Starting /dee2/code/volunteer_pipeline.sh SRR6941570 current disk space = 1551152623616 free memory = 1365913500 SRR6941570 SRAfilesize 11ae9495e8e227a7a29387207426f2f0 SRR6941570.sra SRR6941570.sra file validated SRR6941570 is single end SRR6941570 is conventional basespace SRR6941570 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6941570_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 47 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.17325 34.0 33.0 34.0 32.0 34.0 2 33.311 34.0 33.0 34.0 33.0 34.0 3 32.904 34.0 33.0 34.0 31.0 34.0 4 33.16575 34.0 33.0 34.0 32.0 34.0 5 33.141 34.0 33.0 34.0 31.0 34.0 6 37.0075 38.0 37.0 38.0 36.0 38.0 7 37.31325 38.0 38.0 38.0 37.0 38.0 8 37.499 38.0 38.0 38.0 37.0 38.0 9 37.5535 38.0 38.0 38.0 38.0 38.0 10-11 37.50425 38.0 38.0 38.0 38.0 38.0 12-13 37.420875 38.0 38.0 38.0 37.0 38.0 14-15 37.51075 38.0 38.0 38.0 38.0 38.0 16-17 36.254999999999995 38.0 37.5 38.0 32.0 38.0 18-19 36.900375 38.0 38.0 38.0 33.5 38.0 20-21 36.050875000000005 38.0 37.5 38.0 30.5 38.0 22-23 37.192750000000004 38.0 38.0 38.0 36.5 38.0 24-25 37.431875 38.0 38.0 38.0 37.0 38.0 26-27 37.481125 38.0 38.0 38.0 37.5 38.0 28-29 37.520875000000004 38.0 38.0 38.0 38.0 38.0 30-31 37.453374999999994 38.0 38.0 38.0 37.5 38.0 32-33 37.349875 38.0 38.0 38.0 37.0 38.0 34-35 37.274625 38.0 38.0 38.0 37.0 38.0 36-37 37.220749999999995 38.0 38.0 38.0 37.0 38.0 38-39 37.1905 38.0 38.0 38.0 37.0 38.0 40-41 37.1035 38.0 38.0 38.0 36.5 38.0 42-43 37.088 38.0 38.0 38.0 36.0 38.0 44-45 37.03975 38.0 38.0 38.0 36.0 38.0 46-47 36.948125000000005 38.0 38.0 38.0 36.0 38.0 48-49 37.04675 38.0 38.0 38.0 36.5 38.0 50-51 36.940125 38.0 38.0 38.0 36.0 38.0 52-53 36.93575 38.0 38.0 38.0 36.0 38.0 54-55 37.04025 38.0 38.0 38.0 36.0 38.0 56-57 37.028875 38.0 38.0 38.0 36.0 38.0 58-59 37.19725 38.0 38.0 38.0 37.0 38.0 60-61 37.184 38.0 38.0 38.0 37.0 38.0 62-63 37.04925 38.0 38.0 38.0 36.0 38.0 64-65 36.82925 38.0 38.0 38.0 35.5 38.0 66-67 36.6085 38.0 38.0 38.0 34.5 38.0 68-69 36.6745 38.0 38.0 38.0 34.5 38.0 70-71 36.34025 38.0 37.5 38.0 33.5 38.0 72-73 36.255875 38.0 37.0 38.0 33.0 38.0 74-75 36.075 38.0 37.0 38.0 31.0 38.0 76-77 36.12125 38.0 37.0 38.0 32.0 38.0 78-79 36.22025 38.0 37.5 38.0 33.0 38.0 80-81 36.488 38.0 38.0 38.0 34.5 38.0 82-83 36.52625 38.0 38.0 38.0 35.0 38.0 84-85 36.522875 38.0 38.0 38.0 34.5 38.0 86-87 36.320375 38.0 38.0 38.0 34.0 38.0 88-89 36.514125 38.0 38.0 38.0 34.5 38.0 90-91 36.445375 38.0 38.0 38.0 34.5 38.0 92-93 36.464 38.0 38.0 38.0 34.5 38.0 94-95 36.25325 38.0 38.0 38.0 34.0 38.0 96-97 35.03637500000001 38.0 37.5 38.0 30.5 38.0 98-99 33.008 38.0 35.5 38.0 13.0 38.0 100-101 30.811875 38.0 30.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 10 1.0 11 0.0 12 0.0 13 0.0 14 1.0 15 0.0 16 0.0 17 0.0 18 0.0 19 2.0 20 2.0 21 2.0 22 1.0 23 3.0 24 5.0 25 9.0 26 20.0 27 23.0 28 23.0 29 30.0 30 28.0 31 44.0 32 66.0 33 84.0 34 156.0 35 317.0 36 718.0 37 2465.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 31.175000000000004 20.75 14.725 33.35 2 29.675 37.724999999999994 16.55 16.05 3 30.65 18.05 31.75 19.55 4 26.056514128532132 28.207051762940733 12.028007001750437 33.708427106776696 5 44.85 17.625 19.775000000000002 17.75 6 20.275000000000002 39.800000000000004 23.125 16.8 7 45.800000000000004 21.4 19.85 12.950000000000001 8 19.8 15.475 45.65 19.075 9 16.3 45.9 18.15 19.650000000000002 10-11 36.7375 27.8125 19.537499999999998 15.9125 12-13 17.1125 17.875 20.25 44.7625 14-15 20.4625 33.3625 30.825000000000003 15.35 16-17 28.199999999999996 20.2625 36.225 15.312500000000002 18-19 34.35 25.9625 25.7125 13.975000000000001 20-21 15.687499999999998 24.95 40.0375 19.325 22-23 34.0375 26.2875 24.275 15.4 24-25 32.2625 30.2125 21.6875 15.837499999999999 26-27 36.762499999999996 27.0875 18.6875 17.4625 28-29 17.7875 37.1125 24.3875 20.7125 30-31 21.8125 14.899999999999999 40.4875 22.8 32-33 29.049999999999997 15.937499999999998 30.2875 24.725 34-35 31.7 25.35 27.55 15.4 36-37 36.6375 20.474999999999998 30.7625 12.125 38-39 24.962500000000002 19.45 34.699999999999996 20.8875 40-41 25.624999999999996 14.6125 27.750000000000004 32.0125 42-43 36.5 19.55 22.075 21.875 44-45 49.162499999999994 13.55 18.087500000000002 19.2 46-47 33.175 24.4875 15.662499999999998 26.674999999999997 48-49 25.4625 25.7875 17.7 31.05 50-51 30.3 26.575 9.0625 34.0625 52-53 28.1375 41.449999999999996 8.1125 22.3 54-55 21.4875 28.8375 19.650000000000002 30.025000000000002 56-57 12.85 31.45 16.925 38.775 58-59 17.3125 24.375 27.462500000000002 30.85 60-61 19.6375 27.1625 20.2875 32.9125 62-63 20.4375 24.212500000000002 21.25 34.1 64-65 11.4 26.025 36.0 26.575 66-67 19.025 21.5625 31.025000000000002 28.3875 68-69 25.2875 20.474999999999998 26.0 28.237499999999997 70-71 23.275000000000002 25.474999999999998 30.312499999999996 20.9375 72-73 22.8375 15.737499999999999 31.2625 30.162499999999998 74-75 19.037499999999998 12.65 29.325000000000003 38.987500000000004 76-77 20.6875 13.700000000000001 39.7625 25.85 78-79 22.275 10.6875 38.012499999999996 29.025000000000002 80-81 21.462500000000002 10.0 34.3375 34.2 82-83 26.087500000000002 7.074999999999999 37.8125 29.025000000000002 84-85 20.1125 5.0375000000000005 39.1 35.75 86-87 19.287499999999998 9.637500000000001 42.4375 28.6375 88-89 16.412499999999998 23.200000000000003 37.325 23.0625 90-91 13.325000000000001 27.8375 36.762499999999996 22.075 92-93 18.2875 35.4 29.5375 16.775000000000002 94-95 13.4125 53.075 23.075000000000003 10.4375 96-97 10.075000000000001 68.33749999999999 15.962499999999999 5.625 98-99 6.425 82.4875 7.375 3.7125 100-101 3.4250000000000003 88.3 5.5125 2.7625 >>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 2.5 35 3.0 36 1.0 37 3.5 38 5.0 39 5.0 40 6.0 41 26.0 42 79.0 43 156.5 44 424.0 45 586.0 46 406.5 47 347.5 48 330.0 49 230.0 50 242.0 51 305.0 52 300.5 53 193.0 54 95.5 55 84.0 56 69.0 57 34.0 58 27.0 59 18.5 60 8.0 61 5.5 62 3.0 63 1.5 64 0.0 65 0.5 66 0.5 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 0.0 3 0.0 4 0.025 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 53.474999999999994 #Duplication Level Percentage of deduplicated Percentage of total 1 88.26554464703132 47.199999999999996 2 4.301075268817205 4.6 3 2.0102851799906496 3.225 4 1.168770453482936 2.5 5 1.1220196353436185 3.0 6 0.18700327255726976 0.6 7 0.46750818139317435 1.7500000000000002 8 0.3740065451145395 1.6 9 0.18700327255726976 0.8999999999999999 >10 1.4492753623188406 13.65 >50 0.3272557269752221 11.95 >100 0.1402524544179523 9.025 >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 148 3.6999999999999997 No Hit GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 112 2.8000000000000003 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 101 2.5250000000000004 Illumina Small RNA Adapter 2 (100% over 21bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 98 2.45 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTGGAATTCTCGGGTGCCA 78 1.95 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTGGAATTCTCGGGTGCCAA 71 1.775 No Hit TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 67 1.675 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTTGGAATTCTCGGGTGC 56 1.4000000000000001 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTTGGAATTCTCGGGTG 55 1.375 No Hit CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 53 1.325 RNA PCR Primer, Index 1 (100% over 28bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 46 1.15 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 40 1.0 No Hit TCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTC 30 0.75 RNA PCR Primer, Index 1 (100% over 26bp) CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 24 0.6 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 23 0.575 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATGGAATTCTCGGGTGCCAAGGA 22 0.5499999999999999 RNA PCR Primer, Index 1 (100% over 22bp) AGAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTG 20 0.5 No Hit GAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTGC 19 0.475 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTTGGAATTCTCGGGTGC 19 0.475 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTGAATCTGGAATTC 19 0.475 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTTGGAATTCTCGGGTGCCA 18 0.44999999999999996 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTATGGAATTCTCGGGTGCCAA 18 0.44999999999999996 No Hit AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 17 0.42500000000000004 Illumina Small RNA Adapter 2 (100% over 21bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATGGAATTCTCGGGTG 17 0.42500000000000004 No Hit CGGTCGAGGGCACGCCTGCCTGGGCGTCACGCTGGAATTCTCGGGTGCCA 15 0.375 No Hit CATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAAC 15 0.375 RNA PCR Primer, Index 1 (100% over 24bp) CTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCA 15 0.375 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTTGGAATTCTCGGGTGCC 14 0.35000000000000003 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTGGAATTCTCGGGTG 13 0.325 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTTGGAATTCTCGGGTGCCAAG 13 0.325 No Hit TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTTAGGCATCTCGTATGC 13 0.325 RNA PCR Primer, Index 3 (100% over 50bp) GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 13 0.325 Illumina Small RNA Adapter 2 (100% over 21bp) TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 13 0.325 RNA PCR Primer, Index 1 (100% over 29bp) GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTTGGAATTCTCGGGTGC 13 0.325 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAAATGGAATTCTCGGGT 12 0.3 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTAATGGAATTCTCGGGTGC 11 0.27499999999999997 No Hit ACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCCA 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 28bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGATGGAATTCTC 11 0.27499999999999997 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTGGAATTCTCGGGTGCCAAGG 11 0.27499999999999997 Illumina Small RNA Adapter 2 (100% over 21bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGTGGAATTCTCGGGTGCC 11 0.27499999999999997 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTTGGAATTCTCGGGTGCCAA 10 0.25 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTAATCTGGAATTCT 9 0.22499999999999998 No Hit CTCTGATGATGATCAAACTAATACTTTCGTTCTTCTGGAATTCTCGGGTG 9 0.22499999999999998 No Hit CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 23bp) GGGGATATGGCGAAATCGGTAGACGCTACGGACTTTGGAATTCTCGGGTG 9 0.22499999999999998 No Hit AGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCC 8 0.2 RNA PCR Primer, Index 1 (100% over 27bp) AGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 8 0.2 No Hit TAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAG 8 0.2 RNA PCR Primer, Index 1 (100% over 29bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGGAATTCTCGGGTGC 8 0.2 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTAAATGGAATTCTCGGGTGCC 8 0.2 No Hit TGTCGTGCCAATTCAACATAAACCCCTGGAATTCTCGGGTGCCAAGGAAC 8 0.2 RNA PCR Primer, Index 1 (100% over 24bp) CAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTC 8 0.2 RNA PCR Primer, Index 1 (100% over 26bp) TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGG 8 0.2 No Hit ACCTGCTCTGATACCATGTTGTGATGGAATTCTCGGGTGCCAAGGAACTC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 26bp) TCCGTCGTAGTCTAGGTGGTTAGGATACTCTGGAATTCTCGGGTGCCAAG 7 0.17500000000000002 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGGAATTCTCGGGTGCCA 7 0.17500000000000002 No Hit GACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 23bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCAATGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit AAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit GCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 23bp) ATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACT 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 25bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTAAATGGAATTCTCGGGTG 7 0.17500000000000002 No Hit ATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 23bp) GGGATTGTAGTTCAATTGGACAGAGCACCGCCCTGGAATTCTCGGGTGCC 6 0.15 No Hit GAACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTC 6 0.15 RNA PCR Primer, Index 1 (100% over 26bp) CAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTG 6 0.15 No Hit GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGTTGGAATTCTCGGGT 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAATGGAATTCTCGGGTGCCA 5 0.125 No Hit TTCGGACCAGGCTTCATTCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 5 0.125 RNA PCR Primer, Index 1 (100% over 29bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCTGGAATTCTCGGG 5 0.125 No Hit TGTCGTGCCAATTCAACATAAACCCCTTGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTTGGAATTCT 5 0.125 No Hit GGGTGTTTGGTCTAGTGGTATGATTCTCGCTTGGAATTCTCGGGTGCCAA 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTATGGAATTCTCGGGTGCC 5 0.125 No Hit AACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCC 5 0.125 RNA PCR Primer, Index 1 (100% over 27bp) TGTCGTGCCAATTCAACATAAACCCTGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCAAAAATGGAATTCTCGGGT 5 0.125 No Hit TATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCG 5 0.125 No Hit CATCGAGTAGACCTTGCTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 5 0.125 No Hit GTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTTGGAATTCTCGGGTGCC 5 0.125 No Hit ATGCAGTTACTAATTCATGATCTGGCTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) AAGGGTGCTGAGAATACTTTGAATCTGACACTGGAATTCTCGGGTGCCAA 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTAAAATGGAATTCTCGGGT 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCAAATGGAATTCTCGGGTGC 5 0.125 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCATGGAATTCTCGGGTG 5 0.125 No Hit CTGCCACGATCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAA 5 0.125 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTGGAATTCTCGGGT 5 0.125 No Hit CATCGAGTAGACCTTGTTAATGTGAGAATTTGGAATTCTCGGGTGCCAAG 5 0.125 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGGAATTCTCGGGTGCCAA 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTAAAAATGGAATTCTCGGGTG 5 0.125 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCATGGAATTCTCGGGTGCC 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 0.325 0.0 0.0 0.0 2 0.0 0.35 0.0 0.0 0.0 3 0.0 0.35 0.0 0.0 0.0 4 0.0 0.35 0.0 0.0 0.0 5 0.0 0.35 0.0 0.0 0.0 6 0.0 0.375 0.0 0.0 0.0 7 0.0 0.375 0.0 0.0 0.0 8 0.0 0.375 0.0 0.0 0.0 9 0.0 0.4 0.0 0.0 0.0 10-11 0.0 0.42500000000000004 0.0 0.0 0.0 12-13 0.0 0.45 0.0 0.0 0.0 14-15 0.0 0.4875 0.0 0.0 0.0 16-17 0.0 0.5375 0.0 0.0 0.0 18-19 0.0 0.7125 0.0 0.0 0.0 20-21 0.0 1.2625 0.0 0.0 0.0 22-23 0.0 5.2625 0.0 0.0 0.0 24-25 0.0 14.35 0.0 0.0 0.0 26-27 0.0 24.275 0.0 0.0 0.0 28-29 0.0 29.512500000000003 0.0 0.0 0.0 30-31 0.0 43.075 0.0 0.0 0.0 32-33 0.0 59.349999999999994 0.0 0.0 0.0 34-35 0.0 75.0875 0.0 0.0 0.0 36-37 0.0 86.35 0.0 0.0 0.0 38-39 0.0 90.6125 0.0 0.0 0.0 40-41 0.0 93.375 0.0 0.0 0.0 42-43 0.0 95.5875 0.0 0.0 0.0 44-45 0.0 96.76249999999999 0.0 0.0 0.0 46-47 0.0 97.2375 0.0 0.0 0.0 48-49 0.0 97.38749999999999 0.0 0.0 0.0 50-51 0.0 97.4625 0.0 0.0 0.0 52-53 0.0 97.475 0.0 0.0 0.0 54-55 0.0 97.475 0.0 0.0 0.0 56-57 0.0 97.475 0.0 0.0 0.0 58-59 0.0 97.475 0.0 0.0 0.0 60-61 0.0 97.475 0.0 0.0 0.0 62-63 0.0 97.475 0.0 0.0 0.0 64-65 0.0 97.475 0.0 0.0 0.0 66-67 0.0 97.475 0.0 0.0 0.0 68-69 0.0 97.475 0.0 0.0 0.0 70-71 0.0 97.475 0.0 0.0 0.0 72-73 0.0 97.475 0.0 0.0 0.0 74-75 0.0 97.475 0.0 0.0 0.0 76-77 0.0 97.475 0.0 0.0 0.0 78-79 0.0 97.475 0.0 0.0 0.0 80-81 0.0 97.475 0.0 0.0 0.0 82-83 0.0 97.475 0.0 0.0 0.0 84-85 0.0 97.475 0.0 0.0 0.0 86-87 0.0 97.475 0.0 0.0 0.0 88-89 0.0 97.5 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TAGTTCA 40 5.456968E-12 95.00001 8 AGTTCAA 40 5.456968E-12 95.00001 9 GTAGTTC 40 5.456968E-12 95.00001 7 GTAGACC 75 0.0 95.0 7 TTGTAGT 30 9.458745E-9 95.0 5 AGTAGAC 75 0.0 95.0 6 GGCTGTA 15 6.142176E-4 95.0 4 TAGTTTA 15 6.142176E-4 95.0 9 GATTGTA 25 3.8289727E-7 95.0 3 GCTGTAG 15 6.142176E-4 95.0 5 GAGTAGA 75 0.0 95.0 5 ATTGTAG 30 9.458745E-9 95.0 4 GGGATTG 25 3.8289727E-7 95.0 1 CGAGTAG 75 0.0 95.0 4 GTGGCTG 15 6.142176E-4 95.0 2 GGTGGCT 15 6.142176E-4 95.0 1 AGACCTT 75 0.0 95.0 9 TCGAGTA 75 0.0 95.0 3 GTAGTTT 15 6.142176E-4 95.0 8 CTGTAGT 15 6.142176E-4 95.0 6 >>END_MODULE Rejected 279125 READS because READLEN < 1 Read 279125 spots for SRR6941570.sra Written 279125 spots for SRR6941570.sra Rejected 279125 READS because READLEN < 1 Read 279125 spots for SRR6941570.sra Written 279125 spots for SRR6941570.sra Rejected 279125 READS because READLEN < 1 Read 279125 spots for SRR6941570.sra Written 279125 spots for SRR6941570.sra Rejected 279125 READS because READLEN < 1 Read 279125 spots for SRR6941570.sra Written 279125 spots for SRR6941570.sra Rejected 279125 READS because READLEN < 1 Read 279125 spots for SRR6941570.sra Written 279125 spots for SRR6941570.sra Rejected 279125 READS because READLEN < 1 Read 279125 spots for SRR6941570.sra Written 279125 spots for SRR6941570.sra Rejected 279125 READS because READLEN < 1 Read 279125 spots for SRR6941570.sra Written 279125 spots for SRR6941570.sra Rejected 279125 READS because READLEN < 1 Read 279125 spots for SRR6941570.sra Written 279125 spots for SRR6941570.sra Rejected 279125 READS because READLEN < 1 Read 279125 spots for SRR6941570.sra Written 279125 spots for SRR6941570.sra Rejected 279125 READS because READLEN < 1 Read 279125 spots for SRR6941570.sra Written 279125 spots for SRR6941570.sra Rejected 279125 READS because READLEN < 1 Read 279125 spots for SRR6941570.sra Written 279125 spots for SRR6941570.sra Rejected 279125 READS because READLEN < 1 Read 279125 spots for SRR6941570.sra Written 279125 spots for SRR6941570.sra Rejected 279125 READS because READLEN < 1 Read 279125 spots for SRR6941570.sra Written 279125 spots for SRR6941570.sra Rejected 279125 READS because READLEN < 1 Read 279125 spots for SRR6941570.sra Written 279125 spots for SRR6941570.sra Rejected 279125 READS because READLEN < 1 Read 279125 spots for SRR6941570.sra Written 279125 spots for SRR6941570.sra Rejected 279140 READS because READLEN < 1 Read 279140 spots for SRR6941570.sra Written 279140 spots for SRR6941570.sra Rejected 279125 READS because READLEN < 1 Read 279125 spots for SRR6941570.sra Written 279125 spots for SRR6941570.sra Rejected 279125 READS because READLEN < 1 Read 279125 spots for SRR6941570.sra Written 279125 spots for SRR6941570.sra Rejected 279125 READS because READLEN < 1 Read 279125 spots for SRR6941570.sra Written 279125 spots for SRR6941570.sra Rejected 279125 READS because READLEN < 1 Read 279125 spots for SRR6941570.sra Written 279125 spots for SRR6941570.sra SRR ids: ['SRR6941570.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_5otmxwkb SRR6941570.sra spots: 5582515 blocks: [[1, 279125], [279126, 558250], [558251, 837375], [837376, 1116500], [1116501, 1395625], [1395626, 1674750], [1674751, 1953875], [1953876, 2233000], [2233001, 2512125], [2512126, 2791250], [2791251, 3070375], [3070376, 3349500], [3349501, 3628625], [3628626, 3907750], [3907751, 4186875], [4186876, 4466000], [4466001, 4745125], [4745126, 5024250], [5024251, 5303375], [5303376, 5582515]] SRR6941570 file size 1333491 SRR6941570 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 SRR6941570 SRR6941570_1.fastq Input file: SRR6941570_1.fastq trimmed: SRR6941570-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 11:41:21 2024 >> started Fri Dec 6 11:41:25 2024 >> done (4.404s) 5582515 reads processed; of these: 73 ( 0.00%) short reads filtered out after trimming by size control 15 ( 0.00%) empty reads filtered out after trimming by size control 5582427 (100.00%) reads available; of these: 644903 (11.55%) trimmed reads available after processing 4937524 (88.45%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 6 0.00% 19 8 0.00% 20 4 0.00% 21 9 0.00% 22 5 0.00% 23 8 0.00% 24 14 0.00% 25 10 0.00% 26 12 0.00% 27 25 0.00% 28 28 0.00% 29 36 0.00% 30 41 0.00% 31 37 0.00% 32 53 0.00% 33 37 0.00% 34 38 0.00% 35 59 0.00% 36 56 0.00% 37 69 0.00% 38 71 0.00% 39 85 0.00% 40 122 0.00% 41 105 0.00% 42 132 0.00% 43 147 0.00% 44 127 0.00% 45 158 0.00% 46 154 0.00% 47 154 0.00% 48 147 0.00% 49 153 0.00% 50 144 0.00% 51 132 0.00% 52 103 0.00% 53 79 0.00% 54 74 0.00% 55 60 0.00% 56 33 0.00% 57 33 0.00% 58 31 0.00% 59 33 0.00% 60 48 0.00% 61 60 0.00% 62 64 0.00% 63 56 0.00% 64 62 0.00% 65 53 0.00% 66 69 0.00% 67 93 0.00% 68 141 0.00% 69 167 0.00% 70 258 0.00% 71 255 0.00% 72 307 0.01% 73 840 0.02% 74 5155 0.09% 75 3301 0.06% 76 1171 0.02% 77 438 0.01% 78 553 0.01% 79 597 0.01% 80 698 0.01% 81 673 0.01% 82 751 0.01% 83 912 0.02% 84 1376 0.02% 85 1544 0.03% 86 1786 0.03% 87 2000 0.04% 88 2382 0.04% 89 3194 0.06% 90 4060 0.07% 91 6115 0.11% 92 8387 0.15% 93 15547 0.28% 94 26456 0.47% 95 62584 1.12% 96 72263 1.29% 97 82667 1.48% 98 131148 2.35% 99 142533 2.55% 100 61307 1.10% 101 4937524 88.45% 5582427 reads passed initial QC criterion=sequence-density sequence-density=97.54 sequence-density-rank=1 fanout-score=25.85 fanout-score-rank=1 prefix-density=97.72 prefix-fanout=25.8 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTTAGGCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAA criterion=fanout-score sequence-density=97.54 sequence-density-rank=1 fanout-score=25.85 fanout-score-rank=1 prefix-density=97.72 prefix-fanout=25.8 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTTAGGCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAA 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTTAGGCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAA -o SRR6941570 - Input file: STDIN trimmed: SRR6941570-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTTAGGCATCTCGTATGCCGTCTTCTGCTTGA -- 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 11:41:38 2024 >> started Fri Dec 6 11:41:46 2024 >> done (8.061s) 5468500 reads processed; of these: 22792 ( 0.42%) short reads filtered out after trimming by size control 18572 ( 0.34%) empty reads filtered out after trimming by size control 5427136 (99.24%) reads available; of these: 5393423 (99.38%) trimmed reads available after processing 33713 ( 0.62%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 9465 0.17% 19 22881 0.42% 20 31484 0.58% 21 141316 2.60% 22 146213 2.69% 23 115372 2.13% 24 615425 11.34% 25 149551 2.76% 26 147584 2.72% 27 142210 2.62% 28 144637 2.67% 29 371974 6.85% 30 645806 11.90% 31 440000 8.11% 32 426763 7.86% 33 432503 7.97% 34 366093 6.75% 35 321859 5.93% 36 178475 3.29% 37 123664 2.28% 38 82213 1.51% 39 65692 1.21% 40 68601 1.26% 41 72974 1.34% 42 60432 1.11% 43 19083 0.35% 44 20336 0.37% 45 14142 0.26% 46 4626 0.09% 47 5741 0.11% 48 2341 0.04% 49 1193 0.02% 50 681 0.01% 51 521 0.01% 52 288 0.01% 53 212 0.00% 54 152 0.00% 55 142 0.00% 56 72 0.00% 57 73 0.00% 58 48 0.00% 59 31 0.00% 60 33 0.00% 61 30 0.00% 62 29 0.00% 63 27 0.00% 64 25 0.00% 65 16 0.00% 66 20 0.00% 67 21 0.00% 68 46 0.00% 69 39 0.00% 70 79 0.00% 71 67 0.00% 72 41 0.00% 73 66 0.00% 74 74 0.00% 75 102 0.00% 76 120 0.00% 77 313 0.01% 78 88 0.00% 79 130 0.00% 80 270 0.00% 81 113 0.00% 82 241 0.00% 83 183 0.00% 84 107 0.00% 85 91 0.00% 86 106 0.00% 87 154 0.00% 88 111 0.00% 89 113 0.00% 90 121 0.00% 91 241 0.00% 92 198 0.00% 93 245 0.00% 94 275 0.01% 95 308 0.01% 96 317 0.01% 97 345 0.01% 98 615 0.01% 99 437 0.01% 100 500 0.01% 101 27810 0.51% criterion=sequence-density sequence-density=20.25 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=14 prefix-density=0.00 prefix-fanout=1.0 sequence=CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAA criterion=fanout-score sequence-density=0.42 sequence-density-rank=10 fanout-score=47.58 fanout-score-rank=1 prefix-density=20.00 prefix-fanout=1.0 sequence=ATTGTGAGAATAAAAAA Started job on | Dec 06 11:42:01 Started mapping on | Dec 06 11:42:02 Finished on | Dec 06 11:42:19 Mapping speed, Million of reads per hour | 1173.40 Number of input reads | 5541063 Average input read length | 32 UNIQUE READS: Uniquely mapped reads number | 772820 Uniquely mapped reads % | 13.95% Average mapped length | 27.12 Number of splices: Total | 6377 Number of splices: Annotated (sjdb) | 4078 Number of splices: GT/AG | 5872 Number of splices: GC/AG | 290 Number of splices: AT/AC | 6 Number of splices: Non-canonical | 209 Mismatch rate per base, % | 0.13% Deletion rate per base | 0.00% Deletion average length | 1.56 Insertion rate per base | 0.00% Insertion average length | 1.07 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 3439378 % of reads mapped to multiple loci | 62.07% Number of reads mapped to too many loci | 1124196 % of reads mapped to too many loci | 20.29% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.21% % of reads unmapped: other | 0.48% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1328865 1328865 1328865 N_multimapping 3439378 3439378 3439378 N_noFeature 480544 575310 674591 N_ambiguous 9376 5772 166 UnstrandedReadsAssigned:282900 PositiveStrandReadsAssigned:191738 NegativeStrandReadsAssigned:98063 Dataset is classified unstranded MeadianReadLen=31 20thPercentileLength=25 echo kmer=21 SRR6941570 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: SRR6941570-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 5,541,063 reads, 2,258,973 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 892 rounds 52973 SRR6941570.ke.tsv 35125 SRR6941570.se.tsv 88098 total ==> SRR6941570.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 1 0.323094 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 16.6937 3.00165 KQK14071 474 375 0 0 ==> SRR6941570.se.tsv <== BRADI_1g14170v3 28 BRADI_1g53295v3 0 BRADI_1g59795v3 0 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 2 BRADI_1g74790v3 8 BRADI_1g09890v3 0 BRADI_1g77505v3 0 BRADI_1g48960v3 0 SRR6941570 completed mapping pipeline successfully