Starting /dee2/code/volunteer_pipeline.sh SRR8846506 current disk space = 1507301163008 free memory = 1427313864 SRR8846506 SRAfilesize 18b48921ec3553e2634b8a3a0f2a0fb8 SRR8846506.sra SRR8846506.sra file validated SRR8846506 is single end SRR8846506 is conventional basespace SRR8846506 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8846506_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 45 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.205 34.0 33.0 34.0 30.0 34.0 2 32.8165 34.0 33.0 34.0 30.0 34.0 3 32.9035 34.0 33.0 34.0 32.0 34.0 4 33.1395 34.0 33.0 34.0 32.0 34.0 5 32.9895 34.0 33.0 34.0 32.0 34.0 6 36.7135 38.0 37.0 38.0 34.0 38.0 7 36.94825 38.0 38.0 38.0 35.0 38.0 8 37.2895 38.0 38.0 38.0 36.0 38.0 9 37.26675 38.0 38.0 38.0 36.0 38.0 10-11 37.360375000000005 38.0 38.0 38.0 37.0 38.0 12-13 37.378 38.0 38.0 38.0 37.0 38.0 14-15 37.360749999999996 38.0 38.0 38.0 37.0 38.0 16-17 37.296375 38.0 38.0 38.0 37.0 38.0 18-19 37.321375 38.0 38.0 38.0 37.0 38.0 20-21 37.297250000000005 38.0 38.0 38.0 37.0 38.0 22-23 37.36024999999999 38.0 38.0 38.0 37.0 38.0 24-25 37.376000000000005 38.0 38.0 38.0 37.0 38.0 26-27 37.351375 38.0 38.0 38.0 37.0 38.0 28-29 37.318625 38.0 38.0 38.0 37.0 38.0 30-31 37.363749999999996 38.0 38.0 38.0 37.0 38.0 32-33 37.2635 38.0 38.0 38.0 37.0 38.0 34-35 36.908125 38.0 38.0 38.0 35.5 38.0 36-37 36.830625 38.0 38.0 38.0 35.0 38.0 38-39 36.68575 38.0 38.0 38.0 34.5 38.0 40-41 37.007875 38.0 38.0 38.0 36.0 38.0 42-43 37.02575 38.0 38.0 38.0 36.0 38.0 44-45 36.941375 38.0 38.0 38.0 36.0 38.0 46-47 36.880750000000006 38.0 38.0 38.0 35.5 38.0 48-49 37.01 38.0 38.0 38.0 36.0 38.0 50-51 37.08125 38.0 38.0 38.0 36.0 38.0 52-53 37.169125 38.0 38.0 38.0 36.0 38.0 54-55 36.979124999999996 38.0 38.0 38.0 36.0 38.0 56-57 36.748125 38.0 38.0 38.0 35.0 38.0 58-59 36.6415 38.0 38.0 38.0 34.0 38.0 60-61 36.578625 38.0 38.0 38.0 34.0 38.0 62-63 35.975625 38.0 37.0 38.0 31.0 38.0 64-65 35.60525 38.0 36.5 38.0 29.5 38.0 66-67 35.35475 38.0 36.5 38.0 28.0 38.0 68-69 35.505875 38.0 37.0 38.0 29.0 38.0 70-71 35.049125000000004 38.0 36.0 38.0 28.0 38.0 72-73 34.945499999999996 38.0 36.0 38.0 27.5 38.0 74-75 34.844375 38.0 36.0 38.0 27.5 38.0 76-77 34.42325 38.0 35.0 38.0 26.0 38.0 78-79 34.57525 38.0 35.5 38.0 26.0 38.0 80-81 33.929 38.0 34.5 38.0 24.0 38.0 82-83 34.183 38.0 35.0 38.0 25.0 38.0 84-85 33.930875 38.0 34.5 38.0 24.0 38.0 86-87 33.813874999999996 38.0 34.5 38.0 15.5 38.0 88-89 33.91875 38.0 35.0 38.0 24.0 38.0 90-91 33.016375 38.0 34.0 38.0 15.0 38.0 92-93 32.51575 38.0 34.0 38.0 15.0 38.0 94-95 31.73925 38.0 33.0 38.0 8.0 38.0 96-97 29.253625 38.0 26.5 38.0 2.0 38.0 98-99 25.67675 35.5 8.0 38.0 2.0 38.0 100-101 22.015625 30.0 2.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 19 1.0 20 4.0 21 6.0 22 8.0 23 9.0 24 24.0 25 41.0 26 32.0 27 32.0 28 39.0 29 55.0 30 79.0 31 106.0 32 177.0 33 242.0 34 342.0 35 578.0 36 973.0 37 1252.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 27.32109603617984 29.05027932960894 21.761106677307794 21.86751795690343 2 23.825 31.874999999999996 19.950000000000003 24.349999999999998 3 26.150000000000002 18.45 24.3 31.1 4 30.599999999999998 26.674999999999997 17.724999999999998 25.0 5 35.375 26.650000000000002 19.125 18.85 6 24.131032758189548 32.58314578644661 22.1055263815954 21.180295073768445 7 37.05 21.6 19.7 21.65 8 23.025000000000002 21.175 35.625 20.175 9 23.150000000000002 37.025000000000006 22.15 17.675 10-11 31.4875 27.075 21.7875 19.650000000000002 12-13 21.675 23.0 22.9375 32.3875 14-15 19.900000000000002 36.725 26.0 17.375 16-17 23.45 28.9125 32.087500000000006 15.55 18-19 27.5875 25.8625 25.25 21.3 20-21 20.5875 28.5875 29.549999999999997 21.275 22-23 27.712500000000002 27.575 31.474999999999998 13.237499999999999 24-25 26.5625 24.9125 30.375000000000004 18.15 26-27 37.1875 26.8625 21.8125 14.1375 28-29 18.512500000000003 34.125 27.6 19.7625 30-31 23.3625 16.0 43.45 17.1875 32-33 27.1125 17.0625 30.1875 25.637500000000003 34-35 32.737500000000004 18.3625 26.137500000000003 22.7625 36-37 43.2125 12.962499999999999 25.525 18.3 38-39 31.9875 19.6875 26.424999999999997 21.9 40-41 27.825 19.287499999999998 19.5875 33.300000000000004 42-43 30.012499999999996 31.424999999999997 17.299999999999997 21.2625 44-45 41.375 20.125 13.5375 24.962500000000002 46-47 25.2625 33.725 13.850000000000001 27.1625 48-49 22.5 24.6125 20.3625 32.525 50-51 22.2125 23.5625 13.8125 40.4125 52-53 23.6375 35.375 12.237499999999999 28.749999999999996 54-55 16.6 23.3 20.8 39.300000000000004 56-57 15.425 33.637499999999996 14.9625 35.975 58-59 18.55 29.575000000000003 16.5 35.375 60-61 21.6 22.925 22.875 32.6 62-63 20.7625 23.425 17.962500000000002 37.85 64-65 15.387500000000001 26.650000000000002 29.725 28.237499999999997 66-67 18.75 17.625 28.7375 34.887499999999996 68-69 23.2625 20.0 23.75 32.9875 70-71 19.45 22.912499999999998 33.15 24.4875 72-73 28.762500000000003 11.5875 31.0375 28.6125 74-75 18.625 11.875 28.325 41.175 76-77 20.9125 10.4 43.5375 25.15 78-79 17.875 7.387499999999999 40.1875 34.55 80-81 19.0875 10.75 37.175000000000004 32.9875 82-83 23.2875 12.3125 42.3875 22.0125 84-85 17.7375 16.0875 36.7125 29.462500000000002 86-87 21.462500000000002 25.025 34.137499999999996 19.375 88-89 12.6375 46.35 25.575 15.437500000000002 90-91 9.15 53.337500000000006 25.275 12.237499999999999 92-93 10.9875 62.287499999999994 17.1375 9.5875 94-95 7.9625 72.1375 12.737499999999999 7.1625 96-97 5.7875000000000005 78.7 11.725 3.7875 98-99 5.137499999999999 85.2 6.2375 3.4250000000000003 100-101 2.5375 88.125 4.7875 4.55 >>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 1.0 34 2.5 35 7.5 36 12.0 37 17.0 38 21.0 39 31.5 40 68.0 41 98.5 42 157.5 43 245.0 44 323.0 45 476.5 46 513.0 47 469.5 48 401.0 49 267.5 50 233.0 51 218.0 52 167.5 53 93.5 54 41.0 55 31.0 56 46.0 57 31.5 58 5.0 59 6.5 60 6.5 61 5.0 62 3.0 63 0.5 64 0.0 65 0.0 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 6.0249999999999995 2 0.0 3 0.0 4 0.0 5 0.0 6 0.025 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 57.199999999999996 #Duplication Level Percentage of deduplicated Percentage of total 1 86.93181818181817 49.725 2 6.075174825174825 6.950000000000001 3 2.054195804195804 3.5249999999999995 4 1.048951048951049 2.4 5 0.6993006993006993 2.0 6 0.3933566433566434 1.35 7 0.3933566433566434 1.575 8 0.34965034965034963 1.6 9 0.34965034965034963 1.7999999999999998 >10 1.486013986013986 18.875 >50 0.17482517482517482 7.425 >100 0.043706293706293704 2.775 >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 TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 111 2.775 RNA PCR Primer, Index 1 (100% over 29bp) GGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 99 2.475 RNA PCR Primer, Index 1 (100% over 22bp) AGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 74 1.8499999999999999 No Hit CTCTGATGATGATCAAACTAATACTTTCGTTCTTCTGGAATTCTCGGGTG 70 1.7500000000000002 No Hit GACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 54 1.35 RNA PCR Primer, Index 1 (100% over 23bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 49 1.225 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 47 1.175 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 42 1.05 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 41 1.0250000000000001 Illumina Small RNA Adapter 2 (100% over 21bp) TCTCGGGTGCCAAGGAACTCCAGTCACCATGGCATCTCGTATGCCGTCTT 37 0.9249999999999999 RNA PCR Primer, Index 34 (100% over 50bp) ATATATTTCAAGTTATTTCGGATCTTGGAATTCTCGGGTGCCAAGGAACT 36 0.8999999999999999 RNA PCR Primer, Index 1 (100% over 25bp) CTCGGGTGCCAAGGAACTCCAGTCACCATGGCATCTCGTATGCCGTCTTC 31 0.775 RNA PCR Primer, Index 34 (100% over 50bp) CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 28 0.7000000000000001 Illumina Small RNA Adapter 2 (100% over 21bp) AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 28 0.7000000000000001 Illumina Small RNA Adapter 2 (100% over 21bp) GGGGACGTAGCTCATATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC 28 0.7000000000000001 RNA PCR Primer, Index 2 (100% over 34bp) AAGGGTGCTGAGAATACTTTGAATCTGACACTGGAATTCTCGGGTGCCAA 27 0.675 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 26 0.65 No Hit TCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 26 0.65 No Hit GACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAAC 26 0.65 RNA PCR Primer, Index 1 (100% over 24bp) CATCGAGTAGACCTTGTTATTGTGAGAATAAATGGAATTCTCGGGTGCCA 25 0.625 No Hit TTCGGACCAGGCTTCATTCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 21 0.525 RNA PCR Primer, Index 1 (100% over 29bp) GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 18 0.44999999999999996 No Hit AATTCTCGGGTGCCAAGGAACTCCAGTCACCATGGCATCTCGTATGCCGT 16 0.4 RNA PCR Primer, Index 34 (100% over 50bp) GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 16 0.4 Illumina Small RNA Adapter 2 (100% over 21bp) CACGACTCTCGGCAATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA 16 0.4 RNA PCR Primer, Index 7 (100% over 35bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTCATGGAATTCTCGGGTG 16 0.4 No Hit CATCGAGTAGACCTTGTTATTGTGGAATTCTCGGGTGCCAAGGAACTCCA 15 0.375 RNA PCR Primer, Index 1 (100% over 28bp) GGGGATGTAGCTCAGATGGTAGATGGAATTCTCGGGTGCCAAGGAACTCC 15 0.375 RNA PCR Primer, Index 1 (100% over 27bp) GGGGATATAGCTCAGTTGGTAGATGGAATTCTCGGGTGCCAAGGAACTCC 13 0.325 RNA PCR Primer, Index 1 (100% over 27bp) CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 12 0.3 RNA PCR Primer, Index 1 (100% over 28bp) TTCTCGGGTGCCAAGGAACTCCAGTCACCATGGCATCTCGTATGCCGTCT 12 0.3 RNA PCR Primer, Index 34 (100% over 50bp) TCTCGGACCAGGCTTCATTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 12 0.3 RNA PCR Primer, Index 1 (100% over 29bp) GACACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACT 12 0.3 RNA PCR Primer, Index 1 (100% over 25bp) NCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 29bp) AGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGCCAAG 11 0.27499999999999997 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGAATTCTCGGGTGCCAAGGAACTCCA 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 28bp) TCGTGACCCTGACCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAT 11 0.27499999999999997 RNA PCR Primer, Index 9 (97% over 36bp) AAGGGTGCTGAGAATACTTTGAATCTGACATGGAATTCTCGGGTGCCAAG 10 0.25 No Hit GCACCAGTGGTCTAGTGGTAGAATAGTACCTGGAATTCTCGGGTGCCAAG 10 0.25 No Hit NGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 22bp) TCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTC 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 26bp) CATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGCC 9 0.22499999999999998 No Hit CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 23bp) GGGGATATGGCGAAATCGGTAGACGCTACGGACTTTGGAATTCTCGGGTG 9 0.22499999999999998 No Hit GCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCC 9 0.22499999999999998 No Hit TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 9 0.22499999999999998 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTGGAATTCTCGGGTGCCA 9 0.22499999999999998 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATACTCTGGAATTCTCGGGTGCCAAG 8 0.2 No Hit TCCTGTGGATGAGAAGGCATTTATATTCTGATGATATGGAATTCTCGGGT 8 0.2 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTGGAATTCTCGGGTGCCAAG 8 0.2 No Hit TCCACAGGCTTTCTTGAACTGTGGAATTCTCGGGTGCCAAGGAACTCCAG 8 0.2 RNA PCR Primer, Index 1 (100% over 29bp) ATTCTCGGGTGCCAAGGAACTCCAGTCACCATGGCATCTCGTATGCCGTC 8 0.2 RNA PCR Primer, Index 34 (100% over 50bp) CAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTG 8 0.2 No Hit ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGC 8 0.2 No Hit TTCCATAACTGTTGTTGCTCAAGTGGAATTCTCGGGTGCCAAGGAACTCC 8 0.2 RNA PCR Primer, Index 1 (100% over 27bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTTGGAATTCT 7 0.17500000000000002 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAAAATGGAATTCTCGGGTGC 7 0.17500000000000002 No Hit ATATATTTCAAGTTATTTCGGATCTGGAATTCTCGGGTGCCAAGGAACTC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 26bp) TCCGTCGTAGTCTAGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC 7 0.17500000000000002 RNA PCR Primer, Index 2 (100% over 34bp) ATGCAGTTACTAATTCATGATCTGGCTGGAATTCTCGGGTGCCAAGGAAC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 24bp) GCCCACCCCAAGATGAGTGCTCTCTCTGGAATTCTCGGGTGCCAAGGAAC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 24bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATGGAATTCTCGGGTG 7 0.17500000000000002 No Hit NATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 7 0.17500000000000002 No Hit CTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCA 7 0.17500000000000002 No Hit GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTG 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAAAAATGGAATTCTCGGGTG 6 0.15 No Hit TCTCGGGTGCCAAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC 6 0.15 RNA PCR Primer, Index 2 (100% over 34bp) GGGGATGTAGCTCAGATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC 6 0.15 RNA PCR Primer, Index 2 (100% over 34bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTTGGAATTCTCGGGTGCC 6 0.15 No Hit TTTGGATTGAAGGGAGCTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG 6 0.15 RNA PCR Primer, Index 1 (100% over 29bp) GGGGATGTAGCTCAAATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC 6 0.15 RNA PCR Primer, Index 2 (100% over 34bp) CATCGAGTAGACCTTGTTATTGTGAGAATTATGGAATTCTCGGGTGCCAA 6 0.15 No Hit TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGG 6 0.15 No Hit CACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGG 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATGGAATTCTCGGGTGCCAAGGA 5 0.125 RNA PCR Primer, Index 1 (100% over 22bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAAATGGAATTCTCGGGT 5 0.125 No Hit ATTGTATCCTTAACCATTTCTTTTGGAATTCTCGGGTGCCAAGGAACTCC 5 0.125 RNA PCR Primer, Index 1 (100% over 27bp) ACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTTGGAATTCTCGGGT 5 0.125 No Hit GCACCAGTAGTCTAGTGGTAGAATAGTACCTGGAATTCTCGGGTGCCAAG 5 0.125 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATATGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) TAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAG 5 0.125 RNA PCR Primer, Index 1 (100% over 29bp) CAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGCCAAGGA 5 0.125 RNA PCR Primer, Index 1 (100% over 22bp) GACACGACTCTCGGCAACGGATATCTCGGCTCTCGCTGGAATTCTCGGGT 5 0.125 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGTGGAATTCTCGGGTGCCAAG 5 0.125 No Hit TTCATGGACGTTGATAAGATCCTTCCTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) GAAGTCCTCGTGTTGCATTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA 5 0.125 RNA PCR Primer, Index 1 (100% over 28bp) CATCGAGTAGACCTTGTTATTGTGAGAATAAAAAAATGGAATTCTCGGGT 5 0.125 No Hit ACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 5 0.125 RNA PCR Primer, Index 1 (100% over 31bp) >>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 0.05 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 0.05 0.0 0.0 0.0 6 0.0 0.05 0.0 0.0 0.0 7 0.0 0.05 0.0 0.0 0.0 8 0.0 0.05 0.0 0.0 0.0 9 0.0 0.125 0.0 0.0 0.0 10-11 0.0 0.2375 0.0 0.0 0.0 12-13 0.0 0.425 0.0 0.0 0.0 14-15 0.0 0.8625 0.0 0.0 0.0 16-17 0.0 3.0125 0.0 0.0 0.0 18-19 0.0 5.225 0.0 0.0 0.0 20-21 0.0 8.625 0.0 0.0 0.0 22-23 0.0 18.65 0.0 0.0 0.0 24-25 0.0 33.4875 0.0 0.0 0.0 26-27 0.0 47.7875 0.0 0.0 0.0 28-29 0.0 55.150000000000006 0.0 0.0 0.0 30-31 0.0 65.5 0.0 0.0 0.0 32-33 0.0 73.275 0.0 0.0 0.0 34-35 0.0 80.5875 0.0 0.0 0.0 36-37 0.0 88.4375 0.0 0.0 0.0 38-39 0.0 91.1875 0.0 0.0 0.0 40-41 0.0 92.3 0.0 0.0 0.0 42-43 0.0 93.11250000000001 0.0 0.0 0.0 44-45 0.0 93.4125 0.0 0.0 0.0 46-47 0.0 93.5375 0.0 0.0 0.0 48-49 0.0 93.57499999999999 0.0 0.0 0.0 50-51 0.0 93.6 0.0 0.0 0.0 52-53 0.0 93.625 0.0 0.0 0.0 54-55 0.0 93.625 0.0 0.0 0.0 56-57 0.0 93.625 0.0 0.0 0.0 58-59 0.0 93.625 0.0 0.0 0.0 60-61 0.0 93.625 0.0 0.0 0.0 62-63 0.0 93.625 0.0 0.0 0.0 64-65 0.0 93.625 0.0 0.0 0.0 66-67 0.0 93.625 0.0 0.0 0.0 68-69 0.0 93.625 0.0 0.0 0.0 70-71 0.0 93.625 0.0 0.0 0.0 72-73 0.0 93.625 0.0 0.0 0.0 74-75 0.0 93.625 0.0 0.0 0.0 76-77 0.0 93.625 0.0 0.0 0.0 78-79 0.0 93.625 0.0 0.0 0.0 80-81 0.0 93.6375 0.0 0.0 0.0 82-83 0.0 93.65 0.0 0.0 0.0 84-85 0.0 93.65 0.0 0.0 0.0 86-87 0.0 93.65 0.0 0.0 0.0 88-89 0.0 93.65 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CTCTGAT 15 4.4910912E-4 102.62162 1 GGGATTG 15 4.4910912E-4 102.62162 1 CATCGAG 65 0.0 102.62162 1 TCGGACC 20 1.038194E-5 102.62161 1 GGGGACG 20 1.038194E-5 102.62161 1 GTAGACC 65 0.0 94.925 7 AGTAGAC 65 0.0 94.925 6 GAGTAGA 65 0.0 94.925 5 CGAGTAG 65 0.0 94.925 4 AGACCTT 65 0.0 94.925 9 ATCGAGT 65 0.0 94.925 2 TCGAGTA 65 0.0 94.925 3 GTAGCTC 35 2.3283064E-10 94.925 7 TAGACCT 65 0.0 94.925 8 AGCTCAT 20 1.545283E-5 94.924995 9 AGCTCAG 20 1.545283E-5 94.924995 9 TTGTAGT 15 6.1614934E-4 94.924995 5 ATGATGA 15 6.1614934E-4 94.924995 6 ATGATCA 15 6.1614934E-4 94.924995 9 GGACCAG 20 1.545283E-5 94.924995 3 >>END_MODULE Rejected 705525 READS because READLEN < 1 Read 705525 spots for SRR8846506.sra Written 705525 spots for SRR8846506.sra Rejected 705525 READS because READLEN < 1 Read 705525 spots for SRR8846506.sra Written 705525 spots for SRR8846506.sra Rejected 705525 READS because READLEN < 1 Read 705525 spots for SRR8846506.sra Written 705525 spots for SRR8846506.sra Rejected 705525 READS because READLEN < 1 Read 705525 spots for SRR8846506.sra Written 705525 spots for SRR8846506.sra Rejected 705525 READS because READLEN < 1 Read 705525 spots for SRR8846506.sra Written 705525 spots for SRR8846506.sra Rejected 705525 READS because READLEN < 1 Read 705525 spots for SRR8846506.sra Written 705525 spots for SRR8846506.sra Rejected 705525 READS because READLEN < 1 Read 705525 spots for SRR8846506.sra Written 705525 spots for SRR8846506.sra Rejected 705525 READS because READLEN < 1 Read 705525 spots for SRR8846506.sra Written 705525 spots for SRR8846506.sra Rejected 705525 READS because READLEN < 1 Read 705525 spots for SRR8846506.sra Written 705525 spots for SRR8846506.sra Rejected 705525 READS because READLEN < 1 Read 705525 spots for SRR8846506.sra Written 705525 spots for SRR8846506.sra Rejected 705525 READS because READLEN < 1 Read 705525 spots for SRR8846506.sra Written 705525 spots for SRR8846506.sra Rejected 705525 READS because READLEN < 1 Read 705525 spots for SRR8846506.sra Written 705525 spots for SRR8846506.sra Rejected 705525 READS because READLEN < 1 Read 705525 spots for SRR8846506.sra Written 705525 spots for SRR8846506.sra Rejected 705532 READS because READLEN < 1 Read 705532 spots for SRR8846506.sra Written 705532 spots for SRR8846506.sra Rejected 705525 READS because READLEN < 1 Read 705525 spots for SRR8846506.sra Written 705525 spots for SRR8846506.sra Rejected 705525 READS because READLEN < 1 Read 705525 spots for SRR8846506.sra Written 705525 spots for SRR8846506.sra Rejected 705525 READS because READLEN < 1 Read 705525 spots for SRR8846506.sra Written 705525 spots for SRR8846506.sra Rejected 705525 READS because READLEN < 1 Read 705525 spots for SRR8846506.sra Written 705525 spots for SRR8846506.sra Rejected 705525 READS because READLEN < 1 Read 705525 spots for SRR8846506.sra Written 705525 spots for SRR8846506.sra Rejected 705525 READS because READLEN < 1 Read 705525 spots for SRR8846506.sra Written 705525 spots for SRR8846506.sra SRR ids: ['SRR8846506.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_wsvu1557 SRR8846506.sra spots: 14110507 blocks: [[1, 705525], [705526, 1411050], [1411051, 2116575], [2116576, 2822100], [2822101, 3527625], [3527626, 4233150], [4233151, 4938675], [4938676, 5644200], [5644201, 6349725], [6349726, 7055250], [7055251, 7760775], [7760776, 8466300], [8466301, 9171825], [9171826, 9877350], [9877351, 10582875], [10582876, 11288400], [11288401, 11993925], [11993926, 12699450], [12699451, 13404975], [13404976, 14110507]] SRR8846506 file size 3381908 SRR8846506 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 SRR8846506 SRR8846506_1.fastq Input file: SRR8846506_1.fastq trimmed: SRR8846506-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 03:30:52 2024 >> started Mon Dec 9 03:31:28 2024 >> done (36.070s) 14110507 reads processed; of these: 292 ( 0.00%) short reads filtered out after trimming by size control 44 ( 0.00%) empty reads filtered out after trimming by size control 14110171 (100.00%) reads available; of these: 4566068 (32.36%) trimmed reads available after processing 9544103 (67.64%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 35 0.00% 19 21 0.00% 20 33 0.00% 21 40 0.00% 22 51 0.00% 23 54 0.00% 24 62 0.00% 25 84 0.00% 26 101 0.00% 27 125 0.00% 28 180 0.00% 29 220 0.00% 30 173 0.00% 31 164 0.00% 32 196 0.00% 33 247 0.00% 34 206 0.00% 35 155 0.00% 36 167 0.00% 37 161 0.00% 38 184 0.00% 39 250 0.00% 40 219 0.00% 41 212 0.00% 42 244 0.00% 43 306 0.00% 44 336 0.00% 45 317 0.00% 46 251 0.00% 47 255 0.00% 48 241 0.00% 49 215 0.00% 50 276 0.00% 51 250 0.00% 52 268 0.00% 53 299 0.00% 54 291 0.00% 55 339 0.00% 56 484 0.00% 57 467 0.00% 58 623 0.00% 59 918 0.01% 60 1360 0.01% 61 2294 0.02% 62 3358 0.02% 63 3990 0.03% 64 5954 0.04% 65 8736 0.06% 66 18381 0.13% 67 87217 0.62% 68 85583 0.61% 69 53362 0.38% 70 35232 0.25% 71 32638 0.23% 72 15705 0.11% 73 6587 0.05% 74 6810 0.05% 75 4810 0.03% 76 4338 0.03% 77 4642 0.03% 78 5246 0.04% 79 5801 0.04% 80 6351 0.05% 81 7282 0.05% 82 11784 0.08% 83 11329 0.08% 84 11541 0.08% 85 13570 0.10% 86 17580 0.12% 87 25503 0.18% 88 55817 0.40% 89 97973 0.69% 90 156745 1.11% 91 133101 0.94% 92 129314 0.92% 93 164076 1.16% 94 223621 1.58% 95 431600 3.06% 96 478916 3.39% 97 461131 3.27% 98 717494 5.08% 99 682885 4.84% 100 326691 2.32% 101 9544103 67.64% 14110171 reads passed initial QC criterion=sequence-density sequence-density=92.51 sequence-density-rank=1 fanout-score=31.47 fanout-score-rank=1 prefix-density=92.96 prefix-fanout=31.3 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCATGGCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA criterion=fanout-score sequence-density=92.51 sequence-density-rank=1 fanout-score=31.47 fanout-score-rank=1 prefix-density=92.96 prefix-fanout=31.3 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCATGGCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCATGGCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA -o SRR8846506 - Input file: STDIN trimmed: SRR8846506-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCATGGCATCTCGTATGCCGTCTTCTGCTTGA -- 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 03:34:03 2024 >> started Mon Dec 9 03:35:09 2024 >> done (66.199s) 13806727 reads processed; of these: 714562 ( 5.18%) short reads filtered out after trimming by size control 6582 ( 0.05%) empty reads filtered out after trimming by size control 13085583 (94.78%) reads available; of these: 12426380 (94.96%) trimmed reads available after processing 659203 ( 5.04%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 156822 1.20% 19 243881 1.86% 20 281550 2.15% 21 1108536 8.47% 22 467760 3.57% 23 624354 4.77% 24 2205181 16.85% 25 589384 4.50% 26 467223 3.57% 27 460369 3.52% 28 687745 5.26% 29 680137 5.20% 30 783746 5.99% 31 441018 3.37% 32 451944 3.45% 33 512997 3.92% 34 593524 4.54% 35 616400 4.71% 36 358506 2.74% 37 187121 1.43% 38 134797 1.03% 39 96226 0.74% 40 74915 0.57% 41 87628 0.67% 42 62543 0.48% 43 18540 0.14% 44 17430 0.13% 45 6423 0.05% 46 3337 0.03% 47 1628 0.01% 48 1655 0.01% 49 812 0.01% 50 601 0.00% 51 543 0.00% 52 299 0.00% 53 315 0.00% 54 385 0.00% 55 279 0.00% 56 445 0.00% 57 353 0.00% 58 486 0.00% 59 751 0.01% 60 1129 0.01% 61 2039 0.02% 62 3039 0.02% 63 3697 0.03% 64 5488 0.04% 65 8257 0.06% 66 17631 0.13% 67 84889 0.65% 68 83210 0.64% 69 51609 0.39% 70 33770 0.26% 71 31146 0.24% 72 13667 0.10% 73 4804 0.04% 74 3955 0.03% 75 2624 0.02% 76 2500 0.02% 77 2863 0.02% 78 2621 0.02% 79 2699 0.02% 80 2996 0.02% 81 2339 0.02% 82 2124 0.02% 83 2240 0.02% 84 1671 0.01% 85 1708 0.01% 86 1526 0.01% 87 1413 0.01% 88 1429 0.01% 89 1445 0.01% 90 1675 0.01% 91 2252 0.02% 92 2195 0.02% 93 2240 0.02% 94 2796 0.02% 95 3753 0.03% 96 4435 0.03% 97 5877 0.04% 98 8375 0.06% 99 9985 0.08% 100 12601 0.10% 101 220282 1.68% criterion=sequence-density sequence-density=4.57 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=15 prefix-density=0.00 prefix-fanout=1.0 sequence=TCGGACCAGGCTTCATTCCCCT criterion=fanout-score sequence-density=0.01 sequence-density-rank=38 fanout-score=247.63 fanout-score-rank=1 prefix-density=1.49 prefix-fanout=1.0 sequence=AGCCAAGTGCGGAGAGGATAACTGCTGAAAGCATATAAGTAGTAAGCCCACCCCAAGATGAGTGCTCTCTCCTC Started job on | Dec 09 03:37:04 Started mapping on | Dec 09 03:37:05 Finished on | Dec 09 03:41:22 Mapping speed, Million of reads per hour | 187.55 Number of input reads | 13389027 Average input read length | 31 UNIQUE READS: Uniquely mapped reads number | 3225771 Uniquely mapped reads % | 24.09% Average mapped length | 25.65 Number of splices: Total | 19119 Number of splices: Annotated (sjdb) | 7865 Number of splices: GT/AG | 17773 Number of splices: GC/AG | 1017 Number of splices: AT/AC | 2 Number of splices: Non-canonical | 327 Mismatch rate per base, % | 0.11% Deletion rate per base | 0.00% Deletion average length | 1.37 Insertion rate per base | 0.00% Insertion average length | 1.03 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 5608547 % of reads mapped to multiple loci | 41.89% Number of reads mapped to too many loci | 3368560 % of reads mapped to too many loci | 25.16% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 7.92% % of reads unmapped: other | 0.93% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 4554709 4554709 4554709 N_multimapping 5608547 5608547 5608547 N_noFeature 2099000 2253649 3058024 N_ambiguous 47492 33767 771 UnstrandedReadsAssigned:1079279 PositiveStrandReadsAssigned:938355 NegativeStrandReadsAssigned:166976 Dataset is classified positive stranded MeadianReadLen=27 20thPercentileLength=23 echo kmer=19 SRR8846506 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: SRR8846506-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 13,389,027 reads, 3,155,802 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,033 rounds 52973 SRR8846506.ke.tsv 35125 SRR8846506.se.tsv 88098 total ==> SRR8846506.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 1.87103 0.940431 PNS24247 1044 945 0 0 PNS24249 1928 1829 0 0 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 5.12897 1.57271 PNS24243 293 194 0 0 KQK14069 1603 1504 69.7809 19.5192 KQK14071 474 375 0 0 ==> SRR8846506.se.tsv <== BRADI_1g14170v3 132 BRADI_1g53295v3 1 BRADI_1g59795v3 14 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 12 BRADI_1g74790v3 10 BRADI_1g09890v3 1 BRADI_1g77505v3 2 BRADI_1g48960v3 0 SRR8846506 completed mapping pipeline successfully