Starting /dee2/code/volunteer_pipeline.sh SRR8846503 current disk space = 1500401643520 free memory = 1379069888 SRR8846503 SRAfilesize 325433bb570f3e6a14623e5882101360 SRR8846503.sra SRR8846503.sra file validated SRR8846503 is single end SRR8846503 is conventional basespace SRR8846503 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8846503_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 30.599 33.0 33.0 34.0 25.0 34.0 2 32.72025 34.0 33.0 34.0 28.0 34.0 3 32.9005 34.0 33.0 34.0 32.0 34.0 4 33.074 34.0 33.0 34.0 32.0 34.0 5 33.037 34.0 33.0 34.0 32.0 34.0 6 36.83625 38.0 37.0 38.0 35.0 38.0 7 37.18575 38.0 38.0 38.0 36.0 38.0 8 37.377 38.0 38.0 38.0 37.0 38.0 9 37.44725 38.0 38.0 38.0 37.0 38.0 10-11 37.49475 38.0 38.0 38.0 37.0 38.0 12-13 37.497875 38.0 38.0 38.0 38.0 38.0 14-15 37.426625 38.0 38.0 38.0 37.0 38.0 16-17 37.4155 38.0 38.0 38.0 37.0 38.0 18-19 37.47125 38.0 38.0 38.0 37.0 38.0 20-21 37.42 38.0 38.0 38.0 37.0 38.0 22-23 37.471999999999994 38.0 38.0 38.0 37.0 38.0 24-25 37.476625 38.0 38.0 38.0 37.0 38.0 26-27 37.56 38.0 38.0 38.0 37.5 38.0 28-29 37.440875 38.0 38.0 38.0 37.5 38.0 30-31 37.368875 38.0 38.0 38.0 37.0 38.0 32-33 37.282 38.0 38.0 38.0 37.0 38.0 34-35 37.111374999999995 38.0 38.0 38.0 36.5 38.0 36-37 36.951 38.0 38.0 38.0 35.5 38.0 38-39 36.846374999999995 38.0 38.0 38.0 35.0 38.0 40-41 36.893875 38.0 38.0 38.0 35.5 38.0 42-43 36.785624999999996 38.0 38.0 38.0 35.0 38.0 44-45 37.0165 38.0 38.0 38.0 36.0 38.0 46-47 36.9795 38.0 38.0 38.0 36.0 38.0 48-49 36.966499999999996 38.0 38.0 38.0 36.0 38.0 50-51 37.078875 38.0 38.0 38.0 36.5 38.0 52-53 37.1215 38.0 38.0 38.0 36.0 38.0 54-55 37.050875000000005 38.0 38.0 38.0 36.0 38.0 56-57 36.795500000000004 38.0 38.0 38.0 35.5 38.0 58-59 36.62875 38.0 38.0 38.0 34.5 38.0 60-61 36.4495 38.0 38.0 38.0 34.0 38.0 62-63 35.999125 38.0 37.0 38.0 31.0 38.0 64-65 35.948125000000005 38.0 37.0 38.0 30.5 38.0 66-67 35.62587499999999 38.0 36.5 38.0 28.5 38.0 68-69 35.734624999999994 38.0 37.0 38.0 29.0 38.0 70-71 35.614 38.0 37.0 38.0 29.0 38.0 72-73 35.606750000000005 38.0 37.0 38.0 29.0 38.0 74-75 35.44925 38.0 37.0 38.0 28.5 38.0 76-77 35.183875 38.0 36.5 38.0 27.5 38.0 78-79 35.35825 38.0 37.0 38.0 29.0 38.0 80-81 35.03075 38.0 36.0 38.0 27.5 38.0 82-83 35.001000000000005 38.0 36.5 38.0 28.0 38.0 84-85 34.81275 38.0 36.0 38.0 27.5 38.0 86-87 34.497875 38.0 35.5 38.0 26.5 38.0 88-89 34.388 38.0 35.5 38.0 25.5 38.0 90-91 33.899875 38.0 35.0 38.0 23.0 38.0 92-93 33.502875 38.0 35.0 38.0 18.0 38.0 94-95 32.4075 38.0 34.5 38.0 8.5 38.0 96-97 29.7275 38.0 28.5 38.0 2.0 38.0 98-99 27.0355 37.0 8.5 38.0 2.0 38.0 100-101 24.18675 34.5 2.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 8 2.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 1.0 16 0.0 17 0.0 18 2.0 19 0.0 20 3.0 21 1.0 22 6.0 23 7.0 24 21.0 25 37.0 26 24.0 27 21.0 28 28.0 29 48.0 30 69.0 31 99.0 32 151.0 33 196.0 34 304.0 35 546.0 36 866.0 37 1568.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 35.99132085706537 25.142392188771357 19.582316246270683 19.283970707892596 2 29.025000000000002 26.875 16.075 28.025 3 28.975 18.775 18.125 34.125 4 25.874999999999996 35.65 16.925 21.55 5 27.675 25.374999999999996 24.65 22.3 6 23.75 26.150000000000002 26.974999999999998 23.125 7 38.025 25.4 16.075 20.5 8 19.05 21.825 38.675 20.45 9 23.799999999999997 38.3 20.549999999999997 17.349999999999998 10-11 31.75 23.225 25.637500000000003 19.3875 12-13 21.6875 20.5 23.8625 33.95 14-15 22.3875 40.35 20.575 16.6875 16-17 23.7875 25.8125 32.9375 17.4625 18-19 33.825 23.7375 20.974999999999998 21.462500000000002 20-21 21.2375 28.762500000000003 27.325 22.675 22-23 27.875 30.049999999999997 27.825 14.249999999999998 24-25 29.062500000000004 27.224999999999998 25.3 18.4125 26-27 30.312499999999996 28.775000000000002 22.625 18.2875 28-29 21.837500000000002 26.05 26.8375 25.275 30-31 27.3125 17.849999999999998 33.925 20.9125 32-33 24.9125 16.412499999999998 33.324999999999996 25.35 34-35 32.625 15.4875 29.512500000000003 22.375 36-37 35.75 18.3625 26.987499999999997 18.9 38-39 32.8375 19.8375 27.325 20.0 40-41 28.9 19.5875 23.95 27.5625 42-43 30.9625 24.15 21.475 23.4125 44-45 38.625 21.7375 14.649999999999999 24.9875 46-47 30.45 28.1625 17.0375 24.349999999999998 48-49 26.987499999999997 23.375 18.35 31.2875 50-51 23.3375 25.775 15.6375 35.25 52-53 26.575 29.875 12.4875 31.0625 54-55 23.925 26.9125 16.5625 32.6 56-57 20.5375 26.2125 16.275000000000002 36.975 58-59 20.0 21.4 20.0625 38.5375 60-61 17.05 22.287499999999998 16.2 44.4625 62-63 21.337500000000002 18.5625 20.2875 39.8125 64-65 16.1875 21.7875 24.65 37.375 66-67 19.05 14.799999999999999 26.8375 39.3125 68-69 19.8625 16.3125 25.074999999999996 38.75 70-71 21.712500000000002 15.125 28.1625 35.0 72-73 22.537499999999998 13.9125 28.025 35.525 74-75 18.6125 11.525 30.7 39.1625 76-77 20.575 9.6125 38.3875 31.424999999999997 78-79 19.0125 8.1 38.012499999999996 34.875 80-81 20.837500000000002 10.274999999999999 37.487500000000004 31.4 82-83 20.7625 10.549999999999999 40.825 27.8625 84-85 21.275 12.875 36.95 28.9 86-87 19.9375 20.5875 35.0375 24.4375 88-89 14.924999999999999 34.2375 32.525 18.3125 90-91 13.025 42.0125 28.525 16.4375 92-93 12.6 50.849999999999994 21.7 14.85 94-95 10.674999999999999 58.8375 20.9 9.5875 96-97 8.3625 68.05 16.3 7.2875 98-99 6.6375 75.2875 12.0 6.075 100-101 4.7375 78.9875 10.15 6.125 >>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 0.5 34 0.5 35 0.0 36 2.5 37 5.0 38 6.5 39 8.5 40 11.5 41 35.0 42 68.0 43 117.5 44 167.0 45 209.0 46 319.0 47 375.0 48 394.5 49 422.0 50 350.0 51 287.5 52 314.5 53 297.5 54 185.5 55 96.0 56 75.5 57 113.5 58 86.0 59 17.0 60 8.0 61 8.0 62 6.5 63 4.0 64 3.0 65 4.0 66 1.5 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 warn #Base N-Count 1 7.825 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 55.35 #Duplication Level Percentage of deduplicated Percentage of total 1 83.69467028003614 46.325 2 7.542908762420958 8.35 3 2.935862691960253 4.875 4 1.4001806684733513 3.1 5 0.8581752484191508 2.375 6 0.6775067750677507 2.25 7 0.27100271002710025 1.05 8 0.31616982836495033 1.4000000000000001 9 0.13550135501355012 0.675 >10 1.8970189701897018 16.875 >50 0.22583559168925021 9.700000000000001 >100 0.045167118337850046 3.025 >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 GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 121 3.025 No Hit GGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 91 2.275 RNA PCR Primer, Index 1 (100% over 22bp) TCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 84 2.1 No Hit TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 83 2.075 RNA PCR Primer, Index 1 (100% over 29bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 71 1.775 No Hit AGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 59 1.4749999999999999 No Hit GACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAAC 46 1.15 RNA PCR Primer, Index 1 (100% over 24bp) GACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 32 0.8 RNA PCR Primer, Index 1 (100% over 23bp) CTCTGATGATGATCAAACTAATACTTTCGTTCTTCTGGAATTCTCGGGTG 30 0.75 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 28 0.7000000000000001 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTTGGAATTCT 23 0.575 No Hit CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTC 22 0.5499999999999999 No Hit AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 21 0.525 Illumina Small RNA Adapter 2 (100% over 21bp) CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 20 0.5 No Hit GACACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACT 20 0.5 RNA PCR Primer, Index 1 (100% over 25bp) GCACCAGTGGTCTAGTGGTAGAATAGTACCTGGAATTCTCGGGTGCCAAG 19 0.475 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 18 0.44999999999999996 No Hit TTCGGACCAGGCTTCATTCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 18 0.44999999999999996 RNA PCR Primer, Index 1 (100% over 29bp) GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 18 0.44999999999999996 No Hit AATTCTCGGGTGCCAAGGAACTCCAGTCACGTCCGCATCTCGTATGCCGT 17 0.42500000000000004 RNA PCR Primer, Index 18 (100% over 50bp) GCCCACCCCAAGATGAGTGCTCTCTCTGGAATTCTCGGGTGCCAAGGAAC 17 0.42500000000000004 RNA PCR Primer, Index 1 (100% over 24bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTTGGAATTCTCGGGTGCCA 17 0.42500000000000004 No Hit CTCGGGTGCCAAGGAACTCCAGTCACGTCCGCATCTCGTATGCCGTCTTC 16 0.4 RNA PCR Primer, Index 18 (100% over 50bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 16 0.4 Illumina Small RNA Adapter 2 (100% over 21bp) GGGGATATAGCTCAGTTGGTAGATGGAATTCTCGGGTGCCAAGGAACTCC 16 0.4 RNA PCR Primer, Index 1 (100% over 27bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTCATGGAATTCTCGGGTG 15 0.375 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 14 0.35000000000000003 Illumina Small RNA Adapter 2 (100% over 21bp) TCTCGGGTGCCAAGGAACTCCAGTCACGTCCGCATCTCGTATGCCGTCTT 14 0.35000000000000003 RNA PCR Primer, Index 18 (100% over 50bp) NGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 13 0.325 RNA PCR Primer, Index 1 (100% over 22bp) GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGGAATTCTCGGGTGCCA 13 0.325 No Hit CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 12 0.3 RNA PCR Primer, Index 1 (100% over 23bp) GAAGTCCTCGTGTTGCATTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA 12 0.3 RNA PCR Primer, Index 1 (100% over 28bp) GACACGACTCTCGGCAACGGATATCTCGTGGAATTCTCGGGTGCCAAGGA 12 0.3 RNA PCR Primer, Index 1 (100% over 22bp) NGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 12 0.3 No Hit TCCTGTGGATGAGAAGGCATTTATATTCTGATGATATGGAATTCTCGGGT 11 0.27499999999999997 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 11 0.27499999999999997 Illumina Small RNA Adapter 2 (100% over 21bp) TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 11 0.27499999999999997 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGATGGAATTCTC 11 0.27499999999999997 No Hit NGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 10 0.25 No Hit CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGG 10 0.25 No Hit ATATATTTCAAGTTATTTCGGATCTTGGAATTCTCGGGTGCCAAGGAACT 10 0.25 RNA PCR Primer, Index 1 (100% over 25bp) CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 10 0.25 RNA PCR Primer, Index 1 (100% over 28bp) TCTCGGACCAGGCTTCATTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 10 0.25 RNA PCR Primer, Index 1 (100% over 29bp) CACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACTCC 10 0.25 RNA PCR Primer, Index 1 (100% over 27bp) CACGACTCTCGGCAACGGATATCTCGTGGAATTCTCGGGTGCCAAGGAAC 10 0.25 RNA PCR Primer, Index 1 (100% over 24bp) ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGC 10 0.25 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTGGAATTCTC 10 0.25 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTTGGAATTCTCGGGTGC 10 0.25 No Hit GCACCAGTAGTCTAGTGGTAGAATAGTACCTGGAATTCTCGGGTGCCAAG 9 0.22499999999999998 No Hit GGGGATGTAGCTCAGATGGTAGATGGAATTCTCGGGTGCCAAGGAACTCC 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 27bp) CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGG 9 0.22499999999999998 No Hit CACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAACT 8 0.2 RNA PCR Primer, Index 1 (100% over 25bp) CGACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAA 8 0.2 RNA PCR Primer, Index 1 (100% over 23bp) TCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTC 8 0.2 RNA PCR Primer, Index 1 (100% over 26bp) TCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCG 8 0.2 No Hit NCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 8 0.2 RNA PCR Primer, Index 1 (100% over 29bp) ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGGTGC 8 0.2 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTATGGAATTCTCGGGTGCCAA 8 0.2 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATGGAATTCTCGGGTGCCAAGGA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 22bp) CATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTCTCGTGGAATTCTCGGGTG 7 0.17500000000000002 No Hit GATAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAAC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 24bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTGGAATTCTCGGGTGCCA 7 0.17500000000000002 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATGGAATTCTCGGGTG 7 0.17500000000000002 No Hit CGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTCTC 6 0.15 No Hit GATGAGCTCAACGAGAACAGAAATCTCGTGTGGAATTCTCGGGTGCCAAG 6 0.15 No Hit AGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGT 6 0.15 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTGGAATTCTCGGGTGCCAAG 6 0.15 No Hit GACACGACTCTCGGCAACGTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 6 0.15 RNA PCR Primer, Index 1 (100% over 31bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTGGAATTCTCGGGTG 6 0.15 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTTGGAATTCTCGGGTGCC 6 0.15 No Hit TTCTCGGGTGCCAAGGAACTCCAGTCACGTCCGCATCTCGTATGCCGTCT 6 0.15 RNA PCR Primer, Index 18 (100% over 50bp) GCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCC 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAAAAAATGGAATTCTCGGGT 6 0.15 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGATGGAATTCTCGGGTG 6 0.15 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGTGGAATTCTCGGGTGCC 6 0.15 No Hit TATTCTGGTGTCCTAGGCGTAGAGGATGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) TCAAAAGAGGAAAGGCTTGCGGTGGAATTCTCGGGTGCCAAGGAACTCCA 6 0.15 RNA PCR Primer, Index 1 (100% over 28bp) AGCTGAGGCATCCTAACGAACGAACGATTTGAATGGAATTCTCGGGTGCC 6 0.15 No Hit AGGGCTATAGCTCAGTTCGGTAGAGCAACTCGTTTACACTGGAATTCTCG 5 0.125 No Hit TCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCG 5 0.125 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAATGGAATTCTCGGGTGCCA 5 0.125 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAAT 5 0.125 No Hit GGGGATGTAGCTCAAATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT 5 0.125 RNA PCR Primer, Index 1 (100% over 30bp) TAATTCATGATCTGGCATGTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 5 0.125 RNA PCR Primer, Index 1 (100% over 31bp) CACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAACTC 5 0.125 RNA PCR Primer, Index 1 (100% over 26bp) ATTCTCGGGTGCCAAGGAACTCCAGTCACGTCCGCATCTCGTATGCCGTC 5 0.125 RNA PCR Primer, Index 18 (100% over 50bp) ATAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) ATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGCCA 5 0.125 No Hit GCCCCTATCGTCTAGTGGTTCAGGACATCTCTCTTTCTGGAATTCTCGGG 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATTTGGAATTCTCGGG 5 0.125 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTGAATCTGGAATTC 5 0.125 No Hit CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGGAATTCTCG 5 0.125 No Hit AGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGCCAAG 5 0.125 No Hit GACACGACTCTCGGCAACGGATATTGGAATTCTCGGGTGCCAAGGAACTC 5 0.125 RNA PCR Primer, Index 1 (100% over 26bp) ACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCC 5 0.125 No Hit ATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) >>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 0.05 0.0 0.0 0.0 2 0.0 0.05 0.0 0.0 0.0 3 0.0 0.05 0.0 0.0 0.0 4 0.0 0.05 0.0 0.0 0.0 5 0.0 0.075 0.0 0.0 0.0 6 0.0 0.125 0.0 0.0 0.0 7 0.0 0.15 0.0 0.0 0.0 8 0.0 0.15 0.0 0.0 0.0 9 0.0 0.25 0.0 0.0 0.0 10-11 0.0 0.275 0.0 0.0 0.0 12-13 0.0 0.4 0.0 0.0 0.0 14-15 0.0 0.75 0.0 0.0 0.0 16-17 0.0 1.7375 0.0 0.0 0.0 18-19 0.0 3.4875 0.0 0.0 0.0 20-21 0.0 6.55 0.0 0.0 0.0 22-23 0.0 14.7125 0.0 0.0 0.0 24-25 0.0 25.1625 0.0 0.0 0.0 26-27 0.0 36.45 0.0 0.0 0.0 28-29 0.0 45.4 0.0 0.0 0.0 30-31 0.0 54.712500000000006 0.0 0.0 0.0 32-33 0.0 63.3625 0.0 0.0 0.0 34-35 0.0 74.38749999999999 0.0 0.0 0.0 36-37 0.0 82.7125 0.0 0.0 0.0 38-39 0.0 87.4625 0.0 0.0 0.0 40-41 0.0 90.1375 0.0 0.0 0.0 42-43 0.0 93.0 0.0 0.0 0.0 44-45 0.0 94.48750000000001 0.0 0.0 0.0 46-47 0.0 94.94999999999999 0.0 0.0 0.0 48-49 0.0 95.025 0.0 0.0 0.0 50-51 0.0 95.075 0.0 0.0 0.0 52-53 0.0 95.1 0.0 0.0 0.0 54-55 0.0 95.125 0.0 0.0 0.0 56-57 0.0 95.125 0.0 0.0 0.0 58-59 0.0 95.125 0.0 0.0 0.0 60-61 0.0 95.125 0.0 0.0 0.0 62-63 0.0 95.125 0.0 0.0 0.0 64-65 0.0 95.125 0.0 0.0 0.0 66-67 0.0 95.125 0.0 0.0 0.0 68-69 0.0 95.125 0.0 0.0 0.0 70-71 0.0 95.125 0.0 0.0 0.0 72-73 0.0 95.125 0.0 0.0 0.0 74-75 0.0 95.125 0.0 0.0 0.0 76-77 0.0 95.125 0.0 0.0 0.0 78-79 0.0 95.125 0.0 0.0 0.0 80-81 0.0 95.125 0.0 0.0 0.0 82-83 0.0 95.125 0.0 0.0 0.0 84-85 0.0 95.125 0.0 0.0 0.0 86-87 0.0 95.125 0.0 0.0 0.0 88-89 0.0 95.125 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TCCACTG 15 4.4910912E-4 102.62162 1 GGGATTG 25 2.3796383E-7 102.62162 1 GCGAGCG 15 4.4910912E-4 102.62162 1 CATCGAG 20 1.038194E-5 102.62161 1 GAGCGTA 20 1.545283E-5 94.924995 3 GTAGACC 20 1.545283E-5 94.924995 7 CTGAGAT 15 6.1614934E-4 94.924995 5 TTGTAGT 30 9.511496E-9 94.924995 5 AGTAGAC 20 1.545283E-5 94.924995 6 GGATTGT 30 9.511496E-9 94.924995 2 CGTAGTT 20 1.545283E-5 94.924995 6 CACTGAG 15 6.1614934E-4 94.924995 3 GATTGTA 30 9.511496E-9 94.924995 3 TAGTTCA 50 0.0 94.924995 8 CCACTGA 15 6.1614934E-4 94.924995 2 GAGTAGA 20 1.545283E-5 94.924995 5 ATTGTAG 30 9.511496E-9 94.924995 4 GATCCAG 15 6.1614934E-4 94.924995 9 TGTAGTT 30 9.511496E-9 94.924995 6 CGAGCGT 20 1.545283E-5 94.924995 2 >>END_MODULE Rejected 951762 READS because READLEN < 1 Read 951762 spots for SRR8846503.sra Written 951762 spots for SRR8846503.sra Rejected 951762 READS because READLEN < 1 Read 951762 spots for SRR8846503.sra Written 951762 spots for SRR8846503.sra Rejected 951762 READS because READLEN < 1 Read 951762 spots for SRR8846503.sra Written 951762 spots for SRR8846503.sra Rejected 951762 READS because READLEN < 1 Read 951762 spots for SRR8846503.sra Written 951762 spots for SRR8846503.sra Rejected 951762 READS because READLEN < 1 Read 951762 spots for SRR8846503.sra Written 951762 spots for SRR8846503.sra Rejected 951762 READS because READLEN < 1 Read 951762 spots for SRR8846503.sra Written 951762 spots for SRR8846503.sra Rejected 951762 READS because READLEN < 1 Read 951762 spots for SRR8846503.sra Written 951762 spots for SRR8846503.sra Rejected 951762 READS because READLEN < 1 Read 951762 spots for SRR8846503.sra Written 951762 spots for SRR8846503.sra Rejected 951762 READS because READLEN < 1 Read 951762 spots for SRR8846503.sra Written 951762 spots for SRR8846503.sra Rejected 951762 READS because READLEN < 1 Read 951762 spots for SRR8846503.sra Written 951762 spots for SRR8846503.sra Rejected 951762 READS because READLEN < 1 Read 951762 spots for SRR8846503.sra Written 951762 spots for SRR8846503.sra Rejected 951762 READS because READLEN < 1 Read 951762 spots for SRR8846503.sra Written 951762 spots for SRR8846503.sra Rejected 951762 READS because READLEN < 1 Read 951762 spots for SRR8846503.sra Written 951762 spots for SRR8846503.sra Rejected 951764 READS because READLEN < 1 Read 951764 spots for SRR8846503.sra Written 951764 spots for SRR8846503.sra Rejected 951762 READS because READLEN < 1 Read 951762 spots for SRR8846503.sra Written 951762 spots for SRR8846503.sra Rejected 951762 READS because READLEN < 1 Read 951762 spots for SRR8846503.sra Written 951762 spots for SRR8846503.sra Rejected 951762 READS because READLEN < 1 Read 951762 spots for SRR8846503.sra Written 951762 spots for SRR8846503.sra Rejected 951762 READS because READLEN < 1 Read 951762 spots for SRR8846503.sra Written 951762 spots for SRR8846503.sra Rejected 951762 READS because READLEN < 1 Read 951762 spots for SRR8846503.sra Written 951762 spots for SRR8846503.sra Rejected 951762 READS because READLEN < 1 Read 951762 spots for SRR8846503.sra Written 951762 spots for SRR8846503.sra SRR ids: ['SRR8846503.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_vzhy6tj5 SRR8846503.sra spots: 19035242 blocks: [[1, 951762], [951763, 1903524], [1903525, 2855286], [2855287, 3807048], [3807049, 4758810], [4758811, 5710572], [5710573, 6662334], [6662335, 7614096], [7614097, 8565858], [8565859, 9517620], [9517621, 10469382], [10469383, 11421144], [11421145, 12372906], [12372907, 13324668], [13324669, 14276430], [14276431, 15228192], [15228193, 16179954], [16179955, 17131716], [17131717, 18083478], [18083479, 19035242]] SRR8846503 file size 4569808 SRR8846503 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 SRR8846503 SRR8846503_1.fastq Input file: SRR8846503_1.fastq trimmed: SRR8846503-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 Mon Dec 9 02:04:23 2024 >> started Mon Dec 9 02:05:14 2024 >> done (50.934s) 19035242 reads processed; of these: 467 ( 0.00%) short reads filtered out after trimming by size control 60 ( 0.00%) empty reads filtered out after trimming by size control 19034715 (100.00%) reads available; of these: 5463976 (28.71%) trimmed reads available after processing 13570739 (71.29%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 61 0.00% 19 59 0.00% 20 78 0.00% 21 77 0.00% 22 88 0.00% 23 111 0.00% 24 143 0.00% 25 200 0.00% 26 428 0.00% 27 611 0.00% 28 711 0.00% 29 853 0.00% 30 673 0.00% 31 625 0.00% 32 633 0.00% 33 551 0.00% 34 593 0.00% 35 571 0.00% 36 632 0.00% 37 586 0.00% 38 495 0.00% 39 482 0.00% 40 372 0.00% 41 356 0.00% 42 414 0.00% 43 340 0.00% 44 408 0.00% 45 506 0.00% 46 425 0.00% 47 464 0.00% 48 443 0.00% 49 397 0.00% 50 421 0.00% 51 506 0.00% 52 530 0.00% 53 707 0.00% 54 728 0.00% 55 759 0.00% 56 991 0.01% 57 957 0.01% 58 1089 0.01% 59 1591 0.01% 60 1800 0.01% 61 2380 0.01% 62 3201 0.02% 63 3677 0.02% 64 4700 0.02% 65 6698 0.04% 66 15490 0.08% 67 53652 0.28% 68 62127 0.33% 69 43663 0.23% 70 35359 0.19% 71 44568 0.23% 72 17553 0.09% 73 5963 0.03% 74 7419 0.04% 75 5593 0.03% 76 4624 0.02% 77 4712 0.02% 78 5347 0.03% 79 5723 0.03% 80 6561 0.03% 81 8463 0.04% 82 14063 0.07% 83 13677 0.07% 84 14118 0.07% 85 16447 0.09% 86 20566 0.11% 87 30520 0.16% 88 47319 0.25% 89 81242 0.43% 90 111888 0.59% 91 116136 0.61% 92 165339 0.87% 93 224512 1.18% 94 295059 1.55% 95 617145 3.24% 96 631440 3.32% 97 652843 3.43% 98 866219 4.55% 99 733538 3.85% 100 440967 2.32% 101 13570739 71.29% 19034715 reads passed initial QC criterion=sequence-density sequence-density=94.57 sequence-density-rank=1 fanout-score=33.18 fanout-score-rank=1 prefix-density=95.17 prefix-fanout=33.0 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTCCGCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA criterion=fanout-score sequence-density=94.57 sequence-density-rank=1 fanout-score=33.18 fanout-score-rank=1 prefix-density=95.17 prefix-fanout=33.0 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTCCGCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTCCGCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA -o SRR8846503 - Input file: STDIN trimmed: SRR8846503-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTCCGCATCTCGTATGCCGTCTTCTGCTTGA -- 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 Mon Dec 9 02:08:31 2024 >> started Mon Dec 9 02:10:04 2024 >> done (93.439s) 18633984 reads processed; of these: 461573 ( 2.48%) short reads filtered out after trimming by size control 9079 ( 0.05%) empty reads filtered out after trimming by size control 18163332 (97.47%) reads available; of these: 17678332 (97.33%) trimmed reads available after processing 485000 ( 2.67%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 161596 0.89% 19 285082 1.57% 20 306334 1.69% 21 1118430 6.16% 22 593464 3.27% 23 746039 4.11% 24 1939961 10.68% 25 719666 3.96% 26 929952 5.12% 27 740454 4.08% 28 987025 5.43% 29 808236 4.45% 30 883379 4.86% 31 554062 3.05% 32 1198090 6.60% 33 1046280 5.76% 34 922550 5.08% 35 769546 4.24% 36 878505 4.84% 37 340573 1.88% 38 276835 1.52% 39 257070 1.42% 40 276696 1.52% 41 357875 1.97% 42 290029 1.60% 43 107176 0.59% 44 93823 0.52% 45 37816 0.21% 46 17823 0.10% 47 8846 0.05% 48 7533 0.04% 49 4265 0.02% 50 2875 0.02% 51 2570 0.01% 52 1475 0.01% 53 1207 0.01% 54 1455 0.01% 55 549 0.00% 56 753 0.00% 57 501 0.00% 58 558 0.00% 59 884 0.00% 60 965 0.01% 61 1559 0.01% 62 2389 0.01% 63 2847 0.02% 64 3813 0.02% 65 5732 0.03% 66 14342 0.08% 67 51585 0.28% 68 59682 0.33% 69 41634 0.23% 70 33377 0.18% 71 42107 0.23% 72 14510 0.08% 73 3333 0.02% 74 2799 0.02% 75 2480 0.01% 76 2124 0.01% 77 3118 0.02% 78 2291 0.01% 79 2091 0.01% 80 2995 0.02% 81 2477 0.01% 82 2027 0.01% 83 2850 0.02% 84 1549 0.01% 85 1477 0.01% 86 1383 0.01% 87 1199 0.01% 88 1046 0.01% 89 1226 0.01% 90 1179 0.01% 91 1276 0.01% 92 1348 0.01% 93 1620 0.01% 94 1737 0.01% 95 2358 0.01% 96 2742 0.02% 97 3438 0.02% 98 4779 0.03% 99 5600 0.03% 100 6775 0.04% 101 141635 0.78% criterion=sequence-density sequence-density=4.51 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=12 prefix-density=0.00 prefix-fanout=1.0 sequence=CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAA criterion=fanout-score sequence-density=0.01 sequence-density-rank=45 fanout-score=163.48 fanout-score-rank=1 prefix-density=0.89 prefix-fanout=1.0 sequence=TAGCCAAGTGCGGAGAGGATAACTGCTGAAAGCATATAAGTAGTAAGCCCACCCCAAGATGAGTGCTCTCTCCT Started job on | Dec 09 02:12:40 Started mapping on | Dec 09 02:12:40 Finished on | Dec 09 02:20:50 Mapping speed, Million of reads per hour | 136.39 Number of input reads | 18564063 Average input read length | 32 UNIQUE READS: Uniquely mapped reads number | 2889710 Uniquely mapped reads % | 15.57% Average mapped length | 26.83 Number of splices: Total | 33126 Number of splices: Annotated (sjdb) | 19604 Number of splices: GT/AG | 30191 Number of splices: GC/AG | 2210 Number of splices: AT/AC | 23 Number of splices: Non-canonical | 702 Mismatch rate per base, % | 0.13% Deletion rate per base | 0.00% Deletion average length | 1.33 Insertion rate per base | 0.00% Insertion average length | 1.04 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 7868680 % of reads mapped to multiple loci | 42.39% Number of reads mapped to too many loci | 6692702 % of reads mapped to too many loci | 36.05% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 5.50% % of reads unmapped: other | 0.49% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 7805673 7805673 7805673 N_multimapping 7868680 7868680 7868680 N_noFeature 1736303 1960840 2648931 N_ambiguous 45116 28483 610 UnstrandedReadsAssigned:1108291 PositiveStrandReadsAssigned:900387 NegativeStrandReadsAssigned:240169 Dataset is classified unstranded MeadianReadLen=29 20thPercentileLength=24 echo kmer=19 SRR8846503 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: SRR8846503-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 18,564,063 reads, 5,325,135 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,088 rounds 52973 SRR8846503.ke.tsv 35125 SRR8846503.se.tsv 88098 total ==> SRR8846503.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 10 1.1524 PNS24243 293 194 0 0 KQK14069 1603 1504 117.973 12.4019 KQK14071 474 375 0 0 ==> SRR8846503.se.tsv <== BRADI_1g14170v3 147 BRADI_1g53295v3 0 BRADI_1g59795v3 13 BRADI_1g07683v3 0 BRADI_1g00485v3 2 BRADI_1g20270v3 17 BRADI_1g74790v3 52 BRADI_1g09890v3 0 BRADI_1g77505v3 12 BRADI_1g48960v3 0 SRR8846503 completed mapping pipeline successfully