Starting /dee2/code/volunteer_pipeline.sh SRR8846495 current disk space = 1500824743936 free memory = 1418072240 SRR8846495 SRAfilesize ad5d39d64661429b064749777c38dea7 SRR8846495.sra SRR8846495.sra file validated SRR8846495 is single end SRR8846495 is conventional basespace SRR8846495 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8846495_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 48 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.527 34.0 33.0 34.0 25.0 34.0 2 32.67925 34.0 33.0 34.0 28.0 34.0 3 32.7225 34.0 33.0 34.0 31.0 34.0 4 33.025 34.0 33.0 34.0 32.0 34.0 5 32.92775 34.0 33.0 34.0 32.0 34.0 6 36.5855 38.0 37.0 38.0 34.0 38.0 7 36.8765 38.0 37.0 38.0 35.0 38.0 8 37.1195 38.0 38.0 38.0 36.0 38.0 9 37.17975 38.0 38.0 38.0 36.0 38.0 10-11 37.313874999999996 38.0 38.0 38.0 37.0 38.0 12-13 37.37075 38.0 38.0 38.0 37.0 38.0 14-15 37.3315 38.0 38.0 38.0 37.0 38.0 16-17 37.202375 38.0 38.0 38.0 36.0 38.0 18-19 37.2775 38.0 38.0 38.0 37.0 38.0 20-21 37.237125 38.0 38.0 38.0 36.5 38.0 22-23 37.225750000000005 38.0 38.0 38.0 36.5 38.0 24-25 37.21875 38.0 38.0 38.0 36.0 38.0 26-27 37.2275 38.0 38.0 38.0 37.0 38.0 28-29 37.183499999999995 38.0 38.0 38.0 36.0 38.0 30-31 37.092875 38.0 38.0 38.0 36.0 38.0 32-33 37.050875000000005 38.0 38.0 38.0 36.0 38.0 34-35 36.8115 38.0 38.0 38.0 35.0 38.0 36-37 36.7365 38.0 38.0 38.0 34.5 38.0 38-39 36.55525 38.0 38.0 38.0 34.0 38.0 40-41 36.854375000000005 38.0 38.0 38.0 35.0 38.0 42-43 36.914500000000004 38.0 38.0 38.0 35.5 38.0 44-45 36.83625 38.0 38.0 38.0 35.0 38.0 46-47 36.864875 38.0 38.0 38.0 35.5 38.0 48-49 36.957125 38.0 38.0 38.0 36.0 38.0 50-51 37.032875000000004 38.0 38.0 38.0 36.0 38.0 52-53 37.07325 38.0 38.0 38.0 36.0 38.0 54-55 36.89149999999999 38.0 38.0 38.0 35.5 38.0 56-57 36.792375 38.0 38.0 38.0 35.0 38.0 58-59 36.542125 38.0 38.0 38.0 34.0 38.0 60-61 36.521625 38.0 38.0 38.0 34.0 38.0 62-63 36.094625 38.0 37.0 38.0 32.0 38.0 64-65 35.7765 38.0 37.0 38.0 29.5 38.0 66-67 35.696749999999994 38.0 37.0 38.0 29.5 38.0 68-69 35.701 38.0 37.0 38.0 29.0 38.0 70-71 35.50075 38.0 37.0 38.0 29.0 38.0 72-73 35.408625 38.0 37.0 38.0 28.5 38.0 74-75 35.193875 38.0 36.5 38.0 28.0 38.0 76-77 34.852875 38.0 36.0 38.0 27.0 38.0 78-79 34.842375000000004 38.0 36.0 38.0 27.5 38.0 80-81 34.25875 38.0 35.0 38.0 25.0 38.0 82-83 34.4715 38.0 35.0 38.0 26.0 38.0 84-85 34.258375 38.0 34.5 38.0 24.5 38.0 86-87 34.365375 38.0 35.0 38.0 26.0 38.0 88-89 34.457499999999996 38.0 35.0 38.0 26.0 38.0 90-91 33.810125 38.0 34.0 38.0 24.0 38.0 92-93 33.12175 38.0 34.0 38.0 15.0 38.0 94-95 32.20425 38.0 33.5 38.0 14.5 38.0 96-97 30.058 38.0 29.0 38.0 2.0 38.0 98-99 26.942875 36.0 13.0 38.0 2.0 38.0 100-101 24.083125 34.5 2.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 10 1.0 11 0.0 12 0.0 13 0.0 14 0.0 15 1.0 16 1.0 17 0.0 18 2.0 19 2.0 20 0.0 21 4.0 22 4.0 23 7.0 24 12.0 25 36.0 26 23.0 27 27.0 28 34.0 29 66.0 30 82.0 31 89.0 32 146.0 33 233.0 34 351.0 35 577.0 36 1037.0 37 1265.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 27.48299319727891 28.54421768707483 21.578231292517007 22.39455782312925 2 24.0 30.9 19.45 25.650000000000002 3 25.074999999999996 20.025000000000002 21.099999999999998 33.800000000000004 4 27.375 31.474999999999998 17.45 23.7 5 28.999999999999996 27.575 20.8 22.625 6 23.0 28.7 23.625 24.675 7 35.5 23.974999999999998 19.650000000000002 20.875 8 20.849999999999998 23.075000000000003 32.425 23.65 9 23.474999999999998 33.4 23.05 20.075000000000003 10-11 29.6375 25.624999999999996 23.0375 21.7 12-13 22.8875 23.0875 22.3875 31.637500000000003 14-15 22.4625 35.612500000000004 23.549999999999997 18.375 16-17 24.9125 28.6625 27.9375 18.4875 18-19 29.849999999999998 25.5625 22.475 22.112499999999997 20-21 21.45 30.012499999999996 27.800000000000004 20.7375 22-23 27.400000000000002 26.775 30.662499999999998 15.162500000000001 24-25 27.55 25.2 27.8625 19.3875 26-27 33.324999999999996 27.700000000000003 23.849999999999998 15.125 28-29 23.1625 29.0875 27.250000000000004 20.5 30-31 24.7375 18.6875 37.974999999999994 18.6 32-33 26.35 17.712500000000002 32.9625 22.975 34-35 30.675 16.85 29.862499999999997 22.6125 36-37 38.375 13.7125 28.237499999999997 19.675 38-39 33.4125 19.05 25.924999999999997 21.6125 40-41 31.0375 19.325 21.837500000000002 27.800000000000004 42-43 30.175 26.325 20.825 22.675 44-45 37.4375 21.462500000000002 15.15 25.95 46-47 29.3875 30.2125 14.4375 25.9625 48-49 27.0625 25.137500000000003 17.3125 30.4875 50-51 23.5125 24.5625 14.512500000000001 37.4125 52-53 22.4375 31.412499999999998 12.662499999999998 33.4875 54-55 18.75 24.9375 16.4375 39.875 56-57 18.587500000000002 27.762500000000003 13.275 40.375 58-59 13.375 20.5875 18.099999999999998 47.9375 60-61 15.075 20.599999999999998 20.2125 44.1125 62-63 12.4625 17.7375 19.3625 50.4375 64-65 13.4375 20.075000000000003 25.974999999999998 40.5125 66-67 12.65 15.0 27.787499999999998 44.5625 68-69 16.5 16.037499999999998 24.7375 42.725 70-71 16.675 16.05 30.375000000000004 36.9 72-73 20.8875 11.7125 31.8625 35.5375 74-75 16.6125 11.75 30.9625 40.675 76-77 19.275000000000002 10.174999999999999 39.775 30.775000000000002 78-79 18.425 7.324999999999999 39.050000000000004 35.199999999999996 80-81 20.150000000000002 9.525 37.574999999999996 32.75 82-83 21.15 10.9125 42.075 25.8625 84-85 19.3625 13.850000000000001 37.875 28.9125 86-87 20.5125 21.1875 35.075 23.225 88-89 14.762500000000001 37.237500000000004 29.675 18.325 90-91 11.799999999999999 46.050000000000004 27.700000000000003 14.45 92-93 11.637500000000001 56.074999999999996 19.875 12.4125 94-95 9.3875 65.625 16.325 8.6625 96-97 7.3 72.91250000000001 13.525 6.2625 98-99 5.9375 80.7625 8.387500000000001 4.9125000000000005 100-101 3.5374999999999996 85.28750000000001 6.075 5.1 >>END_MODULE >>Per sequence GC content warn #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 2.0 36 4.0 37 7.0 38 9.5 39 11.0 40 17.5 41 53.0 42 81.5 43 138.5 44 205.0 45 250.5 46 354.5 47 395.5 48 424.0 49 428.5 50 342.0 51 309.5 52 272.0 53 205.0 54 128.0 55 74.0 56 73.0 57 91.0 58 67.5 59 21.0 60 13.0 61 9.5 62 5.5 63 2.0 64 1.5 65 1.5 66 1.0 67 0.5 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 warn #Base N-Count 1 8.125 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 59.25 #Duplication Level Percentage of deduplicated Percentage of total 1 85.0210970464135 50.375 2 6.751054852320674 8.0 3 2.6582278481012658 4.725 4 1.3080168776371308 3.1 5 0.8438818565400843 2.5 6 0.8016877637130801 2.85 7 0.5907172995780591 2.45 8 0.16877637130801687 0.8 9 0.12658227848101267 0.675 >10 1.5611814345991561 17.0 >50 0.16877637130801687 7.5249999999999995 >100 0.0 0.0 >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 GGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 89 2.225 RNA PCR Primer, Index 1 (100% over 22bp) TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 80 2.0 RNA PCR Primer, Index 1 (100% over 29bp) TCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 67 1.675 No Hit AGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 65 1.625 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 34 0.8500000000000001 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 32 0.8 No Hit GACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAAC 32 0.8 RNA PCR Primer, Index 1 (100% over 24bp) CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 32 0.8 No Hit CTCTGATGATGATCAAACTAATACTTTCGTTCTTCTGGAATTCTCGGGTG 31 0.775 No Hit AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 26 0.65 Illumina Small RNA Adapter 2 (100% over 21bp) GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 25 0.625 Illumina Small RNA Adapter 2 (100% over 21bp) CACGACTCTCGGCAACGGATATCTCGTGGAATTCTCGGGTGCCAAGGAAC 24 0.6 RNA PCR Primer, Index 1 (100% over 24bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 23 0.575 Illumina Small RNA Adapter 2 (100% over 21bp) ATATATTTCAAGTTATTTCGGATCTTGGAATTCTCGGGTGCCAAGGAACT 22 0.5499999999999999 RNA PCR Primer, Index 1 (100% over 25bp) TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 22 0.5499999999999999 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 21 0.525 No Hit GACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 20 0.5 RNA PCR Primer, Index 1 (100% over 23bp) GACACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACT 19 0.475 RNA PCR Primer, Index 1 (100% over 25bp) CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTC 19 0.475 No Hit GCCCACCCCAAGATGAGTGCTCTCTCTGGAATTCTCGGGTGCCAAGGAAC 19 0.475 RNA PCR Primer, Index 1 (100% over 24bp) CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 18 0.44999999999999996 RNA PCR Primer, Index 1 (100% over 28bp) AAGGGTGCTGAGAATACTTTGAATCTGACACTGGAATTCTCGGGTGCCAA 18 0.44999999999999996 No Hit GACACGACTCTCGGCAACGGATATCTCGTGGAATTCTCGGGTGCCAAGGA 17 0.42500000000000004 RNA PCR Primer, Index 1 (100% over 22bp) CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 16 0.4 Illumina Small RNA Adapter 2 (100% over 21bp) TCTCGGGTGCCAAGGAACTCCAGTCACCCGTCCATCTCGTATGCCGTCTT 15 0.375 RNA PCR Primer, Index 16 (100% over 50bp) CAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTG 15 0.375 No Hit GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 15 0.375 No Hit CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGG 15 0.375 No Hit GCACCAGTGGTCTAGTGGTAGAATAGTACCTGGAATTCTCGGGTGCCAAG 14 0.35000000000000003 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCATGGAATTCTCGGGTG 13 0.325 No Hit TTCGGACCAGGCTTCATTCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 12 0.3 RNA PCR Primer, Index 1 (100% over 29bp) AATTCTCGGGTGCCAAGGAACTCCAGTCACCCGTCCATCTCGTATGCCGT 12 0.3 RNA PCR Primer, Index 16 (100% over 50bp) GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTG 12 0.3 No Hit CACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACTCC 12 0.3 RNA PCR Primer, Index 1 (100% over 27bp) NGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 22bp) AGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGT 11 0.27499999999999997 No Hit CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 23bp) ACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCC 11 0.27499999999999997 No Hit CGGATAACCGTAGTAATTCTAGAGCTAATACTGGAATTCTCGGGTGCCAA 11 0.27499999999999997 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 10 0.25 No Hit ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGC 10 0.25 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATATGGAATTCTCGGGTGCCAAGGAA 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 23bp) CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGG 9 0.22499999999999998 No Hit CTCGGGTGCCAAGGAACTCCAGTCACCCGTCCATCTCGTATGCCGTCTTC 9 0.22499999999999998 RNA PCR Primer, Index 16 (100% over 50bp) NCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 8 0.2 No Hit CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGG 8 0.2 No Hit TCCTGTGGATGAGAAGGCATTTATATTCTGATGATATGGAATTCTCGGGT 8 0.2 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTGGAATTCTCGGGTGCCAAG 8 0.2 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 7 0.17500000000000002 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAATGGAATTCTCGGGTGCCA 7 0.17500000000000002 No Hit CTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGGAATTCTCGGGTGC 7 0.17500000000000002 No Hit TCGGATAACCGTAGTAATTCTAGAGCTAATACGTGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAAAAATGGAATTCTCGGGTG 7 0.17500000000000002 No Hit CACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAACTC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 26bp) TCCACAGGCTTTCTTGAACTGTGGAATTCTCGGGTGCCAAGGAACTCCAG 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 29bp) CCGGATTATGACTGAACGCCTCTAAGTCATGGAATTCTCGGGTGCCAAGG 7 0.17500000000000002 Illumina Small RNA Adapter 2 (100% over 21bp) ATTCTCGGGTGCCAAGGAACTCCAGTCACCCGTCCATCTCGTATGCCGTC 7 0.17500000000000002 RNA PCR Primer, Index 16 (100% over 50bp) TTCTCGGGTGCCAAGGAACTCCAGTCACCCGTCCATCTCGTATGCCGTCT 7 0.17500000000000002 RNA PCR Primer, Index 16 (100% over 50bp) GAAGTCCTCGTGTTGCATTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 28bp) ACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 31bp) AGCTGAGGCATCCTAACGAACGAACGATTTGAATGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit TCGCTTGGTGCAGATCGGGACTGGAATTCTCGGGTGCCAAGGAACTCCAG 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 29bp) TCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTC 6 0.15 RNA PCR Primer, Index 1 (100% over 26bp) TCCGTCGTAGTCTAGGTGGTTAGGATACTCTGGAATTCTCGGGTGCCAAG 6 0.15 No Hit ATAACCGTAGTAATTCTAGAGCTAATTGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) AGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCC 6 0.15 RNA PCR Primer, Index 1 (100% over 27bp) ATATATTTCAAGTTATTTCGGATCTGGAATTCTCGGGTGCCAAGGAACTC 6 0.15 RNA PCR Primer, Index 1 (100% over 26bp) ATAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAACT 6 0.15 RNA PCR Primer, Index 1 (100% over 25bp) CACGACTCTCGGCAATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCC 6 0.15 RNA PCR Primer, Index 5 (97% over 35bp) AACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC 6 0.15 RNA PCR Primer, Index 2 (100% over 34bp) TCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCG 6 0.15 No Hit NCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 6 0.15 RNA PCR Primer, Index 1 (100% over 29bp) TTCATGGACGTTGATAAGATCCTTCCTGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) GCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCC 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTAAAATGGAATTCTCGGGT 6 0.15 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGAATTCTCGGGTGCCAAGGAACTCCA 6 0.15 RNA PCR Primer, Index 1 (100% over 28bp) AACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAACTCC 6 0.15 RNA PCR Primer, Index 1 (100% over 27bp) ACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTCT 6 0.15 No Hit GCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAA 6 0.15 RNA PCR Primer, Index 1 (100% over 23bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATGGAATTCTCGGGTG 6 0.15 No Hit TAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAACTC 6 0.15 RNA PCR Primer, Index 1 (100% over 26bp) CACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) GACACGACTCTCGGCAACGGATATGGAATTCTCGGGTGCCAAGGAACTCC 5 0.125 RNA PCR Primer, Index 1 (100% over 27bp) CATCGAGTAGACCTTGTTATTGTGGAATTCTCGGGTGCCAAGGAACTCCA 5 0.125 RNA PCR Primer, Index 1 (100% over 28bp) TAATTCATGATCTGGCATGTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 5 0.125 RNA PCR Primer, Index 1 (100% over 31bp) AAGTATGAACTAATTTGAACTGTGAAACTTGGAATTCTCGGGTGCCAAGG 5 0.125 Illumina Small RNA Adapter 2 (100% over 21bp) GACACGACTCTCGGCAACGTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 5 0.125 RNA PCR Primer, Index 1 (100% over 31bp) GCAAGGATTGACAGACTGAGAGCTCTTTCTTGTGGAATTCTCGGGTGCCA 5 0.125 No Hit GATAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGGTGC 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAAAAAATGGAATTCTCGGGT 5 0.125 No Hit CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTCGGGT 5 0.125 No Hit CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGG 5 0.125 No Hit ATAACCGTAGTAATTCTAGAGCTAATATGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTCGGG 5 0.125 No Hit NATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 5 0.125 No Hit NACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) CATCGAGTAGACCTTGTTATTGTGAGAATTATGGAATTCTCGGGTGCCAA 5 0.125 No Hit TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGG 5 0.125 No Hit GCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGGA 5 0.125 RNA PCR Primer, Index 1 (100% over 22bp) ATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) >>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 0.025 0.0 0.0 0.0 2 0.0 0.025 0.0 0.0 0.0 3 0.0 0.025 0.0 0.0 0.0 4 0.0 0.025 0.0 0.0 0.0 5 0.0 0.025 0.0 0.0 0.0 6 0.0 0.025 0.0 0.0 0.0 7 0.0 0.025 0.0 0.0 0.0 8 0.0 0.05 0.0 0.0 0.0 9 0.0 0.1 0.0 0.0 0.0 10-11 0.0 0.1375 0.0 0.0 0.0 12-13 0.0 0.275 0.0 0.0 0.0 14-15 0.0 0.575 0.0 0.0 0.0 16-17 0.0 1.7875 0.0 0.0 0.0 18-19 0.0 3.8875 0.0 0.0 0.0 20-21 0.0 7.025 0.0 0.0 0.0 22-23 0.0 15.7 0.0 0.0 0.0 24-25 0.0 27.2625 0.0 0.0 0.0 26-27 0.0 40.1625 0.0 0.0 0.0 28-29 0.0 49.625 0.0 0.0 0.0 30-31 0.0 60.425 0.0 0.0 0.0 32-33 0.0 68.7125 0.0 0.0 0.0 34-35 0.0 77.375 0.0 0.0 0.0 36-37 0.0 85.76249999999999 0.0 0.0 0.0 38-39 0.0 89.9625 0.0 0.0 0.0 40-41 0.0 91.92500000000001 0.0 0.0 0.0 42-43 0.0 93.38749999999999 0.0 0.0 0.0 44-45 0.0 94.32499999999999 0.0 0.0 0.0 46-47 0.0 94.5625 0.0 0.0 0.0 48-49 0.0 94.575 0.0 0.0 0.0 50-51 0.0 94.575 0.0 0.0 0.0 52-53 0.0 94.625 0.0 0.0 0.0 54-55 0.0 94.625 0.0 0.0 0.0 56-57 0.0 94.625 0.0 0.0 0.0 58-59 0.0 94.625 0.0 0.0 0.0 60-61 0.0 94.625 0.0 0.0 0.0 62-63 0.0 94.65 0.0 0.0 0.0 64-65 0.0 94.65 0.0 0.0 0.0 66-67 0.0 94.65 0.0 0.0 0.0 68-69 0.0 94.65 0.0 0.0 0.0 70-71 0.0 94.65 0.0 0.0 0.0 72-73 0.0 94.65 0.0 0.0 0.0 74-75 0.0 94.65 0.0 0.0 0.0 76-77 0.0 94.65 0.0 0.0 0.0 78-79 0.0 94.675 0.0 0.0 0.0 80-81 0.0 94.6875 0.0 0.0 0.0 82-83 0.0 94.725 0.0 0.0 0.0 84-85 0.0 94.725 0.0 0.0 0.0 86-87 0.0 94.725 0.0 0.0 0.0 88-89 0.0 94.725 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GACACGA 25 2.0123844E-7 105.44445 1 GGGATTG 15 4.0222946E-4 105.44444 1 AGCTGAG 20 9.037147E-6 105.44444 1 GAGGCAT 20 1.5473053E-5 94.9 5 CTGAGGC 20 1.5473053E-5 94.9 3 GCTGAGG 20 1.5473053E-5 94.9 2 TTGTAGT 15 6.16795E-4 94.899994 5 GGACCAG 15 6.16795E-4 94.899994 3 GGATTGT 15 6.16795E-4 94.899994 2 CGGACCA 15 6.16795E-4 94.899994 2 GATTGTA 15 6.16795E-4 94.899994 3 TAGTTCA 15 6.16795E-4 94.899994 8 ATTGTAG 15 6.16795E-4 94.899994 4 AGGCTTC 15 6.16795E-4 94.899994 8 TGTAGTT 15 6.16795E-4 94.899994 6 GGCTTCA 15 6.16795E-4 94.899994 9 CAGGCTT 15 6.16795E-4 94.899994 7 AGTTCAA 15 6.16795E-4 94.899994 9 GTAGTTC 15 6.16795E-4 94.899994 7 CCAGGCT 15 6.16795E-4 94.899994 6 >>END_MODULE Rejected 1053026 READS because READLEN < 1 Read 1053026 spots for SRR8846495.sra Written 1053026 spots for SRR8846495.sra Rejected 1053036 READS because READLEN < 1 Read 1053036 spots for SRR8846495.sra Written 1053036 spots for SRR8846495.sra Rejected 1053026 READS because READLEN < 1 Read 1053026 spots for SRR8846495.sra Written 1053026 spots for SRR8846495.sra Rejected 1053026 READS because READLEN < 1 Read 1053026 spots for SRR8846495.sra Written 1053026 spots for SRR8846495.sra Rejected 1053026 READS because READLEN < 1 Read 1053026 spots for SRR8846495.sra Written 1053026 spots for SRR8846495.sra Rejected 1053026 READS because READLEN < 1 Read 1053026 spots for SRR8846495.sra Written 1053026 spots for SRR8846495.sra Rejected 1053026 READS because READLEN < 1 Read 1053026 spots for SRR8846495.sra Written 1053026 spots for SRR8846495.sra Rejected 1053026 READS because READLEN < 1 Read 1053026 spots for SRR8846495.sra Written 1053026 spots for SRR8846495.sra Rejected 1053026 READS because READLEN < 1 Read 1053026 spots for SRR8846495.sra Written 1053026 spots for SRR8846495.sra Rejected 1053026 READS because READLEN < 1 Read 1053026 spots for SRR8846495.sra Written 1053026 spots for SRR8846495.sra Rejected 1053026 READS because READLEN < 1 Read 1053026 spots for SRR8846495.sra Written 1053026 spots for SRR8846495.sra Rejected 1053026 READS because READLEN < 1 Read 1053026 spots for SRR8846495.sra Written 1053026 spots for SRR8846495.sra Rejected 1053026 READS because READLEN < 1 Read 1053026 spots for SRR8846495.sra Written 1053026 spots for SRR8846495.sra Rejected 1053026 READS because READLEN < 1 Read 1053026 spots for SRR8846495.sra Written 1053026 spots for SRR8846495.sra Rejected 1053026 READS because READLEN < 1 Read 1053026 spots for SRR8846495.sra Written 1053026 spots for SRR8846495.sra Rejected 1053026 READS because READLEN < 1 Read 1053026 spots for SRR8846495.sra Written 1053026 spots for SRR8846495.sra Rejected 1053026 READS because READLEN < 1 Read 1053026 spots for SRR8846495.sra Written 1053026 spots for SRR8846495.sra Rejected 1053026 READS because READLEN < 1 Read 1053026 spots for SRR8846495.sra Written 1053026 spots for SRR8846495.sra Rejected 1053026 READS because READLEN < 1 Read 1053026 spots for SRR8846495.sra Written 1053026 spots for SRR8846495.sra Rejected 1053026 READS because READLEN < 1 Read 1053026 spots for SRR8846495.sra Written 1053026 spots for SRR8846495.sra SRR ids: ['SRR8846495.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_3q41kjes SRR8846495.sra spots: 21060530 blocks: [[1, 1053026], [1053027, 2106052], [2106053, 3159078], [3159079, 4212104], [4212105, 5265130], [5265131, 6318156], [6318157, 7371182], [7371183, 8424208], [8424209, 9477234], [9477235, 10530260], [10530261, 11583286], [11583287, 12636312], [12636313, 13689338], [13689339, 14742364], [14742365, 15795390], [15795391, 16848416], [16848417, 17901442], [17901443, 18954468], [18954469, 20007494], [20007495, 21060530]] SRR8846495 file size 5058329 SRR8846495 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 SRR8846495 SRR8846495_1.fastq Input file: SRR8846495_1.fastq trimmed: SRR8846495-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 Sun Dec 8 22:18:51 2024 >> started Sun Dec 8 22:19:47 2024 >> done (56.123s) 21060530 reads processed; of these: 510 ( 0.00%) short reads filtered out after trimming by size control 64 ( 0.00%) empty reads filtered out after trimming by size control 21059956 (100.00%) reads available; of these: 5857740 (27.81%) trimmed reads available after processing 15202216 (72.19%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 81 0.00% 19 61 0.00% 20 67 0.00% 21 101 0.00% 22 97 0.00% 23 100 0.00% 24 118 0.00% 25 139 0.00% 26 206 0.00% 27 219 0.00% 28 274 0.00% 29 307 0.00% 30 259 0.00% 31 322 0.00% 32 399 0.00% 33 433 0.00% 34 670 0.00% 35 646 0.00% 36 738 0.00% 37 542 0.00% 38 493 0.00% 39 412 0.00% 40 321 0.00% 41 262 0.00% 42 240 0.00% 43 278 0.00% 44 286 0.00% 45 300 0.00% 46 235 0.00% 47 292 0.00% 48 268 0.00% 49 288 0.00% 50 324 0.00% 51 319 0.00% 52 377 0.00% 53 475 0.00% 54 463 0.00% 55 394 0.00% 56 606 0.00% 57 669 0.00% 58 924 0.00% 59 1294 0.01% 60 1655 0.01% 61 2259 0.01% 62 3199 0.02% 63 3749 0.02% 64 4713 0.02% 65 7134 0.03% 66 13020 0.06% 67 50913 0.24% 68 57449 0.27% 69 43836 0.21% 70 38488 0.18% 71 45991 0.22% 72 19656 0.09% 73 7228 0.03% 74 7704 0.04% 75 5079 0.02% 76 4651 0.02% 77 4793 0.02% 78 5490 0.03% 79 5873 0.03% 80 6849 0.03% 81 7901 0.04% 82 10070 0.05% 83 11058 0.05% 84 13147 0.06% 85 17403 0.08% 86 20701 0.10% 87 29322 0.14% 88 50965 0.24% 89 85647 0.41% 90 119553 0.57% 91 133281 0.63% 92 163339 0.78% 93 223882 1.06% 94 309504 1.47% 95 523652 2.49% 96 597366 2.84% 97 644225 3.06% 98 999750 4.75% 99 964934 4.58% 100 577012 2.74% 101 15202216 72.19% 21059956 reads passed initial QC criterion=sequence-density sequence-density=94.19 sequence-density-rank=1 fanout-score=31.91 fanout-score-rank=1 prefix-density=94.61 prefix-fanout=31.8 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCCGTCCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA criterion=fanout-score sequence-density=94.19 sequence-density-rank=1 fanout-score=31.91 fanout-score-rank=1 prefix-density=94.61 prefix-fanout=31.8 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCCGTCCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCCGTCCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA -o SRR8846495 - Input file: STDIN trimmed: SRR8846495-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCCGTCCATCTCGTATGCCGTCTTCTGCTTGA -- 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 Sun Dec 8 22:23:19 2024 >> started Sun Dec 8 22:24:58 2024 >> done (99.294s) 20616589 reads processed; of these: 593912 ( 2.88%) short reads filtered out after trimming by size control 11567 ( 0.06%) empty reads filtered out after trimming by size control 20011110 (97.06%) reads available; of these: 19450536 (97.20%) trimmed reads available after processing 560574 ( 2.80%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 203247 1.02% 19 353174 1.76% 20 369002 1.84% 21 1151354 5.75% 22 735175 3.67% 23 852107 4.26% 24 2555397 12.77% 25 1035005 5.17% 26 1160162 5.80% 27 834322 4.17% 28 1206863 6.03% 29 1106606 5.53% 30 1087401 5.43% 31 715282 3.57% 32 754774 3.77% 33 949534 4.75% 34 1088464 5.44% 35 813328 4.06% 36 843806 4.22% 37 395441 1.98% 38 309618 1.55% 39 236515 1.18% 40 176987 0.88% 41 180608 0.90% 42 164794 0.82% 43 56485 0.28% 44 51537 0.26% 45 21658 0.11% 46 13091 0.07% 47 6704 0.03% 48 6544 0.03% 49 3147 0.02% 50 2097 0.01% 51 2083 0.01% 52 1107 0.01% 53 933 0.00% 54 1251 0.01% 55 467 0.00% 56 674 0.00% 57 525 0.00% 58 672 0.00% 59 987 0.00% 60 1275 0.01% 61 1926 0.01% 62 2765 0.01% 63 3280 0.02% 64 4181 0.02% 65 6479 0.03% 66 12171 0.06% 67 49278 0.25% 68 55444 0.28% 69 41987 0.21% 70 36590 0.18% 71 43823 0.22% 72 16509 0.08% 73 4526 0.02% 74 3073 0.02% 75 1973 0.01% 76 2111 0.01% 77 3554 0.02% 78 2283 0.01% 79 2354 0.01% 80 3383 0.02% 81 2515 0.01% 82 2156 0.01% 83 2578 0.01% 84 1608 0.01% 85 1721 0.01% 86 1490 0.01% 87 1263 0.01% 88 1204 0.01% 89 1225 0.01% 90 1183 0.01% 91 1360 0.01% 92 1396 0.01% 93 1631 0.01% 94 2049 0.01% 95 2997 0.01% 96 3518 0.02% 97 4778 0.02% 98 7203 0.04% 99 8166 0.04% 100 10303 0.05% 101 202873 1.01% criterion=sequence-density sequence-density=5.79 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=15 prefix-density=0.00 prefix-fanout=1.0 sequence=CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATTCAAGAG criterion=fanout-score sequence-density=0.21 sequence-density-rank=21 fanout-score=23.66 fanout-score-rank=1 prefix-density=4.88 prefix-fanout=1.0 sequence=TTGTGAGAATTAAAAA Started job on | Dec 08 22:27:30 Started mapping on | Dec 08 22:27:31 Finished on | Dec 08 22:36:33 Mapping speed, Million of reads per hour | 135.86 Number of input reads | 20454477 Average input read length | 31 UNIQUE READS: Uniquely mapped reads number | 3307208 Uniquely mapped reads % | 16.17% Average mapped length | 26.02 Number of splices: Total | 40060 Number of splices: Annotated (sjdb) | 23181 Number of splices: GT/AG | 37415 Number of splices: GC/AG | 1961 Number of splices: AT/AC | 27 Number of splices: Non-canonical | 657 Mismatch rate per base, % | 0.14% Deletion rate per base | 0.00% Deletion average length | 1.34 Insertion rate per base | 0.00% Insertion average length | 1.02 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 7824646 % of reads mapped to multiple loci | 38.25% Number of reads mapped to too many loci | 8013317 % of reads mapped to too many loci | 39.18% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 5.78% % of reads unmapped: other | 0.62% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 9322623 9322623 9322623 N_multimapping 7824646 7824646 7824646 N_noFeature 2116400 2296856 3109208 N_ambiguous 49247 31028 846 UnstrandedReadsAssigned:1141561 PositiveStrandReadsAssigned:979324 NegativeStrandReadsAssigned:197154 Dataset is classified unstranded MeadianReadLen=28 20thPercentileLength=24 echo kmer=19 SRR8846495 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: SRR8846495-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 20,454,477 reads, 6,038,597 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,097 rounds 52973 SRR8846495.ke.tsv 35125 SRR8846495.se.tsv 88098 total ==> SRR8846495.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 4.00219 0.310145 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 4.99781 0.516305 PNS24243 293 194 2 1.4612 KQK14069 1603 1504 65.3862 6.16196 KQK14071 474 375 5.86496 2.21674 ==> SRR8846495.se.tsv <== BRADI_1g14170v3 94 BRADI_1g53295v3 3 BRADI_1g59795v3 15 BRADI_1g07683v3 3 BRADI_1g00485v3 0 BRADI_1g20270v3 41 BRADI_1g74790v3 45 BRADI_1g09890v3 3 BRADI_1g77505v3 9 BRADI_1g48960v3 0 SRR8846495 completed mapping pipeline successfully