Starting /dee2/code/volunteer_pipeline.sh SRR8846549 current disk space = 1528877613056 free memory = 1607803048 SRR8846549 SRAfilesize f093e5197a9335fdd024630011073ac3 SRR8846549.sra SRR8846549.sra file validated SRR8846549 is single end SRR8846549 is conventional basespace SRR8846549 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8846549_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 fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.425 33.0 33.0 34.0 25.0 34.0 2 32.72775 34.0 33.0 34.0 28.0 34.0 3 32.861 34.0 33.0 34.0 31.0 34.0 4 33.024 34.0 33.0 34.0 32.0 34.0 5 32.87975 34.0 33.0 34.0 32.0 34.0 6 36.563 38.0 37.0 38.0 34.0 38.0 7 37.09225 38.0 38.0 38.0 36.0 38.0 8 37.29925 38.0 38.0 38.0 36.0 38.0 9 37.3115 38.0 38.0 38.0 37.0 38.0 10-11 37.420500000000004 38.0 38.0 38.0 37.0 38.0 12-13 37.449375 38.0 38.0 38.0 37.0 38.0 14-15 37.391999999999996 38.0 38.0 38.0 37.0 38.0 16-17 37.345749999999995 38.0 38.0 38.0 37.0 38.0 18-19 37.358875 38.0 38.0 38.0 37.0 38.0 20-21 37.407125 38.0 38.0 38.0 37.0 38.0 22-23 37.418 38.0 38.0 38.0 37.0 38.0 24-25 37.485375000000005 38.0 38.0 38.0 37.0 38.0 26-27 37.4735 38.0 38.0 38.0 37.5 38.0 28-29 37.380875 38.0 38.0 38.0 37.0 38.0 30-31 37.380250000000004 38.0 38.0 38.0 37.0 38.0 32-33 37.3225 38.0 38.0 38.0 37.0 38.0 34-35 37.12975 38.0 38.0 38.0 36.5 38.0 36-37 37.079625 38.0 38.0 38.0 36.0 38.0 38-39 36.993625 38.0 38.0 38.0 36.0 38.0 40-41 36.9685 38.0 38.0 38.0 36.0 38.0 42-43 36.908625 38.0 38.0 38.0 35.5 38.0 44-45 37.0145 38.0 38.0 38.0 36.0 38.0 46-47 37.089625 38.0 38.0 38.0 36.0 38.0 48-49 37.19525 38.0 38.0 38.0 36.5 38.0 50-51 37.208375000000004 38.0 38.0 38.0 37.0 38.0 52-53 37.247 38.0 38.0 38.0 37.0 38.0 54-55 37.082125000000005 38.0 38.0 38.0 36.0 38.0 56-57 37.016000000000005 38.0 38.0 38.0 36.0 38.0 58-59 36.783125 38.0 38.0 38.0 35.0 38.0 60-61 36.73125 38.0 38.0 38.0 35.0 38.0 62-63 36.413250000000005 38.0 38.0 38.0 33.5 38.0 64-65 36.245875 38.0 37.5 38.0 32.5 38.0 66-67 36.0405 38.0 37.0 38.0 31.0 38.0 68-69 36.025625 38.0 37.0 38.0 31.0 38.0 70-71 36.235125 38.0 37.0 38.0 33.0 38.0 72-73 36.1955 38.0 37.5 38.0 32.0 38.0 74-75 35.8805 38.0 37.0 38.0 30.5 38.0 76-77 35.692875 38.0 37.0 38.0 30.0 38.0 78-79 35.387875 38.0 36.5 38.0 28.0 38.0 80-81 35.373375 38.0 36.5 38.0 28.5 38.0 82-83 35.3965 38.0 37.0 38.0 29.0 38.0 84-85 35.273250000000004 38.0 36.5 38.0 28.5 38.0 86-87 35.5655 38.0 37.0 38.0 30.0 38.0 88-89 35.4445 38.0 37.0 38.0 30.0 38.0 90-91 35.326 38.0 37.0 38.0 30.0 38.0 92-93 35.137 38.0 37.0 38.0 30.0 38.0 94-95 34.113875 38.0 36.0 38.0 25.0 38.0 96-97 32.13175 38.0 34.0 38.0 8.0 38.0 98-99 29.43825 38.0 28.0 38.0 2.0 38.0 100-101 26.156125 36.5 2.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 7 1.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 2.0 15 0.0 16 2.0 17 1.0 18 0.0 19 0.0 20 0.0 21 0.0 22 2.0 23 6.0 24 11.0 25 17.0 26 26.0 27 21.0 28 30.0 29 30.0 30 56.0 31 72.0 32 94.0 33 148.0 34 267.0 35 502.0 36 876.0 37 1836.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 34.25218340611353 23.71724890829694 22.59825327510917 19.432314410480352 2 24.15 28.525 18.175 29.15 3 27.775 18.9 19.275000000000002 34.050000000000004 4 27.275 33.975 15.55 23.200000000000003 5 25.3 25.3 24.175 25.224999999999998 6 25.924999999999997 23.474999999999998 24.925 25.674999999999997 7 35.325 28.225 17.75 18.7 8 17.325 20.925 37.05 24.7 9 23.575 34.575 24.075 17.775 10-11 30.2625 22.175 26.5 21.0625 12-13 23.6125 19.2625 23.9 33.225 14-15 24.25 35.4125 21.1625 19.175 16-17 24.1375 26.974999999999998 30.775000000000002 18.1125 18-19 35.6375 21.275 21.6 21.4875 20-21 23.1125 26.674999999999997 28.1375 22.075 22-23 28.287499999999998 29.062500000000004 27.250000000000004 15.4 24-25 28.287499999999998 25.374999999999996 26.4125 19.925 26-27 31.275 25.5125 24.15 19.0625 28-29 23.7 27.9125 26.0625 22.325 30-31 25.7875 20.4875 34.0125 19.7125 32-33 23.974999999999998 17.125 35.475 23.425 34-35 33.3625 13.65 29.349999999999998 23.6375 36-37 36.4625 16.85 26.8 19.8875 38-39 36.85 16.9625 27.0625 19.125 40-41 29.312500000000004 18.35 23.7125 28.625 42-43 31.874999999999996 25.074999999999996 18.987499999999997 24.0625 44-45 39.1625 23.4125 13.8125 23.6125 46-47 31.574999999999996 31.025000000000002 15.3375 22.0625 48-49 26.200000000000003 25.6125 16.900000000000002 31.2875 50-51 21.65 26.9125 15.437500000000002 36.0 52-53 26.474999999999998 28.95 13.6625 30.912499999999998 54-55 23.2875 29.3375 15.775 31.6 56-57 25.9625 25.2625 18.087500000000002 30.6875 58-59 28.1625 26.2125 14.575 31.05 60-61 23.875 27.5625 19.162499999999998 29.4 62-63 27.224999999999998 21.1125 21.125 30.5375 64-65 22.125 28.0875 23.1125 26.674999999999997 66-67 22.8 19.3 26.787499999999998 31.112499999999997 68-69 23.2125 19.8875 27.3125 29.5875 70-71 24.9875 20.1375 28.8375 26.0375 72-73 25.4625 17.549999999999997 31.374999999999996 25.6125 74-75 18.675 14.149999999999999 30.275000000000002 36.9 76-77 24.6125 10.15 36.15 29.0875 78-79 19.6375 9.825000000000001 37.9375 32.6 80-81 20.0 9.049999999999999 38.425 32.525 82-83 20.3125 9.0125 43.3625 27.3125 84-85 20.5875 11.1 38.574999999999996 29.7375 86-87 21.3125 18.1125 35.3 25.275 88-89 14.2375 34.375 34.7625 16.625 90-91 14.8625 45.1875 25.324999999999996 14.625 92-93 10.7375 55.2 20.225 13.8375 94-95 10.7875 62.9 18.1875 8.125 96-97 7.0874999999999995 73.375 13.3125 6.225 98-99 5.5 80.375 9.85 4.275 100-101 4.025 85.6 6.1375 4.237500000000001 >>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 0.0 32 0.5 33 1.5 34 1.5 35 2.0 36 3.5 37 5.5 38 7.5 39 13.0 40 42.0 41 72.0 42 113.0 43 156.0 44 212.5 45 321.0 46 339.0 47 350.5 48 388.5 49 377.0 50 346.5 51 310.0 52 261.0 53 174.0 54 123.0 55 93.5 56 113.0 57 94.0 58 33.5 59 19.5 60 7.5 61 5.5 62 5.5 63 4.5 64 1.5 65 0.5 66 0.5 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 8.4 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 58.375 #Duplication Level Percentage of deduplicated Percentage of total 1 85.18201284796574 49.725 2 6.980728051391863 8.15 3 2.4839400428265526 4.35 4 1.4132762312633833 3.3000000000000003 5 0.5995717344753747 1.7500000000000002 6 0.47109207708779444 1.6500000000000001 7 0.556745182012848 2.275 8 0.17130620985010706 0.8 9 0.5139186295503212 2.7 >10 1.4561027837259102 16.45 >50 0.1284796573875803 5.675 >100 0.042826552462526764 3.175 >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 GACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 127 3.175 RNA PCR Primer, Index 1 (100% over 23bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 80 2.0 No Hit TCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 74 1.8499999999999999 No Hit TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 73 1.825 RNA PCR Primer, Index 1 (100% over 29bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 49 1.225 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATATGGAATTCTCGGGTGCCAAGGAA 47 1.175 RNA PCR Primer, Index 1 (100% over 23bp) GCCCACCCCAAGATGAGTGCTCTCTCTGGAATTCTCGGGTGCCAAGGAAC 42 1.05 RNA PCR Primer, Index 1 (100% over 24bp) GGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 39 0.975 RNA PCR Primer, Index 1 (100% over 22bp) CACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAACT 30 0.75 RNA PCR Primer, Index 1 (100% over 25bp) AGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 24 0.6 No Hit GACACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACT 23 0.575 RNA PCR Primer, Index 1 (100% over 25bp) CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 21 0.525 No Hit GCACCAGTGGTCTAGTGGTAGAATAGTACCTGGAATTCTCGGGTGCCAAG 21 0.525 No Hit ACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCC 21 0.525 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 20 0.5 Illumina Small RNA Adapter 2 (100% over 21bp) GACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAAC 20 0.5 RNA PCR Primer, Index 1 (100% over 24bp) GCCTTGATGGTGAAATGGTAGACATGGAATTCTCGGGTGCCAAGGAACTC 20 0.5 RNA PCR Primer, Index 1 (100% over 26bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 18 0.44999999999999996 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 18 0.44999999999999996 No Hit CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTC 18 0.44999999999999996 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 17 0.42500000000000004 Illumina Small RNA Adapter 2 (100% over 21bp) NACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 17 0.42500000000000004 RNA PCR Primer, Index 1 (100% over 23bp) GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGGAATTCTCGGGTGCCA 15 0.375 No Hit TTCGGACCAGGCTTCATTCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 14 0.35000000000000003 RNA PCR Primer, Index 1 (100% over 29bp) AGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCC 14 0.35000000000000003 RNA PCR Primer, Index 1 (100% over 27bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTTGGAATTCTCGGGTG 14 0.35000000000000003 No Hit ACCTGCTCTGATACCATGTTGTGATGGAATTCTCGGGTGCCAAGGAACTC 13 0.325 RNA PCR Primer, Index 1 (100% over 26bp) CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 13 0.325 RNA PCR Primer, Index 1 (100% over 28bp) GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 13 0.325 No Hit CTCTGATGATGATCAAACTAATACTTTCGTTCTTCTGGAATTCTCGGGTG 12 0.3 No Hit ATGCAGTTACTAATTCATGATCTGGCTGGAATTCTCGGGTGCCAAGGAAC 12 0.3 RNA PCR Primer, Index 1 (100% over 24bp) TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 12 0.3 No Hit TCCACAGGCTTTCTTGAACTGTGGAATTCTCGGGTGCCAAGGAACTCCAG 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 29bp) AATTCTCGGGTGCCAAGGAACTCCAGTCACGGTAGCATCTCGTATGCCGT 10 0.25 RNA PCR Primer, Index 24 (100% over 50bp) ATATATTTCAAGTTATTTCGGATCTTGGAATTCTCGGGTGCCAAGGAACT 10 0.25 RNA PCR Primer, Index 1 (100% over 25bp) TCTCGGACCAGGCTTCATTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 10 0.25 RNA PCR Primer, Index 1 (100% over 29bp) CAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTC 10 0.25 RNA PCR Primer, Index 1 (100% over 26bp) CAGGGTTCGTTTCCCTGGATGCGCACCATGGAATTCTCGGGTGCCAAGGA 10 0.25 RNA PCR Primer, Index 1 (100% over 22bp) GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 9 0.22499999999999998 No Hit GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTG 9 0.22499999999999998 No Hit GCACCAGTAGTCTAGTGGTAGAATAGTACCTGGAATTCTCGGGTGCCAAG 9 0.22499999999999998 No Hit TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGTAGCATCTCGTATGC 9 0.22499999999999998 RNA PCR Primer, Index 24 (100% over 50bp) ACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAAC 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 24bp) GCGACCCCAGGTCAGGCGGGACTTGGAATTCTCGGGTGCCAAGGAACTCC 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 27bp) TCTCGGGTGCCAAGGAACTCCAGTCACGGTAGCATCTCGTATGCCGTCTT 9 0.22499999999999998 RNA PCR Primer, Index 24 (100% over 50bp) CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 23bp) AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 9 0.22499999999999998 Illumina Small RNA Adapter 2 (100% over 21bp) GACACGACTCTCGGCAACGGATATCTCGTGGAATTCTCGGGTGCCAAGGA 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 22bp) TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTGGAATTCTCGGGTGC 9 0.22499999999999998 No Hit AGGGCTATAGCTCAGTTCGGTAGAGCAACTCGTTTACACCGAGATGGAAT 9 0.22499999999999998 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGGTGGAATTC 8 0.2 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTTGGAATTCT 8 0.2 No Hit CGACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGA 8 0.2 RNA PCR Primer, Index 1 (100% over 22bp) NGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 8 0.2 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGAGTGGAATTCT 7 0.17500000000000002 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTTGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit GAAGTCCTCGTGTTGCATTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 28bp) TGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAA 7 0.17500000000000002 No Hit CACGACTCTCGGCAACGGATATCTCGTGGAATTCTCGGGTGCCAAGGAAC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 24bp) AAGGGTGCTGAGAATACTTTGAATCTGACACTGGAATTCTCGGGTGCCAA 7 0.17500000000000002 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGATGGAATTCTCGGGTGCCAA 7 0.17500000000000002 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTTGGAATTCTCGGGTGCCA 7 0.17500000000000002 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGGAATTCTCGGGTGCCAA 7 0.17500000000000002 No Hit CCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACT 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 25bp) TCCGTCGTAGTCTAGGTGGTTAGGATTGGAATTCTCGGGTGCCAAGGAAC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 24bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTTGGAATTCTCGGGTGC 7 0.17500000000000002 No Hit CACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGC 7 0.17500000000000002 No Hit GCACCAGTGGTCTAGTGGTAGAATAGTATGGAATTCTCGGGTGCCAAGGA 6 0.15 RNA PCR Primer, Index 1 (100% over 22bp) CATCGAGTAGACCTTGTTATTGTGAGAATAAATGGAATTCTCGGGTGCCA 6 0.15 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATACTCTGGAATTCTCGGGTGCCAAG 6 0.15 No Hit TTTGTTTTTATGTTATTTTGTGAAGGTGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) ATCAGCTGACACGAGCAAATCTGAACCTGGAATTCTCGGGTGCCAAGGAA 6 0.15 RNA PCR Primer, Index 1 (100% over 23bp) ATTCTCGGGTGCCAAGGAACTCCAGTCACGGTAGCATCTCGTATGCCGTC 6 0.15 RNA PCR Primer, Index 24 (100% over 50bp) AGTTACTAATTCATGATCTGGCTGGAATTCTCGGGTGCCAAGGAACTCCA 6 0.15 RNA PCR Primer, Index 1 (100% over 28bp) TAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAG 6 0.15 RNA PCR Primer, Index 1 (100% over 29bp) CATCGAGTAGACCTTGTTATTGTGAGAATTAATGGAATTCTCGGGTGCCA 6 0.15 No Hit GCGTCTGTAGTCCAACGGTTAGGATAATTGCCTGGAATTCTCGGGTGCCA 6 0.15 No Hit TCGCTTGGTGCAGATCGGGACTGGAATTCTCGGGTGCCAAGGAACTCCAG 6 0.15 RNA PCR Primer, Index 1 (100% over 29bp) GACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCTGGAATTCTCG 5 0.125 No Hit GTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGGAATTCTCGGGTGCCA 5 0.125 No Hit TAATTCATGATCTGGCATGTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 5 0.125 RNA PCR Primer, Index 1 (100% over 31bp) GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTTGGAATTCTCGGGTGC 5 0.125 No Hit GGGGATATGGCGAAATCGGTAGACGCTACGGACTTTGGAATTCTCGGGTG 5 0.125 No Hit NCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 5 0.125 RNA PCR Primer, Index 1 (100% over 29bp) CATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) CTTAGCGGATACTATGATAGCACCTGGAATTCTCGGGTGCCAAGGAACTC 5 0.125 RNA PCR Primer, Index 1 (100% over 26bp) GCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCC 5 0.125 No Hit TGCCACGATCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAAT 5 0.125 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTAATCCTGGAATTC 5 0.125 No Hit TTGACAGAAGAGAGTGAGCACTGGAATTCTCGGGTGCCAAGGAACTCCAG 5 0.125 RNA PCR Primer, Index 1 (100% over 29bp) GGGGATATAGCTCAGTTGGTAGATGGAATTCTCGGGTGCCAAGGAACTCC 5 0.125 RNA PCR Primer, Index 1 (100% over 27bp) CATCGAGTAGACCTTGTTATTGTGAGAATTATGGAATTCTCGGGTGCCAA 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 0.225 0.0 0.0 0.0 2 0.0 0.225 0.0 0.0 0.0 3 0.0 0.225 0.0 0.0 0.0 4 0.0 0.225 0.0 0.0 0.0 5 0.0 0.225 0.0 0.0 0.0 6 0.0 0.225 0.0 0.0 0.0 7 0.0 0.275 0.0 0.0 0.0 8 0.0 0.35 0.0 0.0 0.0 9 0.0 0.45 0.0 0.0 0.0 10-11 0.0 0.525 0.0 0.0 0.0 12-13 0.0 0.65 0.0 0.0 0.0 14-15 0.0 0.9125000000000001 0.0 0.0 0.0 16-17 0.0 1.6 0.0 0.0 0.0 18-19 0.0 2.625 0.0 0.0 0.0 20-21 0.0 4.8375 0.0 0.0 0.0 22-23 0.0 13.0 0.0 0.0 0.0 24-25 0.0 24.0375 0.0 0.0 0.0 26-27 0.0 37.0625 0.0 0.0 0.0 28-29 0.0 50.1 0.0 0.0 0.0 30-31 0.0 58.125 0.0 0.0 0.0 32-33 0.0 67.275 0.0 0.0 0.0 34-35 0.0 77.3 0.0 0.0 0.0 36-37 0.0 84.5625 0.0 0.0 0.0 38-39 0.0 89.05000000000001 0.0 0.0 0.0 40-41 0.0 91.15 0.0 0.0 0.0 42-43 0.0 93.7875 0.0 0.0 0.0 44-45 0.0 95.5625 0.0 0.0 0.0 46-47 0.0 96.225 0.0 0.0 0.0 48-49 0.0 96.375 0.0 0.0 0.0 50-51 0.0 96.425 0.0 0.0 0.0 52-53 0.0 96.5 0.0 0.0 0.0 54-55 0.0 96.525 0.0 0.0 0.0 56-57 0.0 96.525 0.0 0.0 0.0 58-59 0.0 96.525 0.0 0.0 0.0 60-61 0.0 96.525 0.0 0.0 0.0 62-63 0.0 96.525 0.0 0.0 0.0 64-65 0.0 96.525 0.0 0.0 0.0 66-67 0.0 96.525 0.0 0.0 0.0 68-69 0.0 96.525 0.0 0.0 0.0 70-71 0.0 96.525 0.0 0.0 0.0 72-73 0.0 96.525 0.0 0.0 0.0 74-75 0.0 96.525 0.0 0.0 0.0 76-77 0.0 96.525 0.0 0.0 0.0 78-79 0.0 96.525 0.0 0.0 0.0 80-81 0.0 96.525 0.0 0.0 0.0 82-83 0.0 96.5375 0.0 0.0 0.0 84-85 0.0 96.55 0.0 0.0 0.0 86-87 0.0 96.55 0.0 0.0 0.0 88-89 0.0 96.55 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GACACGA 25 2.1896449E-7 104.0137 1 ACACGAC 25 3.8500548E-7 94.912506 2 TTGTAGT 15 6.164719E-4 94.9125 5 TAGTTCA 15 6.164719E-4 94.9125 8 AGTTCAA 15 6.164719E-4 94.9125 9 GTAGTTC 15 6.164719E-4 94.9125 7 CTCTCGG 30 1.1400607E-6 79.09375 8 ACTCTCG 30 1.1400607E-6 79.09375 7 CACGACT 30 1.1400607E-6 79.09375 3 ACGACTC 30 1.1400607E-6 79.09375 4 GACTCTC 30 1.1400607E-6 79.09375 6 CGACTCT 30 1.1400607E-6 79.09375 5 TCTCGGC 40 6.299526E-6 59.320312 9 AAAAACA 20 5.094958E-4 47.456253 94-95 GATATCT 30 7.616909E-5 39.546875 20-21 GGCAACG 30 7.616909E-5 39.546875 12-13 CGGATAT 30 7.616909E-5 39.546875 18-19 GCAACGG 30 7.616909E-5 39.546875 14-15 GGATATC 30 7.616909E-5 39.546875 18-19 CTCGGCA 30 7.616909E-5 39.546875 10-11 >>END_MODULE Rejected 1144652 READS because READLEN < 1 Read 1144652 spots for SRR8846549.sra Written 1144652 spots for SRR8846549.sra Rejected 1144652 READS because READLEN < 1 Read 1144652 spots for SRR8846549.sra Written 1144652 spots for SRR8846549.sra Rejected 1144652 READS because READLEN < 1 Read 1144652 spots for SRR8846549.sra Written 1144652 spots for SRR8846549.sra Rejected 1144652 READS because READLEN < 1 Read 1144652 spots for SRR8846549.sra Written 1144652 spots for SRR8846549.sra Rejected 1144652 READS because READLEN < 1 Read 1144652 spots for SRR8846549.sra Written 1144652 spots for SRR8846549.sra Rejected 1144652 READS because READLEN < 1 Read 1144652 spots for SRR8846549.sra Written 1144652 spots for SRR8846549.sra Rejected 1144652 READS because READLEN < 1 Read 1144652 spots for SRR8846549.sra Written 1144652 spots for SRR8846549.sra Rejected 1144652 READS because READLEN < 1 Read 1144652 spots for SRR8846549.sra Written 1144652 spots for SRR8846549.sra Rejected 1144652 READS because READLEN < 1 Read 1144652 spots for SRR8846549.sra Written 1144652 spots for SRR8846549.sra Rejected 1144652 READS because READLEN < 1 Read 1144652 spots for SRR8846549.sra Written 1144652 spots for SRR8846549.sra Rejected 1144652 READS because READLEN < 1 Read 1144652 spots for SRR8846549.sra Written 1144652 spots for SRR8846549.sra Rejected 1144652 READS because READLEN < 1 Read 1144652 spots for SRR8846549.sra Written 1144652 spots for SRR8846549.sra Rejected 1144652 READS because READLEN < 1 Read 1144652 spots for SRR8846549.sra Written 1144652 spots for SRR8846549.sra Rejected 1144652 READS because READLEN < 1 Read 1144652 spots for SRR8846549.sra Written 1144652 spots for SRR8846549.sra Rejected 1144652 READS because READLEN < 1 Read 1144652 spots for SRR8846549.sra Written 1144652 spots for SRR8846549.sra Rejected 1144652 READS because READLEN < 1 Read 1144652 spots for SRR8846549.sra Written 1144652 spots for SRR8846549.sra Rejected 1144652 READS because READLEN < 1 Read 1144652 spots for SRR8846549.sra Written 1144652 spots for SRR8846549.sra Rejected 1144652 READS because READLEN < 1 Read 1144652 spots for SRR8846549.sra Written 1144652 spots for SRR8846549.sra Rejected 1144652 READS because READLEN < 1 Read 1144652 spots for SRR8846549.sra Written 1144652 spots for SRR8846549.sra Rejected 1144652 READS because READLEN < 1 Read 1144652 spots for SRR8846549.sra Written 1144652 spots for SRR8846549.sra SRR ids: ['SRR8846549.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_342hjxby SRR8846549.sra spots: 22893040 blocks: [[1, 1144652], [1144653, 2289304], [2289305, 3433956], [3433957, 4578608], [4578609, 5723260], [5723261, 6867912], [6867913, 8012564], [8012565, 9157216], [9157217, 10301868], [10301869, 11446520], [11446521, 12591172], [12591173, 13735824], [13735825, 14880476], [14880477, 16025128], [16025129, 17169780], [17169781, 18314432], [18314433, 19459084], [19459085, 20603736], [20603737, 21748388], [21748389, 22893040]] SRR8846549 file size 5500351 SRR8846549 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 SRR8846549 SRR8846549_1.fastq Input file: SRR8846549_1.fastq trimmed: SRR8846549-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 10:00:11 2024 >> started Mon Dec 9 10:00:22 2024 >> done (10.756s) 22893040 reads processed; of these: 623 ( 0.00%) short reads filtered out after trimming by size control 77 ( 0.00%) empty reads filtered out after trimming by size control 22892340 (100.00%) reads available; of these: 4885180 (21.34%) trimmed reads available after processing 18007160 (78.66%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 74 0.00% 19 63 0.00% 20 69 0.00% 21 75 0.00% 22 88 0.00% 23 90 0.00% 24 133 0.00% 25 171 0.00% 26 232 0.00% 27 339 0.00% 28 418 0.00% 29 490 0.00% 30 442 0.00% 31 403 0.00% 32 374 0.00% 33 334 0.00% 34 343 0.00% 35 269 0.00% 36 265 0.00% 37 259 0.00% 38 256 0.00% 39 250 0.00% 40 264 0.00% 41 303 0.00% 42 394 0.00% 43 365 0.00% 44 419 0.00% 45 420 0.00% 46 404 0.00% 47 411 0.00% 48 352 0.00% 49 274 0.00% 50 334 0.00% 51 328 0.00% 52 312 0.00% 53 356 0.00% 54 362 0.00% 55 416 0.00% 56 462 0.00% 57 511 0.00% 58 484 0.00% 59 609 0.00% 60 796 0.00% 61 868 0.00% 62 1064 0.00% 63 1291 0.01% 64 1810 0.01% 65 2018 0.01% 66 4599 0.02% 67 16663 0.07% 68 20391 0.09% 69 16834 0.07% 70 18958 0.08% 71 30045 0.13% 72 14619 0.06% 73 6975 0.03% 74 20908 0.09% 75 10294 0.04% 76 5311 0.02% 77 4234 0.02% 78 5056 0.02% 79 5802 0.03% 80 7637 0.03% 81 10414 0.05% 82 15857 0.07% 83 15908 0.07% 84 15360 0.07% 85 15942 0.07% 86 20174 0.09% 87 28906 0.13% 88 41107 0.18% 89 54942 0.24% 90 84267 0.37% 91 95170 0.42% 92 120787 0.53% 93 192456 0.84% 94 237032 1.04% 95 514084 2.25% 96 622603 2.72% 97 581515 2.54% 98 836532 3.65% 99 732119 3.20% 100 440615 1.92% 101 18007160 78.66% 22892340 reads passed initial QC criterion=sequence-density sequence-density=96.39 sequence-density-rank=1 fanout-score=35.77 fanout-score-rank=1 prefix-density=96.78 prefix-fanout=35.6 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGTAGCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA criterion=fanout-score sequence-density=96.39 sequence-density-rank=1 fanout-score=35.77 fanout-score-rank=1 prefix-density=96.78 prefix-fanout=35.6 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGTAGCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGTAGCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA -o SRR8846549 - Input file: STDIN trimmed: SRR8846549-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGTAGCATCTCGTATGCCGTCTTCTGCTTGA -- 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 10:01:00 2024 >> started Mon Dec 9 10:01:20 2024 >> done (19.771s) 22420333 reads processed; of these: 463459 ( 2.07%) short reads filtered out after trimming by size control 46597 ( 0.21%) empty reads filtered out after trimming by size control 21910277 (97.73%) reads available; of these: 21615923 (98.66%) trimmed reads available after processing 294354 ( 1.34%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 145483 0.66% 19 274871 1.25% 20 283264 1.29% 21 1242585 5.67% 22 642836 2.93% 23 837751 3.82% 24 2670202 12.19% 25 958032 4.37% 26 1147948 5.24% 27 1688534 7.71% 28 1083225 4.94% 29 834979 3.81% 30 1088402 4.97% 31 830070 3.79% 32 1353552 6.18% 33 1184511 5.41% 34 943786 4.31% 35 834420 3.81% 36 988552 4.51% 37 447368 2.04% 38 348991 1.59% 39 310402 1.42% 40 311421 1.42% 41 308782 1.41% 42 350303 1.60% 43 165903 0.76% 44 181701 0.83% 45 60889 0.28% 46 42971 0.20% 47 19090 0.09% 48 11063 0.05% 49 6713 0.03% 50 4189 0.02% 51 3580 0.02% 52 2088 0.01% 53 1395 0.01% 54 1316 0.01% 55 620 0.00% 56 835 0.00% 57 379 0.00% 58 366 0.00% 59 387 0.00% 60 435 0.00% 61 513 0.00% 62 608 0.00% 63 845 0.00% 64 1279 0.01% 65 1443 0.01% 66 3841 0.02% 67 15595 0.07% 68 19028 0.09% 69 15414 0.07% 70 17292 0.08% 71 27790 0.13% 72 11601 0.05% 73 2315 0.01% 74 1296 0.01% 75 890 0.00% 76 1078 0.00% 77 1441 0.01% 78 1119 0.01% 79 1037 0.00% 80 1995 0.01% 81 1532 0.01% 82 1363 0.01% 83 2123 0.01% 84 1075 0.00% 85 878 0.00% 86 856 0.00% 87 968 0.00% 88 660 0.00% 89 809 0.00% 90 767 0.00% 91 784 0.00% 92 959 0.00% 93 1128 0.01% 94 1160 0.01% 95 1434 0.01% 96 2000 0.01% 97 2709 0.01% 98 4263 0.02% 99 3713 0.02% 100 4670 0.02% 101 135816 0.62% criterion=sequence-density sequence-density=6.20 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=13 prefix-density=0.00 prefix-fanout=1.0 sequence=GGGATTGTAGTTCAATTGGTCAGAGCACCGCCC criterion=fanout-score sequence-density=0.30 sequence-density-rank=16 fanout-score=10.01 fanout-score-rank=1 prefix-density=2.97 prefix-fanout=1.0 sequence=ATTGTGAGAATAAAAA Started job on | Dec 09 10:01:38 Started mapping on | Dec 09 10:01:38 Finished on | Dec 09 10:02:29 Mapping speed, Million of reads per hour | 1579.93 Number of input reads | 22382284 Average input read length | 31 UNIQUE READS: Uniquely mapped reads number | 3652224 Uniquely mapped reads % | 16.32% Average mapped length | 26.88 Number of splices: Total | 45728 Number of splices: Annotated (sjdb) | 29277 Number of splices: GT/AG | 42490 Number of splices: GC/AG | 2380 Number of splices: AT/AC | 30 Number of splices: Non-canonical | 828 Mismatch rate per base, % | 0.16% Deletion rate per base | 0.00% Deletion average length | 1.38 Insertion rate per base | 0.00% Insertion average length | 1.02 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 8378383 % of reads mapped to multiple loci | 37.43% Number of reads mapped to too many loci | 9191189 % of reads mapped to too many loci | 41.06% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.63% % of reads unmapped: other | 0.56% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 10351677 10351677 10351677 N_multimapping 8378383 8378383 8378383 N_noFeature 2157504 2453205 3335067 N_ambiguous 58699 36689 763 UnstrandedReadsAssigned:1436021 PositiveStrandReadsAssigned:1162330 NegativeStrandReadsAssigned:316394 Dataset is classified unstranded MeadianReadLen=28 20thPercentileLength=24 echo kmer=19 SRR8846549 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: SRR8846549-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 22,382,284 reads, 6,654,032 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,149 rounds 52973 SRR8846549.ke.tsv 35125 SRR8846549.se.tsv 88098 total ==> SRR8846549.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 2.52842 0.196555 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 6.931 0.718275 PNS24243 293 194 0 0 KQK14069 1603 1504 390.201 36.8883 KQK14071 474 375 2.34081 0.887529 ==> SRR8846549.se.tsv <== BRADI_1g14170v3 411 BRADI_1g53295v3 6 BRADI_1g59795v3 1 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 45 BRADI_1g74790v3 48 BRADI_1g09890v3 0 BRADI_1g77505v3 3 BRADI_1g48960v3 0 SRR8846549 completed mapping pipeline successfully