Starting /dee2/code/volunteer_pipeline.sh SRR6941567 current disk space = 1551509868544 free memory = 1604689520 SRR6941567 SRAfilesize f3b08ce9139cf065beab08ce754d4e82 SRR6941567.sra SRR6941567.sra file validated SRR6941567 is single end SRR6941567 is conventional basespace SRR6941567 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6941567_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 33.146 34.0 33.0 34.0 32.0 34.0 2 33.29675 34.0 33.0 34.0 32.0 34.0 3 32.8395 34.0 33.0 34.0 31.0 34.0 4 33.117 34.0 33.0 34.0 32.0 34.0 5 33.1605 34.0 33.0 34.0 31.0 34.0 6 36.94 38.0 37.0 38.0 36.0 38.0 7 37.31725 38.0 38.0 38.0 37.0 38.0 8 37.498 38.0 38.0 38.0 37.0 38.0 9 37.50825 38.0 38.0 38.0 37.0 38.0 10-11 37.441375 38.0 38.0 38.0 37.0 38.0 12-13 37.400375 38.0 38.0 38.0 37.0 38.0 14-15 37.442875 38.0 38.0 38.0 37.0 38.0 16-17 36.175250000000005 38.0 37.5 38.0 31.5 38.0 18-19 36.8665 38.0 38.0 38.0 33.5 38.0 20-21 35.950874999999996 38.0 37.5 38.0 30.5 38.0 22-23 37.094625 38.0 38.0 38.0 36.0 38.0 24-25 37.393249999999995 38.0 38.0 38.0 37.0 38.0 26-27 37.399875 38.0 38.0 38.0 37.0 38.0 28-29 37.397125 38.0 38.0 38.0 37.0 38.0 30-31 37.367625000000004 38.0 38.0 38.0 37.0 38.0 32-33 37.223875 38.0 38.0 38.0 36.5 38.0 34-35 37.168125 38.0 38.0 38.0 37.0 38.0 36-37 37.12725 38.0 38.0 38.0 36.5 38.0 38-39 37.093125 38.0 38.0 38.0 36.5 38.0 40-41 37.049375 38.0 38.0 38.0 36.0 38.0 42-43 37.06875 38.0 38.0 38.0 36.0 38.0 44-45 37.06375 38.0 38.0 38.0 36.0 38.0 46-47 36.908125 38.0 38.0 38.0 36.0 38.0 48-49 37.001000000000005 38.0 38.0 38.0 36.0 38.0 50-51 36.83325000000001 38.0 38.0 38.0 35.5 38.0 52-53 36.82825 38.0 38.0 38.0 36.0 38.0 54-55 36.9025 38.0 38.0 38.0 36.0 38.0 56-57 36.97 38.0 38.0 38.0 36.0 38.0 58-59 37.065749999999994 38.0 38.0 38.0 36.5 38.0 60-61 37.072 38.0 38.0 38.0 36.0 38.0 62-63 36.91725 38.0 38.0 38.0 36.0 38.0 64-65 36.53775 38.0 37.5 38.0 34.5 38.0 66-67 36.456 38.0 37.5 38.0 34.0 38.0 68-69 36.656625000000005 38.0 38.0 38.0 34.5 38.0 70-71 36.310625 38.0 37.5 38.0 33.0 38.0 72-73 36.12875 38.0 37.0 38.0 32.0 38.0 74-75 36.16975 38.0 37.0 38.0 33.0 38.0 76-77 36.04625 38.0 37.5 38.0 32.0 38.0 78-79 36.14125 38.0 37.5 38.0 33.5 38.0 80-81 36.385999999999996 38.0 38.0 38.0 34.0 38.0 82-83 36.38225 38.0 38.0 38.0 34.5 38.0 84-85 36.325125 38.0 38.0 38.0 34.0 38.0 86-87 36.128375000000005 38.0 38.0 38.0 34.0 38.0 88-89 36.195875 38.0 38.0 38.0 34.0 38.0 90-91 36.165875 38.0 38.0 38.0 34.0 38.0 92-93 36.031125 38.0 38.0 38.0 34.0 38.0 94-95 35.7115 38.0 38.0 38.0 33.0 38.0 96-97 34.172125 38.0 36.5 38.0 22.0 38.0 98-99 31.963875 38.0 35.0 38.0 2.0 38.0 100-101 29.2135 38.0 25.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 9 1.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 2.0 17 0.0 18 0.0 19 0.0 20 1.0 21 3.0 22 3.0 23 4.0 24 6.0 25 16.0 26 13.0 27 21.0 28 46.0 29 26.0 30 35.0 31 55.0 32 74.0 33 102.0 34 175.0 35 401.0 36 728.0 37 2288.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 30.25 20.9 13.750000000000002 35.099999999999994 2 27.213606803401703 41.295647823911956 15.232616308154077 16.258129064532266 3 28.475 16.775000000000002 34.1 20.65 4 23.125 28.249999999999996 12.5 36.125 5 47.125 16.8 17.875 18.2 6 18.425 41.15 22.125 18.3 7 46.949999999999996 19.5 19.775000000000002 13.775 8 18.45 14.249999999999998 49.225 18.075 9 16.425 48.15 17.775 17.65 10-11 37.8125 28.712500000000002 18.1875 15.287500000000001 12-13 16.2125 16.175 20.0 47.612500000000004 14-15 18.825 31.8625 34.575 14.7375 16-17 29.9375 18.575 37.3 14.1875 18-19 33.175 26.275 27.537499999999998 13.0125 20-21 14.2625 24.4 43.6625 17.675 22-23 34.2 25.0375 26.637499999999996 14.124999999999998 24-25 32.9375 31.2625 21.1625 14.637500000000001 26-27 38.3 28.3875 18.35 14.9625 28-29 16.675 38.3625 26.5 18.462500000000002 30-31 19.8375 13.212499999999999 43.8625 23.0875 32-33 30.837500000000002 14.85 31.324999999999996 22.9875 34-35 33.375 25.3 26.0 15.325 36-37 36.5375 20.0375 30.6375 12.7875 38-39 23.9125 18.2625 35.925000000000004 21.9 40-41 26.200000000000003 13.3125 25.1875 35.3 42-43 38.2125 21.5375 19.0 21.25 44-45 50.4125 14.0125 17.0125 18.5625 46-47 30.9375 25.8625 14.3375 28.8625 48-49 22.7125 28.962500000000002 16.175 32.15 50-51 29.6875 27.3 8.4375 34.575 52-53 27.762500000000003 43.4625 7.025 21.75 54-55 20.0625 28.175 19.162499999999998 32.6 56-57 12.075 29.2 12.4125 46.3125 58-59 20.200000000000003 25.874999999999996 14.0125 39.9125 60-61 12.562499999999998 29.2875 18.9375 39.2125 62-63 14.025000000000002 31.6875 21.8875 32.4 64-65 15.262500000000001 25.6125 21.4125 37.7125 66-67 12.8 25.75 19.35 42.1 68-69 15.587500000000002 29.7125 22.05 32.65 70-71 9.35 35.212500000000006 32.675 22.7625 72-73 14.149999999999999 22.237499999999997 37.6 26.0125 74-75 16.662499999999998 12.587499999999999 31.7125 39.0375 76-77 19.787499999999998 13.925 41.025 25.2625 78-79 20.724999999999998 11.3625 40.4625 27.450000000000003 80-81 20.4125 9.6875 34.175 35.725 82-83 27.150000000000002 6.575 37.5375 28.7375 84-85 19.0625 6.550000000000001 39.574999999999996 34.8125 86-87 18.099999999999998 12.1 43.05 26.75 88-89 15.6 27.775 35.925000000000004 20.7 90-91 12.5125 33.1875 33.7375 20.5625 92-93 17.575 40.8375 27.6625 13.925 94-95 12.4625 60.5375 19.3875 7.6125 96-97 8.275 76.3125 12.025 3.3875 98-99 4.6125 88.3125 4.6 2.475 100-101 2.0875 92.1875 3.1375 2.5875 >>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 1.5 34 2.5 35 5.5 36 5.5 37 3.5 38 6.5 39 10.5 40 14.0 41 30.5 42 88.0 43 184.5 44 520.5 45 695.5 46 450.5 47 350.5 48 309.0 49 204.0 50 225.0 51 283.0 52 255.5 53 146.5 54 65.5 55 58.0 56 38.0 57 10.0 58 13.0 59 14.0 60 5.0 61 2.0 62 1.0 63 0.5 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 0.05 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 50.4 #Duplication Level Percentage of deduplicated Percentage of total 1 87.74801587301587 44.224999999999994 2 4.315476190476191 4.35 3 2.232142857142857 3.375 4 1.3888888888888888 2.8000000000000003 5 0.5952380952380952 1.5 6 0.1984126984126984 0.6 7 0.6448412698412698 2.275 8 0.3472222222222222 1.4000000000000001 9 0.3472222222222222 1.575 >10 1.7857142857142856 17.95 >50 0.2976190476190476 11.774999999999999 >100 0.0992063492063492 8.175 >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 198 4.95 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 129 3.225 Illumina Small RNA Adapter 2 (100% over 21bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTTGGAATTCTCGGGTGCCA 98 2.45 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTGGAATTCTCGGGTGCCAA 90 2.25 No Hit GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 89 2.225 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 76 1.9 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTTGGAATTCTCGGGTG 62 1.55 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTTGGAATTCTCGGGTGC 56 1.4000000000000001 No Hit CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 50 1.25 RNA PCR Primer, Index 1 (100% over 28bp) GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 46 1.15 No Hit TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 42 1.05 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTTGGAATTCTCGGGTGCCA 39 0.975 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 34 0.8500000000000001 No Hit TCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTC 31 0.775 RNA PCR Primer, Index 1 (100% over 26bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 30 0.75 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATGGAATTCTCGGGTGCCAAGGA 26 0.65 RNA PCR Primer, Index 1 (100% over 22bp) CATCGAGTAGACCTTGTTATTGTGAGAATTATGGAATTCTCGGGTGCCAA 26 0.65 No Hit CAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTC 23 0.575 RNA PCR Primer, Index 1 (100% over 26bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 22 0.5499999999999999 No Hit GAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTGC 22 0.5499999999999999 No Hit TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGCCAATATCTCGTATGC 21 0.525 RNA PCR Primer, Index 6 (100% over 50bp) TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 20 0.5 RNA PCR Primer, Index 1 (100% over 29bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGTGGAATTCTCGGGTGCC 19 0.475 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTTGGAATTCTCGGGTGCCAAG 17 0.42500000000000004 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTTGGAATTCTCGGGTGCC 17 0.42500000000000004 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTTGGAATTCTCGGGTGC 16 0.4 No Hit CGGTCGAGGGCACGCCTGCCTGGGCGTCACGCTGGAATTCTCGGGTGCCA 16 0.4 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 16 0.4 Illumina Small RNA Adapter 2 (100% over 21bp) GGGTGTTTGGTCTAGTGGTATGATTCTCGCTTGGAATTCTCGGGTGCCAA 15 0.375 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATGGAATTCTCGGGTG 14 0.35000000000000003 No Hit AGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCC 13 0.325 RNA PCR Primer, Index 1 (100% over 27bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTGGAATTCTCGGGTG 13 0.325 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGGAATTCTCGGGTGCCA 13 0.325 No Hit CTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCA 12 0.3 No Hit ACCTGCTCTGATACCATGTTGTGATGGAATTCTCGGGTGCCAAGGAACTC 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 26bp) GACACGACTCTCGGCAACGGATATCTCGGCTTGGAATTCTCGGGTGCCAA 11 0.27499999999999997 No Hit AGAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTG 11 0.27499999999999997 No Hit AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 11 0.27499999999999997 Illumina Small RNA Adapter 2 (100% over 21bp) GCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAA 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 23bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 10 0.25 Illumina Small RNA Adapter 2 (100% over 21bp) GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTTGGAATTCTCGGGTGC 10 0.25 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTGAATCTGGAATTC 10 0.25 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGATGGAATTCTC 10 0.25 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTGGAATTCTCGGGTGCCAAGG 10 0.25 Illumina Small RNA Adapter 2 (100% over 21bp) TTCGGACCAGGCTTCATTCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 29bp) AACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCC 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 27bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCAATGGAATTCTCGGGTGCC 9 0.22499999999999998 No Hit CATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAAC 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 24bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTAATGGAATTCTCGGGTGC 9 0.22499999999999998 No Hit ACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCCA 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 28bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTAAATGGAATTCTCGGGTG 9 0.22499999999999998 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGGAATTCTCGGGTGC 8 0.2 No Hit GACACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACT 8 0.2 RNA PCR Primer, Index 1 (100% over 25bp) TGTCGTGCCAATTCAACATAAACCCCTGGAATTCTCGGGTGCCAAGGAAC 8 0.2 RNA PCR Primer, Index 1 (100% over 24bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTAAAATGGAATTCTCGGGT 8 0.2 No Hit TTGACAGAAGAGAGTGAGCACTGGAATTCTCGGGTGCCAAGGAACTCCAG 8 0.2 RNA PCR Primer, Index 1 (100% over 29bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGGAATTCTCGGGTGCCAA 8 0.2 No Hit CCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACT 8 0.2 RNA PCR Primer, Index 1 (100% over 25bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAAATGGAATTCTCGGGT 7 0.17500000000000002 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATTGGAATTCTCGGGT 7 0.17500000000000002 No Hit AATATTGGGTAGGTTGTGGTATTTCATTGCTTGGAATTCTCGGGTGCCAA 7 0.17500000000000002 No Hit GACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 23bp) GACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAAC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 24bp) CATCGAGTAGACCTTGTTAATGTGAGAATATGGAATTCTCGGGTGCCAAG 7 0.17500000000000002 No Hit CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 23bp) ACGAACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAAC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 24bp) AAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTAAATGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit CACGACTCTCGGCAACGGATATCTCGGCTTGGAATTCTCGGGTGCCAAGG 7 0.17500000000000002 Illumina Small RNA Adapter 2 (100% over 21bp) CATCGAGTAGACCTTGTTAATGTGAGAATTCTTGGAATTCTCGGGTGCCA 7 0.17500000000000002 No Hit ATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACT 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 25bp) CATCGAGTAGACCTTGTTATTGTGAGAATAAATGGAATTCTCGGGTGCCA 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTATGGAATTCTCGGGTGCC 6 0.15 No Hit AATATTGGGTAGGTTGTGGTATTTCATTGCTGGAATTCTCGGGTGCCAAG 6 0.15 No Hit CATCGAGTAGACCTTGATATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 6 0.15 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATACTGGAATTCTCGGGTGCCAAGGA 5 0.125 RNA PCR Primer, Index 1 (100% over 22bp) TGAAGCTGCCAGCATGATCTGATGGAATTCTCGGGTGCCAAGGAACTCCA 5 0.125 RNA PCR Primer, Index 1 (100% over 28bp) CCGTTACTCGGAGGTTCGAATCCTTCCGTCCCAGCCATGGAATTCTCGGG 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTAAAAATGGAATTCTCGGG 5 0.125 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTATGGAATTCTCGGGTGCCAA 5 0.125 No Hit CATCGAGTAGACCTTGTTAATGTGAGAATTCTGGAATTCTCGGGTGCCAA 5 0.125 No Hit CAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTG 5 0.125 No Hit GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGGAATTCTCGGGTGCC 5 0.125 No Hit ATGCAGTTACTAATTCATGATCTGGCTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCTGGAATTC 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTAAAAAATGGAATTCTCGG 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAAAAATGGAATTCTCGG 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 0.65 0.0 0.0 0.0 2 0.0 0.65 0.0 0.0 0.0 3 0.0 0.65 0.0 0.0 0.0 4 0.0 0.65 0.0 0.0 0.0 5 0.0 0.675 0.0 0.0 0.0 6 0.0 0.725 0.0 0.0 0.0 7 0.0 0.725 0.0 0.0 0.0 8 0.0 0.725 0.0 0.0 0.0 9 0.0 0.75 0.0 0.0 0.0 10-11 0.0 0.7625 0.0 0.0 0.0 12-13 0.0 0.825 0.0 0.0 0.0 14-15 0.0 0.925 0.0 0.0 0.0 16-17 0.0 1.125 0.0 0.0 0.0 18-19 0.0 1.6 0.0 0.0 0.0 20-21 0.0 2.7750000000000004 0.0 0.0 0.0 22-23 0.0 8.1375 0.0 0.0 0.0 24-25 0.0 18.6875 0.0 0.0 0.0 26-27 0.0 29.8625 0.0 0.0 0.0 28-29 0.0 35.375 0.0 0.0 0.0 30-31 0.0 49.7875 0.0 0.0 0.0 32-33 0.0 67.7125 0.0 0.0 0.0 34-35 0.0 82.5375 0.0 0.0 0.0 36-37 0.0 91.5875 0.0 0.0 0.0 38-39 0.0 94.30000000000001 0.0 0.0 0.0 40-41 0.0 95.6625 0.0 0.0 0.0 42-43 0.0 96.9 0.0 0.0 0.0 44-45 0.0 97.36250000000001 0.0 0.0 0.0 46-47 0.0 97.4375 0.0 0.0 0.0 48-49 0.0 97.475 0.0 0.0 0.0 50-51 0.0 97.525 0.0 0.0 0.0 52-53 0.0 97.525 0.0 0.0 0.0 54-55 0.0 97.525 0.0 0.0 0.0 56-57 0.0 97.525 0.0 0.0 0.0 58-59 0.0 97.525 0.0 0.0 0.0 60-61 0.0 97.525 0.0 0.0 0.0 62-63 0.0 97.525 0.0 0.0 0.0 64-65 0.0 97.525 0.0 0.0 0.0 66-67 0.0 97.525 0.0 0.0 0.0 68-69 0.0 97.525 0.0 0.0 0.0 70-71 0.0 97.525 0.0 0.0 0.0 72-73 0.0 97.525 0.0 0.0 0.0 74-75 0.0 97.525 0.0 0.0 0.0 76-77 0.0 97.525 0.0 0.0 0.0 78-79 0.0 97.525 0.0 0.0 0.0 80-81 0.0 97.5375 0.0 0.0 0.0 82-83 0.0 97.575 0.0 0.0 0.0 84-85 0.0 97.575 0.0 0.0 0.0 86-87 0.0 97.575 0.0 0.0 0.0 88-89 0.0 97.575 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGATGTA 15 6.142176E-4 95.0 4 GAGCGTA 25 3.8289727E-7 95.0 3 GTAGACC 90 0.0 95.0 7 AGTAGAC 90 0.0 95.0 6 GATGTAG 15 6.142176E-4 95.0 5 TAGCCAA 15 6.142176E-4 95.0 9 CGTAGTT 25 3.8289727E-7 95.0 6 CGGATGT 15 6.142176E-4 95.0 3 GCGGATG 15 6.142176E-4 95.0 2 TAGTTCA 60 0.0 95.0 8 GAGTAGA 90 0.0 95.0 5 TGTAGCC 15 6.142176E-4 95.0 7 CGAGCGT 25 3.8289727E-7 95.0 2 CGAGTAG 90 0.0 95.0 4 AGACCTT 90 0.0 95.0 9 GCGTAGT 25 3.8289727E-7 95.0 5 ATGTAGC 15 6.142176E-4 95.0 6 AGCGTAG 25 3.8289727E-7 95.0 4 TCGAGTA 90 0.0 95.0 3 AGTTCAA 60 0.0 95.0 9 >>END_MODULE Rejected 268783 READS because READLEN < 1 Read 268783 spots for SRR6941567.sra Written 268783 spots for SRR6941567.sra Rejected 268783 READS because READLEN < 1 Read 268783 spots for SRR6941567.sra Written 268783 spots for SRR6941567.sra Rejected 268783 READS because READLEN < 1 Read 268783 spots for SRR6941567.sra Written 268783 spots for SRR6941567.sra Rejected 268783 READS because READLEN < 1 Read 268783 spots for SRR6941567.sra Written 268783 spots for SRR6941567.sra Rejected 268783 READS because READLEN < 1 Read 268783 spots for SRR6941567.sra Written 268783 spots for SRR6941567.sra Rejected 268783 READS because READLEN < 1 Read 268783 spots for SRR6941567.sra Written 268783 spots for SRR6941567.sra Rejected 268783 READS because READLEN < 1 Read 268783 spots for SRR6941567.sra Written 268783 spots for SRR6941567.sra Rejected 268783 READS because READLEN < 1 Read 268783 spots for SRR6941567.sra Written 268783 spots for SRR6941567.sra Rejected 268783 READS because READLEN < 1 Read 268783 spots for SRR6941567.sra Written 268783 spots for SRR6941567.sra Rejected 268783 READS because READLEN < 1 Read 268783 spots for SRR6941567.sra Written 268783 spots for SRR6941567.sra Rejected 268783 READS because READLEN < 1 Read 268783 spots for SRR6941567.sra Written 268783 spots for SRR6941567.sra Rejected 268783 READS because READLEN < 1 Read 268783 spots for SRR6941567.sra Written 268783 spots for SRR6941567.sra Rejected 268783 READS because READLEN < 1 Read 268783 spots for SRR6941567.sra Written 268783 spots for SRR6941567.sra Rejected 268783 READS because READLEN < 1 Read 268783 spots for SRR6941567.sra Written 268783 spots for SRR6941567.sra Rejected 268783 READS because READLEN < 1 Read 268783 spots for SRR6941567.sra Written 268783 spots for SRR6941567.sra Rejected 268783 READS because READLEN < 1 Read 268783 spots for SRR6941567.sra Written 268783 spots for SRR6941567.sra Rejected 268783 READS because READLEN < 1 Read 268783 spots for SRR6941567.sra Written 268783 spots for SRR6941567.sra Rejected 268783 READS because READLEN < 1 Read 268783 spots for SRR6941567.sra Written 268783 spots for SRR6941567.sra Rejected 268783 READS because READLEN < 1 Read 268783 spots for SRR6941567.sra Written 268783 spots for SRR6941567.sra Rejected 268783 READS because READLEN < 1 Read 268783 spots for SRR6941567.sra Written 268783 spots for SRR6941567.sra SRR ids: ['SRR6941567.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_onta5pb6 SRR6941567.sra spots: 5375660 blocks: [[1, 268783], [268784, 537566], [537567, 806349], [806350, 1075132], [1075133, 1343915], [1343916, 1612698], [1612699, 1881481], [1881482, 2150264], [2150265, 2419047], [2419048, 2687830], [2687831, 2956613], [2956614, 3225396], [3225397, 3494179], [3494180, 3762962], [3762963, 4031745], [4031746, 4300528], [4300529, 4569311], [4569312, 4838094], [4838095, 5106877], [5106878, 5375660]] SRR6941567 file size 1283999 SRR6941567 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 SRR6941567 SRR6941567_1.fastq Input file: SRR6941567_1.fastq trimmed: SRR6941567-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 11:35:17 2024 >> started Fri Dec 6 11:35:20 2024 >> done (3.297s) 5375660 reads processed; of these: 97 ( 0.00%) short reads filtered out after trimming by size control 22 ( 0.00%) empty reads filtered out after trimming by size control 5375541 (100.00%) reads available; of these: 769344 (14.31%) trimmed reads available after processing 4606197 (85.69%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 7 0.00% 19 4 0.00% 20 8 0.00% 21 11 0.00% 22 10 0.00% 23 12 0.00% 24 18 0.00% 25 20 0.00% 26 24 0.00% 27 37 0.00% 28 48 0.00% 29 45 0.00% 30 51 0.00% 31 35 0.00% 32 42 0.00% 33 41 0.00% 34 57 0.00% 35 78 0.00% 36 56 0.00% 37 67 0.00% 38 57 0.00% 39 67 0.00% 40 73 0.00% 41 81 0.00% 42 83 0.00% 43 82 0.00% 44 56 0.00% 45 99 0.00% 46 85 0.00% 47 76 0.00% 48 66 0.00% 49 58 0.00% 50 73 0.00% 51 72 0.00% 52 60 0.00% 53 60 0.00% 54 80 0.00% 55 55 0.00% 56 61 0.00% 57 42 0.00% 58 50 0.00% 59 69 0.00% 60 63 0.00% 61 74 0.00% 62 74 0.00% 63 87 0.00% 64 77 0.00% 65 93 0.00% 66 104 0.00% 67 121 0.00% 68 196 0.00% 69 230 0.00% 70 311 0.01% 71 312 0.01% 72 537 0.01% 73 1388 0.03% 74 9195 0.17% 75 6599 0.12% 76 2201 0.04% 77 666 0.01% 78 863 0.02% 79 806 0.01% 80 927 0.02% 81 879 0.02% 82 991 0.02% 83 1419 0.03% 84 2042 0.04% 85 2346 0.04% 86 2516 0.05% 87 2718 0.05% 88 3031 0.06% 89 3996 0.07% 90 5549 0.10% 91 8089 0.15% 92 11014 0.20% 93 19864 0.37% 94 33590 0.62% 95 75143 1.40% 96 85712 1.59% 97 94348 1.76% 98 143645 2.67% 99 167687 3.12% 100 77665 1.44% 101 4606197 85.69% 5375541 reads passed initial QC criterion=sequence-density sequence-density=97.49 sequence-density-rank=1 fanout-score=25.93 fanout-score-rank=2 prefix-density=97.31 prefix-fanout=25.9 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGCCAATATCTCGTATGCCGTCTTCTGCTTGAAAAA criterion=fanout-score sequence-density=0.01 sequence-density-rank=11 fanout-score=27.53 fanout-score-rank=1 prefix-density=0.30 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGCCAATATCTCGTATGCCGTCTTCTGCTTGAAAAA -o SRR6941567 - Input file: STDIN trimmed: SRR6941567-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGCCAATATCTCGTATGCCGTCTTCTGCTTGA -- 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 11:35:31 2024 >> started Fri Dec 6 11:35:38 2024 >> done (7.053s) 5265836 reads processed; of these: 38450 ( 0.73%) short reads filtered out after trimming by size control 35396 ( 0.67%) empty reads filtered out after trimming by size control 5191990 (98.60%) reads available; of these: 5150787 (99.21%) trimmed reads available after processing 41203 ( 0.79%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 15151 0.29% 19 32582 0.63% 20 45033 0.87% 21 176709 3.40% 22 162721 3.13% 23 133607 2.57% 24 667101 12.85% 25 158714 3.06% 26 150977 2.91% 27 142802 2.75% 28 143498 2.76% 29 377008 7.26% 30 654529 12.61% 31 438753 8.45% 32 432457 8.33% 33 409882 7.89% 34 314934 6.07% 35 284368 5.48% 36 129175 2.49% 37 75737 1.46% 38 43952 0.85% 39 31431 0.61% 40 38063 0.73% 41 37006 0.71% 42 28016 0.54% 43 7157 0.14% 44 7520 0.14% 45 4300 0.08% 46 1688 0.03% 47 1927 0.04% 48 797 0.02% 49 423 0.01% 50 248 0.00% 51 192 0.00% 52 100 0.00% 53 93 0.00% 54 64 0.00% 55 65 0.00% 56 37 0.00% 57 51 0.00% 58 47 0.00% 59 45 0.00% 60 33 0.00% 61 24 0.00% 62 36 0.00% 63 30 0.00% 64 31 0.00% 65 24 0.00% 66 34 0.00% 67 35 0.00% 68 55 0.00% 69 62 0.00% 70 79 0.00% 71 56 0.00% 72 55 0.00% 73 56 0.00% 74 61 0.00% 75 71 0.00% 76 125 0.00% 77 480 0.01% 78 107 0.00% 79 154 0.00% 80 375 0.01% 81 162 0.00% 82 279 0.01% 83 225 0.00% 84 105 0.00% 85 107 0.00% 86 153 0.00% 87 237 0.00% 88 143 0.00% 89 105 0.00% 90 165 0.00% 91 260 0.01% 92 220 0.00% 93 253 0.00% 94 307 0.01% 95 369 0.01% 96 427 0.01% 97 474 0.01% 98 796 0.02% 99 530 0.01% 100 609 0.01% 101 35121 0.68% criterion=sequence-density sequence-density=7.21 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=19 prefix-density=0.00 prefix-fanout=1.0 sequence=GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCGG criterion=fanout-score sequence-density=0.01 sequence-density-rank=33 fanout-score=375.10 fanout-score-rank=1 prefix-density=3.11 prefix-fanout=1.0 sequence=GTAGCCAAGTGCGGAGAGGATAACTGCTGAAAGCATATAAGTAGTAAGCCCACCCCAAGATGAGTGCTCTCTC Started job on | Dec 06 11:35:51 Started mapping on | Dec 06 11:35:51 Finished on | Dec 06 11:36:05 Mapping speed, Million of reads per hour | 1363.29 Number of input reads | 5301695 Average input read length | 31 UNIQUE READS: Uniquely mapped reads number | 741803 Uniquely mapped reads % | 13.99% Average mapped length | 25.99 Number of splices: Total | 5539 Number of splices: Annotated (sjdb) | 2855 Number of splices: GT/AG | 5246 Number of splices: GC/AG | 154 Number of splices: AT/AC | 3 Number of splices: Non-canonical | 136 Mismatch rate per base, % | 0.14% Deletion rate per base | 0.00% Deletion average length | 1.68 Insertion rate per base | 0.00% Insertion average length | 1.08 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 3419375 % of reads mapped to multiple loci | 64.50% Number of reads mapped to too many loci | 931707 % of reads mapped to too many loci | 17.57% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.44% % of reads unmapped: other | 0.50% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1140517 1140517 1140517 N_multimapping 3419375 3419375 3419375 N_noFeature 510512 597153 652220 N_ambiguous 7364 4303 154 UnstrandedReadsAssigned:223927 PositiveStrandReadsAssigned:140347 NegativeStrandReadsAssigned:89429 Dataset is classified unstranded MeadianReadLen=30 20thPercentileLength=24 echo kmer=19 SRR6941567 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: SRR6941567-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 5,301,695 reads, 2,489,875 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 915 rounds 52973 SRR6941567.ke.tsv 35125 SRR6941567.se.tsv 88098 total ==> SRR6941567.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 2 0.249149 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 1 0.166069 PNS24243 293 194 0 0 KQK14069 1603 1504 25.3809 3.84505 KQK14071 474 375 1.69151 1.02775 ==> SRR6941567.se.tsv <== BRADI_1g14170v3 40 BRADI_1g53295v3 2 BRADI_1g59795v3 1 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 0 BRADI_1g74790v3 13 BRADI_1g09890v3 0 BRADI_1g77505v3 0 BRADI_1g48960v3 0 SRR6941567 completed mapping pipeline successfully