Starting /dee2/code/volunteer_pipeline.sh SRR6941581 current disk space = 1551367901184 free memory = 1602414516 SRR6941581 SRAfilesize 53634a6ba8abec6409a7efb66d298057 SRR6941581.sra SRR6941581.sra file validated SRR6941581 is single end SRR6941581 is conventional basespace SRR6941581 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6941581_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 33.2425 34.0 33.0 34.0 32.0 34.0 2 33.3315 34.0 33.0 34.0 33.0 34.0 3 33.11625 34.0 33.0 34.0 31.0 34.0 4 33.2865 34.0 33.0 34.0 33.0 34.0 5 33.24575 34.0 33.0 34.0 33.0 34.0 6 37.06175 38.0 37.0 38.0 36.0 38.0 7 37.3465 38.0 38.0 38.0 37.0 38.0 8 37.49625 38.0 38.0 38.0 37.0 38.0 9 37.543 38.0 38.0 38.0 38.0 38.0 10-11 37.545875 38.0 38.0 38.0 38.0 38.0 12-13 37.44775 38.0 38.0 38.0 38.0 38.0 14-15 37.502375 38.0 38.0 38.0 38.0 38.0 16-17 36.097875 38.0 37.0 38.0 31.0 38.0 18-19 36.934625 38.0 37.5 38.0 33.5 38.0 20-21 36.041124999999994 38.0 38.0 38.0 29.5 38.0 22-23 37.27225 38.0 38.0 38.0 36.5 38.0 24-25 37.490125 38.0 38.0 38.0 37.0 38.0 26-27 37.444500000000005 38.0 38.0 38.0 37.5 38.0 28-29 37.429125 38.0 38.0 38.0 37.5 38.0 30-31 37.376374999999996 38.0 38.0 38.0 37.0 38.0 32-33 37.289375 38.0 38.0 38.0 37.0 38.0 34-35 37.25075 38.0 38.0 38.0 37.0 38.0 36-37 37.24275 38.0 38.0 38.0 37.0 38.0 38-39 37.200625 38.0 38.0 38.0 37.0 38.0 40-41 37.230625 38.0 38.0 38.0 37.0 38.0 42-43 37.242625000000004 38.0 38.0 38.0 37.0 38.0 44-45 37.211 38.0 38.0 38.0 37.0 38.0 46-47 37.068 38.0 38.0 38.0 36.5 38.0 48-49 37.1005 38.0 38.0 38.0 36.5 38.0 50-51 36.942375 38.0 38.0 38.0 36.0 38.0 52-53 36.97925 38.0 38.0 38.0 36.0 38.0 54-55 37.112375 38.0 38.0 38.0 37.0 38.0 56-57 37.06225 38.0 38.0 38.0 36.0 38.0 58-59 37.160875 38.0 38.0 38.0 37.0 38.0 60-61 37.026250000000005 38.0 38.0 38.0 36.0 38.0 62-63 37.073499999999996 38.0 38.0 38.0 36.0 38.0 64-65 36.71325 38.0 38.0 38.0 35.0 38.0 66-67 36.498875 38.0 37.5 38.0 34.0 38.0 68-69 36.603750000000005 38.0 38.0 38.0 34.0 38.0 70-71 36.408875 38.0 37.5 38.0 33.5 38.0 72-73 36.311875 38.0 37.0 38.0 33.0 38.0 74-75 36.278 38.0 37.0 38.0 33.0 38.0 76-77 36.326125000000005 38.0 37.5 38.0 34.0 38.0 78-79 36.546499999999995 38.0 38.0 38.0 34.0 38.0 80-81 36.74275 38.0 38.0 38.0 35.5 38.0 82-83 36.756 38.0 38.0 38.0 35.0 38.0 84-85 36.758125 38.0 38.0 38.0 35.5 38.0 86-87 36.657125 38.0 38.0 38.0 35.0 38.0 88-89 36.720125 38.0 38.0 38.0 35.0 38.0 90-91 36.70025 38.0 38.0 38.0 35.0 38.0 92-93 36.664 38.0 38.0 38.0 35.5 38.0 94-95 36.3605 38.0 38.0 38.0 34.5 38.0 96-97 34.975625 38.0 37.5 38.0 29.5 38.0 98-99 32.750125 38.0 35.5 38.0 8.5 38.0 100-101 30.167125 38.0 27.5 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 15 2.0 16 0.0 17 1.0 18 0.0 19 0.0 20 1.0 21 3.0 22 3.0 23 2.0 24 3.0 25 10.0 26 13.0 27 22.0 28 22.0 29 16.0 30 32.0 31 47.0 32 61.0 33 81.0 34 158.0 35 336.0 36 725.0 37 2462.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 29.625 21.925 14.6 33.85 2 25.674999999999997 41.15 15.85 17.325 3 27.250000000000004 16.625 34.175 21.95 4 25.825 25.6 13.025 35.55 5 46.050000000000004 18.55 17.625 17.775 6 19.425 41.325 21.0 18.25 7 46.1 21.275 19.175 13.450000000000001 8 19.125 15.525 46.075 19.275000000000002 9 16.950000000000003 46.0 18.099999999999998 18.95 10-11 37.225 28.487499999999997 17.849999999999998 16.4375 12-13 17.2125 18.0375 18.675 46.075 14-15 19.287499999999998 32.337500000000006 33.45 14.924999999999999 16-17 29.15 20.025000000000002 36.1125 14.7125 18-19 31.8125 26.687499999999996 27.725 13.775 20-21 15.9125 23.8625 41.625 18.6 22-23 33.875 25.4375 26.0125 14.674999999999999 24-25 31.7625 30.5375 22.0875 15.6125 26-27 39.787499999999994 27.3625 18.625 14.224999999999998 28-29 16.125 39.324999999999996 25.837500000000002 18.712500000000002 30-31 19.85 14.3375 43.824999999999996 21.987499999999997 32-33 31.175000000000004 15.075 31.55 22.2 34-35 32.824999999999996 26.3125 25.362499999999997 15.5 36-37 36.0 19.650000000000002 31.874999999999996 12.475 38-39 25.324999999999996 18.025 35.212500000000006 21.4375 40-41 25.8625 14.4875 24.875 34.775 42-43 38.1875 21.587500000000002 19.8375 20.3875 44-45 49.6375 14.0125 18.1875 18.1625 46-47 31.374999999999996 25.2875 14.299999999999999 29.037499999999998 48-49 23.225 28.6125 16.7625 31.4 50-51 30.599999999999998 26.05 9.375 33.975 52-53 28.012500000000003 42.575 6.812500000000001 22.6 54-55 19.037499999999998 28.6125 19.3875 32.9625 56-57 14.5625 29.5875 12.45 43.4 58-59 22.7125 25.2 15.775 36.3125 60-61 16.05 26.087500000000002 26.775 31.087500000000002 62-63 19.025 24.175 23.9375 32.8625 64-65 18.55 25.025 23.599999999999998 32.824999999999996 66-67 17.4125 21.212500000000002 29.299999999999997 32.074999999999996 68-69 26.724999999999998 19.3375 29.1875 24.75 70-71 19.5625 25.650000000000002 38.837500000000006 15.950000000000001 72-73 19.9875 14.887500000000001 41.112500000000004 24.0125 74-75 19.2375 9.887500000000001 32.337500000000006 38.5375 76-77 20.4375 14.025000000000002 41.712500000000006 23.825 78-79 21.475 9.625 41.6625 27.237499999999997 80-81 21.0 8.537500000000001 34.1875 36.275 82-83 27.237499999999997 6.35 38.4375 27.975 84-85 19.125 5.5625 40.6 34.7125 86-87 18.462500000000002 10.674999999999999 42.8625 28.000000000000004 88-89 16.6125 26.5375 35.925000000000004 20.925 90-91 12.325 31.7875 34.375 21.512500000000003 92-93 17.8 38.6875 28.9 14.6125 94-95 13.15 58.3125 19.662499999999998 8.875 96-97 8.3 73.4 13.7875 4.5125 98-99 5.625 85.2125 6.375 2.7875 100-101 2.6 91.225 3.775 2.4 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 0.0 27 0.0 28 0.0 29 0.0 30 0.0 31 0.0 32 0.5 33 0.5 34 1.0 35 1.0 36 1.0 37 1.5 38 2.0 39 4.0 40 8.0 41 21.5 42 79.5 43 178.5 44 497.5 45 669.0 46 444.0 47 363.0 48 328.0 49 217.0 50 237.5 51 267.5 52 243.0 53 170.0 54 83.5 55 68.0 56 48.0 57 16.0 58 16.0 59 17.5 60 8.0 61 4.0 62 2.5 63 1.0 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 0.0 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 52.349999999999994 #Duplication Level Percentage of deduplicated Percentage of total 1 87.39255014326648 45.75 2 5.253104106972302 5.5 3 2.005730659025788 3.15 4 1.146131805157593 2.4 5 0.5730659025787965 1.5 6 0.38204393505253104 1.2 7 0.5253104106972302 1.925 8 0.3342884431709647 1.4000000000000001 9 0.2387774594078319 1.125 >10 1.7669531996179562 17.125 >50 0.2387774594078319 8.3 >100 0.14326647564469913 10.625 >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 201 5.025 No Hit GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 116 2.9000000000000004 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 108 2.7 Illumina Small RNA Adapter 2 (100% over 21bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTGGAATTCTCGGGTGCCAA 84 2.1 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTGGAATTCTCGGGTGCCA 72 1.7999999999999998 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 71 1.775 No Hit TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 54 1.35 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTTGGAATTCTCGGGTG 51 1.275 No Hit TCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTC 48 1.2 RNA PCR Primer, Index 1 (100% over 26bp) CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 48 1.2 RNA PCR Primer, Index 1 (100% over 28bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 43 1.075 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 41 1.0250000000000001 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 35 0.8750000000000001 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTTGGAATTCTCGGGTGC 31 0.775 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTTGGAATTCTCGGGTGCCA 29 0.7250000000000001 No Hit TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 24 0.6 RNA PCR Primer, Index 1 (100% over 29bp) CATCGAGTAGACCTTGTTATTGTGAGAATGGAATTCTCGGGTGCCAAGGA 23 0.575 RNA PCR Primer, Index 1 (100% over 22bp) CATCGAGTAGACCTTGTTATTGTGAGAATTATGGAATTCTCGGGTGCCAA 22 0.5499999999999999 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 19 0.475 No Hit CGGTCGAGGGCACGCCTGCCTGGGCGTCACGCTGGAATTCTCGGGTGCCA 19 0.475 No Hit GAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTGC 17 0.42500000000000004 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTTGGAATTCTCGGGTGCC 16 0.4 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATGGAATTCTCGGGTG 16 0.4 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTTGGAATTCTCGGGTGC 15 0.375 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGGAATTCTCGGGTGCCA 13 0.325 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTTGGAATTCTCGGGTGCCAAG 13 0.325 No Hit CATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAAC 13 0.325 RNA PCR Primer, Index 1 (100% over 24bp) ACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCCA 13 0.325 RNA PCR Primer, Index 1 (100% over 28bp) AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 13 0.325 Illumina Small RNA Adapter 2 (100% over 21bp) AGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCC 12 0.3 RNA PCR Primer, Index 1 (100% over 27bp) GGGGATATGGCGAAATCGGTAGACGCTACGGACTTTGGAATTCTCGGGTG 12 0.3 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTAAATGGAATTCTCGGGTGCC 12 0.3 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGATGGAATTCTC 12 0.3 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTGGAATTCTCGGGTGCCAAGG 12 0.3 Illumina Small RNA Adapter 2 (100% over 21bp) ACCTGCTCTGATACCATGTTGTGATGGAATTCTCGGGTGCCAAGGAACTC 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 26bp) TCCGTCGTAGTCTAGGTGGTTAGGATACTCTGGAATTCTCGGGTGCCAAG 11 0.27499999999999997 No Hit AGAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTG 11 0.27499999999999997 No Hit GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTTGGAATTCTCGGGTGC 11 0.27499999999999997 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAAATGGAATTCTCGGGT 10 0.25 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 10 0.25 Illumina Small RNA Adapter 2 (100% over 21bp) AAGGGTGCTGAGAATACTTTGAATCTGACACTGGAATTCTCGGGTGCCAA 10 0.25 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGTGGAATTCTCGGGTGCC 10 0.25 No Hit TGTCGTGCCAATTCAACATAAACCCCTGGAATTCTCGGGTGCCAAGGAAC 10 0.25 RNA PCR Primer, Index 1 (100% over 24bp) ATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACT 10 0.25 RNA PCR Primer, Index 1 (100% over 25bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTAAATGGAATTCTCGGGTG 10 0.25 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAATGGAATTCTCGGGTGCCA 9 0.22499999999999998 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTGGAATTCTCGGGTG 9 0.22499999999999998 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTATGGAATTCTCGGGTGCC 9 0.22499999999999998 No Hit GACACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACT 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 25bp) CACGACTCTCGGCAACGGATATCTCGGCTTGGAATTCTCGGGTGCCAAGG 9 0.22499999999999998 Illumina Small RNA Adapter 2 (100% over 21bp) AAGGGTGCTGAGAATACTTTGAATCTGACATGGAATTCTCGGGTGCCAAG 8 0.2 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTTGGAATTCTCGGGTGCCAA 8 0.2 No Hit CATCGAGTAGACCTTGATATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 8 0.2 Illumina Small RNA Adapter 2 (100% over 21bp) GACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAAC 8 0.2 RNA PCR Primer, Index 1 (100% over 24bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCAATGGAATTCTCGGGTGCC 8 0.2 No Hit CAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTG 8 0.2 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTGAATCTGGAATTC 8 0.2 No Hit TAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAG 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 29bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGGAATTCTCGGGTGC 7 0.17500000000000002 No Hit AACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 27bp) CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 23bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTAATGGAATTCTCGGGTGC 7 0.17500000000000002 No Hit TGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAA 7 0.17500000000000002 No Hit GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGTTGGAATTCTCGGGT 7 0.17500000000000002 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTAAAATGGAATTCTCGGGT 7 0.17500000000000002 No Hit CATCGAGTAGACCTTGATATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 7 0.17500000000000002 No Hit TTGACAGAAGAGAGTGAGCACTGGAATTCTCGGGTGCCAAGGAACTCCAG 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 29bp) ATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 23bp) CATCGAGTAGACCTTGTTATTGTGAGAATTAAAATGGAATTCTCGGGTGC 6 0.15 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTAATCTGGAATTCT 6 0.15 No Hit TTCGGACCAGGCTTCATTCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 6 0.15 RNA PCR Primer, Index 1 (100% over 29bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATTGGAATTCTCGGGT 6 0.15 No Hit AGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 6 0.15 No Hit CATCGAGTAGACCTTGTTAATGTGAGAATTGGAATTCTCGGGTGCCAAGG 6 0.15 Illumina Small RNA Adapter 2 (100% over 21bp) ACGAACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) ATCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGG 6 0.15 No Hit CACGACTCTCGGCAACGGATATCTCGGCTCTTGGAATTCTCGGGTGCCAA 5 0.125 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGTGGAATTCT 5 0.125 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTGGAATTCTCGGGTGCCAAG 5 0.125 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTTGGAATTCT 5 0.125 No Hit AATATTGGGTAGGTTGTGGTATTTCATTGCTTGGAATTCTCGGGTGCCAA 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAAAATGGAATTCTCGGGTGC 5 0.125 No Hit GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGTGGAATTCTCGGGTG 5 0.125 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTGAATTGGAATTCT 5 0.125 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTGGAATTCTCGGGT 5 0.125 No Hit CAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTC 5 0.125 RNA PCR Primer, Index 1 (100% over 26bp) TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGG 5 0.125 No Hit CTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCA 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 0.1 0.0 0.0 0.0 6 0.0 0.1 0.0 0.0 0.0 7 0.0 0.1 0.0 0.0 0.0 8 0.0 0.1 0.0 0.0 0.0 9 0.0 0.1 0.0 0.0 0.0 10-11 0.0 0.1125 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 0.4875 0.0 0.0 0.0 20-21 0.0 1.475 0.0 0.0 0.0 22-23 0.0 6.550000000000001 0.0 0.0 0.0 24-25 0.0 17.05 0.0 0.0 0.0 26-27 0.0 27.9125 0.0 0.0 0.0 28-29 0.0 32.85 0.0 0.0 0.0 30-31 0.0 46.8875 0.0 0.0 0.0 32-33 0.0 64.6625 0.0 0.0 0.0 34-35 0.0 78.65 0.0 0.0 0.0 36-37 0.0 88.5875 0.0 0.0 0.0 38-39 0.0 92.375 0.0 0.0 0.0 40-41 0.0 94.0125 0.0 0.0 0.0 42-43 0.0 96.0375 0.0 0.0 0.0 44-45 0.0 96.8625 0.0 0.0 0.0 46-47 0.0 97.2875 0.0 0.0 0.0 48-49 0.0 97.425 0.0 0.0 0.0 50-51 0.0 97.4625 0.0 0.0 0.0 52-53 0.0 97.5 0.0 0.0 0.0 54-55 0.0 97.5 0.0 0.0 0.0 56-57 0.0 97.5 0.0 0.0 0.0 58-59 0.0 97.5 0.0 0.0 0.0 60-61 0.0 97.5 0.0 0.0 0.0 62-63 0.0 97.5 0.0 0.0 0.0 64-65 0.0 97.5 0.0 0.0 0.0 66-67 0.0 97.5 0.0 0.0 0.0 68-69 0.0 97.5 0.0 0.0 0.0 70-71 0.0 97.5 0.0 0.0 0.0 72-73 0.0 97.5 0.0 0.0 0.0 74-75 0.0 97.5 0.0 0.0 0.0 76-77 0.0 97.5 0.0 0.0 0.0 78-79 0.0 97.5 0.0 0.0 0.0 80-81 0.0 97.5 0.0 0.0 0.0 82-83 0.0 97.5 0.0 0.0 0.0 84-85 0.0 97.5 0.0 0.0 0.0 86-87 0.0 97.5 0.0 0.0 0.0 88-89 0.0 97.5 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGATGTA 20 1.5392321E-5 95.00001 4 TTGTAGT 40 5.456968E-12 95.00001 5 GATGTAG 20 1.5392321E-5 95.00001 5 TAGCCAA 20 1.5392321E-5 95.00001 9 CGGATGT 20 1.5392321E-5 95.00001 3 GCGGATG 20 1.5392321E-5 95.00001 2 GATTGTA 40 5.456968E-12 95.00001 3 ATTGTAG 40 5.456968E-12 95.00001 4 TGTAGTT 40 5.456968E-12 95.00001 6 TGTAGCC 20 1.5392321E-5 95.00001 7 ATGTAGC 20 1.5392321E-5 95.00001 6 GTAGCCA 20 1.5392321E-5 95.00001 8 GGCGGAT 20 1.5392321E-5 95.00001 1 GTAGACC 90 0.0 95.0 7 AGCTCAG 15 6.142176E-4 95.0 9 AGTAGAC 90 0.0 95.0 6 AGGATAG 15 6.142176E-4 95.0 4 TCAGGAT 15 6.142176E-4 95.0 2 AGAGGAA 15 6.142176E-4 95.0 6 AAGAGGA 15 6.142176E-4 95.0 5 >>END_MODULE Rejected 292022 READS because READLEN < 1 Read 292022 spots for SRR6941581.sra Written 292022 spots for SRR6941581.sra Rejected 292022 READS because READLEN < 1 Read 292022 spots for SRR6941581.sra Written 292022 spots for SRR6941581.sra Rejected 292022 READS because READLEN < 1 Read 292022 spots for SRR6941581.sra Written 292022 spots for SRR6941581.sra Rejected 292022 READS because READLEN < 1 Read 292022 spots for SRR6941581.sra Written 292022 spots for SRR6941581.sra Rejected 292022 READS because READLEN < 1 Read 292022 spots for SRR6941581.sra Written 292022 spots for SRR6941581.sra Rejected 292022 READS because READLEN < 1 Read 292022 spots for SRR6941581.sra Written 292022 spots for SRR6941581.sra Rejected 292022 READS because READLEN < 1 Read 292022 spots for SRR6941581.sra Written 292022 spots for SRR6941581.sra Rejected 292022 READS because READLEN < 1 Read 292022 spots for SRR6941581.sra Written 292022 spots for SRR6941581.sra Rejected 292022 READS because READLEN < 1 Read 292022 spots for SRR6941581.sra Written 292022 spots for SRR6941581.sra Rejected 292022 READS because READLEN < 1 Read 292022 spots for SRR6941581.sra Written 292022 spots for SRR6941581.sra Rejected 292022 READS because READLEN < 1 Read 292022 spots for SRR6941581.sra Written 292022 spots for SRR6941581.sra Rejected 292022 READS because READLEN < 1 Read 292022 spots for SRR6941581.sra Written 292022 spots for SRR6941581.sra Rejected 292025 READS because READLEN < 1 Read 292025 spots for SRR6941581.sra Written 292025 spots for SRR6941581.sra Rejected 292022 READS because READLEN < 1 Read 292022 spots for SRR6941581.sra Written 292022 spots for SRR6941581.sra Rejected 292022 READS because READLEN < 1 Read 292022 spots for SRR6941581.sra Written 292022 spots for SRR6941581.sra Rejected 292022 READS because READLEN < 1 Read 292022 spots for SRR6941581.sra Written 292022 spots for SRR6941581.sra Rejected 292022 READS because READLEN < 1 Read 292022 spots for SRR6941581.sra Written 292022 spots for SRR6941581.sra Rejected 292022 READS because READLEN < 1 Read 292022 spots for SRR6941581.sra Written 292022 spots for SRR6941581.sra Rejected 292022 READS because READLEN < 1 Read 292022 spots for SRR6941581.sra Written 292022 spots for SRR6941581.sra Rejected 292022 READS because READLEN < 1 Read 292022 spots for SRR6941581.sra Written 292022 spots for SRR6941581.sra SRR ids: ['SRR6941581.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_ff67lvqm SRR6941581.sra spots: 5840443 blocks: [[1, 292022], [292023, 584044], [584045, 876066], [876067, 1168088], [1168089, 1460110], [1460111, 1752132], [1752133, 2044154], [2044155, 2336176], [2336177, 2628198], [2628199, 2920220], [2920221, 3212242], [3212243, 3504264], [3504265, 3796286], [3796287, 4088308], [4088309, 4380330], [4380331, 4672352], [4672353, 4964374], [4964375, 5256396], [5256397, 5548418], [5548419, 5840443]] SRR6941581 file size 1395202 SRR6941581 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 SRR6941581 SRR6941581_1.fastq Input file: SRR6941581_1.fastq trimmed: SRR6941581-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 11:58:15 2024 >> started Fri Dec 6 11:58:18 2024 >> done (2.788s) 5840443 reads processed; of these: 106 ( 0.00%) short reads filtered out after trimming by size control 50 ( 0.00%) empty reads filtered out after trimming by size control 5840287 (100.00%) reads available; of these: 775937 (13.29%) trimmed reads available after processing 5064350 (86.71%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 13 0.00% 19 10 0.00% 20 14 0.00% 21 11 0.00% 22 11 0.00% 23 14 0.00% 24 13 0.00% 25 23 0.00% 26 17 0.00% 27 31 0.00% 28 39 0.00% 29 70 0.00% 30 60 0.00% 31 38 0.00% 32 47 0.00% 33 53 0.00% 34 52 0.00% 35 69 0.00% 36 90 0.00% 37 58 0.00% 38 84 0.00% 39 73 0.00% 40 95 0.00% 41 100 0.00% 42 106 0.00% 43 133 0.00% 44 113 0.00% 45 152 0.00% 46 169 0.00% 47 138 0.00% 48 114 0.00% 49 132 0.00% 50 144 0.00% 51 115 0.00% 52 111 0.00% 53 90 0.00% 54 105 0.00% 55 60 0.00% 56 72 0.00% 57 44 0.00% 58 71 0.00% 59 79 0.00% 60 113 0.00% 61 84 0.00% 62 75 0.00% 63 83 0.00% 64 95 0.00% 65 108 0.00% 66 125 0.00% 67 129 0.00% 68 160 0.00% 69 157 0.00% 70 207 0.00% 71 241 0.00% 72 315 0.01% 73 652 0.01% 74 3622 0.06% 75 2441 0.04% 76 787 0.01% 77 365 0.01% 78 451 0.01% 79 423 0.01% 80 492 0.01% 81 494 0.01% 82 527 0.01% 83 624 0.01% 84 991 0.02% 85 1152 0.02% 86 1301 0.02% 87 1565 0.03% 88 1921 0.03% 89 2859 0.05% 90 3991 0.07% 91 6350 0.11% 92 8826 0.15% 93 17755 0.30% 94 30539 0.52% 95 80164 1.37% 96 93344 1.60% 97 103596 1.77% 98 169233 2.90% 99 172434 2.95% 100 64113 1.10% 101 5064350 86.71% 5840287 reads passed initial QC criterion=sequence-density sequence-density=97.55 sequence-density-rank=1 fanout-score=26.55 fanout-score-rank=1 prefix-density=97.76 prefix-fanout=26.5 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTGAAAAA criterion=fanout-score sequence-density=97.55 sequence-density-rank=1 fanout-score=26.55 fanout-score-rank=1 prefix-density=97.76 prefix-fanout=26.5 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTGAAAAA 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTGAAAAA -o SRR6941581 - Input file: STDIN trimmed: SRR6941581-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTGA -- 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 11:58:34 2024 >> started Fri Dec 6 11:58:40 2024 >> done (5.675s) 5721098 reads processed; of these: 21115 ( 0.37%) short reads filtered out after trimming by size control 12530 ( 0.22%) empty reads filtered out after trimming by size control 5687453 (99.41%) reads available; of these: 5647878 (99.30%) trimmed reads available after processing 39575 ( 0.70%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 10740 0.19% 19 28020 0.49% 20 38097 0.67% 21 182598 3.21% 22 182758 3.21% 23 140457 2.47% 24 797208 14.02% 25 166681 2.93% 26 156070 2.74% 27 144482 2.54% 28 145830 2.56% 29 391668 6.89% 30 669720 11.78% 31 444236 7.81% 32 442924 7.79% 33 429219 7.55% 34 343751 6.04% 35 324039 5.70% 36 170236 2.99% 37 111278 1.96% 38 71231 1.25% 39 52417 0.92% 40 55913 0.98% 41 54837 0.96% 42 43444 0.76% 43 13201 0.23% 44 13489 0.24% 45 9715 0.17% 46 3321 0.06% 47 4066 0.07% 48 1482 0.03% 49 714 0.01% 50 500 0.01% 51 387 0.01% 52 220 0.00% 53 141 0.00% 54 126 0.00% 55 102 0.00% 56 75 0.00% 57 65 0.00% 58 52 0.00% 59 44 0.00% 60 42 0.00% 61 49 0.00% 62 45 0.00% 63 41 0.00% 64 40 0.00% 65 53 0.00% 66 43 0.00% 67 42 0.00% 68 74 0.00% 69 81 0.00% 70 124 0.00% 71 80 0.00% 72 58 0.00% 73 71 0.00% 74 59 0.00% 75 88 0.00% 76 140 0.00% 77 568 0.01% 78 103 0.00% 79 180 0.00% 80 443 0.01% 81 228 0.00% 82 434 0.01% 83 332 0.01% 84 158 0.00% 85 125 0.00% 86 179 0.00% 87 276 0.00% 88 119 0.00% 89 147 0.00% 90 172 0.00% 91 295 0.01% 92 231 0.00% 93 267 0.00% 94 312 0.01% 95 381 0.01% 96 362 0.01% 97 411 0.01% 98 804 0.01% 99 532 0.01% 100 540 0.01% 101 33170 0.58% criterion=sequence-density sequence-density=21.38 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=16 prefix-density=0.00 prefix-fanout=1.0 sequence=CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAA criterion=fanout-score sequence-density=0.45 sequence-density-rank=11 fanout-score=46.61 fanout-score-rank=1 prefix-density=21.09 prefix-fanout=1.0 sequence=ATTGTGAGAATAAAAAA Started job on | Dec 06 11:59:00 Started mapping on | Dec 06 11:59:00 Finished on | Dec 06 11:59:18 Mapping speed, Million of reads per hour | 1161.33 Number of input reads | 5806642 Average input read length | 31 UNIQUE READS: Uniquely mapped reads number | 925857 Uniquely mapped reads % | 15.94% Average mapped length | 26.46 Number of splices: Total | 5979 Number of splices: Annotated (sjdb) | 3560 Number of splices: GT/AG | 5583 Number of splices: GC/AG | 244 Number of splices: AT/AC | 3 Number of splices: Non-canonical | 149 Mismatch rate per base, % | 0.12% Deletion rate per base | 0.00% Deletion average length | 1.56 Insertion rate per base | 0.00% Insertion average length | 1.01 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 3582801 % of reads mapped to multiple loci | 61.70% Number of reads mapped to too many loci | 1078769 % of reads mapped to too many loci | 18.58% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.21% % of reads unmapped: other | 0.57% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1297984 1297984 1297984 N_multimapping 3582801 3582801 3582801 N_noFeature 617895 722380 817722 N_ambiguous 9699 5924 155 UnstrandedReadsAssigned:298263 PositiveStrandReadsAssigned:197553 NegativeStrandReadsAssigned:107980 Dataset is classified unstranded MeadianReadLen=30 20thPercentileLength=24 echo kmer=19 SRR6941581 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: SRR6941581-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 5,806,642 reads, 2,594,884 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 923 rounds 52973 SRR6941581.ke.tsv 35125 SRR6941581.se.tsv 88098 total ==> SRR6941581.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 2.51817 0.40729 KQK14071 474 375 3.9899 2.5882 ==> SRR6941581.se.tsv <== BRADI_1g14170v3 28 BRADI_1g53295v3 2 BRADI_1g59795v3 0 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 4 BRADI_1g74790v3 13 BRADI_1g09890v3 0 BRADI_1g77505v3 0 BRADI_1g48960v3 0 SRR6941581 completed mapping pipeline successfully