Starting /dee2/code/volunteer_pipeline.sh SRR8846550 current disk space = 1528664236032 free memory = 1607770064 SRR8846550 SRAfilesize 42d4c2c1896f87aee47eff6971d6dce4 SRR8846550.sra SRR8846550.sra file validated SRR8846550 is single end SRR8846550 is conventional basespace SRR8846550 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8846550_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 101 %GC 46 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.10725 34.0 33.0 34.0 18.0 34.0 2 32.68825 34.0 33.0 34.0 28.0 34.0 3 32.895 34.0 33.0 34.0 31.0 34.0 4 33.115 34.0 33.0 34.0 32.0 34.0 5 33.15225 34.0 33.0 34.0 32.0 34.0 6 36.938 38.0 37.0 38.0 36.0 38.0 7 37.2725 38.0 38.0 38.0 36.0 38.0 8 37.38675 38.0 38.0 38.0 37.0 38.0 9 37.46475 38.0 38.0 38.0 37.0 38.0 10-11 37.51575 38.0 38.0 38.0 37.0 38.0 12-13 37.509875 38.0 38.0 38.0 37.5 38.0 14-15 37.44725 38.0 38.0 38.0 37.5 38.0 16-17 37.431250000000006 38.0 38.0 38.0 37.0 38.0 18-19 37.439750000000004 38.0 38.0 38.0 37.0 38.0 20-21 37.413375 38.0 38.0 38.0 37.0 38.0 22-23 37.489375 38.0 38.0 38.0 37.5 38.0 24-25 37.478750000000005 38.0 38.0 38.0 37.0 38.0 26-27 37.516875 38.0 38.0 38.0 38.0 38.0 28-29 37.377125 38.0 38.0 38.0 37.0 38.0 30-31 37.37587499999999 38.0 38.0 38.0 37.0 38.0 32-33 37.368125000000006 38.0 38.0 38.0 37.0 38.0 34-35 37.112125 38.0 38.0 38.0 36.5 38.0 36-37 36.94225 38.0 38.0 38.0 36.0 38.0 38-39 36.872875 38.0 38.0 38.0 36.0 38.0 40-41 36.9725 38.0 38.0 38.0 36.0 38.0 42-43 36.81525 38.0 38.0 38.0 35.5 38.0 44-45 37.006249999999994 38.0 38.0 38.0 36.0 38.0 46-47 36.967625 38.0 38.0 38.0 36.0 38.0 48-49 36.979 38.0 38.0 38.0 36.0 38.0 50-51 37.07025 38.0 38.0 38.0 36.0 38.0 52-53 37.147999999999996 38.0 38.0 38.0 36.0 38.0 54-55 36.990125 38.0 38.0 38.0 35.5 38.0 56-57 36.703375 38.0 38.0 38.0 34.5 38.0 58-59 36.645875000000004 38.0 38.0 38.0 34.5 38.0 60-61 36.432500000000005 38.0 38.0 38.0 33.5 38.0 62-63 35.9795 38.0 37.0 38.0 30.0 38.0 64-65 35.9755 38.0 37.0 38.0 31.0 38.0 66-67 35.40375 38.0 37.0 38.0 28.5 38.0 68-69 35.326125 38.0 37.0 38.0 28.5 38.0 70-71 34.908625 38.0 37.0 38.0 27.5 38.0 72-73 34.944625 38.0 37.0 38.0 28.0 38.0 74-75 34.652375000000006 38.0 36.0 38.0 27.0 38.0 76-77 34.527625 38.0 36.0 38.0 26.0 38.0 78-79 34.947 38.0 36.5 38.0 28.0 38.0 80-81 34.775375 38.0 36.5 38.0 27.5 38.0 82-83 34.6995 38.0 36.5 38.0 26.5 38.0 84-85 34.425375 38.0 36.0 38.0 26.0 38.0 86-87 34.24425 38.0 36.0 38.0 24.5 38.0 88-89 34.171625000000006 38.0 36.0 38.0 24.5 38.0 90-91 33.932125 38.0 36.0 38.0 23.0 38.0 92-93 33.685249999999996 38.0 35.5 38.0 15.0 38.0 94-95 32.838125000000005 38.0 34.5 38.0 8.5 38.0 96-97 30.552875 38.0 31.0 38.0 2.0 38.0 98-99 28.074625 37.5 19.5 38.0 2.0 38.0 100-101 25.559375000000003 36.0 2.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 10 1.0 11 0.0 12 1.0 13 0.0 14 0.0 15 0.0 16 2.0 17 2.0 18 1.0 19 1.0 20 2.0 21 4.0 22 8.0 23 17.0 24 25.0 25 60.0 26 37.0 27 29.0 28 28.0 29 46.0 30 50.0 31 70.0 32 113.0 33 162.0 34 279.0 35 514.0 36 874.0 37 1674.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 33.51800554016621 22.686980609418285 19.916897506925206 23.878116343490305 2 28.549999999999997 28.999999999999996 17.25 25.2 3 28.575 18.85 19.825 32.75 4 25.275 34.9 16.775000000000002 23.05 5 28.225 24.5 24.3 22.975 6 26.424999999999997 26.75 26.025 20.8 7 37.625 25.7 18.475 18.2 8 20.9 20.974999999999998 37.875 20.25 9 22.775000000000002 38.0 21.099999999999998 18.125 10-11 30.587500000000002 23.775 25.6 20.0375 12-13 22.725 22.3875 23.175 31.7125 14-15 21.7 39.137499999999996 22.225 16.9375 16-17 23.075000000000003 27.9125 32.587500000000006 16.425 18-19 34.375 24.425 21.3625 19.8375 20-21 21.3125 28.8875 27.737499999999997 22.0625 22-23 28.000000000000004 30.125 27.200000000000003 14.674999999999999 24-25 27.650000000000002 27.8625 25.0125 19.475 26-27 29.775000000000002 28.975 22.775000000000002 18.475 28-29 23.150000000000002 26.2625 26.224999999999998 24.3625 30-31 25.9625 19.475 34.612500000000004 19.950000000000003 32-33 23.7375 17.7625 33.475 25.025 34-35 30.862499999999997 16.675 30.75 21.712500000000002 36-37 35.112500000000004 18.099999999999998 27.987499999999997 18.8 38-39 32.5625 19.775000000000002 28.625 19.037499999999998 40-41 28.1375 18.4125 26.700000000000003 26.75 42-43 30.75 21.1375 22.725 25.387500000000003 44-45 39.7375 20.8 14.75 24.712500000000002 46-47 33.5625 26.3 16.8125 23.325000000000003 48-49 27.750000000000004 23.5875 18.525 30.1375 50-51 22.5875 26.625 16.125 34.6625 52-53 26.25 30.25 13.6375 29.862499999999997 54-55 24.224999999999998 28.675 18.3 28.799999999999997 56-57 20.275000000000002 26.724999999999998 21.2625 31.7375 58-59 17.1375 22.825 26.375 33.6625 60-61 17.9125 23.0125 28.975 30.099999999999998 62-63 20.7875 20.0625 29.099999999999998 30.049999999999997 64-65 16.7 23.275000000000002 32.725 27.3 66-67 18.2375 16.825000000000003 34.575 30.362499999999997 68-69 19.975 16.7 36.5 26.825 70-71 19.875 15.6 38.75 25.775 72-73 22.1 15.687499999999998 35.9375 26.275 74-75 20.1625 13.5875 33.137499999999996 33.1125 76-77 20.6875 10.5875 39.5625 29.1625 78-79 19.900000000000002 8.9375 39.9625 31.2 80-81 21.1375 10.8875 38.6125 29.362500000000004 82-83 20.6125 10.625 40.387499999999996 28.375 84-85 21.5375 10.7875 37.5875 30.0875 86-87 20.0375 17.0375 36.35 26.575 88-89 15.4875 29.5 35.8375 19.175 90-91 13.700000000000001 37.95 31.362499999999997 16.9875 92-93 13.65 47.4375 23.1125 15.8 94-95 11.8125 56.45 21.875 9.8625 96-97 8.5875 67.6875 17.0875 6.6375 98-99 6.6625000000000005 76.8375 12.025 4.475 100-101 4.4125 81.8125 9.1625 4.6125 >>END_MODULE >>Per sequence GC content pass #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 0.5 32 2.5 33 3.5 34 8.5 35 14.0 36 13.0 37 15.5 38 23.0 39 43.5 40 63.0 41 121.0 42 187.5 43 229.0 44 311.5 45 357.5 46 379.5 47 398.5 48 344.5 49 300.0 50 309.0 51 276.5 52 181.5 53 104.5 54 87.0 55 102.5 56 71.0 57 22.0 58 10.5 59 6.5 60 7.0 61 4.0 62 0.0 63 0.5 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 warn #Base N-Count 1 9.75 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 56.89999999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 83.43585237258347 47.475 2 7.6889279437609845 8.75 3 2.987697715289982 5.1 4 1.6256590509666082 3.6999999999999997 5 1.0105448154657293 2.875 6 0.7469244288224955 2.55 7 0.4833040421792618 1.925 8 0.21968365553602814 1.0 9 0.21968365553602814 1.125 >10 1.4499121265377855 19.6 >50 0.13181019332161686 5.8999999999999995 >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 GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 99 2.475 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 79 1.975 No Hit GGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 58 1.4500000000000002 RNA PCR Primer, Index 1 (100% over 22bp) TCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 50 1.25 No Hit GACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAAC 49 1.225 RNA PCR Primer, Index 1 (100% over 24bp) TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 47 1.175 RNA PCR Primer, Index 1 (100% over 29bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 46 1.15 No Hit GACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 45 1.125 RNA PCR Primer, Index 1 (100% over 23bp) AGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 42 1.05 No Hit CTCTGATGATGATCAAACTAATACTTTCGTTCTTCTGGAATTCTCGGGTG 42 1.05 No Hit GACACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACT 37 0.9249999999999999 RNA PCR Primer, Index 1 (100% over 25bp) CTCGGGTGCCAAGGAACTCCAGTCACGTTTCGATCTCGTATGCCGTCTTC 30 0.75 RNA PCR Primer, Index 21 (100% over 50bp) CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 29 0.7250000000000001 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 26 0.65 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTTGGAATTCT 25 0.625 No Hit AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 25 0.625 Illumina Small RNA Adapter 2 (100% over 21bp) TCTCGGGTGCCAAGGAACTCCAGTCACGTTTCGATCTCGTATGCCGTCTT 22 0.5499999999999999 RNA PCR Primer, Index 21 (100% over 50bp) CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGG 21 0.525 No Hit CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTC 21 0.525 No Hit TTCTCGGGTGCCAAGGAACTCCAGTCACGTTTCGATCTCGTATGCCGTCT 19 0.475 RNA PCR Primer, Index 21 (100% over 50bp) AATTCTCGGGTGCCAAGGAACTCCAGTCACGTTTCGATCTCGTATGCCGT 17 0.42500000000000004 RNA PCR Primer, Index 21 (100% over 50bp) GCACCAGTGGTCTAGTGGTAGAATAGTACCTGGAATTCTCGGGTGCCAAG 16 0.4 No Hit CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 16 0.4 RNA PCR Primer, Index 1 (100% over 23bp) TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 15 0.375 No Hit GCCCACCCCAAGATGAGTGCTCTCTCTGGAATTCTCGGGTGCCAAGGAAC 15 0.375 RNA PCR Primer, Index 1 (100% over 24bp) GCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCC 14 0.35000000000000003 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 13 0.325 Illumina Small RNA Adapter 2 (100% over 21bp) CGGATAACCGTAGTAATTCTAGAGCTAATACGTGGAATTCTCGGGTGCCA 12 0.3 No Hit CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 12 0.3 RNA PCR Primer, Index 1 (100% over 28bp) GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 12 0.3 Illumina Small RNA Adapter 2 (100% over 21bp) NGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 12 0.3 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTGGAATTCTCGGGTGCCA 12 0.3 No Hit NGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 22bp) ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGC 11 0.27499999999999997 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATACTCTGGAATTCTCGGGTGCCAAG 10 0.25 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTTGGAATTCTCGGGTGCCA 10 0.25 No Hit TCGGATAACCGTAGTAATTCTAGAGCTAATACGTGGAATTCTCGGGTGCC 9 0.22499999999999998 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCATGGAATTCTCGGGTG 9 0.22499999999999998 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGAATTCTCGGGTGCCAAGGAACTCCA 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 28bp) GGGGATATAGCTCAGTTGGTAGATGGAATTCTCGGGTGCCAAGGAACTCC 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 27bp) CGGATAACCGTAGTAATTCTAGAGCTAATACTGGAATTCTCGGGTGCCAA 9 0.22499999999999998 No Hit NGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 8 0.2 No Hit ATAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAACT 8 0.2 RNA PCR Primer, Index 1 (100% over 25bp) CAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTG 8 0.2 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 8 0.2 Illumina Small RNA Adapter 2 (100% over 21bp) ACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCC 8 0.2 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAATGGAATTCTCGGGTGCCA 7 0.17500000000000002 No Hit CATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTGGAATTCTCGGGTGCCAAG 7 0.17500000000000002 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGGAATTCTCGGGTGCCA 7 0.17500000000000002 No Hit TGCAAGTATGAACTAATTTGAACTGTGAAACTTGGAATTCTCGGGTGCCA 7 0.17500000000000002 No Hit AGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGGT 7 0.17500000000000002 No Hit CACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACTCC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 27bp) CACGACTCTCGGCAACGGATATCTCGTGGAATTCTCGGGTGCCAAGGAAC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 24bp) CATCGAGTAGACCTTGTTATTGTGAGAATTAAAAATGGAATTCTCGGGTG 7 0.17500000000000002 No Hit TAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAACTC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 26bp) CACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGC 7 0.17500000000000002 No Hit TCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTC 6 0.15 RNA PCR Primer, Index 1 (100% over 26bp) CATCGAGTAGACCTTGTTATTGTGAGAATAAAATGGAATTCTCGGGTGCC 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATGGAATTCTCGGGTGCCAAGGA 6 0.15 RNA PCR Primer, Index 1 (100% over 22bp) NGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 6 0.15 Illumina Small RNA Adapter 2 (100% over 21bp) TCCTGTGGATGAGAAGGCATTTATATTCTGATGATATGGAATTCTCGGGT 6 0.15 No Hit GATAACCGTAGTAATTCTAGAGCTAATATGGAATTCTCGGGTGCCAAGGA 6 0.15 RNA PCR Primer, Index 1 (100% over 22bp) GCAAGTATGAACTAATTTGAACTGTGAAACTTGGAATTCTCGGGTGCCAA 6 0.15 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTTGGAATTCTCGGGTGCC 6 0.15 No Hit CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGGAATTCTCG 6 0.15 No Hit GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 6 0.15 No Hit CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGG 6 0.15 No Hit NGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 6 0.15 No Hit ATAACCGTAGTAATTCTAGAGCTAATATGGAATTCTCGGGTGCCAAGGAA 6 0.15 RNA PCR Primer, Index 1 (100% over 23bp) GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTAATCCTGGAATTC 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTATGGAATTCTCGGGTGCCAA 6 0.15 No Hit ATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAA 6 0.15 RNA PCR Primer, Index 1 (100% over 23bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTTGGAATTCTCGGGTGC 6 0.15 No Hit NCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 5 0.125 No Hit CGACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) TTCGGACCAGGCTTCATTCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 5 0.125 RNA PCR Primer, Index 1 (100% over 29bp) GATAACCGTAGTAATTCTAGAGCTAATTGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) AGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGT 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGGAATTCTCGGGTGCCAAGGAACTCCA 5 0.125 RNA PCR Primer, Index 1 (100% over 28bp) GCACCAGTAGTCTAGTGGTAGAATAGTACCTGGAATTCTCGGGTGCCAAG 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAAAAATGGAATTCTCGGGTG 5 0.125 No Hit ATATATTTCAAGTTATTTCGGATCTTGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) CCGGATTATGACTGAACGCCTCTAAGTCATGGAATTCTCGGGTGCCAAGG 5 0.125 Illumina Small RNA Adapter 2 (100% over 21bp) NATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 5 0.125 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATACTCGTGGAATTCTCGGGTGCCAA 5 0.125 No Hit CCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTG 5 0.125 No Hit NTCGGGTGCCAAGGAACTCCAGTCACGTTTCGATCTCGTATGCCGTCTTC 5 0.125 RNA PCR Primer, Index 21 (98% over 50bp) GATAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) NCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 5 0.125 RNA PCR Primer, Index 1 (100% over 29bp) GGGGATGTAGCTCAGATGGTAGATGGAATTCTCGGGTGCCAAGGAACTCC 5 0.125 RNA PCR Primer, Index 1 (100% over 27bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCGTGGAATT 5 0.125 No Hit AGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGCCAAG 5 0.125 No Hit GGGGATGTAGCTCAGATGGTAGAGTGGAATTCTCGGGTGCCAAGGAACTC 5 0.125 RNA PCR Primer, Index 1 (100% over 26bp) GCCTTGATGGTGAAATGGTAGACACGCGAGATGGAATTCTCGGGTGCCAA 5 0.125 No Hit GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGGTG 5 0.125 No Hit CTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCA 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.025 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 0.025 0.0 0.0 0.0 9 0.0 0.125 0.0 0.0 0.0 10-11 0.0 0.225 0.0 0.0 0.0 12-13 0.0 0.325 0.0 0.0 0.0 14-15 0.0 0.6125 0.0 0.0 0.0 16-17 0.0 1.35 0.0 0.0 0.0 18-19 0.0 2.7125000000000004 0.0 0.0 0.0 20-21 0.0 4.925000000000001 0.0 0.0 0.0 22-23 0.0 11.1125 0.0 0.0 0.0 24-25 0.0 20.225 0.0 0.0 0.0 26-27 0.0 31.3375 0.0 0.0 0.0 28-29 0.0 40.825 0.0 0.0 0.0 30-31 0.0 50.25 0.0 0.0 0.0 32-33 0.0 59.5 0.0 0.0 0.0 34-35 0.0 71.7125 0.0 0.0 0.0 36-37 0.0 80.85 0.0 0.0 0.0 38-39 0.0 85.2875 0.0 0.0 0.0 40-41 0.0 87.325 0.0 0.0 0.0 42-43 0.0 90.0875 0.0 0.0 0.0 44-45 0.0 91.57499999999999 0.0 0.0 0.0 46-47 0.0 91.9375 0.0 0.0 0.0 48-49 0.0 92.15 0.0 0.0 0.0 50-51 0.0 92.2375 0.0 0.0 0.0 52-53 0.0 92.2625 0.0 0.0 0.0 54-55 0.0 92.275 0.0 0.0 0.0 56-57 0.0 92.275 0.0 0.0 0.0 58-59 0.0 92.275 0.0 0.0 0.0 60-61 0.0 92.275 0.0 0.0 0.0 62-63 0.0 92.275 0.0 0.0 0.0 64-65 0.0 92.275 0.0 0.0 0.0 66-67 0.0 92.275 0.0 0.0 0.0 68-69 0.0 92.275 0.0 0.0 0.0 70-71 0.0 92.275 0.0 0.0 0.0 72-73 0.0 92.275 0.0 0.0 0.0 74-75 0.0 92.275 0.0 0.0 0.0 76-77 0.0 92.275 0.0 0.0 0.0 78-79 0.0 92.3 0.0 0.0 0.0 80-81 0.0 92.3125 0.0 0.0 0.0 82-83 0.0 92.3375 0.0 0.0 0.0 84-85 0.0 92.425 0.0 0.0 0.0 86-87 0.0 92.425 0.0 0.0 0.0 88-89 0.0 92.425 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CGGATAA 15 3.8020255E-4 106.9155 1 GACACGA 20 8.418772E-6 106.9155 1 GGGATTG 30 4.0181476E-9 106.9155 1 CATCGAG 15 3.8020255E-4 106.9155 1 GTAGACC 15 6.17118E-4 94.887505 7 ACACGAC 25 3.856112E-7 94.887505 2 AGTAGAC 15 6.17118E-4 94.887505 6 CTCTCGG 25 3.856112E-7 94.887505 8 GGATTGT 30 9.536961E-9 94.887505 2 ACTCTCG 25 3.856112E-7 94.887505 7 CACGACT 25 3.856112E-7 94.887505 3 GATTGTA 30 9.536961E-9 94.887505 3 TAGTTCA 35 2.3464963E-10 94.887505 8 GGATAAC 15 6.17118E-4 94.887505 2 TCTCGGC 25 3.856112E-7 94.887505 9 GAGTAGA 15 6.17118E-4 94.887505 5 ATTGTAG 30 9.536961E-9 94.887505 4 CGAGTAG 15 6.17118E-4 94.887505 4 ACGACTC 25 3.856112E-7 94.887505 4 AGACCTT 15 6.17118E-4 94.887505 9 >>END_MODULE Rejected 1025120 READS because READLEN < 1 Read 1025120 spots for SRR8846550.sra Written 1025120 spots for SRR8846550.sra Rejected 1025120 READS because READLEN < 1 Read 1025120 spots for SRR8846550.sra Written 1025120 spots for SRR8846550.sra Rejected 1025120 READS because READLEN < 1 Read 1025120 spots for SRR8846550.sra Written 1025120 spots for SRR8846550.sra Rejected 1025120 READS because READLEN < 1 Read 1025120 spots for SRR8846550.sra Written 1025120 spots for SRR8846550.sra Rejected 1025120 READS because READLEN < 1 Read 1025120 spots for SRR8846550.sra Written 1025120 spots for SRR8846550.sra Rejected 1025120 READS because READLEN < 1 Read 1025120 spots for SRR8846550.sra Written 1025120 spots for SRR8846550.sra Rejected 1025120 READS because READLEN < 1 Read 1025120 spots for SRR8846550.sra Written 1025120 spots for SRR8846550.sra Rejected 1025120 READS because READLEN < 1 Read 1025120 spots for SRR8846550.sra Written 1025120 spots for SRR8846550.sra Rejected 1025120 READS because READLEN < 1 Read 1025120 spots for SRR8846550.sra Written 1025120 spots for SRR8846550.sra Rejected 1025120 READS because READLEN < 1 Read 1025120 spots for SRR8846550.sra Written 1025120 spots for SRR8846550.sra Rejected 1025120 READS because READLEN < 1 Read 1025120 spots for SRR8846550.sra Written 1025120 spots for SRR8846550.sra Rejected 1025120 READS because READLEN < 1 Read 1025120 spots for SRR8846550.sra Written 1025120 spots for SRR8846550.sra Rejected 1025120 READS because READLEN < 1 Read 1025120 spots for SRR8846550.sra Written 1025120 spots for SRR8846550.sra Rejected 1025120 READS because READLEN < 1 Read 1025120 spots for SRR8846550.sra Written 1025120 spots for SRR8846550.sra Rejected 1025120 READS because READLEN < 1 Read 1025120 spots for SRR8846550.sra Written 1025120 spots for SRR8846550.sra Rejected 1025120 READS because READLEN < 1 Read 1025120 spots for SRR8846550.sra Written 1025120 spots for SRR8846550.sra Rejected 1025128 READS because READLEN < 1 Read 1025128 spots for SRR8846550.sra Written 1025128 spots for SRR8846550.sra Rejected 1025120 READS because READLEN < 1 Read 1025120 spots for SRR8846550.sra Written 1025120 spots for SRR8846550.sra Rejected 1025120 READS because READLEN < 1 Read 1025120 spots for SRR8846550.sra Written 1025120 spots for SRR8846550.sra Rejected 1025120 READS because READLEN < 1 Read 1025120 spots for SRR8846550.sra Written 1025120 spots for SRR8846550.sra SRR ids: ['SRR8846550.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_umup7iv0 SRR8846550.sra spots: 20502408 blocks: [[1, 1025120], [1025121, 2050240], [2050241, 3075360], [3075361, 4100480], [4100481, 5125600], [5125601, 6150720], [6150721, 7175840], [7175841, 8200960], [8200961, 9226080], [9226081, 10251200], [10251201, 11276320], [11276321, 12301440], [12301441, 13326560], [13326561, 14351680], [14351681, 15376800], [15376801, 16401920], [16401921, 17427040], [17427041, 18452160], [18452161, 19477280], [19477281, 20502408]] SRR8846550 file size 4923704 SRR8846550 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 SRR8846550 SRR8846550_1.fastq Input file: SRR8846550_1.fastq trimmed: SRR8846550-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 10:08:34 2024 >> started Mon Dec 9 10:08:45 2024 >> done (10.040s) 20502408 reads processed; of these: 517 ( 0.00%) short reads filtered out after trimming by size control 93 ( 0.00%) empty reads filtered out after trimming by size control 20501798 (100.00%) reads available; of these: 5256731 (25.64%) trimmed reads available after processing 15245067 (74.36%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 64 0.00% 19 55 0.00% 20 82 0.00% 21 86 0.00% 22 88 0.00% 23 85 0.00% 24 119 0.00% 25 192 0.00% 26 273 0.00% 27 377 0.00% 28 399 0.00% 29 520 0.00% 30 350 0.00% 31 355 0.00% 32 482 0.00% 33 387 0.00% 34 363 0.00% 35 290 0.00% 36 300 0.00% 37 289 0.00% 38 275 0.00% 39 302 0.00% 40 292 0.00% 41 295 0.00% 42 369 0.00% 43 383 0.00% 44 423 0.00% 45 501 0.00% 46 416 0.00% 47 410 0.00% 48 325 0.00% 49 302 0.00% 50 278 0.00% 51 353 0.00% 52 361 0.00% 53 467 0.00% 54 503 0.00% 55 549 0.00% 56 826 0.00% 57 754 0.00% 58 1029 0.01% 59 1613 0.01% 60 1967 0.01% 61 3219 0.02% 62 3971 0.02% 63 4926 0.02% 64 6820 0.03% 65 10351 0.05% 66 25695 0.13% 67 110229 0.54% 68 124029 0.60% 69 81506 0.40% 70 57840 0.28% 71 60265 0.29% 72 23467 0.11% 73 7014 0.03% 74 8729 0.04% 75 6573 0.03% 76 5447 0.03% 77 5607 0.03% 78 6583 0.03% 79 6638 0.03% 80 7596 0.04% 81 9613 0.05% 82 17287 0.08% 83 16641 0.08% 84 15860 0.08% 85 18648 0.09% 86 23895 0.12% 87 31886 0.16% 88 49596 0.24% 89 79906 0.39% 90 102429 0.50% 91 111451 0.54% 92 156859 0.77% 93 212746 1.04% 94 274111 1.34% 95 525004 2.56% 96 561336 2.74% 97 603934 2.95% 98 741928 3.62% 99 686204 3.35% 100 432743 2.11% 101 15245067 74.36% 20501798 reads passed initial QC criterion=sequence-density sequence-density=92.69 sequence-density-rank=1 fanout-score=34.58 fanout-score-rank=2 prefix-density=93.14 prefix-fanout=34.4 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTTTCGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAATA criterion=fanout-score sequence-density=2.50 sequence-density-rank=6 fanout-score=39.67 fanout-score-rank=1 prefix-density=98.06 prefix-fanout=1.0 sequence=CACGTTTCGATATCGTATGCCGT 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTTTCGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAATA -o SRR8846550 - Input file: STDIN trimmed: SRR8846550-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTTTCGATCTCGTATGCCGTCTTCTGCTTGA -- 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 10:09:19 2024 >> started Mon Dec 9 10:09:40 2024 >> done (21.476s) 20060899 reads processed; of these: 489597 ( 2.44%) short reads filtered out after trimming by size control 9535 ( 0.05%) empty reads filtered out after trimming by size control 19561767 (97.51%) reads available; of these: 18734946 (95.77%) trimmed reads available after processing 826821 ( 4.23%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 163422 0.84% 19 273962 1.40% 20 308281 1.58% 21 916303 4.68% 22 559770 2.86% 23 730136 3.73% 24 1597700 8.17% 25 879114 4.49% 26 1048570 5.36% 27 1000736 5.12% 28 1013222 5.18% 29 915081 4.68% 30 1072143 5.48% 31 746979 3.82% 32 1403707 7.18% 33 1237859 6.33% 34 1107475 5.66% 35 905556 4.63% 36 758313 3.88% 37 401458 2.05% 38 318999 1.63% 39 265035 1.35% 40 252789 1.29% 41 292954 1.50% 42 236665 1.21% 43 106351 0.54% 44 93668 0.48% 45 43851 0.22% 46 20685 0.11% 47 11193 0.06% 48 9437 0.05% 49 5336 0.03% 50 3450 0.02% 51 3029 0.02% 52 2056 0.01% 53 1647 0.01% 54 1822 0.01% 55 841 0.00% 56 1103 0.01% 57 757 0.00% 58 919 0.00% 59 1398 0.01% 60 1764 0.01% 61 3014 0.02% 62 3602 0.02% 63 4565 0.02% 64 6388 0.03% 65 9661 0.05% 66 24707 0.13% 67 107381 0.55% 68 120913 0.62% 69 79162 0.40% 70 55861 0.29% 71 58068 0.30% 72 20609 0.11% 73 4751 0.02% 74 4498 0.02% 75 3691 0.02% 76 3631 0.02% 77 5645 0.03% 78 3675 0.02% 79 3359 0.02% 80 6232 0.03% 81 5660 0.03% 82 4333 0.02% 83 7147 0.04% 84 2878 0.01% 85 2865 0.01% 86 2643 0.01% 87 2177 0.01% 88 1690 0.01% 89 2130 0.01% 90 1890 0.01% 91 1827 0.01% 92 2240 0.01% 93 2468 0.01% 94 2794 0.01% 95 3800 0.02% 96 4632 0.02% 97 5679 0.03% 98 8106 0.04% 99 10163 0.05% 100 12246 0.06% 101 229450 1.17% criterion=sequence-density sequence-density=4.99 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=0.25 sequence-density-rank=16 fanout-score=17.34 fanout-score-rank=1 prefix-density=4.28 prefix-fanout=1.0 sequence=TTGTGAGAATTAAAAA Started job on | Dec 09 10:09:58 Started mapping on | Dec 09 10:09:58 Finished on | Dec 09 10:10:57 Mapping speed, Million of reads per hour | 1220.50 Number of input reads | 20002666 Average input read length | 33 UNIQUE READS: Uniquely mapped reads number | 2628458 Uniquely mapped reads % | 13.14% Average mapped length | 27.96 Number of splices: Total | 41713 Number of splices: Annotated (sjdb) | 26102 Number of splices: GT/AG | 38461 Number of splices: GC/AG | 2499 Number of splices: AT/AC | 25 Number of splices: Non-canonical | 728 Mismatch rate per base, % | 0.15% Deletion rate per base | 0.00% Deletion average length | 1.31 Insertion rate per base | 0.00% Insertion average length | 1.03 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 7645378 % of reads mapped to multiple loci | 38.22% Number of reads mapped to too many loci | 8196470 % of reads mapped to too many loci | 40.98% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 7.28% % of reads unmapped: other | 0.38% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 9728830 9728830 9728830 N_multimapping 7645378 7645378 7645378 N_noFeature 1364490 1537882 2437097 N_ambiguous 49251 30925 492 UnstrandedReadsAssigned:1214717 PositiveStrandReadsAssigned:1059651 NegativeStrandReadsAssigned:190869 Dataset is classified positive stranded MeadianReadLen=30 20thPercentileLength=24 echo kmer=19 SRR8846550 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: SRR8846550-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 20,002,666 reads, 3,178,714 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 973 rounds 52973 SRR8846550.ke.tsv 35125 SRR8846550.se.tsv 88098 total ==> SRR8846550.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 2.43551 1.13002 PNS24247 1044 945 0 0 PNS24249 1928 1829 0 0 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 2.56449 0.725883 PNS24243 293 194 0 0 KQK14069 1603 1504 120.605 31.1413 KQK14071 474 375 12.0077 12.4351 ==> SRR8846550.se.tsv <== BRADI_1g14170v3 205 BRADI_1g53295v3 0 BRADI_1g59795v3 17 BRADI_1g07683v3 2 BRADI_1g00485v3 0 BRADI_1g20270v3 41 BRADI_1g74790v3 17 BRADI_1g09890v3 0 BRADI_1g77505v3 7 BRADI_1g48960v3 0 SRR8846550 completed mapping pipeline successfully