Starting /dee2/code/volunteer_pipeline.sh SRR6941557 current disk space = 1551390097408 free memory = 1604525288 SRR6941557 SRAfilesize bc1d829162de19edd0c66f1b82a84561 SRR6941557.sra SRR6941557.sra file validated SRR6941557 is single end SRR6941557 is conventional basespace SRR6941557 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6941557_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 33.15925 34.0 33.0 34.0 32.0 34.0 2 33.26 34.0 33.0 34.0 33.0 34.0 3 32.89925 34.0 33.0 34.0 31.0 34.0 4 33.184 34.0 33.0 34.0 32.0 34.0 5 33.1525 34.0 33.0 34.0 31.0 34.0 6 36.998 38.0 37.0 38.0 36.0 38.0 7 37.32525 38.0 38.0 38.0 37.0 38.0 8 37.45575 38.0 38.0 38.0 37.0 38.0 9 37.53325 38.0 38.0 38.0 38.0 38.0 10-11 37.53275 38.0 38.0 38.0 38.0 38.0 12-13 37.432500000000005 38.0 38.0 38.0 37.0 38.0 14-15 37.464 38.0 38.0 38.0 37.5 38.0 16-17 36.22925 38.0 37.5 38.0 32.0 38.0 18-19 36.888 38.0 38.0 38.0 34.0 38.0 20-21 35.995999999999995 38.0 37.5 38.0 30.0 38.0 22-23 37.128249999999994 38.0 38.0 38.0 36.5 38.0 24-25 37.425 38.0 38.0 38.0 37.0 38.0 26-27 37.464124999999996 38.0 38.0 38.0 37.0 38.0 28-29 37.493750000000006 38.0 38.0 38.0 38.0 38.0 30-31 37.437749999999994 38.0 38.0 38.0 38.0 38.0 32-33 37.320125000000004 38.0 38.0 38.0 37.0 38.0 34-35 37.32125 38.0 38.0 38.0 37.0 38.0 36-37 37.30475 38.0 38.0 38.0 37.0 38.0 38-39 37.268 38.0 38.0 38.0 37.0 38.0 40-41 37.205 38.0 38.0 38.0 37.0 38.0 42-43 37.232375 38.0 38.0 38.0 37.0 38.0 44-45 37.211875000000006 38.0 38.0 38.0 37.0 38.0 46-47 37.087625 38.0 38.0 38.0 36.5 38.0 48-49 37.2295 38.0 38.0 38.0 37.0 38.0 50-51 37.05275 38.0 38.0 38.0 36.0 38.0 52-53 37.009375 38.0 38.0 38.0 36.0 38.0 54-55 37.153999999999996 38.0 38.0 38.0 37.0 38.0 56-57 37.133375 38.0 38.0 38.0 36.5 38.0 58-59 37.242999999999995 38.0 38.0 38.0 37.0 38.0 60-61 37.17725 38.0 38.0 38.0 37.0 38.0 62-63 36.782125 38.0 38.0 38.0 35.5 38.0 64-65 36.529375 38.0 37.5 38.0 34.0 38.0 66-67 36.28575 38.0 37.5 38.0 32.5 38.0 68-69 36.741375000000005 38.0 38.0 38.0 35.0 38.0 70-71 36.345875 38.0 37.5 38.0 33.5 38.0 72-73 35.846000000000004 38.0 37.0 38.0 29.0 38.0 74-75 35.481875 38.0 36.5 38.0 29.0 38.0 76-77 35.889625 38.0 37.0 38.0 30.0 38.0 78-79 36.362750000000005 38.0 38.0 38.0 34.0 38.0 80-81 36.74525 38.0 38.0 38.0 35.5 38.0 82-83 36.690375 38.0 38.0 38.0 35.5 38.0 84-85 36.703625 38.0 38.0 38.0 35.5 38.0 86-87 36.525125 38.0 38.0 38.0 35.0 38.0 88-89 36.619625 38.0 38.0 38.0 35.0 38.0 90-91 36.68275 38.0 38.0 38.0 35.5 38.0 92-93 36.66075 38.0 38.0 38.0 35.0 38.0 94-95 36.322874999999996 38.0 38.0 38.0 34.5 38.0 96-97 34.450874999999996 38.0 37.5 38.0 23.0 38.0 98-99 32.131875 38.0 35.0 38.0 2.0 38.0 100-101 29.962875 38.0 25.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 0.0 14 0.0 15 1.0 16 0.0 17 1.0 18 0.0 19 1.0 20 1.0 21 1.0 22 2.0 23 6.0 24 7.0 25 9.0 26 13.0 27 19.0 28 19.0 29 18.0 30 27.0 31 49.0 32 49.0 33 90.0 34 169.0 35 446.0 36 690.0 37 2381.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 38.275 23.674999999999997 15.25 22.8 2 32.416208104052025 29.264632316158078 19.909954977488745 18.409204602301152 3 34.699999999999996 20.1 23.175 22.025 4 28.125 32.45 14.674999999999999 24.75 5 38.25 18.575 24.125 19.05 6 23.0 31.4 25.0 20.599999999999998 7 43.175000000000004 22.025 20.375 14.424999999999999 8 22.475 15.525 44.1 17.9 9 18.625 42.975 19.85 18.55 10-11 36.7375 25.05 20.65 17.5625 12-13 17.925 16.925 25.137500000000003 40.0125 14-15 22.875 39.0625 23.6625 14.399999999999999 16-17 27.025 18.525 40.2375 14.2125 18-19 42.175000000000004 20.5125 22.8 14.512500000000001 20-21 14.912500000000001 28.1 35.212500000000006 21.775 22-23 32.1125 29.9625 22.8875 15.037500000000001 24-25 31.137500000000003 29.4125 21.95 17.5 26-27 35.225 25.362499999999997 22.287499999999998 17.125 28-29 18.5 34.275 21.4 25.825 30-31 21.987499999999997 12.3375 40.8375 24.837500000000002 32-33 30.7 11.9375 30.412499999999998 26.950000000000003 34-35 37.012499999999996 21.4875 26.887499999999996 14.6125 36-37 38.9375 21.712500000000002 28.15 11.200000000000001 38-39 22.2625 20.625 36.199999999999996 20.9125 40-41 22.7125 14.149999999999999 27.237499999999997 35.9 42-43 36.875 21.575 19.4375 22.112499999999997 44-45 52.849999999999994 13.875000000000002 15.975 17.299999999999997 46-47 32.6875 23.3625 17.2375 26.7125 48-49 22.3125 25.75 16.412499999999998 35.525 50-51 28.0875 28.1625 8.1875 35.5625 52-53 30.325000000000003 43.55 6.812500000000001 19.3125 54-55 22.4375 30.0875 18.1125 29.362500000000004 56-57 12.837499999999999 31.7 15.712499999999999 39.75 58-59 23.2625 24.95 21.15 30.6375 60-61 24.8 30.3875 16.8625 27.950000000000003 62-63 24.474999999999998 30.8 18.3625 26.3625 64-65 18.8125 27.500000000000004 27.712500000000002 25.974999999999998 66-67 26.0625 23.849999999999998 24.55 25.5375 68-69 32.45 30.175 20.424999999999997 16.950000000000003 70-71 26.787499999999998 35.15 26.387500000000003 11.675 72-73 26.424999999999997 22.1875 29.375 22.0125 74-75 19.8375 11.7125 29.4 39.050000000000004 76-77 20.875 12.237499999999999 41.612500000000004 25.275 78-79 21.675 11.0125 41.099999999999994 26.2125 80-81 21.2375 10.85 34.7625 33.15 82-83 28.025 5.6125 36.8625 29.5 84-85 21.575 6.05 37.012499999999996 35.362500000000004 86-87 18.212500000000002 12.575 42.412499999999994 26.8 88-89 13.3 28.275 37.8875 20.5375 90-91 12.3125 32.625 33.6875 21.375 92-93 18.1375 38.3 27.6625 15.9 94-95 12.950000000000001 55.55 22.9625 8.537500000000001 96-97 10.2875 73.85000000000001 12.65 3.2125 98-99 4.8125 88.075 4.4125 2.7 100-101 2.3 92.21249999999999 3.3125 2.175 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 0.0 27 0.0 28 0.0 29 0.0 30 0.0 31 0.0 32 0.0 33 0.5 34 0.5 35 1.0 36 1.0 37 1.5 38 3.0 39 4.0 40 9.0 41 27.5 42 88.5 43 181.0 44 390.0 45 497.0 46 375.5 47 375.0 48 354.5 49 236.5 50 290.0 51 374.5 52 319.5 53 183.5 54 80.5 55 64.5 56 47.5 57 25.0 58 30.5 59 21.5 60 5.0 61 3.5 62 4.0 63 3.0 64 1.0 65 0.5 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 50.775000000000006 #Duplication Level Percentage of deduplicated Percentage of total 1 87.8877400295421 44.625 2 4.923682914820286 5.0 3 1.8217626784835055 2.775 4 1.3786312161496799 2.8000000000000003 5 0.7385524372230428 1.875 6 0.4923682914820286 1.5 7 0.29542097488921715 1.05 8 0.2461841457410143 1.0 9 0.09847365829640572 0.44999999999999996 >10 1.5263417035942886 15.625 >50 0.4923682914820286 16.3 >100 0.09847365829640572 7.000000000000001 >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 GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 158 3.95 No Hit GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 122 3.05 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 100 2.5 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 88 2.1999999999999997 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTTGGAATTCTCGGGTG 70 1.7500000000000002 No Hit CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 64 1.6 RNA PCR Primer, Index 1 (100% over 28bp) TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 61 1.525 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTTGGAATTCTCGGGTGC 60 1.5 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 54 1.35 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTTGGAATTCTCGGGTGCCAAG 53 1.325 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTGGAATTCTCGGGTGCCAA 51 1.275 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTGGAATTCTCGGGTGCCA 51 1.275 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTTGGAATTCTCGGGTGCCA 50 1.25 No Hit TCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTC 42 1.05 RNA PCR Primer, Index 1 (100% over 26bp) TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 42 1.05 RNA PCR Primer, Index 1 (100% over 29bp) ATATTGGGTAGGTTGTGGTATTTCATTGCTGGAATTCTCGGGTGCCAAGG 41 1.0250000000000001 Illumina Small RNA Adapter 2 (100% over 21bp) CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 36 0.8999999999999999 Illumina Small RNA Adapter 2 (100% over 21bp) CGGTCGAGGGCACGCCTGCCTGGGCGTCACGCTGGAATTCTCGGGTGCCA 32 0.8 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGGAATTCTCGGGTGCCA 27 0.675 No Hit AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 23 0.575 Illumina Small RNA Adapter 2 (100% over 21bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 22 0.5499999999999999 No Hit AGAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTG 21 0.525 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTTGGAATTCTCGGGTGC 21 0.525 No Hit GAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTGC 18 0.44999999999999996 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGGAATTCTCGGGTGC 18 0.44999999999999996 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGTGGAATTCTCGGGTGCC 17 0.42500000000000004 No Hit TTGACAGAAGAGAGTGAGCACTGGAATTCTCGGGTGCCAAGGAACTCCAG 17 0.42500000000000004 RNA PCR Primer, Index 1 (100% over 29bp) TCCTCAGTAGCTCAGTGGTAGAGCGGTCGGCTTGGAATTCTCGGGTGCCA 16 0.4 No Hit GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTTGGAATTCTCGGGTGC 16 0.4 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGGAATTCTCGGGTGCCAA 15 0.375 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTATGGAATTCTCGGGTGCCAA 15 0.375 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 14 0.35000000000000003 Illumina Small RNA Adapter 2 (100% over 21bp) GGGTGTTTGGTCTAGTGGTATGATTCTCGCTTGGAATTCTCGGGTGCCAA 14 0.35000000000000003 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATACTCTGGAATTCTCGGGTGCCAAG 13 0.325 No Hit AGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCC 12 0.3 RNA PCR Primer, Index 1 (100% over 27bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGTGGAATTCT 11 0.27499999999999997 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 11 0.27499999999999997 Illumina Small RNA Adapter 2 (100% over 21bp) CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 11 0.27499999999999997 No Hit AACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCC 10 0.25 RNA PCR Primer, Index 1 (100% over 27bp) TCGGACCAGGCTTCGATCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG 10 0.25 RNA PCR Primer, Index 1 (100% over 29bp) ATATTGGGTAGGTTGTGGTATTTCATTGCTATGGAATTCTCGGGTGCCAA 10 0.25 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGATGGAATTCTC 10 0.25 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTAAATGGAATTCTCGGGTG 10 0.25 No Hit TAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAG 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 29bp) TCGCTTGGTGCAGATCGGGACTGGAATTCTCGGGTGCCAAGGAACTCCAG 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 29bp) GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTAATCTGGAATTCT 8 0.2 No Hit AATATTGGGTAGGTTGTGGTATTTCATTGCTGGAATTCTCGGGTGCCAAG 8 0.2 No Hit ATGCAGTTACTAATTCATGATCTGGCTGGAATTCTCGGGTGCCAAGGAAC 8 0.2 RNA PCR Primer, Index 1 (100% over 24bp) GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGTTGGAATTCTCGGGT 8 0.2 No Hit TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTAGAGATCTCGTATGC 8 0.2 RNA PCR Primer, Index 17 (100% over 50bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTGGAATTCTCGGGTG 7 0.17500000000000002 No Hit AATATTGGGTAGGTTGTGGTATTTCATTGCTTGGAATTCTCGGGTGCCAA 7 0.17500000000000002 No Hit CATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAAC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 24bp) AAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit ATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACT 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 25bp) ATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 23bp) GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTGGAATTCTCGGGT 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATGGAATTCTCGGGTGCCAAGGA 6 0.15 RNA PCR Primer, Index 1 (100% over 22bp) GACACGACTCTCGGCAACGGATATCTCGGCTTGGAATTCTCGGGTGCCAA 6 0.15 No Hit GAACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTC 6 0.15 RNA PCR Primer, Index 1 (100% over 26bp) ACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCCA 6 0.15 RNA PCR Primer, Index 1 (100% over 28bp) TGTCGTGCCAATTCAACATAAACCCCTGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) AAGCTGAAGCGGAAATGCAATTCTCGGGTGAGATGGAATTCTCGGGTGCC 6 0.15 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACCTGGAATTCTCGGGTGCC 6 0.15 No Hit GCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAA 6 0.15 RNA PCR Primer, Index 1 (100% over 23bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATGGAATTCTCGGGTG 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAATGGAATTCTCGGGTGCCA 5 0.125 No Hit GGGATTGTAGTTCAATTGGACAGAGCACCGCCCTGGAATTCTCGGGTGCC 5 0.125 No Hit TTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 5 0.125 RNA PCR Primer, Index 1 (100% over 31bp) GTCCTGCGGCAAAATAGCTCGATGCCAGAATTGGAATTCTCGGGTGCCAA 5 0.125 No Hit TGTCGTGCCAATTCAACATAAACCCCTTGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATTGGAATTCTCGGGT 5 0.125 No Hit GACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) TGTCGTGCCAATTCAACATAAACCCTGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGGAATTCTCGGGTGCC 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTAATGGAATTCTCGGGTGCCA 5 0.125 No Hit AACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGT 5 0.125 RNA PCR Primer, Index 1 (100% over 30bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGAATGGAATTCTCGGGTG 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCAAATGGAATTCTCGGGTGC 5 0.125 No Hit CTGCCACGATCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAA 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 0.3 0.0 0.0 0.0 2 0.0 0.3 0.0 0.0 0.0 3 0.0 0.3 0.0 0.0 0.0 4 0.0 0.3 0.0 0.0 0.0 5 0.0 0.3 0.0 0.0 0.0 6 0.0 0.325 0.0 0.0 0.0 7 0.0 0.325 0.0 0.0 0.0 8 0.0 0.35 0.0 0.0 0.0 9 0.0 0.35 0.0 0.0 0.0 10-11 0.0 0.35 0.0 0.0 0.0 12-13 0.0 0.4125 0.0 0.0 0.0 14-15 0.0 0.44999999999999996 0.0 0.0 0.0 16-17 0.0 0.5 0.0 0.0 0.0 18-19 0.0 0.775 0.0 0.0 0.0 20-21 0.0 1.6375 0.0 0.0 0.0 22-23 0.0 8.375 0.0 0.0 0.0 24-25 0.0 19.125 0.0 0.0 0.0 26-27 0.0 29.275 0.0 0.0 0.0 28-29 0.0 33.5625 0.0 0.0 0.0 30-31 0.0 45.1875 0.0 0.0 0.0 32-33 0.0 62.4375 0.0 0.0 0.0 34-35 0.0 80.9 0.0 0.0 0.0 36-37 0.0 90.51249999999999 0.0 0.0 0.0 38-39 0.0 93.1125 0.0 0.0 0.0 40-41 0.0 94.4625 0.0 0.0 0.0 42-43 0.0 95.9375 0.0 0.0 0.0 44-45 0.0 96.35 0.0 0.0 0.0 46-47 0.0 96.65 0.0 0.0 0.0 48-49 0.0 96.7625 0.0 0.0 0.0 50-51 0.0 96.775 0.0 0.0 0.0 52-53 0.0 96.775 0.0 0.0 0.0 54-55 0.0 96.775 0.0 0.0 0.0 56-57 0.0 96.775 0.0 0.0 0.0 58-59 0.0 96.775 0.0 0.0 0.0 60-61 0.0 96.775 0.0 0.0 0.0 62-63 0.0 96.775 0.0 0.0 0.0 64-65 0.0 96.775 0.0 0.0 0.0 66-67 0.0 96.775 0.0 0.0 0.0 68-69 0.0 96.775 0.0 0.0 0.0 70-71 0.0 96.775 0.0 0.0 0.0 72-73 0.0 96.775 0.0 0.0 0.0 74-75 0.0 96.775 0.0 0.0 0.0 76-77 0.0 96.775 0.0 0.0 0.0 78-79 0.0 96.775 0.0 0.0 0.0 80-81 0.0 96.7875 0.0 0.0 0.0 82-83 0.0 96.8125 0.0 0.0 0.0 84-85 0.0 96.825 0.0 0.0 0.0 86-87 0.0 96.825 0.0 0.0 0.0 88-89 0.0 96.825 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GTAGACC 40 5.456968E-12 95.00001 7 AGTAGAC 40 5.456968E-12 95.00001 6 GAGTAGA 40 5.456968E-12 95.00001 5 CGAGTAG 40 5.456968E-12 95.00001 4 AGACCTT 40 5.456968E-12 95.00001 9 ATCGAGT 40 5.456968E-12 95.00001 2 TCGAGTA 40 5.456968E-12 95.00001 3 TAGACCT 40 5.456968E-12 95.00001 8 CATCGAG 40 5.456968E-12 95.00001 1 AGCTCAG 25 3.8289727E-7 95.0 9 TTGTAGT 30 9.458745E-9 95.0 5 GGGTAGG 15 6.142176E-4 95.0 6 ATTGGGT 15 6.142176E-4 95.0 3 TAGCTCA 25 3.8289727E-7 95.0 8 GGATTGT 30 9.458745E-9 95.0 2 TATTGGG 15 6.142176E-4 95.0 2 GATTGTA 30 9.458745E-9 95.0 3 TTGGGTA 15 6.142176E-4 95.0 4 ATAGCTC 15 6.142176E-4 95.0 7 ATTGTAG 30 9.458745E-9 95.0 4 >>END_MODULE Rejected 278380 READS because READLEN < 1 Read 278380 spots for SRR6941557.sra Written 278380 spots for SRR6941557.sra Rejected 278380 READS because READLEN < 1 Read 278380 spots for SRR6941557.sra Written 278380 spots for SRR6941557.sra Rejected 278380 READS because READLEN < 1 Read 278380 spots for SRR6941557.sra Written 278380 spots for SRR6941557.sra Rejected 278380 READS because READLEN < 1 Read 278380 spots for SRR6941557.sra Written 278380 spots for SRR6941557.sra Rejected 278380 READS because READLEN < 1 Read 278380 spots for SRR6941557.sra Written 278380 spots for SRR6941557.sra Rejected 278380 READS because READLEN < 1 Read 278380 spots for SRR6941557.sra Written 278380 spots for SRR6941557.sra Rejected 278380 READS because READLEN < 1 Read 278380 spots for SRR6941557.sra Written 278380 spots for SRR6941557.sra Rejected 278380 READS because READLEN < 1 Read 278380 spots for SRR6941557.sra Written 278380 spots for SRR6941557.sra Rejected 278380 READS because READLEN < 1 Read 278380 spots for SRR6941557.sra Written 278380 spots for SRR6941557.sra Rejected 278380 READS because READLEN < 1 Read 278380 spots for SRR6941557.sra Written 278380 spots for SRR6941557.sra Rejected 278380 READS because READLEN < 1 Read 278380 spots for SRR6941557.sra Written 278380 spots for SRR6941557.sra Rejected 278380 READS because READLEN < 1 Read 278380 spots for SRR6941557.sra Written 278380 spots for SRR6941557.sra Rejected 278380 READS because READLEN < 1 Read 278380 spots for SRR6941557.sra Written 278380 spots for SRR6941557.sra Rejected 278380 READS because READLEN < 1 Read 278380 spots for SRR6941557.sra Written 278380 spots for SRR6941557.sra Rejected 278380 READS because READLEN < 1 Read 278380 spots for SRR6941557.sra Written 278380 spots for SRR6941557.sra Rejected 278380 READS because READLEN < 1 Read 278380 spots for SRR6941557.sra Written 278380 spots for SRR6941557.sra Rejected 278380 READS because READLEN < 1 Read 278380 spots for SRR6941557.sra Written 278380 spots for SRR6941557.sra Rejected 278380 READS because READLEN < 1 Read 278380 spots for SRR6941557.sra Written 278380 spots for SRR6941557.sra Rejected 278380 READS because READLEN < 1 Read 278380 spots for SRR6941557.sra Written 278380 spots for SRR6941557.sra Rejected 278388 READS because READLEN < 1 Read 278388 spots for SRR6941557.sra Written 278388 spots for SRR6941557.sra SRR ids: ['SRR6941557.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_goj94uqf SRR6941557.sra spots: 5567608 blocks: [[1, 278380], [278381, 556760], [556761, 835140], [835141, 1113520], [1113521, 1391900], [1391901, 1670280], [1670281, 1948660], [1948661, 2227040], [2227041, 2505420], [2505421, 2783800], [2783801, 3062180], [3062181, 3340560], [3340561, 3618940], [3618941, 3897320], [3897321, 4175700], [4175701, 4454080], [4454081, 4732460], [4732461, 5010840], [5010841, 5289220], [5289221, 5567608]] SRR6941557 file size 1329924 SRR6941557 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 SRR6941557 SRR6941557_1.fastq Input file: SRR6941557_1.fastq trimmed: SRR6941557-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 11:15:12 2024 >> started Fri Dec 6 11:15:18 2024 >> done (5.456s) 5567608 reads processed; of these: 100 ( 0.00%) short reads filtered out after trimming by size control 9 ( 0.00%) empty reads filtered out after trimming by size control 5567499 (100.00%) reads available; of these: 709476 (12.74%) trimmed reads available after processing 4858023 (87.26%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 5 0.00% 19 7 0.00% 20 7 0.00% 21 7 0.00% 22 14 0.00% 23 12 0.00% 24 9 0.00% 25 14 0.00% 26 18 0.00% 27 20 0.00% 28 24 0.00% 29 32 0.00% 30 37 0.00% 31 25 0.00% 32 27 0.00% 33 26 0.00% 34 31 0.00% 35 36 0.00% 36 34 0.00% 37 28 0.00% 38 38 0.00% 39 32 0.00% 40 37 0.00% 41 33 0.00% 42 48 0.00% 43 73 0.00% 44 54 0.00% 45 86 0.00% 46 104 0.00% 47 76 0.00% 48 55 0.00% 49 58 0.00% 50 60 0.00% 51 45 0.00% 52 52 0.00% 53 36 0.00% 54 52 0.00% 55 55 0.00% 56 53 0.00% 57 44 0.00% 58 40 0.00% 59 69 0.00% 60 89 0.00% 61 66 0.00% 62 56 0.00% 63 60 0.00% 64 44 0.00% 65 54 0.00% 66 90 0.00% 67 82 0.00% 68 104 0.00% 69 129 0.00% 70 178 0.00% 71 190 0.00% 72 320 0.01% 73 849 0.02% 74 5801 0.10% 75 3906 0.07% 76 1191 0.02% 77 397 0.01% 78 521 0.01% 79 486 0.01% 80 642 0.01% 81 560 0.01% 82 718 0.01% 83 907 0.02% 84 1298 0.02% 85 1383 0.02% 86 1581 0.03% 87 1759 0.03% 88 2039 0.04% 89 2844 0.05% 90 3781 0.07% 91 6867 0.12% 92 9388 0.17% 93 17466 0.31% 94 31639 0.57% 95 89924 1.62% 96 95872 1.72% 97 95492 1.72% 98 140244 2.52% 99 137860 2.48% 100 50986 0.92% 101 4858023 87.26% 5567499 reads passed initial QC criterion=sequence-density sequence-density=97.61 sequence-density-rank=1 fanout-score=26.00 fanout-score-rank=2 prefix-density=97.74 prefix-fanout=26.0 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTAGAGATCTCGTATGCCGTCTTCTGCTTGAAAAAA criterion=fanout-score sequence-density=1.93 sequence-density-rank=6 fanout-score=51.73 fanout-score-rank=1 prefix-density=98.61 prefix-fanout=1.0 sequence=CACGTAGAGATATCGTATGCCGT 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTAGAGATCTCGTATGCCGTCTTCTGCTTGAAAAAA -o SRR6941557 - Input file: STDIN trimmed: SRR6941557-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTAGAGATCTCGTATGCCGTCTTCTGCTTGA -- 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 11:15:40 2024 >> started Fri Dec 6 11:15:46 2024 >> done (6.759s) 5453877 reads processed; of these: 25157 ( 0.46%) short reads filtered out after trimming by size control 21488 ( 0.39%) empty reads filtered out after trimming by size control 5407232 (99.14%) reads available; of these: 5379098 (99.48%) trimmed reads available after processing 28134 ( 0.52%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 11923 0.22% 19 27081 0.50% 20 42073 0.78% 21 219208 4.05% 22 184822 3.42% 23 133705 2.47% 24 806849 14.92% 25 153552 2.84% 26 143234 2.65% 27 120816 2.23% 28 122466 2.26% 29 290524 5.37% 30 547691 10.13% 31 403538 7.46% 32 471595 8.72% 33 610859 11.30% 34 385080 7.12% 35 278035 5.14% 36 125754 2.33% 37 72491 1.34% 38 41232 0.76% 39 31026 0.57% 40 44988 0.83% 41 45373 0.84% 42 30475 0.56% 43 8610 0.16% 44 10021 0.19% 45 6891 0.13% 46 2468 0.05% 47 2759 0.05% 48 920 0.02% 49 449 0.01% 50 284 0.01% 51 233 0.00% 52 120 0.00% 53 86 0.00% 54 74 0.00% 55 60 0.00% 56 30 0.00% 57 42 0.00% 58 30 0.00% 59 34 0.00% 60 41 0.00% 61 21 0.00% 62 28 0.00% 63 26 0.00% 64 13 0.00% 65 21 0.00% 66 23 0.00% 67 32 0.00% 68 28 0.00% 69 40 0.00% 70 49 0.00% 71 32 0.00% 72 34 0.00% 73 43 0.00% 74 36 0.00% 75 52 0.00% 76 101 0.00% 77 341 0.01% 78 61 0.00% 79 72 0.00% 80 458 0.01% 81 131 0.00% 82 271 0.01% 83 176 0.00% 84 64 0.00% 85 71 0.00% 86 116 0.00% 87 161 0.00% 88 113 0.00% 89 101 0.00% 90 109 0.00% 91 175 0.00% 92 171 0.00% 93 179 0.00% 94 225 0.00% 95 307 0.01% 96 294 0.01% 97 367 0.01% 98 562 0.01% 99 376 0.01% 100 417 0.01% 101 23793 0.44% criterion=sequence-density sequence-density=10.93 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=16 prefix-density=0.00 prefix-fanout=1.0 sequence=CATCGAGTAGACCTTGTTATTGTGAGAATTCT criterion=fanout-score sequence-density=0.01 sequence-density-rank=37 fanout-score=45.36 fanout-score-rank=1 prefix-density=0.16 prefix-fanout=1.9 sequence=TGCCAAGGATGTTTTCATTAATCAAGAACGAAAGTTGGGGGCTCGAAGACGATCAGATACCGTCCTAGTCTCAACCATAAACGATGCCGACCAGGGATCGGCGGATGTTGCTTATAGGACTCCGCCGGCACCTTATGAGAAATCAAAGTCTTTGGGTTCCGGGGGGAGTATGGTCGCAAGGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGCGTGGAGCCTGCGGCT Started job on | Dec 06 11:16:00 Started mapping on | Dec 06 11:16:01 Finished on | Dec 06 11:16:19 Mapping speed, Million of reads per hour | 1104.17 Number of input reads | 5520854 Average input read length | 31 UNIQUE READS: Uniquely mapped reads number | 776475 Uniquely mapped reads % | 14.06% Average mapped length | 26.26 Number of splices: Total | 19814 Number of splices: Annotated (sjdb) | 2930 Number of splices: GT/AG | 19100 Number of splices: GC/AG | 583 Number of splices: AT/AC | 4 Number of splices: Non-canonical | 127 Mismatch rate per base, % | 0.99% Deletion rate per base | 0.01% Deletion average length | 1.35 Insertion rate per base | 0.00% Insertion average length | 1.25 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 3521009 % of reads mapped to multiple loci | 63.78% Number of reads mapped to too many loci | 958776 % of reads mapped to too many loci | 17.37% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.15% % of reads unmapped: other | 0.64% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1223370 1223370 1223370 N_multimapping 3521009 3521009 3521009 N_noFeature 490120 598752 663515 N_ambiguous 9675 4945 481 UnstrandedReadsAssigned:276680 PositiveStrandReadsAssigned:172778 NegativeStrandReadsAssigned:112479 Dataset is classified unstranded MeadianReadLen=30 20thPercentileLength=24 echo kmer=19 SRR6941557 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: SRR6941557-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 5,520,854 reads, 2,313,688 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 933 rounds 52973 SRR6941557.ke.tsv 35125 SRR6941557.se.tsv 88098 total ==> SRR6941557.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 1 1.14229 KQK14069 1603 1504 23.1153 3.40589 KQK14071 474 375 0 0 ==> SRR6941557.se.tsv <== BRADI_1g14170v3 36 BRADI_1g53295v3 2 BRADI_1g59795v3 0 BRADI_1g07683v3 0 BRADI_1g00485v3 3 BRADI_1g20270v3 2 BRADI_1g74790v3 6 BRADI_1g09890v3 17 BRADI_1g77505v3 0 BRADI_1g48960v3 0 SRR6941557 completed mapping pipeline successfully