Starting /dee2/code/volunteer_pipeline.sh SRR6941564 current disk space = 1551436414976 free memory = 1600867160 SRR6941564 SRAfilesize 63ef1890e7b3adc5777db44b10823e00 SRR6941564.sra SRR6941564.sra file validated SRR6941564 is single end SRR6941564 is conventional basespace SRR6941564 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6941564_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 33.3665 34.0 33.0 34.0 33.0 34.0 2 33.42425 34.0 33.0 34.0 33.0 34.0 3 33.3095 34.0 33.0 34.0 33.0 34.0 4 33.3995 34.0 33.0 34.0 33.0 34.0 5 33.3275 34.0 33.0 34.0 33.0 34.0 6 37.12925 38.0 37.0 38.0 36.0 38.0 7 37.45225 38.0 38.0 38.0 37.0 38.0 8 37.59125 38.0 38.0 38.0 38.0 38.0 9 37.633 38.0 38.0 38.0 38.0 38.0 10-11 37.6155 38.0 38.0 38.0 38.0 38.0 12-13 37.587125 38.0 38.0 38.0 38.0 38.0 14-15 37.53425 38.0 38.0 38.0 38.0 38.0 16-17 36.1005 38.0 37.0 38.0 31.5 38.0 18-19 36.917625 38.0 37.5 38.0 33.5 38.0 20-21 36.218 38.0 38.0 38.0 30.5 38.0 22-23 37.380875 38.0 38.0 38.0 36.5 38.0 24-25 37.538 38.0 38.0 38.0 38.0 38.0 26-27 37.48625 38.0 38.0 38.0 37.5 38.0 28-29 37.487875 38.0 38.0 38.0 37.0 38.0 30-31 37.420625 38.0 38.0 38.0 37.0 38.0 32-33 37.366249999999994 38.0 38.0 38.0 37.0 38.0 34-35 37.35275 38.0 38.0 38.0 37.0 38.0 36-37 37.273875000000004 38.0 38.0 38.0 37.0 38.0 38-39 37.237750000000005 38.0 38.0 38.0 37.0 38.0 40-41 37.219 38.0 38.0 38.0 37.0 38.0 42-43 37.183625 38.0 38.0 38.0 37.0 38.0 44-45 37.212625 38.0 38.0 38.0 37.0 38.0 46-47 37.161875 38.0 38.0 38.0 36.5 38.0 48-49 37.248374999999996 38.0 38.0 38.0 37.0 38.0 50-51 36.985625 38.0 38.0 38.0 36.0 38.0 52-53 37.097625 38.0 38.0 38.0 37.0 38.0 54-55 37.227875 38.0 38.0 38.0 37.0 38.0 56-57 37.150125 38.0 38.0 38.0 36.5 38.0 58-59 37.237125 38.0 38.0 38.0 37.0 38.0 60-61 37.219125 38.0 38.0 38.0 37.0 38.0 62-63 36.8725 38.0 38.0 38.0 35.5 38.0 64-65 36.593125 38.0 37.5 38.0 34.5 38.0 66-67 36.251 38.0 37.5 38.0 32.5 38.0 68-69 36.771375000000006 38.0 38.0 38.0 35.0 38.0 70-71 36.095625 38.0 37.5 38.0 31.0 38.0 72-73 35.587125 38.0 36.5 38.0 28.5 38.0 74-75 35.696125 38.0 37.0 38.0 29.0 38.0 76-77 35.99275 38.0 37.0 38.0 31.0 38.0 78-79 36.503625 38.0 38.0 38.0 34.0 38.0 80-81 36.87175 38.0 38.0 38.0 36.0 38.0 82-83 36.899625 38.0 38.0 38.0 36.0 38.0 84-85 36.888 38.0 38.0 38.0 36.0 38.0 86-87 36.90475 38.0 38.0 38.0 36.0 38.0 88-89 36.873000000000005 38.0 38.0 38.0 36.0 38.0 90-91 36.886250000000004 38.0 38.0 38.0 35.5 38.0 92-93 36.790875 38.0 38.0 38.0 35.5 38.0 94-95 36.451375 38.0 38.0 38.0 34.5 38.0 96-97 34.776375 38.0 37.5 38.0 28.5 38.0 98-99 32.826750000000004 38.0 35.5 38.0 8.5 38.0 100-101 30.63525 38.0 28.5 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 15 1.0 16 1.0 17 0.0 18 1.0 19 0.0 20 0.0 21 0.0 22 1.0 23 2.0 24 2.0 25 6.0 26 10.0 27 20.0 28 18.0 29 22.0 30 28.0 31 35.0 32 60.0 33 87.0 34 142.0 35 386.0 36 724.0 37 2454.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 26.650000000000002 19.85 14.2 39.300000000000004 2 24.74355766825119 44.933700275206405 14.83612709532149 15.486614961220916 3 24.5 16.3 40.400000000000006 18.8 4 22.525000000000002 25.2 11.799999999999999 40.475 5 51.800000000000004 16.5 17.575 14.124999999999998 6 16.85 46.650000000000006 20.0 16.5 7 52.675000000000004 18.025 16.825000000000003 12.475 8 17.65 13.700000000000001 54.15 14.499999999999998 9 15.575 53.87499999999999 15.775 14.774999999999999 10-11 38.3 31.775 16.325 13.600000000000001 12-13 14.4375 16.0 18.625 50.9375 14-15 16.6375 30.162499999999998 39.675 13.525 16-17 30.837500000000002 17.4 39.5875 12.174999999999999 18-19 31.225 28.037499999999998 29.175 11.5625 20-21 13.100000000000001 22.4625 47.2625 17.175 22-23 35.475 22.95 28.125 13.450000000000001 24-25 34.699999999999996 34.2 18.875 12.225 26-27 39.5875 31.025000000000002 16.575 12.812499999999998 28-29 14.2625 39.975 27.875 17.8875 30-31 19.075 12.950000000000001 46.0625 21.912499999999998 32-33 33.025 14.4875 31.0 21.4875 34-35 33.475 28.037499999999998 24.75 13.737499999999999 36-37 36.1 20.25 31.612499999999997 12.0375 38-39 22.4875 17.8625 36.9125 22.7375 40-41 25.874999999999996 13.65 25.0625 35.4125 42-43 39.8375 21.2875 19.1 19.775000000000002 44-45 51.0375 12.325 17.974999999999998 18.6625 46-47 31.075000000000003 24.4 14.2375 30.2875 48-49 22.55 29.299999999999997 15.45 32.7 50-51 31.7375 27.525 8.0 32.737500000000004 52-53 27.700000000000003 45.275 6.1125 20.9125 54-55 19.287499999999998 28.9875 19.5625 32.1625 56-57 11.975 32.225 14.124999999999998 41.675000000000004 58-59 21.45 31.087500000000002 15.325 32.1375 60-61 15.950000000000001 23.4375 24.275 36.3375 62-63 20.849999999999998 31.162499999999998 16.35 31.637500000000003 64-65 18.725 32.175 23.575 25.525 66-67 15.6125 24.099999999999998 26.8625 33.425 68-69 25.650000000000002 29.6375 19.025 25.687500000000004 70-71 18.0 32.05 30.0875 19.8625 72-73 20.474999999999998 18.9 32.9875 27.6375 74-75 20.2125 11.4 29.075 39.3125 76-77 20.837500000000002 14.149999999999999 42.0125 23.0 78-79 21.1625 10.5375 40.4875 27.8125 80-81 22.325 8.2875 32.5 36.8875 82-83 28.000000000000004 5.625 38.012499999999996 28.3625 84-85 18.9375 5.8999999999999995 40.2875 34.875 86-87 17.5625 11.25 43.824999999999996 27.3625 88-89 15.712499999999999 26.8625 35.449999999999996 21.975 90-91 12.3 31.424999999999997 35.125 21.15 92-93 18.1375 38.6375 29.625 13.600000000000001 94-95 13.175 59.9125 18.875 8.0375 96-97 8.4625 76.525 11.862499999999999 3.15 98-99 4.7 88.7125 4.575 2.0125 100-101 1.9375 93.8 2.6625 1.6 >>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 0.0 34 0.5 35 1.5 36 1.5 37 2.0 38 3.5 39 5.0 40 11.5 41 29.0 42 84.0 43 213.0 44 619.5 45 819.5 46 495.0 47 299.0 48 252.5 49 182.5 50 195.5 51 244.0 52 225.5 53 133.5 54 62.0 55 46.5 56 36.0 57 14.0 58 12.0 59 10.0 60 1.0 61 0.5 62 0.0 63 0.0 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 0.075 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 46.525 #Duplication Level Percentage of deduplicated Percentage of total 1 86.45889306824289 40.225 2 4.997313272434175 4.65 3 2.0956475013433637 2.9250000000000003 4 1.7732401934443847 3.3000000000000003 5 0.6448146157979581 1.5 6 0.5910800644814616 1.6500000000000001 7 0.2686727565824825 0.8750000000000001 8 0.42987641053197206 1.6 9 0.42987641053197206 1.7999999999999998 >10 1.8269747447608813 16.925 >50 0.2686727565824825 8.55 >100 0.21493820526598603 16.0 >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 235 5.875 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 150 3.75 Illumina Small RNA Adapter 2 (100% over 21bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTGGAATTCTCGGGTGCCAA 138 3.45 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTGGAATTCTCGGGTGCCA 117 2.9250000000000003 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 95 2.375 No Hit GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 72 1.7999999999999998 No Hit CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 60 1.5 RNA PCR Primer, Index 1 (100% over 28bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTTGGAATTCTCGGGTG 59 1.4749999999999999 No Hit TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 56 1.4000000000000001 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTTGGAATTCTCGGGTGC 49 1.225 No Hit TCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTC 47 1.175 RNA PCR Primer, Index 1 (100% over 26bp) CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 45 1.125 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 44 1.0999999999999999 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 44 1.0999999999999999 No Hit TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 31 0.775 RNA PCR Primer, Index 1 (100% over 29bp) CATCGAGTAGACCTTGTTATTGTGAGAATTATGGAATTCTCGGGTGCCAA 27 0.675 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 21 0.525 Illumina Small RNA Adapter 2 (100% over 21bp) CATCGAGTAGACCTTGTTATTGTGAGAATGGAATTCTCGGGTGCCAAGGA 20 0.5 RNA PCR Primer, Index 1 (100% over 22bp) GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTTGGAATTCTCGGGTGC 20 0.5 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTTGGAATTCTCGGGTGCCA 20 0.5 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATGGAATTCTCGGGTG 20 0.5 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGGAATTCTCGGGTGCCA 19 0.475 No Hit GAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTGC 18 0.44999999999999996 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTTGGAATTCTCGGGTGCCAAG 17 0.42500000000000004 No Hit AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 17 0.42500000000000004 Illumina Small RNA Adapter 2 (100% over 21bp) ACCTGCTCTGATACCATGTTGTGATGGAATTCTCGGGTGCCAAGGAACTC 16 0.4 RNA PCR Primer, Index 1 (100% over 26bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGGAATTCTCGGGTGC 15 0.375 No Hit CATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAAC 14 0.35000000000000003 RNA PCR Primer, Index 1 (100% over 24bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTAATGGAATTCTCGGGTGC 14 0.35000000000000003 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTAAATGGAATTCTCGGGTG 14 0.35000000000000003 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATACTCTGGAATTCTCGGGTGCCAAG 13 0.325 No Hit GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTTGGAATTCTCGGGTGC 13 0.325 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 12 0.3 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCAATGGAATTCTCGGGTGCC 12 0.3 No Hit CATCGAGTAGACCTTGTTAATGTGAGAATTTGGAATTCTCGGGTGCCAAG 12 0.3 No Hit TGTCGTGCCAATTCAACATAAACCCTGGAATTCTCGGGTGCCAAGGAACT 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 25bp) CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 23bp) ACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCCA 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 28bp) CATCGAGTAGACCTTGTTATTGTGAGAATAAATGGAATTCTCGGGTGCCA 10 0.25 No Hit TTCGGACCAGGCTTCATTCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 10 0.25 RNA PCR Primer, Index 1 (100% over 29bp) CGGTCGAGGGCACGCCTGCCTGGGCGTCACGCTGGAATTCTCGGGTGCCA 10 0.25 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTATGGAATTCTCGGGTGCC 10 0.25 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTTGGAATTCTCGGGTGCC 10 0.25 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAAATGGAATTCTCGGGT 9 0.22499999999999998 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATTGGAATTCTCGGGT 9 0.22499999999999998 No Hit GAACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTC 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 26bp) AACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCC 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 27bp) ATGCAGTTACTAATTCATGATCTGGCTGGAATTCTCGGGTGCCAAGGAAC 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 24bp) ATATTGGGTAGGTTGTGGTATTTCATTGCTGGAATTCTCGGGTGCCAAGG 9 0.22499999999999998 Illumina Small RNA Adapter 2 (100% over 21bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGTGGAATTCTCGGGTGCC 9 0.22499999999999998 No Hit ATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACT 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 25bp) CATCGAGTAGACCTTGATATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 8 0.2 Illumina Small RNA Adapter 2 (100% over 21bp) CAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTG 8 0.2 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTAAATGGAATTCTCGGGTGCC 8 0.2 No Hit TGTCGTGCCAATTCAACATAAACCCCTGGAATTCTCGGGTGCCAAGGAAC 8 0.2 RNA PCR Primer, Index 1 (100% over 24bp) CATCGAGTAGACCTTGTTAATGTGAGAATTCTTGGAATTCTCGGGTGCCA 8 0.2 No Hit CATCGAGTAGACCTTGATATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 8 0.2 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTGGAATTCTCGGGT 8 0.2 No Hit GCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAA 8 0.2 RNA PCR Primer, Index 1 (100% over 23bp) CATCGAGTAGACCTTGTTATTGTGAGAATTAAAATGGAATTCTCGGGTGC 7 0.17500000000000002 No Hit AGAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTG 7 0.17500000000000002 No Hit CATCGAGTAGACCTTGGTATTGTGAGAATTCTTGGAATTCTCGGGTGCCA 7 0.17500000000000002 No Hit TTGACAGAAGAGAGTGAGCACTGGAATTCTCGGGTGCCAAGGAACTCCAG 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 29bp) CTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCA 7 0.17500000000000002 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 6 0.15 Illumina Small RNA Adapter 2 (100% over 21bp) TGACAGAAGAGAGTGAGCACTGGAATTCTCGGGTGCCAAGGAACTCCAGT 6 0.15 RNA PCR Primer, Index 1 (100% over 30bp) TTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 6 0.15 RNA PCR Primer, Index 1 (100% over 31bp) TGTCGTGCCAATTCAACATAAACCCCTTGGAATTCTCGGGTGCCAAGGAA 6 0.15 RNA PCR Primer, Index 1 (100% over 23bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTGGAATTCTCGGGTG 6 0.15 No Hit ACGAACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) CATCGAGTAGACCTTGTTACTGTGAGAATTTGGAATTCTCGGGTGCCAAG 6 0.15 No Hit AAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTGCC 6 0.15 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTTGGAATTCTCGGG 6 0.15 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGATGGAATTCTC 6 0.15 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGGAATTCTCGGGTGCCAA 6 0.15 No Hit ATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGG 5 0.125 No Hit GCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGT 5 0.125 No Hit GGGATTGTAGTTCAATTGGACAGAGCACCGCCCTGGAATTCTCGGGTGCC 5 0.125 No Hit AGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCC 5 0.125 RNA PCR Primer, Index 1 (100% over 27bp) CATCGAGTAGACCTTGATATTGTGAGAATTCTGGAATTCTCGGGTGCCAA 5 0.125 No Hit TAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAG 5 0.125 RNA PCR Primer, Index 1 (100% over 29bp) CATCGAGTAGACCTTGTTAATGTGAGAATTGGAATTCTCGGGTGCCAAGG 5 0.125 Illumina Small RNA Adapter 2 (100% over 21bp) AGAAGAGAGAGAGTACAGCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG 5 0.125 RNA PCR Primer, Index 1 (100% over 29bp) CATCGAGTAGACCTTGTTATTGTGAGAATCTGGAATTCTCGGGTGCCAAG 5 0.125 No Hit AACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGT 5 0.125 RNA PCR Primer, Index 1 (100% over 30bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTCATGGAATTCTCGGGTG 5 0.125 No Hit TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGG 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 0.1 0.0 0.0 0.0 2 0.0 0.1 0.0 0.0 0.0 3 0.0 0.1 0.0 0.0 0.0 4 0.0 0.1 0.0 0.0 0.0 5 0.0 0.125 0.0 0.0 0.0 6 0.0 0.125 0.0 0.0 0.0 7 0.0 0.125 0.0 0.0 0.0 8 0.0 0.125 0.0 0.0 0.0 9 0.0 0.125 0.0 0.0 0.0 10-11 0.0 0.125 0.0 0.0 0.0 12-13 0.0 0.125 0.0 0.0 0.0 14-15 0.0 0.125 0.0 0.0 0.0 16-17 0.0 0.1625 0.0 0.0 0.0 18-19 0.0 0.5 0.0 0.0 0.0 20-21 0.0 1.65 0.0 0.0 0.0 22-23 0.0 7.75 0.0 0.0 0.0 24-25 0.0 17.85 0.0 0.0 0.0 26-27 0.0 28.362499999999997 0.0 0.0 0.0 28-29 0.0 32.7625 0.0 0.0 0.0 30-31 0.0 47.9125 0.0 0.0 0.0 32-33 0.0 67.35 0.0 0.0 0.0 34-35 0.0 82.175 0.0 0.0 0.0 36-37 0.0 91.92500000000001 0.0 0.0 0.0 38-39 0.0 95.1 0.0 0.0 0.0 40-41 0.0 96.2125 0.0 0.0 0.0 42-43 0.0 97.0625 0.0 0.0 0.0 44-45 0.0 97.38749999999999 0.0 0.0 0.0 46-47 0.0 97.5875 0.0 0.0 0.0 48-49 0.0 97.6375 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 97.6625 0.0 0.0 0.0 64-65 0.0 97.675 0.0 0.0 0.0 66-67 0.0 97.675 0.0 0.0 0.0 68-69 0.0 97.675 0.0 0.0 0.0 70-71 0.0 97.675 0.0 0.0 0.0 72-73 0.0 97.675 0.0 0.0 0.0 74-75 0.0 97.675 0.0 0.0 0.0 76-77 0.0 97.675 0.0 0.0 0.0 78-79 0.0 97.675 0.0 0.0 0.0 80-81 0.0 97.675 0.0 0.0 0.0 82-83 0.0 97.675 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 GTAGACC 100 0.0 95.0 7 AGCTCAG 15 6.142176E-4 95.0 9 TTGTAGT 50 0.0 95.0 5 AGTAGAC 100 0.0 95.0 6 GGATTGT 50 0.0 95.0 2 GATTGTA 50 0.0 95.0 3 TAGTTCA 55 0.0 95.0 8 GAGTAGA 100 0.0 95.0 5 ATTGTAG 50 0.0 95.0 4 TGTAGTT 50 0.0 95.0 6 GGGATTG 50 0.0 95.0 1 CGAGTAG 100 0.0 95.0 4 AGACCTT 100 0.0 95.0 9 TCGAGTA 100 0.0 95.0 3 AGTTCAA 55 0.0 95.0 9 GTAGTTC 55 0.0 95.0 7 TAGACCT 100 0.0 95.0 8 CATCGAG 105 0.0 90.47619 1 ATCGAGT 110 0.0 86.36364 2 TAGCTCA 20 0.0019257745 71.25 8 >>END_MODULE Rejected 322827 READS because READLEN < 1 Read 322827 spots for SRR6941564.sra Written 322827 spots for SRR6941564.sra Rejected 322827 READS because READLEN < 1 Read 322827 spots for SRR6941564.sra Written 322827 spots for SRR6941564.sra Rejected 322827 READS because READLEN < 1 Read 322827 spots for SRR6941564.sra Written 322827 spots for SRR6941564.sra Rejected 322827 READS because READLEN < 1 Read 322827 spots for SRR6941564.sra Written 322827 spots for SRR6941564.sra Rejected 322827 READS because READLEN < 1 Read 322827 spots for SRR6941564.sra Written 322827 spots for SRR6941564.sra Rejected 322827 READS because READLEN < 1 Read 322827 spots for SRR6941564.sra Written 322827 spots for SRR6941564.sra Rejected 322827 READS because READLEN < 1 Read 322827 spots for SRR6941564.sra Written 322827 spots for SRR6941564.sra Rejected 322827 READS because READLEN < 1 Read 322827 spots for SRR6941564.sra Written 322827 spots for SRR6941564.sra Rejected 322841 READS because READLEN < 1 Read 322841 spots for SRR6941564.sra Written 322841 spots for SRR6941564.sra Rejected 322827 READS because READLEN < 1 Read 322827 spots for SRR6941564.sra Written 322827 spots for SRR6941564.sra Rejected 322827 READS because READLEN < 1 Read 322827 spots for SRR6941564.sra Written 322827 spots for SRR6941564.sra Rejected 322827 READS because READLEN < 1 Read 322827 spots for SRR6941564.sra Written 322827 spots for SRR6941564.sra Rejected 322827 READS because READLEN < 1 Read 322827 spots for SRR6941564.sra Written 322827 spots for SRR6941564.sra Rejected 322827 READS because READLEN < 1 Read 322827 spots for SRR6941564.sra Written 322827 spots for SRR6941564.sra Rejected 322827 READS because READLEN < 1 Read 322827 spots for SRR6941564.sra Written 322827 spots for SRR6941564.sra Rejected 322827 READS because READLEN < 1 Read 322827 spots for SRR6941564.sra Written 322827 spots for SRR6941564.sra Rejected 322827 READS because READLEN < 1 Read 322827 spots for SRR6941564.sra Written 322827 spots for SRR6941564.sra Rejected 322827 READS because READLEN < 1 Read 322827 spots for SRR6941564.sra Written 322827 spots for SRR6941564.sra Rejected 322827 READS because READLEN < 1 Read 322827 spots for SRR6941564.sra Written 322827 spots for SRR6941564.sra Rejected 322827 READS because READLEN < 1 Read 322827 spots for SRR6941564.sra Written 322827 spots for SRR6941564.sra SRR ids: ['SRR6941564.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_nsbfgi3j SRR6941564.sra spots: 6456554 blocks: [[1, 322827], [322828, 645654], [645655, 968481], [968482, 1291308], [1291309, 1614135], [1614136, 1936962], [1936963, 2259789], [2259790, 2582616], [2582617, 2905443], [2905444, 3228270], [3228271, 3551097], [3551098, 3873924], [3873925, 4196751], [4196752, 4519578], [4519579, 4842405], [4842406, 5165232], [5165233, 5488059], [5488060, 5810886], [5810887, 6133713], [6133714, 6456554]] SRR6941564 file size 1542611 SRR6941564 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 SRR6941564 SRR6941564_1.fastq Input file: SRR6941564_1.fastq trimmed: SRR6941564-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 11:28:46 2024 >> started Fri Dec 6 11:28:50 2024 >> done (3.693s) 6456554 reads processed; of these: 96 ( 0.00%) short reads filtered out after trimming by size control 19 ( 0.00%) empty reads filtered out after trimming by size control 6456439 (100.00%) reads available; of these: 798296 (12.36%) trimmed reads available after processing 5658143 (87.64%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 11 0.00% 19 4 0.00% 20 8 0.00% 21 9 0.00% 22 17 0.00% 23 22 0.00% 24 11 0.00% 25 12 0.00% 26 13 0.00% 27 17 0.00% 28 35 0.00% 29 53 0.00% 30 68 0.00% 31 29 0.00% 32 79 0.00% 33 52 0.00% 34 54 0.00% 35 61 0.00% 36 55 0.00% 37 58 0.00% 38 74 0.00% 39 74 0.00% 40 92 0.00% 41 65 0.00% 42 114 0.00% 43 121 0.00% 44 104 0.00% 45 150 0.00% 46 185 0.00% 47 122 0.00% 48 92 0.00% 49 95 0.00% 50 115 0.00% 51 106 0.00% 52 92 0.00% 53 83 0.00% 54 81 0.00% 55 67 0.00% 56 96 0.00% 57 68 0.00% 58 66 0.00% 59 105 0.00% 60 106 0.00% 61 96 0.00% 62 101 0.00% 63 92 0.00% 64 88 0.00% 65 75 0.00% 66 78 0.00% 67 92 0.00% 68 126 0.00% 69 161 0.00% 70 191 0.00% 71 184 0.00% 72 289 0.00% 73 626 0.01% 74 3784 0.06% 75 2679 0.04% 76 925 0.01% 77 324 0.01% 78 426 0.01% 79 460 0.01% 80 534 0.01% 81 527 0.01% 82 613 0.01% 83 718 0.01% 84 1092 0.02% 85 1277 0.02% 86 1270 0.02% 87 1649 0.03% 88 2025 0.03% 89 3152 0.05% 90 4803 0.07% 91 7621 0.12% 92 10824 0.17% 93 22116 0.34% 94 38454 0.60% 95 94440 1.46% 96 104298 1.62% 97 103910 1.61% 98 149835 2.32% 99 166959 2.59% 100 68441 1.06% 101 5658143 87.64% 6456439 reads passed initial QC criterion=sequence-density sequence-density=97.56 sequence-density-rank=1 fanout-score=24.61 fanout-score-rank=2 prefix-density=97.80 prefix-fanout=24.5 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCGTATGCCGTCTTCTGCTTGAAAAAA criterion=fanout-score sequence-density=2.71 sequence-density-rank=5 fanout-score=36.60 fanout-score-rank=1 prefix-density=98.46 prefix-fanout=1.0 sequence=CACGATCAGATATCGTATGCCGT 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCGTATGCCGTCTTCTGCTTGAAAAAA -o SRR6941564 - Input file: STDIN trimmed: SRR6941564-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCAGATCTCGTATGCCGTCTTCTGCTTGA -- 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 11:29:02 2024 >> started Fri Dec 6 11:29:09 2024 >> done (7.593s) 6324675 reads processed; of these: 29928 ( 0.47%) short reads filtered out after trimming by size control 14624 ( 0.23%) empty reads filtered out after trimming by size control 6280123 (99.30%) reads available; of these: 6239107 (99.35%) trimmed reads available after processing 41016 ( 0.65%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 15670 0.25% 19 40378 0.64% 20 54469 0.87% 21 245770 3.91% 22 207099 3.30% 23 150013 2.39% 24 890186 14.17% 25 165445 2.63% 26 150121 2.39% 27 139661 2.22% 28 156000 2.48% 29 472424 7.52% 30 861865 13.72% 31 534176 8.51% 32 538470 8.57% 33 484685 7.72% 34 352123 5.61% 35 318060 5.06% 36 153843 2.45% 37 90453 1.44% 38 53113 0.85% 39 37428 0.60% 40 38066 0.61% 41 36502 0.58% 42 28427 0.45% 43 7487 0.12% 44 7910 0.13% 45 4332 0.07% 46 1457 0.02% 47 1680 0.03% 48 746 0.01% 49 417 0.01% 50 212 0.00% 51 188 0.00% 52 93 0.00% 53 88 0.00% 54 60 0.00% 55 64 0.00% 56 40 0.00% 57 37 0.00% 58 38 0.00% 59 54 0.00% 60 60 0.00% 61 42 0.00% 62 36 0.00% 63 49 0.00% 64 38 0.00% 65 30 0.00% 66 29 0.00% 67 27 0.00% 68 43 0.00% 69 55 0.00% 70 64 0.00% 71 51 0.00% 72 42 0.00% 73 46 0.00% 74 47 0.00% 75 71 0.00% 76 77 0.00% 77 206 0.00% 78 72 0.00% 79 123 0.00% 80 220 0.00% 81 132 0.00% 82 182 0.00% 83 132 0.00% 84 86 0.00% 85 91 0.00% 86 91 0.00% 87 137 0.00% 88 86 0.00% 89 124 0.00% 90 164 0.00% 91 218 0.00% 92 188 0.00% 93 264 0.00% 94 307 0.00% 95 374 0.01% 96 365 0.01% 97 450 0.01% 98 723 0.01% 99 501 0.01% 100 552 0.01% 101 34178 0.54% criterion=sequence-density sequence-density=6.88 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=14 prefix-density=0.00 prefix-fanout=1.0 sequence=GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCG criterion=fanout-score sequence-density=0.19 sequence-density-rank=20 fanout-score=156.05 fanout-score-rank=1 prefix-density=29.16 prefix-fanout=1.0 sequence=TATTGTGAGAAAAAA Started job on | Dec 06 11:29:21 Started mapping on | Dec 06 11:29:21 Finished on | Dec 06 11:29:40 Mapping speed, Million of reads per hour | 1214.88 Number of input reads | 6411887 Average input read length | 31 UNIQUE READS: Uniquely mapped reads number | 964458 Uniquely mapped reads % | 15.04% Average mapped length | 25.27 Number of splices: Total | 4842 Number of splices: Annotated (sjdb) | 2200 Number of splices: GT/AG | 4544 Number of splices: GC/AG | 187 Number of splices: AT/AC | 3 Number of splices: Non-canonical | 108 Mismatch rate per base, % | 0.12% Deletion rate per base | 0.00% Deletion average length | 1.46 Insertion rate per base | 0.00% Insertion average length | 1.02 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 4375350 % of reads mapped to multiple loci | 68.24% Number of reads mapped to too many loci | 831219 % of reads mapped to too many loci | 12.96% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.23% % of reads unmapped: other | 0.52% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1072079 1072079 1072079 N_multimapping 4375350 4375350 4375350 N_noFeature 698078 794179 865306 N_ambiguous 7075 3853 210 UnstrandedReadsAssigned:259305 PositiveStrandReadsAssigned:166426 NegativeStrandReadsAssigned:98942 Dataset is classified unstranded MeadianReadLen=30 20thPercentileLength=24 echo kmer=19 SRR6941564 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: SRR6941564-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 6,411,887 reads, 3,363,011 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 974 rounds 52973 SRR6941564.ke.tsv 35125 SRR6941564.se.tsv 88098 total ==> SRR6941564.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 0 0 PNS24243 293 194 0 0 KQK14069 1603 1504 12.1535 1.54337 KQK14071 474 375 0 0 ==> SRR6941564.se.tsv <== BRADI_1g14170v3 18 BRADI_1g53295v3 0 BRADI_1g59795v3 0 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 1 BRADI_1g74790v3 25 BRADI_1g09890v3 0 BRADI_1g77505v3 1 BRADI_1g48960v3 0 SRR6941564 completed mapping pipeline successfully