Starting /dee2/code/volunteer_pipeline.sh SRR6941569 current disk space = 1551166423040 free memory = 1604059976 SRR6941569 SRAfilesize 9a35c953405dd288bdf7f68bb953092a SRR6941569.sra SRR6941569.sra file validated SRR6941569 is single end SRR6941569 is conventional basespace SRR6941569 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6941569_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 101 %GC 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.24275 34.0 33.0 34.0 32.0 34.0 2 33.32325 34.0 33.0 34.0 33.0 34.0 3 33.1335 34.0 33.0 34.0 31.0 34.0 4 33.249 34.0 33.0 34.0 32.0 34.0 5 33.23825 34.0 33.0 34.0 33.0 34.0 6 37.11175 38.0 37.0 38.0 36.0 38.0 7 37.4475 38.0 38.0 38.0 37.0 38.0 8 37.56525 38.0 38.0 38.0 38.0 38.0 9 37.6065 38.0 38.0 38.0 38.0 38.0 10-11 37.529125 38.0 38.0 38.0 38.0 38.0 12-13 37.460499999999996 38.0 38.0 38.0 38.0 38.0 14-15 37.494125 38.0 38.0 38.0 37.5 38.0 16-17 36.181375 38.0 37.5 38.0 32.0 38.0 18-19 36.888625000000005 38.0 38.0 38.0 33.5 38.0 20-21 36.146375000000006 38.0 38.0 38.0 30.0 38.0 22-23 37.291875000000005 38.0 38.0 38.0 36.5 38.0 24-25 37.514875 38.0 38.0 38.0 37.0 38.0 26-27 37.444625 38.0 38.0 38.0 37.5 38.0 28-29 37.498374999999996 38.0 38.0 38.0 38.0 38.0 30-31 37.36775 38.0 38.0 38.0 37.0 38.0 32-33 37.2545 38.0 38.0 38.0 37.0 38.0 34-35 37.2685 38.0 38.0 38.0 37.0 38.0 36-37 37.21525 38.0 38.0 38.0 36.5 38.0 38-39 37.196749999999994 38.0 38.0 38.0 37.0 38.0 40-41 37.112875 38.0 38.0 38.0 37.0 38.0 42-43 37.1485 38.0 38.0 38.0 37.0 38.0 44-45 37.17725 38.0 38.0 38.0 37.0 38.0 46-47 37.049125000000004 38.0 38.0 38.0 36.5 38.0 48-49 37.123000000000005 38.0 38.0 38.0 37.0 38.0 50-51 37.040375 38.0 38.0 38.0 36.0 38.0 52-53 37.021875 38.0 38.0 38.0 36.0 38.0 54-55 37.080625 38.0 38.0 38.0 36.0 38.0 56-57 37.054249999999996 38.0 38.0 38.0 36.0 38.0 58-59 37.191625 38.0 38.0 38.0 37.0 38.0 60-61 37.066375 38.0 38.0 38.0 37.0 38.0 62-63 36.738875 38.0 38.0 38.0 35.0 38.0 64-65 36.380125 38.0 37.5 38.0 33.5 38.0 66-67 36.035125 38.0 37.5 38.0 31.5 38.0 68-69 36.723875 38.0 38.0 38.0 35.0 38.0 70-71 36.23725 38.0 37.5 38.0 32.0 38.0 72-73 35.81725 38.0 37.0 38.0 29.5 38.0 74-75 35.737624999999994 38.0 37.0 38.0 29.0 38.0 76-77 35.97875 38.0 37.5 38.0 32.0 38.0 78-79 36.26625 38.0 38.0 38.0 33.5 38.0 80-81 36.682500000000005 38.0 38.0 38.0 35.5 38.0 82-83 36.726 38.0 38.0 38.0 36.0 38.0 84-85 36.661625 38.0 38.0 38.0 35.5 38.0 86-87 36.451875 38.0 38.0 38.0 34.5 38.0 88-89 36.445125000000004 38.0 38.0 38.0 35.0 38.0 90-91 36.488875 38.0 38.0 38.0 35.0 38.0 92-93 36.2775 38.0 38.0 38.0 34.5 38.0 94-95 35.774375 38.0 38.0 38.0 34.0 38.0 96-97 33.522625000000005 38.0 36.5 38.0 13.5 38.0 98-99 30.65025 38.0 30.0 38.0 2.0 38.0 100-101 27.637875 38.0 24.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 17 1.0 18 0.0 19 2.0 20 1.0 21 2.0 22 2.0 23 4.0 24 5.0 25 13.0 26 13.0 27 23.0 28 23.0 29 35.0 30 35.0 31 49.0 32 74.0 33 94.0 34 191.0 35 449.0 36 769.0 37 2215.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 26.650000000000002 23.625 15.075 34.65 2 24.7935951963973 41.65624218163623 16.537403052289218 17.012759569677257 3 26.400000000000002 17.05 36.85 19.7 4 22.85 26.3 12.45 38.4 5 47.699999999999996 18.425 18.4 15.475 6 17.5 45.050000000000004 22.05 15.4 7 47.9 18.224999999999998 20.5 13.375 8 17.974999999999998 15.675 48.475 17.875 9 16.7 48.699999999999996 17.599999999999998 17.0 10-11 37.1 31.075000000000003 16.900000000000002 14.924999999999999 12-13 16.4875 16.162499999999998 19.412499999999998 47.9375 14-15 17.825 31.65 36.1125 14.4125 16-17 29.025000000000002 18.25 39.5125 13.212499999999999 18-19 31.887500000000003 26.3625 29.037499999999998 12.712499999999999 20-21 13.5625 23.875 44.5375 18.025 22-23 34.65 23.175 28.012500000000003 14.1625 24-25 33.35 30.599999999999998 22.5625 13.487499999999999 26-27 42.025 28.825 16.537499999999998 12.612499999999999 28-29 12.975 42.0875 26.85 18.087500000000002 30-31 17.875 10.237499999999999 49.5 22.3875 32-33 31.95 12.712499999999999 30.125 25.2125 34-35 35.6625 24.349999999999998 23.6125 16.375 36-37 40.7375 17.6375 28.9875 12.6375 38-39 23.6875 17.1875 35.362500000000004 23.7625 40-41 24.95 15.387500000000001 21.462500000000002 38.2 42-43 37.775 27.237499999999997 16.6875 18.3 44-45 51.74999999999999 15.6375 14.899999999999999 17.712500000000002 46-47 26.337500000000002 29.75 14.475 29.4375 48-49 19.5 27.950000000000003 17.6625 34.887499999999996 50-51 29.2 25.75 8.575000000000001 36.475 52-53 27.5625 44.65 6.6625000000000005 21.125 54-55 15.675 28.825 21.475 34.025 56-57 8.612499999999999 35.2625 10.925 45.2 58-59 17.65 31.7125 15.55 35.0875 60-61 24.1375 29.575000000000003 18.3 27.987499999999997 62-63 21.075 26.3625 25.3125 27.250000000000004 64-65 9.0375 35.1625 23.75 32.05 66-67 18.099999999999998 25.362499999999997 24.175 32.3625 68-69 29.7 23.962500000000002 22.237499999999997 24.099999999999998 70-71 22.3625 27.425 34.1875 16.025 72-73 25.3125 13.075000000000001 36.525 25.087500000000002 74-75 20.3375 9.1 28.487499999999997 42.075 76-77 21.3125 13.1625 43.6375 21.8875 78-79 20.025000000000002 9.325 41.7625 28.8875 80-81 21.375 8.8125 33.050000000000004 36.762499999999996 82-83 27.975 6.9125000000000005 39.225 25.887500000000003 84-85 18.212500000000002 8.0625 40.1625 33.5625 86-87 18.387500000000003 16.075 41.275 24.2625 88-89 14.8375 36.7875 30.112499999999997 18.2625 90-91 10.15 41.462500000000006 30.2375 18.15 92-93 16.3625 47.75 24.099999999999998 11.7875 94-95 10.8875 66.0875 16.037499999999998 6.987500000000001 96-97 7.3999999999999995 79.625 9.9875 2.9875 98-99 4.6125 89.25 3.7624999999999997 2.375 100-101 2.075 92.07499999999999 3.075 2.775 >>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 3.5 35 6.0 36 3.5 37 2.5 38 4.0 39 7.5 40 22.0 41 51.0 42 116.5 43 260.0 44 644.0 45 799.5 46 487.0 47 324.0 48 252.5 49 146.5 50 162.5 51 209.0 52 195.5 53 130.0 54 62.0 55 41.0 56 29.5 57 11.0 58 12.5 59 7.5 60 1.5 61 1.5 62 0.5 63 0.0 64 0.0 65 1.5 66 2.0 67 1.0 68 0.5 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 47.025 #Duplication Level Percentage of deduplicated Percentage of total 1 87.08133971291866 40.949999999999996 2 4.9973418394471025 4.7 3 2.2328548644338118 3.15 4 1.1164274322169059 2.1 5 0.531632110579479 1.25 6 0.5847953216374269 1.6500000000000001 7 0.3189792663476874 1.05 8 0.2658160552897395 1.0 9 0.21265284423179162 0.8999999999999999 >10 2.1796916533758637 20.125 >50 0.3189792663476874 11.575000000000001 >100 0.1594896331738437 11.55 >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 212 5.3 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 144 3.5999999999999996 Illumina Small RNA Adapter 2 (100% over 21bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTGGAATTCTCGGGTGCCAA 106 2.65 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 94 2.35 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTGGAATTCTCGGGTGCCA 87 2.175 No Hit GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 83 2.075 No Hit CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 80 2.0 RNA PCR Primer, Index 1 (100% over 28bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTTGGAATTCTCGGGTG 65 1.625 No Hit TCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTC 54 1.35 RNA PCR Primer, Index 1 (100% over 26bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTTGGAATTCTCGGGTGC 48 1.2 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 46 1.15 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 42 1.05 No Hit TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 41 1.0250000000000001 No Hit TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 39 0.975 RNA PCR Primer, Index 1 (100% over 29bp) CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 36 0.8999999999999999 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTATGGAATTCTCGGGTGCCAA 30 0.75 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATGGAATTCTCGGGTGCCAAGGA 29 0.7250000000000001 RNA PCR Primer, Index 1 (100% over 22bp) ACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCCA 27 0.675 RNA PCR Primer, Index 1 (100% over 28bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTTGGAATTCTCGGGTGCCA 26 0.65 No Hit ACCTGCTCTGATACCATGTTGTGATGGAATTCTCGGGTGCCAAGGAACTC 21 0.525 RNA PCR Primer, Index 1 (100% over 26bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATGGAATTCTCGGGTG 20 0.5 No Hit GAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTGC 18 0.44999999999999996 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 18 0.44999999999999996 Illumina Small RNA Adapter 2 (100% over 21bp) TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACAGTGATCTCGTATGC 18 0.44999999999999996 RNA PCR Primer, Index 5 (100% over 50bp) ATATTGGGTAGGTTGTGGTATTTCATTGCTGGAATTCTCGGGTGCCAAGG 18 0.44999999999999996 Illumina Small RNA Adapter 2 (100% over 21bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTATGGAATTCTCGGGTGCC 17 0.42500000000000004 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTTGGAATTCTCGGGTGCC 17 0.42500000000000004 No Hit TGTCGTGCCAATTCAACATAAACCCCTGGAATTCTCGGGTGCCAAGGAAC 17 0.42500000000000004 RNA PCR Primer, Index 1 (100% over 24bp) ATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACT 17 0.42500000000000004 RNA PCR Primer, Index 1 (100% over 25bp) ATATTGGGTAGGTTGTGGTATTTCATTGCTTGGAATTCTCGGGTGCCAAG 16 0.4 No Hit TAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAG 16 0.4 RNA PCR Primer, Index 1 (100% over 29bp) CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTA 16 0.4 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTAATGGAATTCTCGGGTGC 15 0.375 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 14 0.35000000000000003 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 13 0.325 Illumina Small RNA Adapter 2 (100% over 21bp) GACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACG 13 0.325 No Hit AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 13 0.325 Illumina Small RNA Adapter 2 (100% over 21bp) CGGTCGAGGGCACGCCTGCCTGGGCGTCACGCTGGAATTCTCGGGTGCCA 12 0.3 No Hit CATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAAC 12 0.3 RNA PCR Primer, Index 1 (100% over 24bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGTGGAATTCTCGGGTGCC 12 0.3 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAAATGGAATTCTCGGGT 11 0.27499999999999997 No Hit AGAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTG 11 0.27499999999999997 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTTGGAATTCTCGGGTGC 11 0.27499999999999997 No Hit GAACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTC 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 26bp) AACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCC 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 27bp) GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTTGGAATTCTCGGGTGC 11 0.27499999999999997 No Hit ACGAACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAAC 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 24bp) GAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 33bp) TTCGGACCAGGCTTCATTCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 10 0.25 RNA PCR Primer, Index 1 (100% over 29bp) CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 10 0.25 RNA PCR Primer, Index 1 (100% over 23bp) TCCGTCGTAGTCTAGGTGGTTAGGATACTCTGGAATTCTCGGGTGCCAAG 9 0.22499999999999998 No Hit TTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 31bp) GGGTGTTTGGTCTAGTGGTATGATTCTCGCTTGGAATTCTCGGGTGCCAA 9 0.22499999999999998 No Hit CCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCC 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 27bp) CATCGAGTAGACCTTGTTATTGTGAGAATAAATGGAATTCTCGGGTGCCA 8 0.2 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAAAAATGGAATTCTCGGGTG 8 0.2 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGGAATTCTCGGGTGCCA 8 0.2 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGATGGAATTCTC 8 0.2 No Hit TTGACAGAAGAGAGTGAGCACTGGAATTCTCGGGTGCCAAGGAACTCCAG 8 0.2 RNA PCR Primer, Index 1 (100% over 29bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGGAATTCTCGGGTGC 7 0.17500000000000002 No Hit GGGGATATGGCGAAATCGGTAGACGCTACGGACTTTGGAATTCTCGGGTG 7 0.17500000000000002 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCAATGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTGAATCTGGAATTC 7 0.17500000000000002 No Hit ACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGT 7 0.17500000000000002 No Hit AAGGGTGCTGAGAATACTTTGAATCTGACACTGGAATTCTCGGGTGCCAA 7 0.17500000000000002 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTAAAATGGAATTCTCGGGTGC 6 0.15 No Hit GGTAGTTCGACCGCGGAATTTGGAATTCTCGGGTGCCAAGGAACTCCAGT 6 0.15 RNA PCR Primer, Index 1 (100% over 30bp) CGAACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACT 6 0.15 RNA PCR Primer, Index 1 (100% over 25bp) CATCGAGTAGACCTTGATATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 6 0.15 Illumina Small RNA Adapter 2 (100% over 21bp) TCCCGTGCTGTAAAATAACTGATTTGCCTATCTGATCTGGAATTCTCGGG 6 0.15 No Hit TCTCATGGAGAGTTCGATCCTGGCTTGGAATTCTCGGGTGCCAAGGAACT 6 0.15 RNA PCR Primer, Index 1 (100% over 25bp) ATGCAGTTACTAATTCATGATCTGGCTGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) CATCGAGTAGACCTTGTTATTGTGAGAATTAATGGAATTCTCGGGTGCCA 6 0.15 No Hit CATCGAGTAGACCTTGATATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 6 0.15 No Hit CATCGAGTAGACCTTGTTAATGTGAGAATTTGGAATTCTCGGGTGCCAAG 6 0.15 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCATGGAATTCTCGGGTGCC 6 0.15 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTGGAATTCTCGGGT 5 0.125 No Hit AGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCC 5 0.125 RNA PCR Primer, Index 1 (100% over 27bp) TGACAGAAGAGAGTGAGCACTGGAATTCTCGGGTGCCAAGGAACTCCAGT 5 0.125 RNA PCR Primer, Index 1 (100% over 30bp) TGAAGCTGCCAGCATGATCTGATGGAATTCTCGGGTGCCAAGGAACTCCA 5 0.125 RNA PCR Primer, Index 1 (100% over 28bp) GGGATTGTAGTTCAATAGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 5 0.125 No Hit CATCGAGTAGACCTTGTTAATGTGAGAATTGGAATTCTCGGGTGCCAAGG 5 0.125 Illumina Small RNA Adapter 2 (100% over 21bp) CAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTG 5 0.125 No Hit CATCGAGTAGACCTTGTTACTGTGAGAATTTGGAATTCTCGGGTGCCAAG 5 0.125 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGAATTCTCGGGTGCCAAGGAACTCCA 5 0.125 RNA PCR Primer, Index 1 (100% over 28bp) 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 0.55 0.0 0.0 0.0 2 0.0 0.575 0.0 0.0 0.0 3 0.0 0.575 0.0 0.0 0.0 4 0.0 0.575 0.0 0.0 0.0 5 0.0 0.575 0.0 0.0 0.0 6 0.0 0.575 0.0 0.0 0.0 7 0.0 0.575 0.0 0.0 0.0 8 0.0 0.6 0.0 0.0 0.0 9 0.0 0.6 0.0 0.0 0.0 10-11 0.0 0.6375 0.0 0.0 0.0 12-13 0.0 0.7375 0.0 0.0 0.0 14-15 0.0 0.8125 0.0 0.0 0.0 16-17 0.0 1.0625 0.0 0.0 0.0 18-19 0.0 1.9375 0.0 0.0 0.0 20-21 0.0 3.2375 0.0 0.0 0.0 22-23 0.0 11.3625 0.0 0.0 0.0 24-25 0.0 25.3 0.0 0.0 0.0 26-27 0.0 38.1875 0.0 0.0 0.0 28-29 0.0 41.7375 0.0 0.0 0.0 30-31 0.0 55.625 0.0 0.0 0.0 32-33 0.0 71.61250000000001 0.0 0.0 0.0 34-35 0.0 84.375 0.0 0.0 0.0 36-37 0.0 92.025 0.0 0.0 0.0 38-39 0.0 94.125 0.0 0.0 0.0 40-41 0.0 94.775 0.0 0.0 0.0 42-43 0.0 95.5875 0.0 0.0 0.0 44-45 0.0 95.925 0.0 0.0 0.0 46-47 0.0 96.05 0.0 0.0 0.0 48-49 0.0 96.075 0.0 0.0 0.0 50-51 0.0 96.075 0.0 0.0 0.0 52-53 0.0 96.075 0.0 0.0 0.0 54-55 0.0 96.075 0.0 0.0 0.0 56-57 0.0 96.075 0.0 0.0 0.0 58-59 0.0 96.075 0.0 0.0 0.0 60-61 0.0 96.075 0.0 0.0 0.0 62-63 0.0 96.075 0.0 0.0 0.0 64-65 0.0 96.075 0.0 0.0 0.0 66-67 0.0 96.075 0.0 0.0 0.0 68-69 0.0 96.075 0.0 0.0 0.0 70-71 0.0 96.0875 0.0 0.0 0.0 72-73 0.0 96.1 0.0 0.0 0.0 74-75 0.0 96.1 0.0 0.0 0.0 76-77 0.0 96.125 0.0 0.0 0.0 78-79 0.0 96.2125 0.0 0.0 0.0 80-81 0.0 96.275 0.0 0.0 0.0 82-83 0.0 96.32499999999999 0.0 0.0 0.0 84-85 0.0 96.4 0.0 0.0 0.0 86-87 0.0 96.4125 0.0 0.0 0.0 88-89 0.0 96.425 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 GTAGACC 110 0.0 95.0 7 TTGTAGT 30 9.458745E-9 95.0 5 AGTAGAC 110 0.0 95.0 6 TAGCCAA 15 6.142176E-4 95.0 9 CGGATGT 15 6.142176E-4 95.0 3 GCGGATG 15 6.142176E-4 95.0 2 GATTGTA 30 9.458745E-9 95.0 3 GAGTAGA 110 0.0 95.0 5 ATTGTAG 30 9.458745E-9 95.0 4 TGTAGCC 15 6.142176E-4 95.0 7 GGGATTG 30 9.458745E-9 95.0 1 CGAGTAG 110 0.0 95.0 4 AGACCTT 110 0.0 95.0 9 TCGAGTA 110 0.0 95.0 3 TAGACCT 110 0.0 95.0 8 GTAGCCA 15 6.142176E-4 95.0 8 GGCGGAT 15 6.142176E-4 95.0 1 GTAGTTC 45 1.6370905E-11 84.44444 7 >>END_MODULE Rejected 290912 READS because READLEN < 1 Read 290912 spots for SRR6941569.sra Written 290912 spots for SRR6941569.sra Rejected 290912 READS because READLEN < 1 Read 290912 spots for SRR6941569.sra Written 290912 spots for SRR6941569.sra Rejected 290912 READS because READLEN < 1 Read 290912 spots for SRR6941569.sra Written 290912 spots for SRR6941569.sra Rejected 290912 READS because READLEN < 1 Read 290912 spots for SRR6941569.sra Written 290912 spots for SRR6941569.sra Rejected 290912 READS because READLEN < 1 Read 290912 spots for SRR6941569.sra Written 290912 spots for SRR6941569.sra Rejected 290912 READS because READLEN < 1 Read 290912 spots for SRR6941569.sra Written 290912 spots for SRR6941569.sra Rejected 290912 READS because READLEN < 1 Read 290912 spots for SRR6941569.sra Written 290912 spots for SRR6941569.sra Rejected 290912 READS because READLEN < 1 Read 290912 spots for SRR6941569.sra Written 290912 spots for SRR6941569.sra Rejected 290912 READS because READLEN < 1 Read 290912 spots for SRR6941569.sra Written 290912 spots for SRR6941569.sra Rejected 290912 READS because READLEN < 1 Read 290912 spots for SRR6941569.sra Written 290912 spots for SRR6941569.sra Rejected 290912 READS because READLEN < 1 Read 290912 spots for SRR6941569.sra Written 290912 spots for SRR6941569.sra Rejected 290912 READS because READLEN < 1 Read 290912 spots for SRR6941569.sra Written 290912 spots for SRR6941569.sra Rejected 290912 READS because READLEN < 1 Read 290912 spots for SRR6941569.sra Written 290912 spots for SRR6941569.sra Rejected 290912 READS because READLEN < 1 Read 290912 spots for SRR6941569.sra Written 290912 spots for SRR6941569.sra Rejected 290924 READS because READLEN < 1 Read 290924 spots for SRR6941569.sra Written 290924 spots for SRR6941569.sra Rejected 290912 READS because READLEN < 1 Read 290912 spots for SRR6941569.sra Written 290912 spots for SRR6941569.sra Rejected 290912 READS because READLEN < 1 Read 290912 spots for SRR6941569.sra Written 290912 spots for SRR6941569.sra Rejected 290912 READS because READLEN < 1 Read 290912 spots for SRR6941569.sra Written 290912 spots for SRR6941569.sra Rejected 290912 READS because READLEN < 1 Read 290912 spots for SRR6941569.sra Written 290912 spots for SRR6941569.sra Rejected 290912 READS because READLEN < 1 Read 290912 spots for SRR6941569.sra Written 290912 spots for SRR6941569.sra SRR ids: ['SRR6941569.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_cn34nj54 SRR6941569.sra spots: 5818252 blocks: [[1, 290912], [290913, 581824], [581825, 872736], [872737, 1163648], [1163649, 1454560], [1454561, 1745472], [1745473, 2036384], [2036385, 2327296], [2327297, 2618208], [2618209, 2909120], [2909121, 3200032], [3200033, 3490944], [3490945, 3781856], [3781857, 4072768], [4072769, 4363680], [4363681, 4654592], [4654593, 4945504], [4945505, 5236416], [5236417, 5527328], [5527329, 5818252]] SRR6941569 file size 1389893 SRR6941569 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 SRR6941569 SRR6941569_1.fastq Input file: SRR6941569_1.fastq trimmed: SRR6941569-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 11:40:38 2024 >> started Fri Dec 6 11:40:42 2024 >> done (3.816s) 5818252 reads processed; of these: 86 ( 0.00%) short reads filtered out after trimming by size control 18 ( 0.00%) empty reads filtered out after trimming by size control 5818148 (100.00%) reads available; of these: 975468 (16.77%) trimmed reads available after processing 4842680 (83.23%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 11 0.00% 19 2 0.00% 20 11 0.00% 21 9 0.00% 22 15 0.00% 23 10 0.00% 24 12 0.00% 25 19 0.00% 26 21 0.00% 27 21 0.00% 28 32 0.00% 29 49 0.00% 30 53 0.00% 31 35 0.00% 32 33 0.00% 33 46 0.00% 34 51 0.00% 35 55 0.00% 36 46 0.00% 37 59 0.00% 38 40 0.00% 39 40 0.00% 40 48 0.00% 41 52 0.00% 42 64 0.00% 43 76 0.00% 44 67 0.00% 45 99 0.00% 46 98 0.00% 47 70 0.00% 48 64 0.00% 49 62 0.00% 50 68 0.00% 51 54 0.00% 52 57 0.00% 53 37 0.00% 54 45 0.00% 55 39 0.00% 56 40 0.00% 57 49 0.00% 58 44 0.00% 59 43 0.00% 60 58 0.00% 61 53 0.00% 62 54 0.00% 63 49 0.00% 64 67 0.00% 65 53 0.00% 66 69 0.00% 67 80 0.00% 68 158 0.00% 69 180 0.00% 70 253 0.00% 71 249 0.00% 72 460 0.01% 73 1383 0.02% 74 9501 0.16% 75 6129 0.11% 76 1866 0.03% 77 620 0.01% 78 864 0.01% 79 812 0.01% 80 977 0.02% 81 957 0.02% 82 1249 0.02% 83 1592 0.03% 84 2675 0.05% 85 2917 0.05% 86 3108 0.05% 87 3517 0.06% 88 4029 0.07% 89 5990 0.10% 90 8418 0.14% 91 13060 0.22% 92 16230 0.28% 93 29333 0.50% 94 48357 0.83% 95 124087 2.13% 96 126485 2.17% 97 118104 2.03% 98 182883 3.14% 99 187217 3.22% 100 69479 1.19% 101 4842680 83.23% 5818148 reads passed initial QC criterion=sequence-density sequence-density=96.15 sequence-density-rank=1 fanout-score=23.64 fanout-score-rank=3 prefix-density=96.01 prefix-fanout=23.6 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACAGTGATCTCGTATGCCGTCTTCTGCTTGAAAAAA criterion=fanout-score sequence-density=0.01 sequence-density-rank=10 fanout-score=86.85 fanout-score-rank=1 prefix-density=0.92 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACAGTGATCTCGTATGCCGTCTTCTGCTTGAAAAAA -o SRR6941569 - Input file: STDIN trimmed: SRR6941569-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACAGTGATCTCGTATGCCGTCTTCTGCTTGA -- 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 11:41:14 2024 >> started Fri Dec 6 11:41:21 2024 >> done (7.093s) 5698186 reads processed; of these: 65476 ( 1.15%) short reads filtered out after trimming by size control 35869 ( 0.63%) empty reads filtered out after trimming by size control 5596841 (98.22%) reads available; of these: 5483382 (97.97%) trimmed reads available after processing 113459 ( 2.03%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 20680 0.37% 19 50866 0.91% 20 60681 1.08% 21 312590 5.59% 22 240535 4.30% 23 146361 2.62% 24 1047280 18.71% 25 143999 2.57% 26 118650 2.12% 27 98166 1.75% 28 114502 2.05% 29 416049 7.43% 30 697712 12.47% 31 395766 7.07% 32 400848 7.16% 33 384249 6.87% 34 275743 4.93% 35 244315 4.37% 36 97601 1.74% 37 52398 0.94% 38 27834 0.50% 39 18913 0.34% 40 26641 0.48% 41 28119 0.50% 42 23391 0.42% 43 4857 0.09% 44 5415 0.10% 45 3501 0.06% 46 1146 0.02% 47 1737 0.03% 48 656 0.01% 49 370 0.01% 50 210 0.00% 51 229 0.00% 52 149 0.00% 53 115 0.00% 54 106 0.00% 55 137 0.00% 56 96 0.00% 57 167 0.00% 58 170 0.00% 59 117 0.00% 60 75 0.00% 61 55 0.00% 62 88 0.00% 63 53 0.00% 64 85 0.00% 65 56 0.00% 66 71 0.00% 67 75 0.00% 68 267 0.00% 69 250 0.00% 70 426 0.01% 71 211 0.00% 72 137 0.00% 73 207 0.00% 74 180 0.00% 75 334 0.01% 76 557 0.01% 77 3565 0.06% 78 361 0.01% 79 824 0.01% 80 2518 0.04% 81 1046 0.02% 82 2101 0.04% 83 1760 0.03% 84 649 0.01% 85 584 0.01% 86 830 0.01% 87 1553 0.03% 88 521 0.01% 89 399 0.01% 90 420 0.01% 91 1110 0.02% 92 610 0.01% 93 535 0.01% 94 502 0.01% 95 604 0.01% 96 798 0.01% 97 816 0.01% 98 1803 0.03% 99 1019 0.02% 100 1500 0.03% 101 104219 1.86% criterion=sequence-density sequence-density=7.27 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=14 prefix-density=0.00 prefix-fanout=1.0 sequence=GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCGGAAGCTGCGGGTTCGAGCCCCGTCAGTCCCGCCA criterion=fanout-score sequence-density=0.17 sequence-density-rank=20 fanout-score=148.01 fanout-score-rank=1 prefix-density=25.00 prefix-fanout=1.0 sequence=TATTGTGAGAAAAA Started job on | Dec 06 11:41:35 Started mapping on | Dec 06 11:41:36 Finished on | Dec 06 11:41:47 Mapping speed, Million of reads per hour | 1870.95 Number of input reads | 5716803 Average input read length | 31 UNIQUE READS: Uniquely mapped reads number | 1139938 Uniquely mapped reads % | 19.94% Average mapped length | 25.61 Number of splices: Total | 3412 Number of splices: Annotated (sjdb) | 1058 Number of splices: GT/AG | 3180 Number of splices: GC/AG | 147 Number of splices: AT/AC | 2 Number of splices: Non-canonical | 83 Mismatch rate per base, % | 0.10% Deletion rate per base | 0.00% Deletion average length | 1.38 Insertion rate per base | 0.00% Insertion average length | 1.08 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 3781670 % of reads mapped to multiple loci | 66.15% Number of reads mapped to too many loci | 574178 % of reads mapped to too many loci | 10.04% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.14% % of reads unmapped: other | 0.72% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 795195 795195 795195 N_multimapping 3781670 3781670 3781670 N_noFeature 839820 944736 1031513 N_ambiguous 10399 6693 231 UnstrandedReadsAssigned:289719 PositiveStrandReadsAssigned:188509 NegativeStrandReadsAssigned:108194 Dataset is classified unstranded MeadianReadLen=30 20thPercentileLength=24 echo kmer=19 SRR6941569 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: SRR6941569-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 5,716,803 reads, 2,932,816 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 962 rounds 52973 SRR6941569.ke.tsv 35125 SRR6941569.se.tsv 88098 total ==> SRR6941569.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 0 0 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 1 0.154733 PNS24243 293 194 0 0 KQK14069 1603 1504 13.57 1.91544 KQK14071 474 375 1.75026 0.990855 ==> SRR6941569.se.tsv <== BRADI_1g14170v3 15 BRADI_1g53295v3 1 BRADI_1g59795v3 0 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 2 BRADI_1g74790v3 5 BRADI_1g09890v3 0 BRADI_1g77505v3 0 BRADI_1g48960v3 0 SRR6941569 completed mapping pipeline successfully