Starting /dee2/code/volunteer_pipeline.sh SRR6941559 current disk space = 1551308914688 free memory = 1599154760 SRR6941559 SRAfilesize 2438679adc7be764a9426235f4d040bc SRR6941559.sra SRR6941559.sra file validated SRR6941559 is single end SRR6941559 is conventional basespace SRR6941559 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6941559_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 46 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.312 34.0 33.0 34.0 33.0 34.0 2 33.38725 34.0 33.0 34.0 33.0 34.0 3 33.21675 34.0 33.0 34.0 33.0 34.0 4 33.31675 34.0 33.0 34.0 33.0 34.0 5 33.29775 34.0 33.0 34.0 33.0 34.0 6 37.0735 38.0 37.0 38.0 36.0 38.0 7 37.38875 38.0 38.0 38.0 37.0 38.0 8 37.5665 38.0 38.0 38.0 38.0 38.0 9 37.649 38.0 38.0 38.0 38.0 38.0 10-11 37.6195 38.0 38.0 38.0 38.0 38.0 12-13 37.478750000000005 38.0 38.0 38.0 38.0 38.0 14-15 37.518125 38.0 38.0 38.0 38.0 38.0 16-17 36.205 38.0 37.5 38.0 32.0 38.0 18-19 36.989625000000004 38.0 38.0 38.0 34.5 38.0 20-21 36.237125000000006 38.0 38.0 38.0 31.0 38.0 22-23 37.286874999999995 38.0 38.0 38.0 36.5 38.0 24-25 37.491 38.0 38.0 38.0 38.0 38.0 26-27 37.416375 38.0 38.0 38.0 37.5 38.0 28-29 37.4955 38.0 38.0 38.0 38.0 38.0 30-31 37.426249999999996 38.0 38.0 38.0 38.0 38.0 32-33 37.35825 38.0 38.0 38.0 37.0 38.0 34-35 37.327875 38.0 38.0 38.0 37.0 38.0 36-37 37.284499999999994 38.0 38.0 38.0 37.0 38.0 38-39 37.27775 38.0 38.0 38.0 37.0 38.0 40-41 37.224000000000004 38.0 38.0 38.0 37.0 38.0 42-43 37.2325 38.0 38.0 38.0 37.0 38.0 44-45 37.22775 38.0 38.0 38.0 37.0 38.0 46-47 37.125 38.0 38.0 38.0 36.5 38.0 48-49 37.21925 38.0 38.0 38.0 37.0 38.0 50-51 37.062 38.0 38.0 38.0 36.0 38.0 52-53 37.1545 38.0 38.0 38.0 37.0 38.0 54-55 37.217749999999995 38.0 38.0 38.0 37.0 38.0 56-57 37.213375 38.0 38.0 38.0 37.0 38.0 58-59 37.389624999999995 38.0 38.0 38.0 37.0 38.0 60-61 37.27525 38.0 38.0 38.0 37.0 38.0 62-63 37.2415 38.0 38.0 38.0 37.0 38.0 64-65 37.07125 38.0 38.0 38.0 36.5 38.0 66-67 36.81175 38.0 38.0 38.0 35.5 38.0 68-69 36.987 38.0 38.0 38.0 36.0 38.0 70-71 36.733 38.0 38.0 38.0 35.0 38.0 72-73 36.455749999999995 38.0 37.0 38.0 34.0 38.0 74-75 36.187 38.0 37.0 38.0 33.0 38.0 76-77 36.320375 38.0 37.5 38.0 33.5 38.0 78-79 36.63 38.0 38.0 38.0 34.5 38.0 80-81 36.901875000000004 38.0 38.0 38.0 36.0 38.0 82-83 36.824625 38.0 38.0 38.0 36.0 38.0 84-85 36.784 38.0 38.0 38.0 35.5 38.0 86-87 36.73825 38.0 38.0 38.0 35.5 38.0 88-89 36.7155 38.0 38.0 38.0 35.5 38.0 90-91 36.693625 38.0 38.0 38.0 35.5 38.0 92-93 36.70825 38.0 38.0 38.0 35.5 38.0 94-95 36.458625 38.0 38.0 38.0 34.5 38.0 96-97 35.1335 38.0 37.5 38.0 31.0 38.0 98-99 33.1505 38.0 36.0 38.0 13.5 38.0 100-101 30.862875000000003 38.0 32.5 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 11 1.0 12 0.0 13 1.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 1.0 21 2.0 22 3.0 23 3.0 24 5.0 25 8.0 26 10.0 27 23.0 28 17.0 29 21.0 30 21.0 31 41.0 32 47.0 33 67.0 34 131.0 35 322.0 36 697.0 37 2579.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 37.95 21.099999999999998 14.399999999999999 26.55 2 32.6081520380095 32.958239559889975 15.878969742435608 18.554638659664917 3 33.275 17.65 27.55 21.525 4 27.224999999999998 29.925 13.15 29.7 5 42.275 16.900000000000002 23.35 17.474999999999998 6 19.950000000000003 35.625 25.4 19.025 7 45.4 21.175 20.525 12.9 8 22.3 13.950000000000001 45.225 18.525 9 16.8 45.5 20.7 17.0 10-11 36.6 26.55 20.6625 16.1875 12-13 17.1 16.75 23.2125 42.9375 14-15 19.875 38.5375 26.724999999999998 14.8625 16-17 27.800000000000004 19.1375 39.1125 13.950000000000001 18-19 40.0 22.775000000000002 23.325000000000003 13.900000000000002 20-21 15.312500000000002 25.8125 39.1 19.775000000000002 22-23 33.0875 29.475 22.0 15.437500000000002 24-25 31.674999999999997 32.025 20.8875 15.412500000000001 26-27 34.925 26.400000000000002 20.3625 18.3125 28-29 18.1875 34.675 22.6 24.5375 30-31 23.05 13.700000000000001 38.675 24.575 32-33 29.9875 14.174999999999999 30.062499999999996 25.775 34-35 33.375 23.0125 28.762500000000003 14.85 36-37 37.1125 22.0 29.5375 11.35 38-39 23.5 22.5 35.3 18.7 40-41 22.725 13.8125 29.95 33.5125 42-43 35.449999999999996 18.987499999999997 22.4625 23.1 44-45 51.475 12.587499999999999 18.0 17.9375 46-47 34.8 22.5125 16.925 25.7625 48-49 25.137500000000003 24.6 18.15 32.1125 50-51 28.349999999999998 26.637499999999996 9.1 35.9125 52-53 30.575000000000003 42.5875 6.950000000000001 19.8875 54-55 23.474999999999998 30.362499999999997 18.625 27.537499999999998 56-57 13.65 32.175 14.7125 39.4625 58-59 13.737499999999999 28.4 22.912499999999998 34.949999999999996 60-61 17.9125 22.900000000000002 22.05 37.1375 62-63 15.012500000000001 24.4 31.674999999999997 28.9125 64-65 9.6125 30.0 31.887500000000003 28.499999999999996 66-67 13.8625 20.474999999999998 30.9875 34.675 68-69 18.3625 20.1125 34.8125 26.7125 70-71 14.025000000000002 22.8375 41.5875 21.55 72-73 13.700000000000001 16.037499999999998 44.800000000000004 25.4625 74-75 14.05 12.225 35.9875 37.737500000000004 76-77 19.125 12.925 41.75 26.200000000000003 78-79 21.625 10.174999999999999 41.2625 26.937499999999996 80-81 19.2 11.7125 37.0625 32.025 82-83 27.650000000000002 6.7125 36.662499999999994 28.975 84-85 20.3 5.35 36.85 37.5 86-87 19.45 9.4 42.675000000000004 28.475 88-89 14.4375 22.787499999999998 40.637499999999996 22.1375 90-91 13.5875 26.224999999999998 36.1125 24.075 92-93 19.412499999999998 32.2 30.325000000000003 18.0625 94-95 13.8875 49.175000000000004 25.8625 11.075 96-97 11.600000000000001 66.5625 16.662499999999998 5.175 98-99 6.1 82.4125 7.6125 3.875 100-101 3.5125 88.2 5.3625 2.9250000000000003 >>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 0.0 33 0.5 34 2.0 35 3.5 36 3.0 37 2.0 38 2.5 39 10.0 40 27.5 41 67.0 42 133.5 43 363.5 44 531.0 45 386.5 46 327.0 47 329.0 48 231.5 49 280.0 50 390.0 51 355.5 52 218.0 53 107.0 54 85.5 55 67.0 56 28.5 57 22.0 58 16.0 59 3.5 60 3.0 61 2.0 62 1.0 63 1.0 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 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 51.55 #Duplication Level Percentage of deduplicated Percentage of total 1 87.05140640155189 44.875 2 5.286129970902037 5.45 3 2.2308438409311346 3.45 4 1.066925315227934 2.1999999999999997 5 1.0184287099903007 2.625 6 0.38797284190106696 1.2 7 0.24248302618816686 0.8750000000000001 8 0.24248302618816686 1.0 9 0.24248302618816686 1.125 >10 1.7458777885548011 15.975 >50 0.3394762366634336 11.325000000000001 >100 0.1454898157129001 9.9 >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 GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 156 3.9 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 131 3.2750000000000004 No Hit GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 109 2.725 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTTGGAATTCTCGGGTGC 76 1.9 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTTGGAATTCTCGGGTG 74 1.8499999999999999 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTGGAATTCTCGGGTGCCAA 71 1.775 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTGGAATTCTCGGGTGCCA 70 1.7500000000000002 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 55 1.375 No Hit TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 55 1.375 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 52 1.3 Illumina Small RNA Adapter 2 (100% over 21bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 48 1.2 No Hit TCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTC 37 0.9249999999999999 RNA PCR Primer, Index 1 (100% over 26bp) CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 35 0.8750000000000001 RNA PCR Primer, Index 1 (100% over 28bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTTGGAATTCTCGGGTGCCA 31 0.775 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTGAATCTGGAATTC 27 0.675 No Hit GAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTGC 22 0.5499999999999999 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGATGGAATTCTC 21 0.525 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGTGGAATTCTCGGGTGCC 21 0.525 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATACTCTGGAATTCTCGGGTGCCAAG 19 0.475 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 18 0.44999999999999996 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 18 0.44999999999999996 No Hit CTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCA 18 0.44999999999999996 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTTGGAATTCTCGGGTGC 17 0.42500000000000004 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTTGGAATTCTCGGGTGCCAAG 17 0.42500000000000004 No Hit TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 17 0.42500000000000004 RNA PCR Primer, Index 1 (100% over 29bp) GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTTGGAATTCTCGGGTGC 17 0.42500000000000004 No Hit ACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCCA 17 0.42500000000000004 RNA PCR Primer, Index 1 (100% over 28bp) ATATTGGGTAGGTTGTGGTATTTCATTGCTGGAATTCTCGGGTGCCAAGG 17 0.42500000000000004 Illumina Small RNA Adapter 2 (100% over 21bp) CGGTCGAGGGCACGCCTGCCTGGGCGTCACGCTGGAATTCTCGGGTGCCA 16 0.4 No Hit AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 16 0.4 Illumina Small RNA Adapter 2 (100% over 21bp) GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTAATCTGGAATTCT 15 0.375 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTGGAATTCTCGGGTG 15 0.375 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATGGAATTCTCGGGTGCCAAGGA 14 0.35000000000000003 RNA PCR Primer, Index 1 (100% over 22bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 13 0.325 Illumina Small RNA Adapter 2 (100% over 21bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGGAATTCTCGGGTGC 13 0.325 No Hit AGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCC 12 0.3 RNA PCR Primer, Index 1 (100% over 27bp) GAACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTC 12 0.3 RNA PCR Primer, Index 1 (100% over 26bp) GACACGACTCTCGGCAACGGATATCTCGGCTTGGAATTCTCGGGTGCCAA 11 0.27499999999999997 No Hit TGTCGTGCCAATTCAACATAAACCCCTTGGAATTCTCGGGTGCCAAGGAA 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 23bp) GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGGAATTCTCGGGTGCCA 11 0.27499999999999997 No Hit TGTCGTGCCAATTCAACATAAACCCCTGGAATTCTCGGGTGCCAAGGAAC 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 24bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATGGAATTCTCGGGTG 11 0.27499999999999997 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTAAATGGAATTCTCGGGTG 11 0.27499999999999997 No Hit ACCTGCTCTGATACCATGTTGTGATGGAATTCTCGGGTGCCAAGGAACTC 10 0.25 RNA PCR Primer, Index 1 (100% over 26bp) GGGTGTTTGGTCTAGTGGTATGATTCTCGCTTGGAATTCTCGGGTGCCAA 10 0.25 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTATGGAATTCTCGGGTGCC 10 0.25 No Hit TGTCGTGCCAATTCAACATAAACCCTGGAATTCTCGGGTGCCAAGGAACT 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 25bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTTTGGAATTCTCGGGTGCC 9 0.22499999999999998 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCTGGAATTC 9 0.22499999999999998 No Hit GCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAA 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 23bp) CATCGAGTAGACCTTGTTATTGTGAGAATTATGGAATTCTCGGGTGCCAA 9 0.22499999999999998 No Hit TTCGGACCAGGCTTCATTCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 8 0.2 RNA PCR Primer, Index 1 (100% over 29bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCTGGAATTCTCGGG 8 0.2 No Hit CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 8 0.2 RNA PCR Primer, Index 1 (100% over 23bp) AAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTGCC 8 0.2 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCATGGAATTCTCGGGTGCC 8 0.2 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGAGTGGAATTCT 7 0.17500000000000002 No Hit CAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTG 7 0.17500000000000002 No Hit CACGACTCTCGGCAACGGATATCTCGGCTTGGAATTCTCGGGTGCCAAGG 7 0.17500000000000002 Illumina Small RNA Adapter 2 (100% over 21bp) TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTAGCTTATCTCGTATGC 7 0.17500000000000002 RNA PCR Primer, Index 10 (100% over 50bp) TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGG 7 0.17500000000000002 No Hit TCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCAATGGAATTCTCGGGTGCC 6 0.15 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTATGGAATTCTCGGGTGCCAA 6 0.15 No Hit CATCGAGTAGACCTTGTTAATGTGAGAATTCTGGAATTCTCGGGTGCCAA 6 0.15 No Hit AGAAGAGAGAGAGTACAGCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG 6 0.15 RNA PCR Primer, Index 1 (100% over 29bp) CATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) CATCGAGTAGACCTTGTTATTGTGAGAATTAAATGGAATTCTCGGGTGCC 6 0.15 No Hit TGCCACGATCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAAT 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAATGGAATTCTCGGGTGCCA 5 0.125 No Hit TCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) GGTAGTTCGACCGCGGAATTTGGAATTCTCGGGTGCCAAGGAACTCCAGT 5 0.125 RNA PCR Primer, Index 1 (100% over 30bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGTGGAATTCT 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATTGGAATTCTCGGGT 5 0.125 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTTGGAATTCT 5 0.125 No Hit GGGATTGTAGTTCAATAGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 5 0.125 No Hit AATATTGGGTAGGTTGTGGTATTTCATTGCTTGGAATTCTCGGGTGCCAA 5 0.125 No Hit TAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAG 5 0.125 RNA PCR Primer, Index 1 (100% over 29bp) GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 5 0.125 Illumina Small RNA Adapter 2 (100% over 21bp) AACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCC 5 0.125 RNA PCR Primer, Index 1 (100% over 27bp) AATATTGGGTAGGTTGTGGTATTTCATTGCTGGAATTCTCGGGTGCCAAG 5 0.125 No Hit GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGTGGAATTCTCGGGTG 5 0.125 No Hit ACGAACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) TCTCATGGAGAGTTCGATCCTGGCTTGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTAATGGAATTCTCGGGTGC 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTAATGGAATTCTCGGGTGCCA 5 0.125 No Hit ACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCC 5 0.125 No Hit CAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTC 5 0.125 RNA PCR Primer, Index 1 (100% over 26bp) ATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) TCGCTTGGTGCAGATCGGGACTGGAATTCTCGGGTGCCAAGGAACTCCAG 5 0.125 RNA PCR Primer, Index 1 (100% over 29bp) >>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 0.2 0.0 0.0 0.0 2 0.0 0.2 0.0 0.0 0.0 3 0.0 0.2 0.0 0.0 0.0 4 0.0 0.2 0.0 0.0 0.0 5 0.0 0.2 0.0 0.0 0.0 6 0.0 0.2 0.0 0.0 0.0 7 0.0 0.2 0.0 0.0 0.0 8 0.0 0.2 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 0.25 0.0 0.0 0.0 14-15 0.0 0.2625 0.0 0.0 0.0 16-17 0.0 0.35 0.0 0.0 0.0 18-19 0.0 0.48750000000000004 0.0 0.0 0.0 20-21 0.0 1.4125 0.0 0.0 0.0 22-23 0.0 5.5125 0.0 0.0 0.0 24-25 0.0 14.25 0.0 0.0 0.0 26-27 0.0 23.2375 0.0 0.0 0.0 28-29 0.0 27.8375 0.0 0.0 0.0 30-31 0.0 39.2 0.0 0.0 0.0 32-33 0.0 56.075 0.0 0.0 0.0 34-35 0.0 74.9625 0.0 0.0 0.0 36-37 0.0 86.4375 0.0 0.0 0.0 38-39 0.0 90.4625 0.0 0.0 0.0 40-41 0.0 92.575 0.0 0.0 0.0 42-43 0.0 95.6875 0.0 0.0 0.0 44-45 0.0 96.9375 0.0 0.0 0.0 46-47 0.0 97.32499999999999 0.0 0.0 0.0 48-49 0.0 97.475 0.0 0.0 0.0 50-51 0.0 97.525 0.0 0.0 0.0 52-53 0.0 97.55 0.0 0.0 0.0 54-55 0.0 97.5625 0.0 0.0 0.0 56-57 0.0 97.575 0.0 0.0 0.0 58-59 0.0 97.575 0.0 0.0 0.0 60-61 0.0 97.575 0.0 0.0 0.0 62-63 0.0 97.575 0.0 0.0 0.0 64-65 0.0 97.575 0.0 0.0 0.0 66-67 0.0 97.575 0.0 0.0 0.0 68-69 0.0 97.575 0.0 0.0 0.0 70-71 0.0 97.575 0.0 0.0 0.0 72-73 0.0 97.575 0.0 0.0 0.0 74-75 0.0 97.575 0.0 0.0 0.0 76-77 0.0 97.575 0.0 0.0 0.0 78-79 0.0 97.575 0.0 0.0 0.0 80-81 0.0 97.575 0.0 0.0 0.0 82-83 0.0 97.575 0.0 0.0 0.0 84-85 0.0 97.5875 0.0 0.0 0.0 86-87 0.0 97.6 0.0 0.0 0.0 88-89 0.0 97.6 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GAGCGTA 20 1.5392321E-5 95.00001 3 CGTAGTT 20 1.5392321E-5 95.00001 6 CGAGCGT 20 1.5392321E-5 95.00001 2 GCGTAGT 20 1.5392321E-5 95.00001 5 AGCGTAG 20 1.5392321E-5 95.00001 4 GCGAGCG 20 1.5392321E-5 95.00001 1 GTAGACC 30 9.458745E-9 95.0 7 CCAATTC 15 6.142176E-4 95.0 8 TTGTAGT 25 3.8289727E-7 95.0 5 AGTAGAC 30 9.458745E-9 95.0 6 GTCGTGC 15 6.142176E-4 95.0 2 TAGCCAA 15 6.142176E-4 95.0 9 GGATTGT 25 3.8289727E-7 95.0 2 CAATTCA 15 6.142176E-4 95.0 9 CGGATGT 15 6.142176E-4 95.0 3 GCGGATG 15 6.142176E-4 95.0 2 GATTGTA 25 3.8289727E-7 95.0 3 TCGTGCC 15 6.142176E-4 95.0 3 TAGTTCA 45 0.0 95.0 8 GAGTAGA 30 9.458745E-9 95.0 5 >>END_MODULE Rejected 299470 READS because READLEN < 1 Read 299470 spots for SRR6941559.sra Written 299470 spots for SRR6941559.sra Rejected 299470 READS because READLEN < 1 Read 299470 spots for SRR6941559.sra Written 299470 spots for SRR6941559.sra Rejected 299470 READS because READLEN < 1 Read 299470 spots for SRR6941559.sra Written 299470 spots for SRR6941559.sra Rejected 299470 READS because READLEN < 1 Read 299470 spots for SRR6941559.sra Written 299470 spots for SRR6941559.sra Rejected 299470 READS because READLEN < 1 Read 299470 spots for SRR6941559.sra Written 299470 spots for SRR6941559.sra Rejected 299470 READS because READLEN < 1 Read 299470 spots for SRR6941559.sra Written 299470 spots for SRR6941559.sra Rejected 299470 READS because READLEN < 1 Read 299470 spots for SRR6941559.sra Written 299470 spots for SRR6941559.sra Rejected 299470 READS because READLEN < 1 Read 299470 spots for SRR6941559.sra Written 299470 spots for SRR6941559.sra Rejected 299470 READS because READLEN < 1 Read 299470 spots for SRR6941559.sra Written 299470 spots for SRR6941559.sra Rejected 299470 READS because READLEN < 1 Read 299470 spots for SRR6941559.sra Written 299470 spots for SRR6941559.sra Rejected 299470 READS because READLEN < 1 Read 299470 spots for SRR6941559.sra Written 299470 spots for SRR6941559.sra Rejected 299470 READS because READLEN < 1 Read 299470 spots for SRR6941559.sra Written 299470 spots for SRR6941559.sra Rejected 299472 READS because READLEN < 1 Read 299472 spots for SRR6941559.sra Written 299472 spots for SRR6941559.sra Rejected 299470 READS because READLEN < 1 Read 299470 spots for SRR6941559.sra Written 299470 spots for SRR6941559.sra Rejected 299470 READS because READLEN < 1 Read 299470 spots for SRR6941559.sra Written 299470 spots for SRR6941559.sra Rejected 299470 READS because READLEN < 1 Read 299470 spots for SRR6941559.sra Written 299470 spots for SRR6941559.sra Rejected 299470 READS because READLEN < 1 Read 299470 spots for SRR6941559.sra Written 299470 spots for SRR6941559.sra Rejected 299470 READS because READLEN < 1 Read 299470 spots for SRR6941559.sra Written 299470 spots for SRR6941559.sra Rejected 299470 READS because READLEN < 1 Read 299470 spots for SRR6941559.sra Written 299470 spots for SRR6941559.sra Rejected 299470 READS because READLEN < 1 Read 299470 spots for SRR6941559.sra Written 299470 spots for SRR6941559.sra SRR ids: ['SRR6941559.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_gg06h7hp SRR6941559.sra spots: 5989402 blocks: [[1, 299470], [299471, 598940], [598941, 898410], [898411, 1197880], [1197881, 1497350], [1497351, 1796820], [1796821, 2096290], [2096291, 2395760], [2395761, 2695230], [2695231, 2994700], [2994701, 3294170], [3294171, 3593640], [3593641, 3893110], [3893111, 4192580], [4192581, 4492050], [4492051, 4791520], [4791521, 5090990], [5090991, 5390460], [5390461, 5689930], [5689931, 5989402]] SRR6941559 file size 1430842 SRR6941559 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 SRR6941559 SRR6941559_1.fastq Input file: SRR6941559_1.fastq trimmed: SRR6941559-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 11:16:50 2024 >> started Fri Dec 6 11:16:52 2024 >> done (2.722s) 5989402 reads processed; of these: 79 ( 0.00%) short reads filtered out after trimming by size control 26 ( 0.00%) empty reads filtered out after trimming by size control 5989297 (100.00%) reads available; of these: 748362 (12.49%) trimmed reads available after processing 5240935 (87.51%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 7 0.00% 19 10 0.00% 20 13 0.00% 21 4 0.00% 22 11 0.00% 23 15 0.00% 24 14 0.00% 25 10 0.00% 26 10 0.00% 27 22 0.00% 28 31 0.00% 29 50 0.00% 30 43 0.00% 31 38 0.00% 32 34 0.00% 33 31 0.00% 34 37 0.00% 35 44 0.00% 36 49 0.00% 37 53 0.00% 38 52 0.00% 39 57 0.00% 40 66 0.00% 41 56 0.00% 42 59 0.00% 43 73 0.00% 44 59 0.00% 45 90 0.00% 46 85 0.00% 47 98 0.00% 48 61 0.00% 49 54 0.00% 50 67 0.00% 51 65 0.00% 52 55 0.00% 53 46 0.00% 54 37 0.00% 55 34 0.00% 56 50 0.00% 57 24 0.00% 58 33 0.00% 59 37 0.00% 60 35 0.00% 61 55 0.00% 62 34 0.00% 63 60 0.00% 64 50 0.00% 65 43 0.00% 66 60 0.00% 67 58 0.00% 68 108 0.00% 69 137 0.00% 70 194 0.00% 71 189 0.00% 72 327 0.01% 73 707 0.01% 74 4403 0.07% 75 2814 0.05% 76 907 0.02% 77 338 0.01% 78 494 0.01% 79 509 0.01% 80 575 0.01% 81 537 0.01% 82 642 0.01% 83 820 0.01% 84 1211 0.02% 85 1342 0.02% 86 1477 0.02% 87 1811 0.03% 88 2104 0.04% 89 2842 0.05% 90 3889 0.06% 91 6154 0.10% 92 8691 0.15% 93 16806 0.28% 94 29526 0.49% 95 72772 1.22% 96 83469 1.39% 97 96393 1.61% 98 164613 2.75% 99 170774 2.85% 100 68608 1.15% 101 5240935 87.51% 5989297 reads passed initial QC criterion=sequence-density sequence-density=97.74 sequence-density-rank=1 fanout-score=27.04 fanout-score-rank=1 prefix-density=97.95 prefix-fanout=27.0 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTAGCTTATCTCGTATGCCGTCTTCTGCTTGAAAAAA criterion=fanout-score sequence-density=97.74 sequence-density-rank=1 fanout-score=27.04 fanout-score-rank=1 prefix-density=97.95 prefix-fanout=27.0 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTAGCTTATCTCGTATGCCGTCTTCTGCTTGAAAAAA 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTAGCTTATCTCGTATGCCGTCTTCTGCTTGAAAAAA -o SRR6941559 - Input file: STDIN trimmed: SRR6941559-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTAGCTTATCTCGTATGCCGTCTTCTGCTTGA -- 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 11:17:18 2024 >> started Fri Dec 6 11:17:23 2024 >> done (5.483s) 5867067 reads processed; of these: 20907 ( 0.36%) short reads filtered out after trimming by size control 14894 ( 0.25%) empty reads filtered out after trimming by size control 5831266 (99.39%) reads available; of these: 5796804 (99.41%) trimmed reads available after processing 34462 ( 0.59%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 9358 0.16% 19 24733 0.42% 20 33744 0.58% 21 152450 2.61% 22 147214 2.52% 23 119205 2.04% 24 635447 10.90% 25 154583 2.65% 26 153713 2.64% 27 149224 2.56% 28 151284 2.59% 29 335191 5.75% 30 614103 10.53% 31 445676 7.64% 32 499514 8.57% 33 627217 10.76% 34 430112 7.38% 35 349962 6.00% 36 177226 3.04% 37 122507 2.10% 38 77258 1.32% 39 63469 1.09% 40 83412 1.43% 41 89726 1.54% 42 76946 1.32% 43 21035 0.36% 44 22592 0.39% 45 13722 0.24% 46 4593 0.08% 47 5657 0.10% 48 2007 0.03% 49 1038 0.02% 50 591 0.01% 51 454 0.01% 52 259 0.00% 53 179 0.00% 54 111 0.00% 55 60 0.00% 56 60 0.00% 57 47 0.00% 58 42 0.00% 59 24 0.00% 60 23 0.00% 61 28 0.00% 62 28 0.00% 63 23 0.00% 64 23 0.00% 65 24 0.00% 66 20 0.00% 67 26 0.00% 68 45 0.00% 69 27 0.00% 70 53 0.00% 71 48 0.00% 72 44 0.00% 73 45 0.00% 74 48 0.00% 75 70 0.00% 76 107 0.00% 77 284 0.00% 78 71 0.00% 79 90 0.00% 80 300 0.01% 81 125 0.00% 82 199 0.00% 83 183 0.00% 84 78 0.00% 85 79 0.00% 86 97 0.00% 87 179 0.00% 88 91 0.00% 89 119 0.00% 90 129 0.00% 91 196 0.00% 92 179 0.00% 93 229 0.00% 94 315 0.01% 95 346 0.01% 96 402 0.01% 97 435 0.01% 98 780 0.01% 99 516 0.01% 100 516 0.01% 101 28901 0.50% criterion=sequence-density sequence-density=14.35 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=12 prefix-density=0.00 prefix-fanout=1.0 sequence=CATCGAGTAGACCTTGTTATTGTGAGAATTCT criterion=fanout-score sequence-density=0.30 sequence-density-rank=13 fanout-score=47.19 fanout-score-rank=1 prefix-density=14.15 prefix-fanout=1.0 sequence=ATTGTGAGAATAAAAA Started job on | Dec 06 11:17:42 Started mapping on | Dec 06 11:17:43 Finished on | Dec 06 11:18:01 Mapping speed, Million of reads per hour | 1190.70 Number of input reads | 5953496 Average input read length | 32 UNIQUE READS: Uniquely mapped reads number | 719471 Uniquely mapped reads % | 12.08% Average mapped length | 27.20 Number of splices: Total | 12548 Number of splices: Annotated (sjdb) | 3336 Number of splices: GT/AG | 11908 Number of splices: GC/AG | 411 Number of splices: AT/AC | 3 Number of splices: Non-canonical | 226 Mismatch rate per base, % | 0.55% Deletion rate per base | 0.01% Deletion average length | 1.46 Insertion rate per base | 0.00% Insertion average length | 1.08 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 3827978 % of reads mapped to multiple loci | 64.30% Number of reads mapped to too many loci | 1142638 % of reads mapped to too many loci | 19.19% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.02% % of reads unmapped: other | 0.40% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1406047 1406047 1406047 N_multimapping 3827978 3827978 3827978 N_noFeature 437998 548262 605500 N_ambiguous 9425 5445 332 UnstrandedReadsAssigned:272048 PositiveStrandReadsAssigned:165764 NegativeStrandReadsAssigned:113639 Dataset is classified unstranded MeadianReadLen=31 20thPercentileLength=25 echo kmer=21 SRR6941559 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=21 [quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20 [index] k-mer length: 21 [index] number of targets: 52,972 [index] number of k-mers: 65,978,135 [index] number of equivalence classes: 190,841 [quant] running in single-end mode [quant] will process file 1: SRR6941559-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 5,953,496 reads, 2,350,483 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 890 rounds 52973 SRR6941559.ke.tsv 35125 SRR6941559.se.tsv 88098 total ==> SRR6941559.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 2 0.226322 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 0 0 PNS24243 293 194 2 2.13373 KQK14069 1603 1504 14.8049 2.03736 KQK14071 474 375 1.61978 0.893996 ==> SRR6941559.se.tsv <== BRADI_1g14170v3 17 BRADI_1g53295v3 0 BRADI_1g59795v3 0 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 0 BRADI_1g74790v3 10 BRADI_1g09890v3 0 BRADI_1g77505v3 0 BRADI_1g48960v3 0 SRR6941559 completed mapping pipeline successfully