Starting /dee2/code/volunteer_pipeline.sh SRR6941580 current disk space = 1551397756928 free memory = 1598854716 SRR6941580 SRAfilesize 69581f9f4c6e24278201b53f85d08fca SRR6941580.sra SRR6941580.sra file validated SRR6941580 is single end SRR6941580 is conventional basespace SRR6941580 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6941580_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 33.07975 34.0 33.0 34.0 32.0 34.0 2 33.202 34.0 33.0 34.0 32.0 34.0 3 32.63525 34.0 33.0 34.0 29.0 34.0 4 32.99575 34.0 33.0 34.0 32.0 34.0 5 33.0745 34.0 33.0 34.0 31.0 34.0 6 36.95725 38.0 37.0 38.0 36.0 38.0 7 37.2275 38.0 38.0 38.0 36.0 38.0 8 37.441 38.0 38.0 38.0 37.0 38.0 9 37.479 38.0 38.0 38.0 37.0 38.0 10-11 37.445125000000004 38.0 38.0 38.0 37.0 38.0 12-13 37.365625 38.0 38.0 38.0 37.0 38.0 14-15 37.4025 38.0 38.0 38.0 37.0 38.0 16-17 36.14875 38.0 37.5 38.0 31.5 38.0 18-19 36.848625 38.0 37.5 38.0 33.5 38.0 20-21 35.80375 38.0 37.5 38.0 30.5 38.0 22-23 36.8755 38.0 38.0 38.0 35.0 38.0 24-25 37.265249999999995 38.0 38.0 38.0 37.0 38.0 26-27 37.171125 38.0 38.0 38.0 36.5 38.0 28-29 37.188375 38.0 38.0 38.0 36.5 38.0 30-31 37.25075 38.0 38.0 38.0 37.0 38.0 32-33 37.193375 38.0 38.0 38.0 36.5 38.0 34-35 37.216875 38.0 38.0 38.0 37.0 38.0 36-37 37.100750000000005 38.0 38.0 38.0 36.5 38.0 38-39 37.075375 38.0 38.0 38.0 36.0 38.0 40-41 37.000625 38.0 38.0 38.0 36.0 38.0 42-43 37.00375 38.0 38.0 38.0 36.0 38.0 44-45 37.089875 38.0 38.0 38.0 36.5 38.0 46-47 36.970375 38.0 38.0 38.0 36.0 38.0 48-49 37.12 38.0 38.0 38.0 36.5 38.0 50-51 36.886125 38.0 38.0 38.0 36.0 38.0 52-53 36.840374999999995 38.0 38.0 38.0 35.5 38.0 54-55 36.95 38.0 38.0 38.0 36.0 38.0 56-57 36.804625 38.0 38.0 38.0 35.0 38.0 58-59 36.951875 38.0 38.0 38.0 36.0 38.0 60-61 36.859 38.0 38.0 38.0 36.0 38.0 62-63 36.612624999999994 38.0 38.0 38.0 34.5 38.0 64-65 36.100624999999994 38.0 37.5 38.0 31.5 38.0 66-67 35.849000000000004 38.0 37.0 38.0 31.0 38.0 68-69 36.40975 38.0 38.0 38.0 33.5 38.0 70-71 35.929249999999996 38.0 37.0 38.0 30.0 38.0 72-73 35.487875 38.0 37.0 38.0 28.0 38.0 74-75 34.774125 38.0 36.0 38.0 25.0 38.0 76-77 35.442875 38.0 36.5 38.0 28.5 38.0 78-79 35.99325 38.0 37.5 38.0 32.0 38.0 80-81 36.416375 38.0 38.0 38.0 34.5 38.0 82-83 36.371875 38.0 38.0 38.0 34.5 38.0 84-85 36.28625 38.0 38.0 38.0 34.0 38.0 86-87 36.139624999999995 38.0 38.0 38.0 33.5 38.0 88-89 36.056125 38.0 38.0 38.0 33.5 38.0 90-91 35.876875 38.0 38.0 38.0 33.5 38.0 92-93 35.757125 38.0 38.0 38.0 33.5 38.0 94-95 35.27975 38.0 38.0 38.0 32.0 38.0 96-97 33.212500000000006 38.0 36.0 38.0 8.5 38.0 98-99 30.813375 38.0 31.0 38.0 2.0 38.0 100-101 28.215125 38.0 24.5 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 6 1.0 7 0.0 8 0.0 9 1.0 10 0.0 11 1.0 12 0.0 13 1.0 14 0.0 15 2.0 16 0.0 17 2.0 18 1.0 19 1.0 20 3.0 21 3.0 22 2.0 23 4.0 24 8.0 25 9.0 26 11.0 27 21.0 28 24.0 29 46.0 30 58.0 31 70.0 32 79.0 33 118.0 34 209.0 35 477.0 36 794.0 37 2054.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 39.975 23.474999999999998 14.649999999999999 21.9 2 33.31665832916458 28.36418209104552 20.08504252126063 18.234117058529264 3 33.900000000000006 18.65 23.575 23.875 4 26.088044022011005 34.242121060530266 14.932466233116559 24.73736868434217 5 41.025 17.95 25.650000000000002 15.375 6 22.225 31.374999999999996 27.150000000000002 19.25 7 44.15 22.025 19.950000000000003 13.875000000000002 8 22.475 14.249999999999998 46.475 16.8 9 18.2 44.175 22.45 15.174999999999999 10-11 38.625 24.1625 20.3375 16.875 12-13 17.675 14.2625 25.95 42.112500000000004 14-15 20.075000000000003 41.925000000000004 24.3875 13.612499999999999 16-17 27.05 16.7125 42.3625 13.875000000000002 18-19 44.6125 19.425 22.85 13.112499999999999 20-21 13.8 27.750000000000004 38.012499999999996 20.4375 22-23 31.624999999999996 30.325000000000003 22.75 15.299999999999999 24-25 31.7 29.65 21.8625 16.7875 26-27 37.0 25.35 19.537499999999998 18.1125 28-29 17.925 35.2875 20.95 25.837500000000002 30-31 22.85 11.025 42.725 23.400000000000002 32-33 28.287499999999998 12.1875 29.362500000000004 30.162499999999998 34-35 37.5 19.775000000000002 27.0125 15.712499999999999 36-37 42.262499999999996 21.55 25.112499999999997 11.075 38-39 23.05 22.8125 35.4375 18.7 40-41 20.5375 14.512500000000001 27.2625 37.6875 42-43 32.6125 24.6 20.4625 22.325 44-45 55.275 12.85 14.4125 17.4625 46-47 31.7625 26.575 17.525 24.1375 48-49 22.9375 22.237499999999997 18.7625 36.0625 50-51 25.337500000000002 27.125 8.475000000000001 39.0625 52-53 32.2875 42.9375 6.2625 18.512500000000003 54-55 24.587500000000002 29.25 18.125 28.037499999999998 56-57 15.512500000000001 34.7375 11.7875 37.9625 58-59 25.174999999999997 26.1 18.4 30.325000000000003 60-61 27.3625 22.1 22.4625 28.075 62-63 35.5 20.837500000000002 19.2625 24.4 64-65 20.2375 30.85 22.925 25.9875 66-67 28.8875 17.974999999999998 24.875 28.262500000000003 68-69 42.4625 20.2375 18.7375 18.5625 70-71 33.825 22.5125 32.3625 11.3 72-73 32.375 15.262500000000001 31.924999999999997 20.4375 74-75 19.5 10.3875 29.549999999999997 40.5625 76-77 22.2 11.075 42.175000000000004 24.55 78-79 21.7375 9.925 41.275 27.0625 80-81 21.325 12.812499999999998 35.175 30.6875 82-83 28.575 7.7 36.225 27.500000000000004 84-85 20.6125 7.9750000000000005 35.3375 36.075 86-87 19.375 14.0625 40.9875 25.575 88-89 11.875 32.65 36.0875 19.3875 90-91 11.2375 35.6375 32.5625 20.5625 92-93 17.7875 40.475 24.9375 16.8 94-95 12.375 54.725 23.9375 8.9625 96-97 11.2875 71.72500000000001 13.225000000000001 3.7624999999999997 98-99 5.175 86.85000000000001 5.2124999999999995 2.7625 100-101 2.9749999999999996 90.85 3.6999999999999997 2.475 >>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 0.0 34 0.5 35 1.5 36 3.5 37 4.5 38 4.5 39 4.0 40 7.0 41 14.0 42 29.0 43 85.5 44 198.5 45 437.0 46 521.5 47 387.5 48 348.5 49 295.5 50 211.0 51 287.0 52 382.5 53 341.5 54 208.0 55 78.0 56 51.5 57 44.0 58 16.5 59 14.0 60 14.5 61 4.0 62 1.5 63 0.5 64 1.5 65 1.5 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 0.05 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 50.9 #Duplication Level Percentage of deduplicated Percentage of total 1 87.62278978388997 44.6 2 4.174852652259331 4.25 3 2.5540275049115913 3.9 4 1.1787819253438114 2.4 5 0.9332023575638507 2.375 6 0.343811394891945 1.05 7 0.4911591355599214 1.7500000000000002 8 0.29469548133595286 1.2 9 0.2455795677799607 1.125 >10 1.719056974459725 19.125 >50 0.3929273084479371 14.249999999999998 >100 0.04911591355599214 3.975 >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 159 3.975 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 100 2.5 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTTGGAATTCTCGGGTG 94 2.35 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 92 2.3 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 65 1.625 No Hit GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 64 1.6 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTGGAATTCTCGGGTGCCAA 53 1.325 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTTGGAATTCTCGGGTGCCA 51 1.275 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTTGGAATTCTCGGGTGC 51 1.275 No Hit CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 49 1.225 RNA PCR Primer, Index 1 (100% over 28bp) ATATTGGGTAGGTTGTGGTATTTCATTGCTTGGAATTCTCGGGTGCCAAG 46 1.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTGGAATTCTCGGGTGCCA 45 1.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 42 1.05 Illumina Small RNA Adapter 2 (100% over 21bp) TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 41 1.0250000000000001 RNA PCR Primer, Index 1 (100% over 29bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 40 1.0 No Hit TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 33 0.8250000000000001 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTGGAATTCTCGGGTGCCAAGG 30 0.75 Illumina Small RNA Adapter 2 (100% over 21bp) GAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTGC 27 0.675 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGGAATTCTCGGGTGCCA 26 0.65 No Hit TCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTC 24 0.6 RNA PCR Primer, Index 1 (100% over 26bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 24 0.6 Illumina Small RNA Adapter 2 (100% over 21bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGGAATTCTCGGGTGC 24 0.6 No Hit GGGTGTTTGGTCTAGTGGTATGATTCTCGCTTGGAATTCTCGGGTGCCAA 21 0.525 No Hit TCGCTTGGTGCAGATCGGGACTGGAATTCTCGGGTGCCAAGGAACTCCAG 20 0.5 RNA PCR Primer, Index 1 (100% over 29bp) GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTTGGAATTCTCGGGTGC 18 0.44999999999999996 No Hit ACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCCA 18 0.44999999999999996 RNA PCR Primer, Index 1 (100% over 28bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGGAATTCTCGGGTGCCAA 18 0.44999999999999996 No Hit CGGTCGAGGGCACGCCTGCCTGGGCGTCACGCTGGAATTCTCGGGTGCCA 17 0.42500000000000004 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 16 0.4 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACCTGGAATTCTCGGGTGCC 16 0.4 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTAATCTGGAATTCT 15 0.375 No Hit GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTTGGAATTCTCGGGTGC 15 0.375 No Hit TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGAGTGGATCTCGTATGC 14 0.35000000000000003 RNA PCR Primer, Index 23 (100% over 50bp) CATCGAGTAGACCTTGTTATTGTGAGAATGGAATTCTCGGGTGCCAAGGA 13 0.325 RNA PCR Primer, Index 1 (100% over 22bp) CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTA 13 0.325 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATACTCTGGAATTCTCGGGTGCCAAG 12 0.3 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 12 0.3 Illumina Small RNA Adapter 2 (100% over 21bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGATGGAATTCTC 12 0.3 No Hit AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 12 0.3 Illumina Small RNA Adapter 2 (100% over 21bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGTGGAATTCTCGGGTGCC 11 0.27499999999999997 No Hit TTTCGTGCTTATCCTAGTTGTTGGTTTAGTTGGAATTCTCGGGTGCCAAG 11 0.27499999999999997 No Hit GGGATTGTAGTTCAATTGGACAGAGCACCGCCCTGGAATTCTCGGGTGCC 10 0.25 No Hit TTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 10 0.25 RNA PCR Primer, Index 1 (100% over 31bp) TTGACAGAAGAGAGTGAGCACTGGAATTCTCGGGTGCCAAGGAACTCCAG 10 0.25 RNA PCR Primer, Index 1 (100% over 29bp) GAACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTC 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 26bp) TAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAG 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 29bp) AATATTGGGTAGGTTGTGGTATTTCATTGCTGGAATTCTCGGGTGCCAAG 9 0.22499999999999998 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCTGGAATTC 9 0.22499999999999998 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTATGGAATTCTCGGGTGCCAA 9 0.22499999999999998 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAATGGAATTCTCGGGTGCCA 8 0.2 No Hit CACCATGCGCGGGTTCAATTCCCGTCGTTCGCCCCATGGAATTCTCGGGT 8 0.2 No Hit TGTCGTGCCAATTCAACATAAACCCTGGAATTCTCGGGTGCCAAGGAACT 8 0.2 RNA PCR Primer, Index 1 (100% over 25bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCAATGGAATTCTCGGGTGCC 8 0.2 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTGAATCTGGAATTC 8 0.2 No Hit GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGTTGGAATTCTCGGGT 8 0.2 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTGGAATTCTCGGGT 7 0.17500000000000002 No Hit AGAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTG 7 0.17500000000000002 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCTGGAATTCTCGGG 7 0.17500000000000002 No Hit TCGGACCAGGCTTCGATCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 29bp) CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 23bp) GTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTTGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit CACGACTCTCGGCAACGGATATCTCGGCTTGGAATTCTCGGGTGCCAAGG 7 0.17500000000000002 Illumina Small RNA Adapter 2 (100% over 21bp) CTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCCAG 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 29bp) ATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACT 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 25bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTAAATGGAATTCTCGGGTG 7 0.17500000000000002 No Hit AATATTGGGTAGGTTGTGGTATTTCATTGCTTGGAATTCTCGGGTGCCAA 6 0.15 No Hit GTCAGGATAGCTCAGTTGGGAGAGCAGAGGACTTGGAATTCTCGGGTGCC 6 0.15 No Hit CTCTGATGATGATCAAACTAATACTTTCGTTCTTCTGGAATTCTCGGGTG 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTAATGGAATTCTCGGGTGC 6 0.15 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTTGGAATTCTCGGG 6 0.15 No Hit CAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTC 6 0.15 RNA PCR Primer, Index 1 (100% over 26bp) CCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACT 6 0.15 RNA PCR Primer, Index 1 (100% over 25bp) TGAAGCTGCCAGCATGATCTGATGGAATTCTCGGGTGCCAAGGAACTCCA 5 0.125 RNA PCR Primer, Index 1 (100% over 28bp) GGGATTGTAGTTCAATAGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 5 0.125 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATATGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) GGGCCTGTAGCTCAGAGGATTAGAGCACGTGGCTGGAATTCTCGGGTGCC 5 0.125 No Hit GTCAGGATAGCTCAGTTGGAAGAGCAGAGGACTTGGAATTCTCGGGTGCC 5 0.125 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTATGGAATTCTCGGGTGCCAA 5 0.125 No Hit ACGAACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTTTGGAATTCTCGGGTGCC 5 0.125 No Hit AGAAGAGAGAGAGTACAGCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG 5 0.125 RNA PCR Primer, Index 1 (100% over 29bp) CAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTG 5 0.125 No Hit GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTTTGGAATTCTCGGGTG 5 0.125 No Hit CATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) GACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACG 5 0.125 No Hit TGCCACGATCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAAT 5 0.125 No Hit GAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC 5 0.125 RNA PCR Primer, Index 1 (100% over 33bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCAAATGGAATTCTCGGGTGC 5 0.125 No Hit GCGAGCGTAGTTCAATTGTAAAACATCTCCTTTGGAATTCTCGGGTGCCA 5 0.125 No Hit GGGATTGTAGTTCAATGGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATGGAATTCTCGGGTG 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 0.425 0.0 0.0 0.0 2 0.0 0.425 0.0 0.0 0.0 3 0.0 0.425 0.0 0.0 0.0 4 0.0 0.45 0.0 0.0 0.0 5 0.0 0.475 0.0 0.0 0.0 6 0.0 0.475 0.0 0.0 0.0 7 0.0 0.475 0.0 0.0 0.0 8 0.0 0.5 0.0 0.0 0.0 9 0.0 0.55 0.0 0.0 0.0 10-11 0.0 0.6000000000000001 0.0 0.0 0.0 12-13 0.0 0.6875 0.0 0.0 0.0 14-15 0.0 0.8625 0.0 0.0 0.0 16-17 0.0 1.4125 0.0 0.0 0.0 18-19 0.0 2.325 0.0 0.0 0.0 20-21 0.0 3.65 0.0 0.0 0.0 22-23 0.0 10.3625 0.0 0.0 0.0 24-25 0.0 22.05 0.0 0.0 0.0 26-27 0.0 33.075 0.0 0.0 0.0 28-29 0.0 36.3625 0.0 0.0 0.0 30-31 0.0 46.5625 0.0 0.0 0.0 32-33 0.0 61.3 0.0 0.0 0.0 34-35 0.0 80.6375 0.0 0.0 0.0 36-37 0.0 90.375 0.0 0.0 0.0 38-39 0.0 92.94999999999999 0.0 0.0 0.0 40-41 0.0 94.0 0.0 0.0 0.0 42-43 0.0 95.9 0.0 0.0 0.0 44-45 0.0 96.61250000000001 0.0 0.0 0.0 46-47 0.0 96.85 0.0 0.0 0.0 48-49 0.0 96.875 0.0 0.0 0.0 50-51 0.0 96.875 0.0 0.0 0.0 52-53 0.0 96.875 0.0 0.0 0.0 54-55 0.0 96.875 0.0 0.0 0.0 56-57 0.0 96.875 0.0 0.0 0.0 58-59 0.0 96.875 0.0 0.0 0.0 60-61 0.0 96.875 0.0 0.0 0.0 62-63 0.0 96.875 0.0 0.0 0.0 64-65 0.0 96.875 0.0 0.0 0.0 66-67 0.0 96.875 0.0 0.0 0.0 68-69 0.0 96.875 0.0 0.0 0.0 70-71 0.0 96.875 0.0 0.0 0.0 72-73 0.0 96.875 0.0 0.0 0.0 74-75 0.0 96.9 0.0 0.0 0.0 76-77 0.0 96.9125 0.0 0.0 0.0 78-79 0.0 96.925 0.0 0.0 0.0 80-81 0.0 96.9375 0.0 0.0 0.0 82-83 0.0 96.975 0.0 0.0 0.0 84-85 0.0 96.975 0.0 0.0 0.0 86-87 0.0 96.975 0.0 0.0 0.0 88-89 0.0 96.975 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GTAGACC 50 0.0 95.0 7 AGGATAG 30 9.458745E-9 95.0 4 TCAGGAT 30 9.458745E-9 95.0 2 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 TAGTTCA 50 0.0 95.0 8 GGATAGC 30 9.458745E-9 95.0 5 ATAGCTC 30 9.458745E-9 95.0 7 TGTAGCC 15 6.142176E-4 95.0 7 GGGATTG 30 9.458745E-9 95.0 1 CGAGTAG 50 0.0 95.0 4 AGACCTT 50 0.0 95.0 9 CAGGATA 30 9.458745E-9 95.0 3 ATCGAGT 50 0.0 95.0 2 GTCAGGA 30 9.458745E-9 95.0 1 TCGAGTA 50 0.0 95.0 3 AGTTCAA 45 0.0 95.0 9 GTAGTTC 45 0.0 95.0 7 >>END_MODULE Rejected 253476 READS because READLEN < 1 Read 253476 spots for SRR6941580.sra Written 253476 spots for SRR6941580.sra Rejected 253476 READS because READLEN < 1 Read 253476 spots for SRR6941580.sra Written 253476 spots for SRR6941580.sra Rejected 253476 READS because READLEN < 1 Read 253476 spots for SRR6941580.sra Written 253476 spots for SRR6941580.sra Rejected 253476 READS because READLEN < 1 Read 253476 spots for SRR6941580.sra Written 253476 spots for SRR6941580.sra Rejected 253476 READS because READLEN < 1 Read 253476 spots for SRR6941580.sra Written 253476 spots for SRR6941580.sra Rejected 253476 READS because READLEN < 1 Read 253476 spots for SRR6941580.sra Written 253476 spots for SRR6941580.sra Rejected 253476 READS because READLEN < 1 Read 253476 spots for SRR6941580.sra Written 253476 spots for SRR6941580.sra Rejected 253476 READS because READLEN < 1 Read 253476 spots for SRR6941580.sra Written 253476 spots for SRR6941580.sra Rejected 253476 READS because READLEN < 1 Read 253476 spots for SRR6941580.sra Written 253476 spots for SRR6941580.sra Rejected 253476 READS because READLEN < 1 Read 253476 spots for SRR6941580.sra Written 253476 spots for SRR6941580.sra Rejected 253476 READS because READLEN < 1 Read 253476 spots for SRR6941580.sra Written 253476 spots for SRR6941580.sra Rejected 253476 READS because READLEN < 1 Read 253476 spots for SRR6941580.sra Written 253476 spots for SRR6941580.sra Rejected 253476 READS because READLEN < 1 Read 253476 spots for SRR6941580.sra Written 253476 spots for SRR6941580.sra Rejected 253476 READS because READLEN < 1 Read 253476 spots for SRR6941580.sra Written 253476 spots for SRR6941580.sra Rejected 253476 READS because READLEN < 1 Read 253476 spots for SRR6941580.sra Written 253476 spots for SRR6941580.sra Rejected 253476 READS because READLEN < 1 Read 253476 spots for SRR6941580.sra Written 253476 spots for SRR6941580.sra Rejected 253476 READS because READLEN < 1 Read 253476 spots for SRR6941580.sra Written 253476 spots for SRR6941580.sra Rejected 253482 READS because READLEN < 1 Read 253482 spots for SRR6941580.sra Written 253482 spots for SRR6941580.sra Rejected 253476 READS because READLEN < 1 Read 253476 spots for SRR6941580.sra Written 253476 spots for SRR6941580.sra Rejected 253476 READS because READLEN < 1 Read 253476 spots for SRR6941580.sra Written 253476 spots for SRR6941580.sra SRR ids: ['SRR6941580.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_iai6eop5 SRR6941580.sra spots: 5069526 blocks: [[1, 253476], [253477, 506952], [506953, 760428], [760429, 1013904], [1013905, 1267380], [1267381, 1520856], [1520857, 1774332], [1774333, 2027808], [2027809, 2281284], [2281285, 2534760], [2534761, 2788236], [2788237, 3041712], [3041713, 3295188], [3295189, 3548664], [3548665, 3802140], [3802141, 4055616], [4055617, 4309092], [4309093, 4562568], [4562569, 4816044], [4816045, 5069526]] SRR6941580 file size 1210754 SRR6941580 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 SRR6941580 SRR6941580_1.fastq Input file: SRR6941580_1.fastq trimmed: SRR6941580-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 11:55:31 2024 >> started Fri Dec 6 11:55:35 2024 >> done (3.183s) 5069526 reads processed; of these: 97 ( 0.00%) short reads filtered out after trimming by size control 14 ( 0.00%) empty reads filtered out after trimming by size control 5069415 (100.00%) reads available; of these: 826956 (16.31%) trimmed reads available after processing 4242459 (83.69%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 10 0.00% 19 4 0.00% 20 11 0.00% 21 11 0.00% 22 16 0.00% 23 18 0.00% 24 22 0.00% 25 22 0.00% 26 16 0.00% 27 40 0.00% 28 40 0.00% 29 53 0.00% 30 47 0.00% 31 31 0.00% 32 54 0.00% 33 41 0.00% 34 52 0.00% 35 50 0.00% 36 69 0.00% 37 54 0.00% 38 49 0.00% 39 69 0.00% 40 71 0.00% 41 95 0.00% 42 96 0.00% 43 97 0.00% 44 77 0.00% 45 124 0.00% 46 129 0.00% 47 115 0.00% 48 96 0.00% 49 89 0.00% 50 76 0.00% 51 83 0.00% 52 90 0.00% 53 91 0.00% 54 88 0.00% 55 87 0.00% 56 107 0.00% 57 85 0.00% 58 92 0.00% 59 124 0.00% 60 164 0.00% 61 104 0.00% 62 97 0.00% 63 102 0.00% 64 92 0.00% 65 89 0.00% 66 141 0.00% 67 134 0.00% 68 196 0.00% 69 215 0.00% 70 330 0.01% 71 331 0.01% 72 440 0.01% 73 1131 0.02% 74 7091 0.14% 75 4349 0.09% 76 1491 0.03% 77 525 0.01% 78 681 0.01% 79 714 0.01% 80 744 0.01% 81 847 0.02% 82 1004 0.02% 83 1319 0.03% 84 2451 0.05% 85 2813 0.06% 86 3210 0.06% 87 3960 0.08% 88 5131 0.10% 89 6984 0.14% 90 10513 0.21% 91 14198 0.28% 92 16857 0.33% 93 27573 0.54% 94 43192 0.85% 95 111615 2.20% 96 101144 2.00% 97 95536 1.88% 98 166842 3.29% 99 141856 2.80% 100 48059 0.95% 101 4242459 83.69% 5069415 reads passed initial QC criterion=sequence-density sequence-density=97.26 sequence-density-rank=1 fanout-score=26.68 fanout-score-rank=3 prefix-density=97.25 prefix-fanout=26.7 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGAGTGGATCTCGTATGCCGTCTTCTGCTTGAAAAAAA criterion=fanout-score sequence-density=0.01 sequence-density-rank=13 fanout-score=97.42 fanout-score-rank=1 prefix-density=0.54 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGAGTGGATCTCGTATGCCGTCTTCTGCTTGAAAAAAA -o SRR6941580 - Input file: STDIN trimmed: SRR6941580-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGAGTGGATCTCGTATGCCGTCTTCTGCTTGA -- 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 11:55:52 2024 >> started Fri Dec 6 11:55:58 2024 >> done (6.287s) 4965958 reads processed; of these: 67644 ( 1.36%) short reads filtered out after trimming by size control 24284 ( 0.49%) empty reads filtered out after trimming by size control 4874030 (98.15%) reads available; of these: 4828569 (99.07%) trimmed reads available after processing 45461 ( 0.93%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 19454 0.40% 19 36747 0.75% 20 46793 0.96% 21 248783 5.10% 22 156352 3.21% 23 117502 2.41% 24 820109 16.83% 25 115809 2.38% 26 97729 2.01% 27 86067 1.77% 28 92798 1.90% 29 267465 5.49% 30 438142 8.99% 31 320206 6.57% 32 401228 8.23% 33 577142 11.84% 34 336213 6.90% 35 268088 5.50% 36 109866 2.25% 37 59739 1.23% 38 32291 0.66% 39 25341 0.52% 40 40241 0.83% 41 42320 0.87% 42 31260 0.64% 43 8588 0.18% 44 11552 0.24% 45 7738 0.16% 46 2853 0.06% 47 2428 0.05% 48 904 0.02% 49 554 0.01% 50 294 0.01% 51 270 0.01% 52 128 0.00% 53 114 0.00% 54 82 0.00% 55 65 0.00% 56 58 0.00% 57 70 0.00% 58 53 0.00% 59 55 0.00% 60 83 0.00% 61 52 0.00% 62 43 0.00% 63 30 0.00% 64 24 0.00% 65 31 0.00% 66 46 0.00% 67 36 0.00% 68 56 0.00% 69 61 0.00% 70 81 0.00% 71 72 0.00% 72 44 0.00% 73 61 0.00% 74 72 0.00% 75 136 0.00% 76 166 0.00% 77 821 0.02% 78 109 0.00% 79 181 0.00% 80 1184 0.02% 81 367 0.01% 82 736 0.02% 83 467 0.01% 84 148 0.00% 85 137 0.00% 86 295 0.01% 87 464 0.01% 88 188 0.00% 89 141 0.00% 90 165 0.00% 91 317 0.01% 92 244 0.01% 93 245 0.01% 94 320 0.01% 95 408 0.01% 96 397 0.01% 97 392 0.01% 98 862 0.02% 99 508 0.01% 100 582 0.01% 101 39767 0.82% criterion=sequence-density sequence-density=4.92 sequence-density-rank=1 fanout-score=1.00 fanout-score-rank=13 prefix-density=0.04 prefix-fanout=1.0 sequence=GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTGAATCC criterion=fanout-score sequence-density=0.01 sequence-density-rank=40 fanout-score=88.08 fanout-score-rank=1 prefix-density=0.52 prefix-fanout=1.0 sequence=CCATCGAGTAGACCTTGTTATTGTGAGAATTCT Started job on | Dec 06 11:56:15 Started mapping on | Dec 06 11:56:16 Finished on | Dec 06 11:56:35 Mapping speed, Million of reads per hour | 943.10 Number of input reads | 4977487 Average input read length | 31 UNIQUE READS: Uniquely mapped reads number | 788434 Uniquely mapped reads % | 15.84% Average mapped length | 25.91 Number of splices: Total | 21362 Number of splices: Annotated (sjdb) | 1842 Number of splices: GT/AG | 20590 Number of splices: GC/AG | 646 Number of splices: AT/AC | 4 Number of splices: Non-canonical | 122 Mismatch rate per base, % | 1.05% Deletion rate per base | 0.01% Deletion average length | 1.26 Insertion rate per base | 0.00% Insertion average length | 1.27 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 3232036 % of reads mapped to multiple loci | 64.93% Number of reads mapped to too many loci | 690308 % of reads mapped to too many loci | 13.87% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.70% % of reads unmapped: other | 0.66% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 957017 957017 957017 N_multimapping 3232036 3232036 3232036 N_noFeature 513330 617336 680198 N_ambiguous 9619 4911 565 UnstrandedReadsAssigned:265485 PositiveStrandReadsAssigned:166187 NegativeStrandReadsAssigned:107671 Dataset is classified unstranded MeadianReadLen=30 20thPercentileLength=24 echo kmer=19 SRR6941580 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: SRR6941580-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 4,977,487 reads, 2,261,442 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 942 rounds 52973 SRR6941580.ke.tsv 35125 SRR6941580.se.tsv 88098 total ==> SRR6941580.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 0.950947 KQK14069 1603 1504 24.2195 2.97082 KQK14071 474 375 0 0 ==> SRR6941580.se.tsv <== BRADI_1g14170v3 61 BRADI_1g53295v3 3 BRADI_1g59795v3 1 BRADI_1g07683v3 0 BRADI_1g00485v3 2 BRADI_1g20270v3 2 BRADI_1g74790v3 5 BRADI_1g09890v3 17 BRADI_1g77505v3 0 BRADI_1g48960v3 0 SRR6941580 completed mapping pipeline successfully