38.0 38.0 38.0 37.0 38.0 42-43 37.170500000000004 38.0 38.0 38.0 37.0 38.0 44-45 37.126625000000004 38.0 38.0 38.0 36.5 38.0 46-47 37.052625 38.0 38.0 38.0 36.5 38.0 48-49 37.21725 38.0 38.0 38.0 37.0 38.0 50-51 37.012625 38.0 38.0 38.0 36.0 38.0 52-53 37.11625 38.0 38.0 38.0 36.5 38.0 54-55 37.188625 38.0 38.0 38.0 37.0 38.0 56-57 37.02775 38.0 38.0 38.0 36.0 38.0 58-59 37.24575 38.0 38.0 38.0 37.0 38.0 60-61 37.116875 38.0 38.0 38.0 37.0 38.0 62-63 36.65775 38.0 38.0 38.0 35.0 38.0 64-65 36.414249999999996 38.0 37.5 38.0 33.5 38.0 66-67 36.008875 38.0 37.0 38.0 32.0 38.0 68-69 36.871125 38.0 38.0 38.0 36.0 38.0 70-71 36.67225 38.0 38.0 38.0 34.5 38.0 72-73 36.375625 38.0 37.5 38.0 34.0 38.0 74-75 35.904624999999996 38.0 37.0 38.0 31.0 38.0 76-77 36.156 38.0 37.5 38.0 33.5 38.0 78-79 36.461124999999996 38.0 38.0 38.0 34.5 38.0 80-81 36.71875 38.0 38.0 38.0 36.0 38.0 82-83 36.651250000000005 38.0 38.0 38.0 36.0 38.0 84-85 36.734375 38.0 38.0 38.0 36.0 38.0 86-87 36.475375 38.0 38.0 38.0 35.0 38.0 88-89 36.4295 38.0 38.0 38.0 34.0 38.0 90-91 36.3535 38.0 38.0 38.0 34.5 38.0 92-93 36.27325 38.0 38.0 38.0 34.5 38.0 94-95 35.743625 38.0 38.0 38.0 33.5 38.0 96-97 32.563625 38.0 35.0 38.0 8.0 38.0 98-99 28.836125 37.5 18.0 38.0 2.0 38.0 100-101 24.273 34.5 2.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 8 1.0 9 0.0 10 0.0 11 1.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 1.0 18 1.0 19 2.0 20 0.0 21 3.0 22 2.0 23 4.0 24 9.0 25 9.0 26 8.0 27 18.0 28 40.0 29 31.0 30 35.0 31 50.0 32 73.0 33 101.0 34 199.0 35 554.0 36 884.0 37 1974.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 33.975 30.275000000000002 17.0 18.75 2 28.75718929732433 26.65666416604151 21.605401350337583 22.980745186296573 3 32.475 19.950000000000003 23.875 23.7 4 25.825 32.175 17.349999999999998 24.65 5 38.6 21.25 23.75 16.400000000000002 6 23.575 27.925 25.4 23.1 7 38.175 23.275000000000002 22.2 16.35 8 21.25 18.45 41.65 18.65 9 21.425 39.85 21.5 17.224999999999998 10-11 36.25 24.575 19.3 19.875 12-13 19.287499999999998 16.525000000000002 27.3125 36.875 14-15 21.212500000000002 36.8875 23.425 18.475 16-17 25.087500000000002 18.1875 40.7875 15.937499999999998 18-19 38.7875 19.425 24.762500000000003 17.025000000000002 20-21 16.125 26.8125 34.1625 22.900000000000002 22-23 31.887500000000003 28.237499999999997 24.55 15.325 24-25 29.825000000000003 28.3875 25.8125 15.975 26-27 41.2875 24.625 19.9625 14.124999999999998 28-29 14.787500000000001 40.050000000000004 22.287499999999998 22.875 30-31 18.462500000000002 10.0 48.825 22.7125 32-33 28.537499999999998 8.7625 31.874999999999996 30.825000000000003 34-35 40.849999999999994 15.187500000000002 25.587500000000002 18.375 36-37 50.0125 16.7875 21.6 11.600000000000001 38-39 24.175 20.9375 34.8375 20.05 40-41 19.875 15.55 22.2125 42.3625 42-43 31.4875 33.6875 15.7625 19.0625 44-45 56.39999999999999 15.787499999999998 11.1875 16.625 46-47 26.474999999999998 32.6375 16.85 24.0375 48-49 17.837500000000002 22.0875 20.5625 39.5125 50-51 22.537499999999998 23.65 9.6125 44.2 52-53 30.2625 43.7125 6.9625 19.0625 54-55 17.1625 24.2375 21.9375 36.662499999999994 56-57 7.025 30.5125 20.7 41.7625 58-59 13.600000000000001 14.374999999999998 34.075 37.95 60-61 20.8125 23.9875 30.575000000000003 24.625 62-63 11.9625 30.2625 33.375 24.4 64-65 5.55 26.787499999999998 36.6 31.0625 66-67 13.275 10.375 38.737500000000004 37.6125 68-69 21.625 17.349999999999998 36.449999999999996 24.575 70-71 18.099999999999998 27.224999999999998 41.75 12.925 72-73 22.662499999999998 20.0 35.8 21.5375 74-75 13.1375 10.237499999999999 28.9125 47.712500000000006 76-77 21.762500000000003 8.4875 46.5125 23.2375 78-79 17.4625 7.7 44.125 30.7125 80-81 18.5 10.362499999999999 37.2875 33.85 82-83 29.612500000000004 5.2124999999999995 40.45 24.725 84-85 20.0625 8.649999999999999 36.0875 35.199999999999996 86-87 20.9875 18.862499999999997 40.112500000000004 20.0375 88-89 10.100000000000001 45.300000000000004 29.4125 15.187500000000002 90-91 8.7 49.075 25.6 16.625 92-93 14.5875 53.37499999999999 19.9375 12.1 94-95 9.175 65.55 18.875 6.4 96-97 8.8375 79.4125 9.4 2.35 98-99 3.25 91.0125 3.75 1.9875 100-101 1.3875 91.95 4.1625000000000005 2.5 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 0.0 27 0.0 28 0.0 29 0.0 30 0.0 31 0.0 32 1.0 33 1.5 34 3.5 35 6.0 36 4.0 37 3.5 38 6.5 39 18.0 40 47.0 41 102.5 42 215.5 43 536.5 44 645.0 45 446.0 46 373.0 47 296.5 48 202.5 49 246.5 50 307.5 51 231.0 52 123.0 53 60.0 54 38.0 55 25.5 56 11.5 57 23.5 58 21.0 59 2.0 60 0.5 61 0.5 62 0.0 63 0.5 64 0.5 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 0.0 2 0.025 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-11 0.0 12-13 0.0 14-15 0.0 16-17 0.0 18-19 0.0 20-21 0.0 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.0 30-31 0.0 32-33 0.0 34-35 0.0 36-37 0.0 38-39 0.0 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0 54-55 0.0 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0 66-67 0.0 68-69 0.0 70-71 0.0 72-73 0.0 74-75 0.0 76-77 0.0 78-79 0.0 80-81 0.0 82-83 0.0 84-85 0.0 86-87 0.0 88-89 0.0 90-91 0.0 92-93 0.0 94-95 0.0 96-97 0.0 98-99 0.0 100-101 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 101 4000.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 52.400000000000006 #Duplication Level Percentage of deduplicated Percentage of total 1 88.35877862595419 46.300000000000004 2 4.437022900763359 4.65 3 2.1946564885496183 3.45 4 1.1927480916030535 2.5 5 0.5248091603053435 1.375 6 0.33396946564885494 1.05 7 0.2862595419847328 1.05 8 0.4770992366412214 2.0 9 0.1431297709923664 0.675 >10 1.6698473282442747 20.025000000000002 >50 0.2862595419847328 11.4 >100 0.09541984732824427 5.525 >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 TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 111 2.775 RNA PCR Primer, Index 1 (100% over 29bp) GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 110 2.75 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 100 2.5 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTTGGAATTCTCGGGTGC 91 2.275 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 85 2.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTGGAATTCTCGGGTGCCAA 62 1.55 No Hit GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 60 1.5 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTTGGAATTCTCGGGTGCCA 58 1.4500000000000002 No Hit CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 46 1.15 RNA PCR Primer, Index 1 (100% over 28bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTTGGAATTCTCGGGTG 44 1.0999999999999999 No Hit ACCTGCTCTGATACCATGTTGTGATGGAATTCTCGGGTGCCAAGGAACTC 43 1.075 RNA PCR Primer, Index 1 (100% over 26bp) ACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCCA 41 1.0250000000000001 RNA PCR Primer, Index 1 (100% over 28bp) ATATTGGGTAGGTTGTGGTATTTCATTGCTTGGAATTCTCGGGTGCCAAG 37 0.9249999999999999 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 37 0.9249999999999999 Illumina Small RNA Adapter 2 (100% over 21bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 32 0.8 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTGGAATTCTCGGGTGCCAAGG 31 0.775 Illumina Small RNA Adapter 2 (100% over 21bp) CGGTCGAGGGCACGCCTGCCTGGGCGTCACGCTGGAATTCTCGGGTGCCA 30 0.75 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTGGAATTCTCGGGTGCCA 30 0.75 No Hit TCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTC 29 0.7250000000000001 RNA PCR Primer, Index 1 (100% over 26bp) GAACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTC 29 0.7250000000000001 RNA PCR Primer, Index 1 (100% over 26bp) TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 26 0.65 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 25 0.625 Illumina Small RNA Adapter 2 (100% over 21bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGTGGAATTCTCGGGTGCC 24 0.6 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 21 0.525 No Hit TTCGGACCAGGCTTCATTCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 21 0.525 RNA PCR Primer, Index 1 (100% over 29bp) AACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCC 21 0.525 RNA PCR Primer, Index 1 (100% over 27bp) GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTTGGAATTCTCGGGTGC 21 0.525 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTTGGAATTCTCGGGTGC 20 0.5 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGGAATTCTCGGGTGCCA 18 0.44999999999999996 No Hit TCGCTTGGTGCAGATCGGGACTGGAATTCTCGGGTGCCAAGGAACTCCAG 17 0.42500000000000004 RNA PCR Primer, Index 1 (100% over 29bp) TTGACAGAAGAGAGTGAGCACTGGAATTCTCGGGTGCCAAGGAACTCCAG 15 0.375 RNA PCR Primer, Index 1 (100% over 29bp) AGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCC 14 0.35000000000000003 RNA PCR Primer, Index 1 (100% over 27bp) GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACCTGGAATTCTCGGGTGCC 14 0.35000000000000003 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 13 0.325 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTATGGAATTCTCGGGTGCCAA 13 0.325 No Hit TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTCGTATGC 13 0.325 RNA PCR Primer, Index 12 (100% over 50bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGGAATTCTCGGGTGCCAA 12 0.3 No Hit GGTAGTTCGACCGCGGAATTTGGAATTCTCGGGTGCCAAGGAACTCCAGT 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 30bp) TAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAG 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 29bp) GTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTTGGAATTCTCGGGTGCC 11 0.27499999999999997 No Hit AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 11 0.27499999999999997 Illumina Small RNA Adapter 2 (100% over 21bp) CATCGAGTAGACCTTGTTATTGTGAGAATTATGGAATTCTCGGGTGCCAA 10 0.25 No Hit ATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACT 10 0.25 RNA PCR Primer, Index 1 (100% over 25bp) GAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTGC 9 0.22499999999999998 No Hit AGAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTG 9 0.22499999999999998 No Hit TGAAGCTGCCAGCATGATCTGATGGAATTCTCGGGTGCCAAGGAACTCCA 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 28bp) GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTGGAATTCTCGGGT 8 0.2 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTAATCTGGAATTCT 8 0.2 No Hit CGAACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACT 8 0.2 RNA PCR Primer, Index 1 (100% over 25bp) TAGAACTCCACATCCTTGGCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 8 0.2 RNA PCR Primer, Index 1 (100% over 29bp) GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 8 0.2 Illumina Small RNA Adapter 2 (100% over 21bp) CCCTATAGAACTCCACATCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG 8 0.2 RNA PCR Primer, Index 1 (100% over 29bp) TGTCGTGCCAATTCAACATAAACCCTGGAATTCTCGGGTGCCAAGGAACT 8 0.2 RNA PCR Primer, Index 1 (100% over 25bp) AAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTGCC 8 0.2 No Hit GCGTCTGTAGTCCAACGGTTAGGATAATTGCCTTGGAATTCTCGGGTGCC 8 0.2 No Hit CAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTC 8 0.2 RNA PCR Primer, Index 1 (100% over 26bp) TGTCGTGCCAATTCAACATAAACCCCTTGGAATTCTCGGGTGCCAAGGAA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 23bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTGGAATTCTCGGGTG 7 0.17500000000000002 No Hit GGGTGTTTGGTCTAGTGGTATGATTCTCGCTTGGAATTCTCGGGTGCCAA 7 0.17500000000000002 No Hit TGTCGTGCCAATTCAACATAAACCCCTGGAATTCTCGGGTGCCAAGGAAC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 24bp) CTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCCAG 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 29bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATGGAATTCTCGGGTG 7 0.17500000000000002 No Hit GGGATTGTAGTTCAATTGGACAGAGCACCGCCCTGGAATTCTCGGGTGCC 6 0.15 No Hit TGACAGAAGAGAGTGAGCACTGGAATTCTCGGGTGCCAAGGAACTCCAGT 6 0.15 RNA PCR Primer, Index 1 (100% over 30bp) GTCAGGATAGCTCAGTAGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 6 0.15 No Hit AATATTGGGTAGGTTGTGGTATTTCATTGCTTGGAATTCTCGGGTGCCAA 6 0.15 No Hit CATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGATGGAATTCTC 6 0.15 No Hit GAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC 6 0.15 RNA PCR Primer, Index 1 (100% over 33bp) TTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 5 0.125 RNA PCR Primer, Index 1 (100% over 31bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTTGGAATTCT 5 0.125 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGGAATTCTCGGGTGC 5 0.125 No Hit GACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGTGGAATTCTCGGGTG 5 0.125 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGTGGAATTCTCGGGTGCCAAG 5 0.125 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTGAATCTGGAATTC 5 0.125 No Hit CCCGCCTTGCACCAAGTGAATTGGAATTCTCGGGTGCCAAGGAACTCCAG 5 0.125 RNA PCR Primer, Index 1 (100% over 29bp) ATGCAGTTACTAATTCATGATCTGGCTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) CATCGAGTAGACCTTGTTATTGTGAGAATTAATGGAATTCTCGGGTGCCA 5 0.125 No Hit AAGCTGAAGCGGAAATGCAATTCTCGGGTGAGATGGAATTCTCGGGTGCC 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 0.475 0.0 0.0 0.0 2 0.0 0.475 0.0 0.0 0.0 3 0.0 0.475 0.0 0.0 0.0 4 0.0 0.475 0.0 0.0 0.0 5 0.0 0.475 0.0 0.0 0.0 6 0.0 0.475 0.0 0.0 0.0 7 0.0 0.475 0.0 0.0 0.0 8 0.0 0.475 0.0 0.0 0.0 9 0.0 0.475 0.0 0.0 0.0 10-11 0.0 0.5125 0.0 0.0 0.0 12-13 0.0 0.6 0.0 0.0 0.0 14-15 0.0 0.6625000000000001 0.0 0.0 0.0 16-17 0.0 0.8875 0.0 0.0 0.0 18-19 0.0 1.4875 0.0 0.0 0.0 20-21 0.0 2.9875 0.0 0.0 0.0 22-23 0.0 14.1625 0.0 0.0 0.0 24-25 0.0 31.1875 0.0 0.0 0.0 26-27 0.0 46.6375 0.0 0.0 0.0 28-29 0.0 49.6625 0.0 0.0 0.0 30-31 0.0 58.25 0.0 0.0 0.0 32-33 0.0 70.6875 0.0 0.0 0.0 34-35 0.0 86.8625 0.0 0.0 0.0 36-37 0.0 94.30000000000001 0.0 0.0 0.0 38-39 0.0 95.825 0.0 0.0 0.0 40-41 0.0 96.35 0.0 0.0 0.0 42-43 0.0 97.2625 0.0 0.0 0.0 44-45 0.0 97.6 0.0 0.0 0.0 46-47 0.0 97.65 0.0 0.0 0.0 48-49 0.0 97.65 0.0 0.0 0.0 50-51 0.0 97.65 0.0 0.0 0.0 52-53 0.0 97.65 0.0 0.0 0.0 54-55 0.0 97.65 0.0 0.0 0.0 56-57 0.0 97.65 0.0 0.0 0.0 58-59 0.0 97.65 0.0 0.0 0.0 60-61 0.0 97.65 0.0 0.0 0.0 62-63 0.0 97.65 0.0 0.0 0.0 64-65 0.0 97.65 0.0 0.0 0.0 66-67 0.0 97.65 0.0 0.0 0.0 68-69 0.0 97.65 0.0 0.0 0.0 70-71 0.0 97.65 0.0 0.0 0.0 72-73 0.0 97.65 0.0 0.0 0.0 74-75 0.0 97.65 0.0 0.0 0.0 76-77 0.0 97.65 0.0 0.0 0.0 78-79 0.0 97.65 0.0 0.0 0.0 80-81 0.0 97.65 0.0 0.0 0.0 82-83 0.0 97.65 0.0 0.0 0.0 84-85 0.0 97.675 0.0 0.0 0.0 86-87 0.0 97.675 0.0 0.0 0.0 88-89 0.0 97.675 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTGTAGT 40 5.456968E-12 95.00001 5 GGCTGTA 20 1.5392321E-5 95.00001 4 GTGGCTG 20 1.5392321E-5 95.00001 2 GGTGGCT 20 1.5392321E-5 95.00001 1 TGGCTGT 20 1.5392321E-5 95.00001 3 GGATGTA 15 6.142176E-4 95.0 4 GTAGACC 45 0.0 95.0 7 AGCTCAG 45 0.0 95.0 9 AGTAGAC 45 0.0 95.0 6 AGGATAG 45 0.0 95.0 4 TCAGGAT 45 0.0 95.0 2 GATGTAG 15 6.142176E-4 95.0 5 TAGCTCA 45 0.0 95.0 8 TAGCCAA 15 6.142176E-4 95.0 9 TAGTTTA 15 6.142176E-4 95.0 9 CGGATGT 15 6.142176E-4 95.0 3 GCGGATG 15 6.142176E-4 95.0 2 TAGTTCA 45 0.0 95.0 8 GGATAGC 45 0.0 95.0 5 ATAGCTC 45 0.0 95.0 7 >>END_MODULE Rejected 304711 READS because READLEN < 1 Read 304711 spots for SRR6941544.sra Written 304711 spots for SRR6941544.sra Rejected 304711 READS because READLEN < 1 Read 304711 spots for SRR6941544.sra Written 304711 spots for SRR6941544.sra Rejected 304711 READS because READLEN < 1 Read 304711 spots for SRR6941544.sra Written 304711 spots for SRR6941544.sra Rejected 304711 READS because READLEN < 1 Read 304711 spots for SRR6941544.sra Written 304711 spots for SRR6941544.sra Rejected 304711 READS because READLEN < 1 Read 304711 spots for SRR6941544.sra Written 304711 spots for SRR6941544.sra Rejected 304711 READS because READLEN < 1 Read 304711 spots for SRR6941544.sra Written 304711 spots for SRR6941544.sra Rejected 304711 READS because READLEN < 1 Read 304711 spots for SRR6941544.sra Written 304711 spots for SRR6941544.sra Rejected 304711 READS because READLEN < 1 Read 304711 spots for SRR6941544.sra Written 304711 spots for SRR6941544.sra Rejected 304711 READS because READLEN < 1 Read 304711 spots for SRR6941544.sra Written 304711 spots for SRR6941544.sra Rejected 304711 READS because READLEN < 1 Read 304711 spots for SRR6941544.sra Written 304711 spots for SRR6941544.sra Rejected 304711 READS because READLEN < 1 Read 304711 spots for SRR6941544.sra Written 304711 spots for SRR6941544.sra Rejected 304711 READS because READLEN < 1 Read 304711 spots for SRR6941544.sra Written 304711 spots for SRR6941544.sra Rejected 304711 READS because READLEN < 1 Read 304711 spots for SRR6941544.sra Written 304711 spots for SRR6941544.sra Rejected 304711 READS because READLEN < 1 Read 304711 spots for SRR6941544.sra Written 304711 spots for SRR6941544.sra Rejected 304711 READS because READLEN < 1 Read 304711 spots for SRR6941544.sra Written 304711 spots for SRR6941544.sra Rejected 304712 READS because READLEN < 1 Read 304712 spots for SRR6941544.sra Written 304712 spots for SRR6941544.sra Rejected 304711 READS because READLEN < 1 Read 304711 spots for SRR6941544.sra Written 304711 spots for SRR6941544.sra Rejected 304711 READS because READLEN < 1 Read 304711 spots for SRR6941544.sra Written 304711 spots for SRR6941544.sra Rejected 304711 READS because READLEN < 1 Read 304711 spots for SRR6941544.sra Written 304711 spots for SRR6941544.sra Rejected 304711 READS because READLEN < 1 Read 304711 spots for SRR6941544.sra Written 304711 spots for SRR6941544.sra SRR ids: ['SRR6941544.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_u4622x0j SRR6941544.sra spots: 6094221 blocks: [[1, 304711], [304712, 609422], [609423, 914133], [914134, 1218844], [1218845, 1523555], [1523556, 1828266], [1828267, 2132977], [2132978, 2437688], [2437689, 2742399], [2742400, 3047110], [3047111, 3351821], [3351822, 3656532], [3656533, 3961243], [3961244, 4265954], [4265955, 4570665], [4570666, 4875376], [4875377, 5180087], [5180088, 5484798], [5484799, 5789509], [5789510, 6094221]] SRR6941544 file size 1455920 SRR6941544 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 SRR6941544 SRR6941544_1.fastq Input file: SRR6941544_1.fastq trimmed: SRR6941544-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 Fri Dec 6 10:46:34 2024 >> started Fri Dec 6 10:46:38 2024 >> done (3.598s) 6094221 reads processed; of these: 107 ( 0.00%) short reads filtered out after trimming by size control 17 ( 0.00%) empty reads filtered out after trimming by size control 6094097 (100.00%) reads available; of these: 1560776 (25.61%) trimmed reads available after processing 4533321 (74.39%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 7 0.00% 19 8 0.00% 20 8 0.00% 21 11 0.00% 22 21 0.00% 23 11 0.00% 24 14 0.00% 25 25 0.00% 26 34 0.00% 27 54 0.00% 28 63 0.00% 29 71 0.00% 30 73 0.00% 31 61 0.00% 32 44 0.00% 33 54 0.00% 34 60 0.00% 35 39 0.00% 36 33 0.00% 37 26 0.00% 38 14 0.00% 39 23 0.00% 40 18 0.00% 41 18 0.00% 42 24 0.00% 43 28 0.00% 44 20 0.00% 45 42 0.00% 46 44 0.00% 47 43 0.00% 48 29 0.00% 49 31 0.00% 50 25 0.00% 51 30 0.00% 52 25 0.00% 53 23 0.00% 54 17 0.00% 55 22 0.00% 56 31 0.00% 57 38 0.00% 58 13 0.00% 59 27 0.00% 60 38 0.00% 61 32 0.00% 62 45 0.00% 63 53 0.00% 64 65 0.00% 65 69 0.00% 66 71 0.00% 67 89 0.00% 68 160 0.00% 69 161 0.00% 70 241 0.00% 71 233 0.00% 72 381 0.01% 73 1028 0.02% 74 5840 0.10% 75 4213 0.07% 76 1300 0.02% 77 470 0.01% 78 572 0.01% 79 572 0.01% 80 692 0.01% 81 687 0.01% 82 876 0.01% 83 1082 0.02% 84 1626 0.03% 85 1987 0.03% 86 2481 0.04% 87 3094 0.05% 88 4284 0.07% 89 6597 0.11% 90 10504 0.17% 91 15016 0.25% 92 19076 0.31% 93 36149 0.59% 94 65693 1.08% 95 218103 3.58% 96 206534 3.39% 97 183901 3.02% 98 324458 5.32% 99 341102 5.60% 100 99899 1.64% 101 4533321 74.39% 6094097 reads passed initial QC criterion=sequence-density sequence-density=97.83 sequence-density-rank=1 fanout-score=27.24 fanout-score-rank=2 prefix-density=97.91 prefix-fanout=27.2 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTCGTATGCCGTCTTCTGCTTGAAAAAA criterion=fanout-score sequence-density=1.77 sequence-density-rank=8 fanout-score=56.09 fanout-score-rank=1 prefix-density=98.50 prefix-fanout=1.0 sequence=CACCTTGTAATATCGTATGCCGT 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTCGTATGCCGTCTTCTGCTTGAAAAAA -o SRR6941544 - Input file: STDIN trimmed: SRR6941544-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTCGTATGCCGTCTTCTGCTTGA -- 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 Fri Dec 6 10:47:01 2024 >> started Fri Dec 6 10:47:10 2024 >> done (8.709s) 5969728 reads processed; of these: 54962 ( 0.92%) short reads filtered out after trimming by size control 20881 ( 0.35%) empty reads filtered out after trimming by size control 5893885 (98.73%) reads available; of these: 5856136 (99.36%) trimmed reads available after processing 37749 ( 0.64%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 22299 0.38% 19 54965 0.93% 20 72624 1.23% 21 534329 9.07% 22 262702 4.46% 23 195240 3.31% 24 1436231 24.37% 25 168352 2.86% 26 126635 2.15% 27 100699 1.71% 28 93118 1.58% 29 259053 4.40% 30 437737 7.43% 31 314651 5.34% 32 393048 6.67% 33 551263 9.35% 34 369346 6.27% 35 195565 3.32% 36 93796 1.59% 37 44260 0.75% 38 19868 0.34% 39 13816 0.23% 40 24032 0.41% 41 30806 0.52% 42 20732 0.35% 43 4278 0.07% 44 7192 0.12% 45 2699 0.05% 46 929 0.02% 47 910 0.02% 48 371 0.01% 49 187 0.00% 50 109 0.00% 51 107 0.00% 52 60 0.00% 53 62 0.00% 54 46 0.00% 55 32 0.00% 56 32 0.00% 57 50 0.00% 58 34 0.00% 59 23 0.00% 60 19 0.00% 61 20 0.00% 62 35 0.00% 63 31 0.00% 64 26 0.00% 65 22 0.00% 66 23 0.00% 67 20 0.00% 68 47 0.00% 69 69 0.00% 70 120 0.00% 71 64 0.00% 72 59 0.00% 73 68 0.00% 74 58 0.00% 75 98 0.00% 76 146 0.00% 77 658 0.01% 78 102 0.00% 79 199 0.00% 80 494 0.01% 81 232 0.00% 82 464 0.01% 83 469 0.01% 84 173 0.00% 85 148 0.00% 86 246 0.00% 87 327 0.01% 88 153 0.00% 89 125 0.00% 90 182 0.00% 91 310 0.01% 92 217 0.00% 93 297 0.01% 94 318 0.01% 95 434 0.01% 96 443 0.01% 97 601 0.01% 98 973 0.02% 99 676 0.01% 100 677 0.01% 101 31754 0.54% criterion=sequence-density sequence-density=8.79 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=10 prefix-density=0.00 prefix-fanout=1.0 sequence=CATCGAGTAGACCTTGTTATTGTGAGAATTCT criterion=fanout-score sequence-density=0.17 sequence-density-rank=25 fanout-score=53.09 fanout-score-rank=1 prefix-density=5.47 prefix-fanout=1.6 sequence=GTGAGAATTCTAAAAA Started job on | Dec 06 10:47:32 Started mapping on | Dec 06 10:47:32 Finished on | Dec 06 10:47:48 Mapping speed, Million of reads per hour | 1354.11 Number of input reads | 6018254 Average input read length | 29 UNIQUE READS: Uniquely mapped reads number | 1570307 Uniquely mapped reads % | 26.09% Average mapped length | 24.83 Number of splices: Total | 5609 Number of splices: Annotated (sjdb) | 1982 Number of splices: GT/AG | 5389 Number of splices: GC/AG | 146 Number of splices: AT/AC | 0 Number of splices: Non-canonical | 74 Mismatch rate per base, % | 0.11% Deletion rate per base | 0.00% Deletion average length | 1.51 Insertion rate per base | 0.00% Insertion average length | 1.07 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 3465659 % of reads mapped to multiple loci | 57.59% Number of reads mapped to too many loci | 725018 % of reads mapped to too many loci | 12.05% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.49% % of reads unmapped: other | 0.79% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 982288 982288 982288 N_multimapping 3465659 3465659 3465659 N_noFeature 1166688 1317056 1415203 N_ambiguous 10793 5761 344 UnstrandedReadsAssigned:392826 PositiveStrandReadsAssigned:247490 NegativeStrandReadsAssigned:154760 Dataset is classified unstranded MeadianReadLen=27 20thPercentileLength=24 echo kmer=19 SRR6941544 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: SRR6941544-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 6,018,254 reads, 2,815,021 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 976 rounds 52973 SRR6941544.ke.tsv 35125 SRR6941544.se.tsv 88098 total ==> SRR6941544.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 0 0 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 1 0.151746 PNS24243 293 194 1 1.07318 KQK14069 1603 1504 44.5816 6.17135 KQK14071 474 375 9.50524 5.27721 ==> SRR6941544.se.tsv <== BRADI_1g14170v3 91 BRADI_1g53295v3 1 BRADI_1g59795v3 2 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 0 BRADI_1g74790v3 16 BRADI_1g09890v3 0 BRADI_1g77505v3 1 BRADI_1g48960v3 1 SRR6941544 completed mapping pipeline successfully