Starting /dee2/code/volunteer_pipeline.sh SRR6941568 current disk space = 1551519842304 free memory = 1604669668 SRR6941568 SRAfilesize d6bf8590e8b1cacbdbdb064d8f9ffe56 SRR6941568.sra SRR6941568.sra file validated SRR6941568 is single end SRR6941568 is conventional basespace SRR6941568 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6941568_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 33.0755 34.0 33.0 34.0 32.0 34.0 2 33.24525 34.0 33.0 34.0 32.0 34.0 3 32.70025 34.0 33.0 34.0 30.0 34.0 4 33.02725 34.0 33.0 34.0 32.0 34.0 5 33.02625 34.0 33.0 34.0 31.0 34.0 6 36.854 38.0 37.0 38.0 36.0 38.0 7 37.21175 38.0 38.0 38.0 36.0 38.0 8 37.408 38.0 38.0 38.0 37.0 38.0 9 37.45625 38.0 38.0 38.0 37.0 38.0 10-11 37.408874999999995 38.0 38.0 38.0 37.0 38.0 12-13 37.4035 38.0 38.0 38.0 37.0 38.0 14-15 37.434625 38.0 38.0 38.0 37.0 38.0 16-17 36.116625 38.0 37.0 38.0 31.5 38.0 18-19 36.787499999999994 38.0 37.5 38.0 33.5 38.0 20-21 35.780875 38.0 37.5 38.0 29.5 38.0 22-23 37.043 38.0 38.0 38.0 35.0 38.0 24-25 37.30975 38.0 38.0 38.0 37.0 38.0 26-27 37.349999999999994 38.0 38.0 38.0 37.0 38.0 28-29 37.348375000000004 38.0 38.0 38.0 37.0 38.0 30-31 37.264250000000004 38.0 38.0 38.0 37.0 38.0 32-33 37.087625 38.0 38.0 38.0 37.0 38.0 34-35 37.091499999999996 38.0 38.0 38.0 37.0 38.0 36-37 37.042375 38.0 38.0 38.0 36.5 38.0 38-39 37.046625 38.0 38.0 38.0 36.0 38.0 40-41 36.89 38.0 38.0 38.0 36.0 38.0 42-43 36.898125 38.0 38.0 38.0 36.0 38.0 44-45 36.929625 38.0 38.0 38.0 36.0 38.0 46-47 36.74925 38.0 38.0 38.0 35.0 38.0 48-49 36.953125 38.0 38.0 38.0 36.0 38.0 50-51 36.685375 38.0 38.0 38.0 35.0 38.0 52-53 36.76375 38.0 38.0 38.0 36.0 38.0 54-55 36.885000000000005 38.0 38.0 38.0 36.0 38.0 56-57 36.8575 38.0 38.0 38.0 35.5 38.0 58-59 37.0075 38.0 38.0 38.0 36.0 38.0 60-61 36.984 38.0 38.0 38.0 36.0 38.0 62-63 36.701750000000004 38.0 38.0 38.0 35.5 38.0 64-65 36.397875 38.0 37.5 38.0 34.0 38.0 66-67 36.07925 38.0 37.0 38.0 31.5 38.0 68-69 36.47825 38.0 38.0 38.0 34.0 38.0 70-71 36.013374999999996 38.0 37.5 38.0 31.5 38.0 72-73 35.63975 38.0 37.0 38.0 29.0 38.0 74-75 35.591125 38.0 37.0 38.0 29.0 38.0 76-77 35.724125 38.0 37.0 38.0 29.5 38.0 78-79 36.042125 38.0 37.5 38.0 32.0 38.0 80-81 36.50675 38.0 38.0 38.0 34.5 38.0 82-83 36.43 38.0 38.0 38.0 34.5 38.0 84-85 36.382 38.0 38.0 38.0 34.5 38.0 86-87 36.137375000000006 38.0 38.0 38.0 33.5 38.0 88-89 36.25325 38.0 38.0 38.0 34.0 38.0 90-91 36.242625000000004 38.0 38.0 38.0 34.0 38.0 92-93 36.162625 38.0 38.0 38.0 34.0 38.0 94-95 35.602375 38.0 38.0 38.0 32.5 38.0 96-97 34.095875 38.0 36.5 38.0 21.5 38.0 98-99 31.575625 38.0 34.0 38.0 2.0 38.0 100-101 28.717375 38.0 25.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 6 1.0 7 0.0 8 1.0 9 0.0 10 1.0 11 0.0 12 1.0 13 0.0 14 0.0 15 3.0 16 0.0 17 3.0 18 0.0 19 1.0 20 3.0 21 3.0 22 3.0 23 4.0 24 9.0 25 9.0 26 24.0 27 25.0 28 26.0 29 26.0 30 47.0 31 58.0 32 66.0 33 103.0 34 200.0 35 404.0 36 842.0 37 2137.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 28.475 22.55 14.524999999999999 34.449999999999996 2 26.056514128532132 41.68542135533884 16.004001000250064 16.25406351587897 3 27.800000000000004 17.525 34.9 19.775000000000002 4 25.974999999999998 26.724999999999998 12.275 35.025 5 45.45 18.3 19.400000000000002 16.85 6 19.125 41.675000000000004 20.825 18.375 7 46.575 21.05 19.025 13.350000000000001 8 17.675 15.775 47.925000000000004 18.625 9 17.5 47.125 16.6 18.775 10-11 37.55 29.625 17.45 15.375 12-13 16.3875 17.05 20.1625 46.400000000000006 14-15 19.075 31.825 33.725 15.375 16-17 29.099999999999998 18.7625 37.55 14.5875 18-19 32.375 26.575 27.450000000000003 13.600000000000001 20-21 14.9375 23.45 42.762499999999996 18.85 22-23 34.7625 24.45 26.1625 14.625 24-25 32.9125 31.2 22.925 12.962499999999999 26-27 39.0875 28.4375 18.8 13.675 28-29 14.1875 39.137499999999996 27.35 19.325 30-31 19.275000000000002 12.1875 44.824999999999996 23.7125 32-33 31.724999999999998 13.7625 30.725 23.7875 34-35 35.2625 25.575 24.5 14.662500000000001 36-37 37.325 19.375 31.0375 12.2625 38-39 23.200000000000003 17.8875 35.475 23.4375 40-41 25.2375 14.975 23.549999999999997 36.2375 42-43 38.95 23.1625 18.45 19.4375 44-45 50.925 14.0625 16.6875 18.325 46-47 28.962500000000002 26.825 14.387500000000001 29.825000000000003 48-49 22.237499999999997 27.85 16.5 33.4125 50-51 29.675 27.6 7.9375 34.7875 52-53 27.487499999999997 43.824999999999996 8.05 20.6375 54-55 17.25 27.900000000000002 21.85 33.0 56-57 12.7 30.7625 14.7 41.8375 58-59 21.0 24.224999999999998 21.4 33.375 60-61 11.475 30.375000000000004 17.625 40.525 62-63 10.95 31.887500000000003 19.45 37.7125 64-65 14.8375 27.212500000000002 29.9 28.050000000000004 66-67 13.3875 22.8125 24.7875 39.0125 68-69 18.0375 29.45 17.5875 34.925 70-71 11.2125 33.650000000000006 27.525 27.6125 72-73 15.35 20.625 31.125000000000004 32.9 74-75 16.675 13.375 28.537499999999998 41.4125 76-77 19.8375 14.174999999999999 42.0375 23.95 78-79 20.6125 10.212499999999999 40.4375 28.7375 80-81 20.599999999999998 9.2 33.4375 36.762499999999996 82-83 28.1625 6.15 37.75 27.9375 84-85 18.224999999999998 6.75 40.575 34.449999999999996 86-87 18.4 13.750000000000002 41.775 26.075 88-89 14.912500000000001 30.837500000000002 34.1625 20.0875 90-91 11.6875 35.275 32.8125 20.225 92-93 17.6625 42.625 26.625 13.087499999999999 94-95 11.9125 62.0875 18.4125 7.5874999999999995 96-97 8.375 77.14999999999999 11.0375 3.4375000000000004 98-99 4.3 88.675 4.475 2.55 100-101 1.875 92.5125 2.9250000000000003 2.6875 >>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 0.5 33 0.5 34 1.0 35 2.5 36 3.5 37 4.5 38 5.5 39 8.0 40 17.0 41 38.0 42 101.5 43 201.5 44 523.5 45 716.5 46 460.5 47 346.0 48 324.5 49 214.5 50 222.5 51 254.0 52 210.5 53 132.0 54 69.5 55 56.5 56 44.0 57 12.0 58 10.0 59 9.0 60 4.0 61 3.0 62 1.0 63 1.0 64 1.0 65 0.5 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 50.724999999999994 #Duplication Level Percentage of deduplicated Percentage of total 1 87.28437654016757 44.275 2 5.076392311483489 5.1499999999999995 3 2.4149827501232135 3.675 4 0.8871365204534253 1.7999999999999998 5 0.7885657959586003 2.0 6 0.39428289797930016 1.2 7 0.4928536224741252 1.7500000000000002 8 0.44356826022671264 1.7999999999999998 9 0.09857072449482504 0.44999999999999996 >10 1.6757023164120255 16.400000000000002 >50 0.2957121734844751 11.35 >100 0.14785608674223755 10.15 >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 CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 183 4.575 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 120 3.0 Illumina Small RNA Adapter 2 (100% over 21bp) GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 103 2.5749999999999997 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 98 2.45 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTGGAATTCTCGGGTGCCAA 88 2.1999999999999997 No Hit CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 81 2.025 RNA PCR Primer, Index 1 (100% over 28bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTTGGAATTCTCGGGTGCCA 73 1.825 No Hit TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 59 1.4749999999999999 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 55 1.375 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTTGGAATTCTCGGGTG 41 1.0250000000000001 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTTGGAATTCTCGGGTGC 41 1.0250000000000001 No Hit TCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTC 36 0.8999999999999999 RNA PCR Primer, Index 1 (100% over 26bp) GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 35 0.8750000000000001 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTTGGAATTCTCGGGTGCCA 35 0.8750000000000001 No Hit TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 33 0.8250000000000001 RNA PCR Primer, Index 1 (100% over 29bp) CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 33 0.8250000000000001 No Hit GAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTGC 27 0.675 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTATGGAATTCTCGGGTGCCAA 25 0.625 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATGGAATTCTCGGGTG 23 0.575 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATGGAATTCTCGGGTGCCAAGGA 21 0.525 RNA PCR Primer, Index 1 (100% over 22bp) GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTTGGAATTCTCGGGTGC 20 0.5 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTTGGAATTCTCGGGTGCC 18 0.44999999999999996 No Hit AGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCC 16 0.4 RNA PCR Primer, Index 1 (100% over 27bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 15 0.375 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTTGGAATTCTCGGGTGC 15 0.375 No Hit ACCTGCTCTGATACCATGTTGTGATGGAATTCTCGGGTGCCAAGGAACTC 14 0.35000000000000003 RNA PCR Primer, Index 1 (100% over 26bp) AACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCC 14 0.35000000000000003 RNA PCR Primer, Index 1 (100% over 27bp) ATATTGGGTAGGTTGTGGTATTTCATTGCTGGAATTCTCGGGTGCCAAGG 14 0.35000000000000003 Illumina Small RNA Adapter 2 (100% over 21bp) AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 14 0.35000000000000003 Illumina Small RNA Adapter 2 (100% over 21bp) TTCGGACCAGGCTTCATTCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 13 0.325 RNA PCR Primer, Index 1 (100% over 29bp) CGGTCGAGGGCACGCCTGCCTGGGCGTCACGCTGGAATTCTCGGGTGCCA 13 0.325 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATTGGAATTCTCGGGT 13 0.325 No Hit GAACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTC 13 0.325 RNA PCR Primer, Index 1 (100% over 26bp) ACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCCA 13 0.325 RNA PCR Primer, Index 1 (100% over 28bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGTGGAATTCTCGGGTGCC 13 0.325 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATACTCTGGAATTCTCGGGTGCCAAG 12 0.3 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAAATGGAATTCTCGGGT 12 0.3 No Hit AGAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTG 12 0.3 No Hit TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTGACCAATCTCGTATGC 11 0.27499999999999997 RNA PCR Primer, Index 4 (100% over 50bp) GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGGAATTCTCGGGTGCCA 11 0.27499999999999997 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 10 0.25 Illumina Small RNA Adapter 2 (100% over 21bp) TAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAG 10 0.25 RNA PCR Primer, Index 1 (100% over 29bp) CATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAAC 10 0.25 RNA PCR Primer, Index 1 (100% over 24bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCAATGGAATTCTCGGGTGCC 9 0.22499999999999998 No Hit AAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTGCC 9 0.22499999999999998 No Hit CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 8 0.2 RNA PCR Primer, Index 1 (100% over 23bp) GGGGATATGGCGAAATCGGTAGACGCTACGGACTTTGGAATTCTCGGGTG 8 0.2 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTAATGGAATTCTCGGGTGC 8 0.2 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTAAATGGAATTCTCGGGTGCC 8 0.2 No Hit GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGTTGGAATTCTCGGGT 8 0.2 No Hit CACGACTCTCGGCAACGGATATCTCGGCTTGGAATTCTCGGGTGCCAAGG 8 0.2 Illumina Small RNA Adapter 2 (100% over 21bp) CATCGAGTAGACCTTGTTAATGTGAGAATTTGGAATTCTCGGGTGCCAAG 8 0.2 No Hit CAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTC 8 0.2 RNA PCR Primer, Index 1 (100% over 26bp) ATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACT 8 0.2 RNA PCR Primer, Index 1 (100% over 25bp) TGTCGTGCCAATTCAACATAAACCCCTTGGAATTCTCGGGTGCCAAGGAA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 23bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTATGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 7 0.17500000000000002 Illumina Small RNA Adapter 2 (100% over 21bp) CATCGAGTAGACCTTGTTAATGTGAGAATTCTGGAATTCTCGGGTGCCAA 7 0.17500000000000002 No Hit AAGGGTGCTGAGAATACTTTGAATCTGACACTGGAATTCTCGGGTGCCAA 7 0.17500000000000002 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGATGGAATTCTC 7 0.17500000000000002 No Hit CATCGAGTAGACCTTGATATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 7 0.17500000000000002 No Hit TTGACAGAAGAGAGTGAGCACTGGAATTCTCGGGTGCCAAGGAACTCCAG 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 29bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTAAATGGAATTCTCGGGTG 7 0.17500000000000002 No Hit CTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCA 7 0.17500000000000002 No Hit AAGGGTGCTGAGAATACTTTGAATCTGACATGGAATTCTCGGGTGCCAAG 6 0.15 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTTGGAATTCTCGGGTGCCAA 6 0.15 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTGGAATTCTCGGGTG 6 0.15 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTTGGAATTCTCGGGTGCCAAG 6 0.15 No Hit ATGCAGTTACTAATTCATGATCTGGCTGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTTATGGAATTCTCGGGTGC 6 0.15 No Hit GAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC 6 0.15 RNA PCR Primer, Index 1 (100% over 33bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCAAATGGAATTCTCGGGTGC 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTAAAAAAATGGAATTCTCGGG 5 0.125 No Hit TGAAGCTGCCAGCATGATCTGATGGAATTCTCGGGTGCCAAGGAACTCCA 5 0.125 RNA PCR Primer, Index 1 (100% over 28bp) CATCGAGTAGACCTTGATATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 5 0.125 Illumina Small RNA Adapter 2 (100% over 21bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGGAATTCTCGGGTGC 5 0.125 No Hit CCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCC 5 0.125 RNA PCR Primer, Index 1 (100% over 27bp) GGTAGTTCGACCGCGGAATTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 5 0.125 RNA PCR Primer, Index 1 (100% over 31bp) CAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTG 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATCTGGAATTCTCGGGTGCCAAG 5 0.125 No Hit GGGGATGTAGCTCAGATGGTAGATGGAATTCTCGGGTGCCAAGGAACTCC 5 0.125 RNA PCR Primer, Index 1 (100% over 27bp) CATCGAGTAGACCTTGTTATTGTGAGAATTAATGGAATTCTCGGGTGCCA 5 0.125 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACG 5 0.125 No Hit CTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCCAG 5 0.125 RNA PCR Primer, Index 1 (100% over 29bp) AAGCTGAAGCGGAAATGCAATTCTCGGGTGAGATGGAATTCTCGGGTGCC 5 0.125 No Hit GCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGG 5 0.125 No Hit CCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) >>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 0.375 0.0 0.0 0.0 2 0.0 0.375 0.0 0.0 0.0 3 0.0 0.375 0.0 0.0 0.0 4 0.0 0.375 0.0 0.0 0.0 5 0.0 0.4 0.0 0.0 0.0 6 0.0 0.4 0.0 0.0 0.0 7 0.0 0.4 0.0 0.0 0.0 8 0.0 0.4 0.0 0.0 0.0 9 0.0 0.4 0.0 0.0 0.0 10-11 0.0 0.4375 0.0 0.0 0.0 12-13 0.0 0.45 0.0 0.0 0.0 14-15 0.0 0.5125 0.0 0.0 0.0 16-17 0.0 0.6000000000000001 0.0 0.0 0.0 18-19 0.0 1.1 0.0 0.0 0.0 20-21 0.0 2.6 0.0 0.0 0.0 22-23 0.0 8.9625 0.0 0.0 0.0 24-25 0.0 21.175 0.0 0.0 0.0 26-27 0.0 32.0375 0.0 0.0 0.0 28-29 0.0 36.7625 0.0 0.0 0.0 30-31 0.0 51.0 0.0 0.0 0.0 32-33 0.0 68.36250000000001 0.0 0.0 0.0 34-35 0.0 82.7125 0.0 0.0 0.0 36-37 0.0 91.175 0.0 0.0 0.0 38-39 0.0 93.9625 0.0 0.0 0.0 40-41 0.0 95.05000000000001 0.0 0.0 0.0 42-43 0.0 95.95 0.0 0.0 0.0 44-45 0.0 96.3875 0.0 0.0 0.0 46-47 0.0 96.525 0.0 0.0 0.0 48-49 0.0 96.5375 0.0 0.0 0.0 50-51 0.0 96.55 0.0 0.0 0.0 52-53 0.0 96.55 0.0 0.0 0.0 54-55 0.0 96.575 0.0 0.0 0.0 56-57 0.0 96.575 0.0 0.0 0.0 58-59 0.0 96.575 0.0 0.0 0.0 60-61 0.0 96.575 0.0 0.0 0.0 62-63 0.0 96.575 0.0 0.0 0.0 64-65 0.0 96.5875 0.0 0.0 0.0 66-67 0.0 96.6 0.0 0.0 0.0 68-69 0.0 96.6 0.0 0.0 0.0 70-71 0.0 96.6 0.0 0.0 0.0 72-73 0.025 96.6 0.0 0.0 0.0 74-75 0.025 96.6 0.0 0.0 0.0 76-77 0.025 96.6 0.0 0.0 0.0 78-79 0.025 96.6 0.0 0.0 0.0 80-81 0.025 96.6125 0.0 0.0 0.0 82-83 0.025 96.67500000000001 0.0 0.0 0.0 84-85 0.025 96.725 0.0 0.0 0.0 86-87 0.025 96.725 0.0 0.0 0.0 88-89 0.025 96.75 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 ATTGTAG 40 5.456968E-12 95.00001 4 TGTAGTT 40 5.456968E-12 95.00001 6 GGATGTA 15 6.142176E-4 95.0 4 GTAGACC 60 0.0 95.0 7 GATGTAG 15 6.142176E-4 95.0 5 TAGCCAA 15 6.142176E-4 95.0 9 CGGATGT 15 6.142176E-4 95.0 3 GCGGATG 15 6.142176E-4 95.0 2 TGTAGCC 15 6.142176E-4 95.0 7 CGAGTAG 60 0.0 95.0 4 AGACCTT 60 0.0 95.0 9 ATGTAGC 15 6.142176E-4 95.0 6 ATCGAGT 60 0.0 95.0 2 TCGAGTA 60 0.0 95.0 3 TAGACCT 60 0.0 95.0 8 CATCGAG 60 0.0 95.0 1 GATTGTA 35 2.3101165E-10 94.99999 3 GGGATTG 35 2.3101165E-10 94.99999 1 AGTAGAC 65 0.0 87.69231 6 >>END_MODULE Rejected 249468 READS because READLEN < 1 Read 249468 spots for SRR6941568.sra Written 249468 spots for SRR6941568.sra Rejected 249468 READS because READLEN < 1 Read 249468 spots for SRR6941568.sra Written 249468 spots for SRR6941568.sra Rejected 249468 READS because READLEN < 1 Read 249468 spots for SRR6941568.sra Written 249468 spots for SRR6941568.sra Rejected 249478 READS because READLEN < 1 Read 249478 spots for SRR6941568.sra Written 249478 spots for SRR6941568.sra Rejected 249468 READS because READLEN < 1 Read 249468 spots for SRR6941568.sra Written 249468 spots for SRR6941568.sra Rejected 249468 READS because READLEN < 1 Read 249468 spots for SRR6941568.sra Written 249468 spots for SRR6941568.sra Rejected 249468 READS because READLEN < 1 Read 249468 spots for SRR6941568.sra Written 249468 spots for SRR6941568.sra Rejected 249468 READS because READLEN < 1 Read 249468 spots for SRR6941568.sra Written 249468 spots for SRR6941568.sra Rejected 249468 READS because READLEN < 1 Read 249468 spots for SRR6941568.sra Written 249468 spots for SRR6941568.sra Rejected 249468 READS because READLEN < 1 Read 249468 spots for SRR6941568.sra Written 249468 spots for SRR6941568.sra Rejected 249468 READS because READLEN < 1 Read 249468 spots for SRR6941568.sra Written 249468 spots for SRR6941568.sra Rejected 249468 READS because READLEN < 1 Read 249468 spots for SRR6941568.sra Written 249468 spots for SRR6941568.sra Rejected 249468 READS because READLEN < 1 Read 249468 spots for SRR6941568.sra Written 249468 spots for SRR6941568.sra Rejected 249468 READS because READLEN < 1 Read 249468 spots for SRR6941568.sra Written 249468 spots for SRR6941568.sra Rejected 249468 READS because READLEN < 1 Read 249468 spots for SRR6941568.sra Written 249468 spots for SRR6941568.sra Rejected 249468 READS because READLEN < 1 Read 249468 spots for SRR6941568.sra Written 249468 spots for SRR6941568.sra Rejected 249468 READS because READLEN < 1 Read 249468 spots for SRR6941568.sra Written 249468 spots for SRR6941568.sra Rejected 249468 READS because READLEN < 1 Read 249468 spots for SRR6941568.sra Written 249468 spots for SRR6941568.sra Rejected 249468 READS because READLEN < 1 Read 249468 spots for SRR6941568.sra Written 249468 spots for SRR6941568.sra Rejected 249468 READS because READLEN < 1 Read 249468 spots for SRR6941568.sra Written 249468 spots for SRR6941568.sra SRR ids: ['SRR6941568.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_s6i2lqdm SRR6941568.sra spots: 4989370 blocks: [[1, 249468], [249469, 498936], [498937, 748404], [748405, 997872], [997873, 1247340], [1247341, 1496808], [1496809, 1746276], [1746277, 1995744], [1995745, 2245212], [2245213, 2494680], [2494681, 2744148], [2744149, 2993616], [2993617, 3243084], [3243085, 3492552], [3492553, 3742020], [3742021, 3991488], [3991489, 4240956], [4240957, 4490424], [4490425, 4739892], [4739893, 4989370]] SRR6941568 file size 1191576 SRR6941568 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 SRR6941568 SRR6941568_1.fastq Input file: SRR6941568_1.fastq trimmed: SRR6941568-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 11:36:30 2024 >> started Fri Dec 6 11:36:34 2024 >> done (3.276s) 4989370 reads processed; of these: 66 ( 0.00%) short reads filtered out after trimming by size control 19 ( 0.00%) empty reads filtered out after trimming by size control 4989285 (100.00%) reads available; of these: 785754 (15.75%) trimmed reads available after processing 4203531 (84.25%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 7 0.00% 19 6 0.00% 20 4 0.00% 21 13 0.00% 22 3 0.00% 23 11 0.00% 24 4 0.00% 25 14 0.00% 26 13 0.00% 27 28 0.00% 28 34 0.00% 29 44 0.00% 30 55 0.00% 31 27 0.00% 32 47 0.00% 33 40 0.00% 34 47 0.00% 35 46 0.00% 36 50 0.00% 37 53 0.00% 38 66 0.00% 39 87 0.00% 40 83 0.00% 41 62 0.00% 42 61 0.00% 43 77 0.00% 44 71 0.00% 45 85 0.00% 46 70 0.00% 47 67 0.00% 48 62 0.00% 49 51 0.00% 50 42 0.00% 51 46 0.00% 52 45 0.00% 53 43 0.00% 54 45 0.00% 55 31 0.00% 56 31 0.00% 57 29 0.00% 58 27 0.00% 59 32 0.00% 60 40 0.00% 61 38 0.00% 62 29 0.00% 63 41 0.00% 64 46 0.00% 65 46 0.00% 66 53 0.00% 67 67 0.00% 68 110 0.00% 69 136 0.00% 70 210 0.00% 71 187 0.00% 72 289 0.01% 73 755 0.02% 74 4359 0.09% 75 3176 0.06% 76 1149 0.02% 77 458 0.01% 78 500 0.01% 79 501 0.01% 80 610 0.01% 81 601 0.01% 82 699 0.01% 83 884 0.02% 84 1331 0.03% 85 1503 0.03% 86 1642 0.03% 87 1922 0.04% 88 2361 0.05% 89 3187 0.06% 90 4754 0.10% 91 7127 0.14% 92 9530 0.19% 93 18787 0.38% 94 32878 0.66% 95 77676 1.56% 96 90878 1.82% 97 99202 1.99% 98 151922 3.04% 99 183044 3.67% 100 81267 1.63% 101 4203531 84.25% 4989285 reads passed initial QC criterion=sequence-density sequence-density=97.15 sequence-density-rank=1 fanout-score=24.48 fanout-score-rank=3 prefix-density=97.33 prefix-fanout=24.4 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTGACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAA criterion=fanout-score sequence-density=0.01 sequence-density-rank=12 fanout-score=52.41 fanout-score-rank=1 prefix-density=0.45 prefix-fanout=1.0 sequence=CCATCGAGTAGACCTTGTTATTGTGAGAATT 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTGACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAA -o SRR6941568 - Input file: STDIN trimmed: SRR6941568-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTGACCAATCTCGTATGCCGTCTTCTGCTTGA -- 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 11:36:59 2024 >> started Fri Dec 6 11:37:05 2024 >> done (5.797s) 4887463 reads processed; of these: 31020 ( 0.63%) short reads filtered out after trimming by size control 17046 ( 0.35%) empty reads filtered out after trimming by size control 4839397 (99.02%) reads available; of these: 4787961 (98.94%) trimmed reads available after processing 51436 ( 1.06%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 12614 0.26% 19 32505 0.67% 20 42125 0.87% 21 197593 4.08% 22 193091 3.99% 23 131855 2.72% 24 793707 16.40% 25 143209 2.96% 26 126619 2.62% 27 115085 2.38% 28 122355 2.53% 29 353441 7.30% 30 591560 12.22% 31 365424 7.55% 32 369450 7.63% 33 349023 7.21% 34 268778 5.55% 35 239900 4.96% 36 117081 2.42% 37 66543 1.38% 38 38670 0.80% 39 25430 0.53% 40 25877 0.53% 41 24790 0.51% 42 18844 0.39% 43 4923 0.10% 44 5185 0.11% 45 3486 0.07% 46 1139 0.02% 47 1422 0.03% 48 635 0.01% 49 331 0.01% 50 200 0.00% 51 155 0.00% 52 78 0.00% 53 66 0.00% 54 65 0.00% 55 46 0.00% 56 26 0.00% 57 54 0.00% 58 42 0.00% 59 28 0.00% 60 44 0.00% 61 22 0.00% 62 33 0.00% 63 28 0.00% 64 41 0.00% 65 25 0.00% 66 34 0.00% 67 39 0.00% 68 92 0.00% 69 73 0.00% 70 140 0.00% 71 80 0.00% 72 69 0.00% 73 97 0.00% 74 79 0.00% 75 132 0.00% 76 175 0.00% 77 712 0.01% 78 130 0.00% 79 262 0.01% 80 688 0.01% 81 311 0.01% 82 668 0.01% 83 527 0.01% 84 229 0.00% 85 198 0.00% 86 272 0.01% 87 363 0.01% 88 181 0.00% 89 165 0.00% 90 175 0.00% 91 399 0.01% 92 284 0.01% 93 270 0.01% 94 306 0.01% 95 379 0.01% 96 458 0.01% 97 483 0.01% 98 1007 0.02% 99 634 0.01% 100 760 0.02% 101 44883 0.93% criterion=sequence-density sequence-density=6.87 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=17 prefix-density=0.00 prefix-fanout=1.0 sequence=GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCGGAAGCTGCGGGTTCGAGCCCCGTCAGTCCCGCCA criterion=fanout-score sequence-density=0.14 sequence-density-rank=27 fanout-score=162.29 fanout-score-rank=1 prefix-density=23.03 prefix-fanout=1.0 sequence=TATTGTGAGAAAAAA Started job on | Dec 06 11:37:25 Started mapping on | Dec 06 11:37:26 Finished on | Dec 06 11:37:43 Mapping speed, Million of reads per hour | 1046.38 Number of input reads | 4941219 Average input read length | 31 UNIQUE READS: Uniquely mapped reads number | 844735 Uniquely mapped reads % | 17.10% Average mapped length | 25.65 Number of splices: Total | 3940 Number of splices: Annotated (sjdb) | 1804 Number of splices: GT/AG | 3687 Number of splices: GC/AG | 151 Number of splices: AT/AC | 3 Number of splices: Non-canonical | 99 Mismatch rate per base, % | 0.12% Deletion rate per base | 0.00% Deletion average length | 1.47 Insertion rate per base | 0.00% Insertion average length | 1.01 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 3120344 % of reads mapped to multiple loci | 63.15% Number of reads mapped to too many loci | 779544 % of reads mapped to too many loci | 15.78% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.34% % of reads unmapped: other | 0.64% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 976140 976140 976140 N_multimapping 3120344 3120344 3120344 N_noFeature 598394 678611 761792 N_ambiguous 7527 4598 220 UnstrandedReadsAssigned:238814 PositiveStrandReadsAssigned:161526 NegativeStrandReadsAssigned:82723 Dataset is classified unstranded MeadianReadLen=30 20thPercentileLength=24 echo kmer=19 SRR6941568 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: SRR6941568-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 4,941,219 reads, 2,268,612 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 940 rounds 52973 SRR6941568.ke.tsv 35125 SRR6941568.se.tsv 88098 total ==> SRR6941568.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0.333333 0.104489 PNS24249 1928 1829 0 0 PNS24246 1044 945 0.333333 0.104489 PNS24248 1044 945 0.333333 0.104489 PNS24244 1471 1372 0 0 PNS24243 293 194 0 0 KQK14069 1603 1504 25.898 5.10084 KQK14071 474 375 0 0 ==> SRR6941568.se.tsv <== BRADI_1g14170v3 24 BRADI_1g53295v3 1 BRADI_1g59795v3 1 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 1 BRADI_1g74790v3 17 BRADI_1g09890v3 0 BRADI_1g77505v3 0 BRADI_1g48960v3 0 SRR6941568 completed mapping pipeline successfully