Starting /dee2/code/volunteer_pipeline.sh SRR8846480 current disk space = 1506291806208 free memory = 1398945264 SRR8846480 SRAfilesize e9ba7cab8bd17eb7d140c9fd4f91704d SRR8846480.sra SRR8846480.sra file validated SRR8846480 is single end SRR8846480 is conventional basespace SRR8846480 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8846480_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 pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.6015 34.0 33.0 34.0 32.0 34.0 2 32.9725 34.0 33.0 34.0 32.0 34.0 3 33.0055 34.0 33.0 34.0 32.0 34.0 4 33.15 34.0 33.0 34.0 32.0 34.0 5 33.1345 34.0 33.0 34.0 32.0 34.0 6 36.82375 38.0 37.0 38.0 35.0 38.0 7 37.09525 38.0 38.0 38.0 36.0 38.0 8 37.34675 38.0 38.0 38.0 37.0 38.0 9 37.3435 38.0 38.0 38.0 37.0 38.0 10-11 37.458749999999995 38.0 38.0 38.0 37.0 38.0 12-13 37.423249999999996 38.0 38.0 38.0 37.0 38.0 14-15 37.425875000000005 38.0 38.0 38.0 37.0 38.0 16-17 37.349375 38.0 38.0 38.0 37.0 38.0 18-19 37.401875000000004 38.0 38.0 38.0 37.0 38.0 20-21 37.427875 38.0 38.0 38.0 37.0 38.0 22-23 37.369125 38.0 38.0 38.0 37.0 38.0 24-25 37.38175 38.0 38.0 38.0 37.0 38.0 26-27 37.371375 38.0 38.0 38.0 37.0 38.0 28-29 37.414625 38.0 38.0 38.0 37.0 38.0 30-31 37.42525 38.0 38.0 38.0 37.0 38.0 32-33 37.307625 38.0 38.0 38.0 37.0 38.0 34-35 37.113375 38.0 38.0 38.0 36.5 38.0 36-37 37.028125 38.0 38.0 38.0 36.0 38.0 38-39 36.88375 38.0 38.0 38.0 35.5 38.0 40-41 37.0815 38.0 38.0 38.0 36.0 38.0 42-43 37.0645 38.0 38.0 38.0 36.0 38.0 44-45 37.03425 38.0 38.0 38.0 36.0 38.0 46-47 36.873000000000005 38.0 38.0 38.0 35.5 38.0 48-49 37.0025 38.0 38.0 38.0 36.0 38.0 50-51 37.058125000000004 38.0 38.0 38.0 36.0 38.0 52-53 37.116749999999996 38.0 38.0 38.0 36.0 38.0 54-55 36.918 38.0 38.0 38.0 36.0 38.0 56-57 36.88175 38.0 38.0 38.0 35.5 38.0 58-59 36.883125 38.0 38.0 38.0 35.5 38.0 60-61 36.860749999999996 38.0 38.0 38.0 35.0 38.0 62-63 36.47325 38.0 38.0 38.0 34.0 38.0 64-65 36.152875 38.0 37.0 38.0 32.0 38.0 66-67 35.6845 38.0 37.0 38.0 29.0 38.0 68-69 35.860625 38.0 37.0 38.0 29.5 38.0 70-71 35.446375 38.0 37.0 38.0 28.5 38.0 72-73 35.429125 38.0 37.0 38.0 28.5 38.0 74-75 35.188375 38.0 36.5 38.0 28.0 38.0 76-77 34.947375 38.0 36.0 38.0 27.5 38.0 78-79 35.240875 38.0 36.0 38.0 29.0 38.0 80-81 34.853624999999994 38.0 36.0 38.0 27.0 38.0 82-83 35.039 38.0 36.0 38.0 28.0 38.0 84-85 34.917625 38.0 36.0 38.0 28.0 38.0 86-87 35.001875 38.0 36.0 38.0 28.0 38.0 88-89 35.01625 38.0 36.0 38.0 28.0 38.0 90-91 34.665125 38.0 36.0 38.0 27.0 38.0 92-93 34.52525 38.0 36.0 38.0 27.0 38.0 94-95 34.064 38.0 35.5 38.0 24.5 38.0 96-97 32.85025 38.0 34.0 38.0 14.5 38.0 98-99 30.63475 38.0 31.5 38.0 2.0 38.0 100-101 27.81225 37.5 20.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 3.0 20 2.0 21 2.0 22 3.0 23 2.0 24 15.0 25 23.0 26 24.0 27 13.0 28 33.0 29 34.0 30 55.0 31 83.0 32 97.0 33 129.0 34 279.0 35 455.0 36 1073.0 37 1674.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 26.966587740068405 29.150223625361747 19.205472244146275 24.677716390423573 2 26.075 31.574999999999996 19.025 23.325000000000003 3 24.349999999999998 21.325 23.974999999999998 30.349999999999998 4 26.3 30.425 18.075 25.2 5 32.1 25.324999999999996 21.275 21.3 6 23.825 30.45 22.85 22.875 7 35.6 25.25 18.025 21.125 8 21.25 22.15 34.55 22.05 9 23.0 34.0 23.375 19.625 10-11 29.175 27.725 22.05 21.05 12-13 23.225 23.2125 20.775 32.7875 14-15 22.912499999999998 32.887499999999996 25.362499999999997 18.8375 16-17 25.362499999999997 27.237499999999997 28.599999999999998 18.8 18-19 28.175 27.5625 23.0375 21.224999999999998 20-21 22.9375 28.3625 28.549999999999997 20.150000000000002 22-23 28.462500000000002 27.725 28.487499999999997 15.325 24-25 27.075 25.662499999999998 27.8125 19.45 26-27 34.525 28.237499999999997 22.2125 15.024999999999999 28-29 22.125 31.6 26.0125 20.2625 30-31 25.0 20.8125 37.375 16.8125 32-33 24.75 20.825 33.1875 21.2375 34-35 28.6125 19.075 30.85 21.462500000000002 36-37 36.575 14.549999999999999 30.1875 18.6875 38-39 33.1 18.0125 28.7375 20.150000000000002 40-41 31.125000000000004 16.4875 23.9 28.487499999999997 42-43 31.275 24.425 22.85 21.45 44-45 40.637499999999996 18.0125 16.2375 25.112499999999997 46-47 31.125000000000004 30.9375 13.200000000000001 24.7375 48-49 29.45 24.837500000000002 18.387500000000003 27.325 50-51 24.85 25.8 13.6375 35.712500000000006 52-53 23.6375 34.825 12.275 29.262500000000003 54-55 20.325 28.1625 18.387500000000003 33.125 56-57 18.5625 32.9875 15.312500000000002 33.137499999999996 58-59 14.399999999999999 31.2875 24.2625 30.049999999999997 60-61 16.125 28.075 24.5625 31.2375 62-63 12.8875 32.975 21.587500000000002 32.550000000000004 64-65 13.4125 30.8125 30.4875 25.2875 66-67 11.4125 25.5 31.5125 31.574999999999996 68-69 15.6 27.400000000000002 28.237499999999997 28.762500000000003 70-71 14.787500000000001 25.724999999999998 35.575 23.9125 72-73 19.9125 19.2 33.862500000000004 27.025 74-75 16.037499999999998 19.287499999999998 30.175 34.5 76-77 20.1 15.037500000000001 39.2625 25.6 78-79 18.925 9.925 37.4375 33.7125 80-81 19.3125 10.375 37.3375 32.975 82-83 22.6 9.1875 41.8125 26.400000000000002 84-85 18.3125 9.1 39.95 32.6375 86-87 22.325 13.425 38.7875 25.4625 88-89 16.3 29.25 33.5875 20.8625 90-91 13.175 37.3 32.1 17.424999999999997 92-93 14.149999999999999 48.8125 23.65 13.3875 94-95 10.725 60.775 18.7 9.8 96-97 8.3 70.025 15.2 6.4750000000000005 98-99 6.3125 80.45 9.2625 3.975 100-101 3.8 87.2375 5.575 3.3875 >>END_MODULE >>Per sequence GC content fail #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 1.5 32 3.0 33 2.5 34 3.5 35 8.5 36 12.5 37 16.0 38 50.0 39 72.0 40 98.0 41 167.0 42 225.0 43 370.5 44 410.0 45 388.0 46 404.0 47 341.0 48 317.5 49 285.0 50 222.0 51 149.0 52 93.0 53 88.5 54 117.5 55 86.0 56 26.5 57 16.0 58 11.5 59 5.0 60 4.0 61 3.5 62 2.0 63 0.0 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 pass #Base N-Count 1 4.9750000000000005 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 60.4 #Duplication Level Percentage of deduplicated Percentage of total 1 86.29966887417218 52.125 2 6.622516556291391 8.0 3 1.8625827814569538 3.375 4 1.1175496688741722 2.7 5 0.7450331125827815 2.25 6 0.6208609271523179 2.25 7 0.5380794701986755 2.275 8 0.24834437086092717 1.2 9 0.24834437086092717 1.35 >10 1.5728476821192054 18.6 >50 0.08278145695364239 3.15 >100 0.041390728476821195 2.725 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences fail #Sequence Count Percentage Possible Source GGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 109 2.725 RNA PCR Primer, Index 1 (100% over 22bp) AGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 66 1.6500000000000001 No Hit TCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 60 1.5 No Hit TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 46 1.15 RNA PCR Primer, Index 1 (100% over 29bp) CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 43 1.075 No Hit GACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 42 1.05 RNA PCR Primer, Index 1 (100% over 23bp) AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 41 1.0250000000000001 Illumina Small RNA Adapter 2 (100% over 21bp) CTCTGATGATGATCAAACTAATACTTTCGTTCTTCTGGAATTCTCGGGTG 29 0.7250000000000001 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 28 0.7000000000000001 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 28 0.7000000000000001 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 28 0.7000000000000001 Illumina Small RNA Adapter 2 (100% over 21bp) GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 26 0.65 Illumina Small RNA Adapter 2 (100% over 21bp) GACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAAC 26 0.65 RNA PCR Primer, Index 1 (100% over 24bp) TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 26 0.65 No Hit CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTC 25 0.625 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 24 0.6 No Hit ATATATTTCAAGTTATTTCGGATCTTGGAATTCTCGGGTGCCAAGGAACT 21 0.525 RNA PCR Primer, Index 1 (100% over 25bp) GACACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACT 20 0.5 RNA PCR Primer, Index 1 (100% over 25bp) CTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCA 17 0.42500000000000004 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 16 0.4 Illumina Small RNA Adapter 2 (100% over 21bp) GCCCACCCCAAGATGAGTGCTCTCTCTGGAATTCTCGGGTGCCAAGGAAC 16 0.4 RNA PCR Primer, Index 1 (100% over 24bp) GCACCAGTGGTCTAGTGGTAGAATAGTACCTGGAATTCTCGGGTGCCAAG 15 0.375 No Hit CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGG 14 0.35000000000000003 No Hit CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 14 0.35000000000000003 RNA PCR Primer, Index 1 (100% over 23bp) TCTCGGGTGCCAAGGAACTCCAGTCACATGTCAATCTCGTATGCCGTCTT 14 0.35000000000000003 RNA PCR Primer, Index 15 (100% over 50bp) CACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGC 14 0.35000000000000003 No Hit ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGC 13 0.325 No Hit CGGATAACCGTAGTAATTCTAGAGCTAATACTGGAATTCTCGGGTGCCAA 13 0.325 No Hit AGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGT 12 0.3 No Hit AAGGGTGCTGAGAATACTTTGAATCTGACACTGGAATTCTCGGGTGCCAA 12 0.3 No Hit AATTCTCGGGTGCCAAGGAACTCCAGTCACATGTCAATCTCGTATGCCGT 12 0.3 RNA PCR Primer, Index 15 (100% over 50bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATGGAATTCTCGGGTG 12 0.3 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTTGGAATTCTCGGGTGC 12 0.3 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAATGGAATTCTCGGGTGCCA 11 0.27499999999999997 No Hit GATAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAAC 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 24bp) CAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTG 11 0.27499999999999997 No Hit ATTCTCGGGTGCCAAGGAACTCCAGTCACATGTCAATCTCGTATGCCGTC 11 0.27499999999999997 RNA PCR Primer, Index 15 (100% over 50bp) GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 11 0.27499999999999997 No Hit CACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAACT 10 0.25 RNA PCR Primer, Index 1 (100% over 25bp) ATATTGGGTAGGTTGTGGTATTTCATTGCTGGAATTCTCGGGTGCCAAGG 10 0.25 Illumina Small RNA Adapter 2 (100% over 21bp) ACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCC 10 0.25 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATACTCTGGAATTCTCGGGTGCCAAG 9 0.22499999999999998 No Hit TTCGGACCAGGCTTCATTCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 29bp) AAGGGTGCTGAGAATACTTTGAATCTGACATGGAATTCTCGGGTGCCAAG 9 0.22499999999999998 No Hit ATATATTTCAAGTTATTTCGGATCTGGAATTCTCGGGTGCCAAGGAACTC 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 26bp) GCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCC 9 0.22499999999999998 No Hit CAGGGTTCGTTTCCCTGGATGCGCACCATGGAATTCTCGGGTGCCAAGGA 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 22bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 8 0.2 No Hit CGGATAACCGTAGTAATTCTAGAGCTAATACGTGGAATTCTCGGGTGCCA 8 0.2 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATATGGAATTCTCGGGTGCCAAGGAA 8 0.2 RNA PCR Primer, Index 1 (100% over 23bp) ATAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAACT 8 0.2 RNA PCR Primer, Index 1 (100% over 25bp) GACACGACTCTCGGCAACGGATATCTCGTGGAATTCTCGGGTGCCAAGGA 8 0.2 RNA PCR Primer, Index 1 (100% over 22bp) GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGGTG 8 0.2 No Hit GATAACCGTAGTAATTCTAGAGCTAATTGGAATTCTCGGGTGCCAAGGAA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 23bp) TAAGATGAGCTCAACGAGAACAGAAATCTCGTGTGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit CTCGGGTGCCAAGGAACTCCAGTCACATGTCAATCTCGTATGCCGTCTTC 7 0.17500000000000002 RNA PCR Primer, Index 15 (100% over 50bp) CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 28bp) CCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTG 7 0.17500000000000002 No Hit GATAACCGTAGTAATTCTAGAGCTAATACTGGAATTCTCGGGTGCCAAGG 7 0.17500000000000002 Illumina Small RNA Adapter 2 (100% over 21bp) CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGG 7 0.17500000000000002 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTAAATGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit TGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAA 7 0.17500000000000002 No Hit ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGGTGC 7 0.17500000000000002 No Hit NGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 7 0.17500000000000002 No Hit ACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTCT 7 0.17500000000000002 No Hit ATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACT 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 25bp) TCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTC 6 0.15 RNA PCR Primer, Index 1 (100% over 26bp) GATGAGCTCAACGAGAACAGAAATCTCGTGTGGAATTCTCGGGTGCCAAG 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATGGAATTCTCGGGTGCCAAGGA 6 0.15 RNA PCR Primer, Index 1 (100% over 22bp) TTCTCGGGTGCCAAGGAACTCCAGTCACATGTCAATCTCGTATGCCGTCT 6 0.15 RNA PCR Primer, Index 15 (100% over 50bp) TAATTCATGATCTGGCATGTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 6 0.15 RNA PCR Primer, Index 1 (100% over 31bp) GACACGACTCTCGGCAACGGATATCTCGGCTGGAATTCTCGGGTGCCAAG 6 0.15 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTTGGAATTCTCGGGTGCCAAG 6 0.15 No Hit GGGGATATGGCGAAATCGGTAGACGCTACGGACTTTGGAATTCTCGGGTG 6 0.15 No Hit CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGG 6 0.15 No Hit CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGG 6 0.15 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGAATTCTCGGGTGCCAAGGAACTCCA 6 0.15 RNA PCR Primer, Index 1 (100% over 28bp) ATTGTATCCTTAACCATTTCTTTTTGGAATTCTCGGGTGCCAAGGAACTC 6 0.15 RNA PCR Primer, Index 1 (100% over 26bp) NATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTATGGAATTCTCGGGTGCCAA 6 0.15 No Hit TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGG 6 0.15 No Hit NCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 5 0.125 No Hit NGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 5 0.125 RNA PCR Primer, Index 1 (100% over 22bp) GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAAATGGAATTCTCGGGTGCC 5 0.125 No Hit TCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) TCGGATAACCGTAGTAATTCTAGAGCTAATACGTGGAATTCTCGGGTGCC 5 0.125 No Hit GCACCAGTAGTCTAGTGGTAGAATAGTACCTGGAATTCTCGGGTGCCAAG 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAAAAATGGAATTCTCGGGTG 5 0.125 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTTGGAATTCT 5 0.125 No Hit ACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) ATATTGGGTAGGTTGTGGTATTTCATTGCTATGGAATTCTCGGGTGCCAA 5 0.125 No Hit TCTCGGACCAGGCTTCATTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 5 0.125 RNA PCR Primer, Index 1 (100% over 29bp) AGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGGT 5 0.125 No Hit CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGGAATTCTCG 5 0.125 No Hit ACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 5 0.125 RNA PCR Primer, Index 1 (100% over 31bp) CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTCGGG 5 0.125 No Hit TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTGGAATTCTCGGGTGC 5 0.125 No Hit CTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCA 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 0.05 0.0 0.0 0.0 2 0.0 0.05 0.0 0.0 0.0 3 0.0 0.075 0.0 0.0 0.0 4 0.0 0.075 0.0 0.0 0.0 5 0.0 0.075 0.0 0.0 0.0 6 0.0 0.075 0.0 0.0 0.0 7 0.0 0.1 0.0 0.0 0.0 8 0.0 0.1 0.0 0.0 0.0 9 0.0 0.175 0.0 0.0 0.0 10-11 0.0 0.2625 0.0 0.0 0.0 12-13 0.0 0.44999999999999996 0.0 0.0 0.0 14-15 0.0 0.7 0.0 0.0 0.0 16-17 0.0 1.225 0.0 0.0 0.0 18-19 0.0 1.7625000000000002 0.0 0.0 0.0 20-21 0.0 3.375 0.0 0.0 0.0 22-23 0.0 8.4 0.0 0.0 0.0 24-25 0.0 18.8125 0.0 0.0 0.0 26-27 0.0 31.2875 0.0 0.0 0.0 28-29 0.0 41.025000000000006 0.0 0.0 0.0 30-31 0.0 53.525 0.0 0.0 0.0 32-33 0.0 63.537499999999994 0.0 0.0 0.0 34-35 0.0 73.3875 0.0 0.0 0.0 36-37 0.0 82.825 0.0 0.0 0.0 38-39 0.0 87.75 0.0 0.0 0.0 40-41 0.0 90.2125 0.0 0.0 0.0 42-43 0.0 92.3125 0.0 0.0 0.0 44-45 0.0 93.575 0.0 0.0 0.0 46-47 0.0 93.9375 0.0 0.0 0.0 48-49 0.0 94.1375 0.0 0.0 0.0 50-51 0.0 94.175 0.0 0.0 0.0 52-53 0.0 94.1875 0.0 0.0 0.0 54-55 0.0 94.2 0.0 0.0 0.0 56-57 0.0 94.2 0.0 0.0 0.0 58-59 0.0 94.2 0.0 0.0 0.0 60-61 0.0 94.2 0.0 0.0 0.0 62-63 0.0 94.2 0.0 0.0 0.0 64-65 0.0 94.2 0.0 0.0 0.0 66-67 0.0 94.2 0.0 0.0 0.0 68-69 0.0 94.2 0.0 0.0 0.0 70-71 0.0 94.2 0.0 0.0 0.0 72-73 0.0 94.2 0.0 0.0 0.0 74-75 0.0 94.2 0.0 0.0 0.0 76-77 0.0 94.2 0.0 0.0 0.0 78-79 0.0 94.2 0.0 0.0 0.0 80-81 0.0 94.2 0.0 0.0 0.0 82-83 0.0 94.2 0.0 0.0 0.0 84-85 0.0 94.2 0.0 0.0 0.0 86-87 0.0 94.2 0.0 0.0 0.0 88-89 0.0 94.2 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GACACGA 20 1.1111353E-5 101.26667 1 CATCGAG 45 0.0 101.26666 1 GAGTAGA 50 0.0 94.93751 5 GTAGACC 45 0.0 94.9375 7 ACACGAC 20 1.5442722E-5 94.9375 2 CACCAGT 15 6.1582687E-4 94.9375 2 CGAGTAG 45 0.0 94.9375 4 AGACCTT 45 0.0 94.9375 9 ATCGAGT 45 0.0 94.9375 2 TCGAGTA 45 0.0 94.9375 3 TAGACCT 45 0.0 94.9375 8 AGTAGAC 50 0.0 85.443756 6 GCATCCT 40 6.2896906E-6 59.335938 2 GGCATCC 35 1.7821995E-4 57.86667 1 CTCTCGG 35 2.472862E-4 54.25 8 ACTCTCG 35 2.472862E-4 54.25 7 CACGACT 35 2.472862E-4 54.25 3 ACGACTC 35 2.472862E-4 54.25 4 GACTCTC 35 2.472862E-4 54.25 6 CGACTCT 35 2.472862E-4 54.25 5 >>END_MODULE Rejected 685362 READS because READLEN < 1 Read 685362 spots for SRR8846480.sra Written 685362 spots for SRR8846480.sra Rejected 685362 READS because READLEN < 1 Read 685362 spots for SRR8846480.sra Written 685362 spots for SRR8846480.sra Rejected 685362 READS because READLEN < 1 Read 685362 spots for SRR8846480.sra Written 685362 spots for SRR8846480.sra Rejected 685362 READS because READLEN < 1 Read 685362 spots for SRR8846480.sra Written 685362 spots for SRR8846480.sra Rejected 685362 READS because READLEN < 1 Read 685362 spots for SRR8846480.sra Written 685362 spots for SRR8846480.sra Rejected 685362 READS because READLEN < 1 Read 685362 spots for SRR8846480.sra Written 685362 spots for SRR8846480.sra Rejected 685362 READS because READLEN < 1 Read 685362 spots for SRR8846480.sra Written 685362 spots for SRR8846480.sra Rejected 685362 READS because READLEN < 1 Read 685362 spots for SRR8846480.sra Written 685362 spots for SRR8846480.sra Rejected 685362 READS because READLEN < 1 Read 685362 spots for SRR8846480.sra Written 685362 spots for SRR8846480.sra Rejected 685362 READS because READLEN < 1 Read 685362 spots for SRR8846480.sra Written 685362 spots for SRR8846480.sra Rejected 685362 READS because READLEN < 1 Read 685362 spots for SRR8846480.sra Written 685362 spots for SRR8846480.sra Rejected 685362 READS because READLEN < 1 Read 685362 spots for SRR8846480.sra Written 685362 spots for SRR8846480.sra Rejected 685362 READS because READLEN < 1 Read 685362 spots for SRR8846480.sra Written 685362 spots for SRR8846480.sra Rejected 685362 READS because READLEN < 1 Read 685362 spots for SRR8846480.sra Written 685362 spots for SRR8846480.sra Rejected 685362 READS because READLEN < 1 Read 685362 spots for SRR8846480.sra Written 685362 spots for SRR8846480.sra Rejected 685362 READS because READLEN < 1 Read 685362 spots for SRR8846480.sra Written 685362 spots for SRR8846480.sra Rejected 685362 READS because READLEN < 1 Read 685362 spots for SRR8846480.sra Written 685362 spots for SRR8846480.sra Rejected 685362 READS because READLEN < 1 Read 685362 spots for SRR8846480.sra Written 685362 spots for SRR8846480.sra Rejected 685362 READS because READLEN < 1 Read 685362 spots for SRR8846480.sra Written 685362 spots for SRR8846480.sra Rejected 685362 READS because READLEN < 1 Read 685362 spots for SRR8846480.sra Written 685362 spots for SRR8846480.sra SRR ids: ['SRR8846480.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_cs2rb_ra SRR8846480.sra spots: 13707240 blocks: [[1, 685362], [685363, 1370724], [1370725, 2056086], [2056087, 2741448], [2741449, 3426810], [3426811, 4112172], [4112173, 4797534], [4797535, 5482896], [5482897, 6168258], [6168259, 6853620], [6853621, 7538982], [7538983, 8224344], [8224345, 8909706], [8909707, 9595068], [9595069, 10280430], [10280431, 10965792], [10965793, 11651154], [11651155, 12336516], [12336517, 13021878], [13021879, 13707240]] SRR8846480 file size 3284635 SRR8846480 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 SRR8846480 SRR8846480_1.fastq Input file: SRR8846480_1.fastq trimmed: SRR8846480-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- minimum overlap length for adapter detection (-k): inf -- number of concurrent threads (-t): 20 Sun Dec 8 16:23:42 2024 >> started Sun Dec 8 16:24:18 2024 >> done (35.592s) 13707240 reads processed; of these: 250 ( 0.00%) short reads filtered out after trimming by size control 46 ( 0.00%) empty reads filtered out after trimming by size control 13706944 (100.00%) reads available; of these: 2492074 (18.18%) trimmed reads available after processing 11214870 (81.82%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 35 0.00% 19 23 0.00% 20 31 0.00% 21 48 0.00% 22 31 0.00% 23 32 0.00% 24 31 0.00% 25 42 0.00% 26 55 0.00% 27 70 0.00% 28 100 0.00% 29 83 0.00% 30 92 0.00% 31 92 0.00% 32 85 0.00% 33 88 0.00% 34 118 0.00% 35 88 0.00% 36 113 0.00% 37 103 0.00% 38 136 0.00% 39 145 0.00% 40 158 0.00% 41 183 0.00% 42 167 0.00% 43 193 0.00% 44 178 0.00% 45 177 0.00% 46 172 0.00% 47 199 0.00% 48 186 0.00% 49 193 0.00% 50 200 0.00% 51 204 0.00% 52 157 0.00% 53 146 0.00% 54 123 0.00% 55 100 0.00% 56 123 0.00% 57 126 0.00% 58 156 0.00% 59 206 0.00% 60 279 0.00% 61 434 0.00% 62 613 0.00% 63 745 0.01% 64 1016 0.01% 65 1554 0.01% 66 3216 0.02% 67 15482 0.11% 68 19381 0.14% 69 15428 0.11% 70 16670 0.12% 71 24805 0.18% 72 12117 0.09% 73 4188 0.03% 74 5263 0.04% 75 3193 0.02% 76 2269 0.02% 77 2383 0.02% 78 2647 0.02% 79 2954 0.02% 80 3629 0.03% 81 4198 0.03% 82 6141 0.04% 83 6566 0.05% 84 7303 0.05% 85 8746 0.06% 86 9870 0.07% 87 12890 0.09% 88 20582 0.15% 89 27519 0.20% 90 36923 0.27% 91 40975 0.30% 92 50770 0.37% 93 75168 0.55% 94 100604 0.73% 95 190367 1.39% 96 244863 1.79% 97 270500 1.97% 98 471705 3.44% 99 508373 3.71% 100 254757 1.86% 101 11214870 81.82% 13706944 reads passed initial QC criterion=sequence-density sequence-density=94.38 sequence-density-rank=1 fanout-score=32.34 fanout-score-rank=2 prefix-density=95.04 prefix-fanout=32.1 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGTCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA criterion=fanout-score sequence-density=2.26 sequence-density-rank=4 fanout-score=43.87 fanout-score-rank=1 prefix-density=98.30 prefix-fanout=1.0 sequence=CACATGTCAATATCGTATGCCGT 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGTCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA -o SRR8846480 - Input file: STDIN trimmed: SRR8846480-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGTCAATCTCGTATGCCGTCTTCTGCTTGA -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- minimum overlap length for adapter detection (-k): 3 -- number of concurrent threads (-t): 20 Sun Dec 8 16:26:50 2024 >> started Sun Dec 8 16:27:57 2024 >> done (66.168s) 13418377 reads processed; of these: 222925 ( 1.66%) short reads filtered out after trimming by size control 10710 ( 0.08%) empty reads filtered out after trimming by size control 13184742 (98.26%) reads available; of these: 12916861 (97.97%) trimmed reads available after processing 267881 ( 2.03%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 65231 0.49% 19 118281 0.90% 20 124652 0.95% 21 490514 3.72% 22 281414 2.13% 23 420703 3.19% 24 1615818 12.26% 25 625891 4.75% 26 603297 4.58% 27 635600 4.82% 28 843649 6.40% 29 789214 5.99% 30 921042 6.99% 31 613842 4.66% 32 645900 4.90% 33 721830 5.47% 34 756081 5.73% 35 664215 5.04% 36 578641 4.39% 37 318982 2.42% 38 250169 1.90% 39 181192 1.37% 40 146810 1.11% 41 155934 1.18% 42 152852 1.16% 43 61333 0.47% 44 63660 0.48% 45 27396 0.21% 46 13827 0.10% 47 7967 0.06% 48 5997 0.05% 49 2999 0.02% 50 1814 0.01% 51 1641 0.01% 52 883 0.01% 53 612 0.00% 54 666 0.01% 55 294 0.00% 56 285 0.00% 57 209 0.00% 58 177 0.00% 59 192 0.00% 60 234 0.00% 61 398 0.00% 62 532 0.00% 63 657 0.00% 64 877 0.01% 65 1387 0.01% 66 3012 0.02% 67 14940 0.11% 68 18763 0.14% 69 14811 0.11% 70 16020 0.12% 71 23855 0.18% 72 10671 0.08% 73 2715 0.02% 74 1386 0.01% 75 935 0.01% 76 978 0.01% 77 2105 0.02% 78 1031 0.01% 79 1158 0.01% 80 1767 0.01% 81 1338 0.01% 82 1214 0.01% 83 1716 0.01% 84 838 0.01% 85 845 0.01% 86 715 0.01% 87 656 0.00% 88 523 0.00% 89 569 0.00% 90 557 0.00% 91 626 0.00% 92 649 0.00% 93 799 0.01% 94 961 0.01% 95 1472 0.01% 96 1704 0.01% 97 2415 0.02% 98 3839 0.03% 99 4002 0.03% 100 4907 0.04% 101 124459 0.94% criterion=sequence-density sequence-density=6.93 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=14 prefix-density=0.00 prefix-fanout=1.0 sequence=CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAA criterion=fanout-score sequence-density=0.28 sequence-density-rank=15 fanout-score=22.07 fanout-score-rank=1 prefix-density=6.21 prefix-fanout=1.0 sequence=TTGTGAGAATTAAAAA Started job on | Dec 08 16:30:11 Started mapping on | Dec 08 16:30:11 Finished on | Dec 08 16:37:02 Mapping speed, Million of reads per hour | 118.01 Number of input reads | 13473309 Average input read length | 32 UNIQUE READS: Uniquely mapped reads number | 2207948 Uniquely mapped reads % | 16.39% Average mapped length | 26.77 Number of splices: Total | 26338 Number of splices: Annotated (sjdb) | 18754 Number of splices: GT/AG | 24703 Number of splices: GC/AG | 1111 Number of splices: AT/AC | 12 Number of splices: Non-canonical | 512 Mismatch rate per base, % | 0.13% Deletion rate per base | 0.00% Deletion average length | 1.34 Insertion rate per base | 0.00% Insertion average length | 1.00 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 5081389 % of reads mapped to multiple loci | 37.71% Number of reads mapped to too many loci | 5408012 % of reads mapped to too many loci | 40.14% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 5.10% % of reads unmapped: other | 0.66% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 6183972 6183972 6183972 N_multimapping 5081389 5081389 5081389 N_noFeature 1363883 1498829 2062516 N_ambiguous 32670 21861 426 UnstrandedReadsAssigned:811395 PositiveStrandReadsAssigned:687258 NegativeStrandReadsAssigned:145006 Dataset is classified unstranded MeadianReadLen=29 20thPercentileLength=24 echo kmer=19 SRR8846480 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: SRR8846480-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 13,473,309 reads, 4,094,419 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,069 rounds 52973 SRR8846480.ke.tsv 35125 SRR8846480.se.tsv 88098 total ==> SRR8846480.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 2 0.257287 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 0 0 PNS24243 293 194 0 0 KQK14069 1603 1504 0.000121538 1.90137e-05 KQK14071 474 375 0 0 ==> SRR8846480.se.tsv <== BRADI_1g14170v3 82 BRADI_1g53295v3 1 BRADI_1g59795v3 8 BRADI_1g07683v3 3 BRADI_1g00485v3 2 BRADI_1g20270v3 8 BRADI_1g74790v3 26 BRADI_1g09890v3 0 BRADI_1g77505v3 7 BRADI_1g48960v3 0 SRR8846480 completed mapping pipeline successfully