Starting /dee2/code/volunteer_pipeline.sh SRR8846513 current disk space = 1515390021632 free memory = 1592127072 SRR8846513 SRAfilesize 248841f9539b1842f4bbd04dcd533487 SRR8846513.sra SRR8846513.sra file validated SRR8846513 is single end SRR8846513 is conventional basespace SRR8846513 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8846513_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 30.77675 33.0 33.0 34.0 27.0 34.0 2 32.7515 34.0 33.0 34.0 28.0 34.0 3 32.91175 34.0 33.0 34.0 32.0 34.0 4 32.984 34.0 33.0 34.0 32.0 34.0 5 32.916 34.0 33.0 34.0 32.0 34.0 6 36.5605 38.0 37.0 38.0 34.0 38.0 7 37.141 38.0 38.0 38.0 36.0 38.0 8 37.37875 38.0 38.0 38.0 37.0 38.0 9 37.29325 38.0 38.0 38.0 37.0 38.0 10-11 37.447874999999996 38.0 38.0 38.0 37.0 38.0 12-13 37.4875 38.0 38.0 38.0 37.5 38.0 14-15 37.452375 38.0 38.0 38.0 37.0 38.0 16-17 37.370625 38.0 38.0 38.0 37.0 38.0 18-19 37.4535 38.0 38.0 38.0 37.0 38.0 20-21 37.449124999999995 38.0 38.0 38.0 37.5 38.0 22-23 37.488875 38.0 38.0 38.0 38.0 38.0 24-25 37.49975 38.0 38.0 38.0 37.5 38.0 26-27 37.520125 38.0 38.0 38.0 38.0 38.0 28-29 37.458749999999995 38.0 38.0 38.0 37.0 38.0 30-31 37.457750000000004 38.0 38.0 38.0 37.5 38.0 32-33 37.402249999999995 38.0 38.0 38.0 37.0 38.0 34-35 37.2355 38.0 38.0 38.0 37.0 38.0 36-37 37.20325 38.0 38.0 38.0 37.0 38.0 38-39 37.158500000000004 38.0 38.0 38.0 36.5 38.0 40-41 37.1275 38.0 38.0 38.0 36.5 38.0 42-43 36.970625 38.0 38.0 38.0 36.5 38.0 44-45 37.084374999999994 38.0 38.0 38.0 36.0 38.0 46-47 37.114625000000004 38.0 38.0 38.0 36.0 38.0 48-49 37.2595 38.0 38.0 38.0 37.0 38.0 50-51 37.323750000000004 38.0 38.0 38.0 37.0 38.0 52-53 37.307375 38.0 38.0 38.0 37.0 38.0 54-55 37.13825 38.0 38.0 38.0 37.0 38.0 56-57 37.091375 38.0 38.0 38.0 36.0 38.0 58-59 37.01349999999999 38.0 38.0 38.0 36.0 38.0 60-61 37.02225 38.0 38.0 38.0 36.0 38.0 62-63 36.763 38.0 38.0 38.0 35.0 38.0 64-65 36.705749999999995 38.0 38.0 38.0 34.5 38.0 66-67 36.5685 38.0 38.0 38.0 34.0 38.0 68-69 36.533500000000004 38.0 38.0 38.0 34.0 38.0 70-71 36.4045 38.0 38.0 38.0 34.0 38.0 72-73 36.300124999999994 38.0 37.5 38.0 33.5 38.0 74-75 36.169 38.0 37.0 38.0 33.5 38.0 76-77 35.676249999999996 38.0 37.0 38.0 30.0 38.0 78-79 35.544375 38.0 37.0 38.0 29.0 38.0 80-81 35.573 38.0 37.0 38.0 29.5 38.0 82-83 35.587 38.0 37.0 38.0 29.0 38.0 84-85 35.566125 38.0 37.0 38.0 29.5 38.0 86-87 36.0095 38.0 37.0 38.0 33.0 38.0 88-89 35.795375 38.0 37.0 38.0 32.5 38.0 90-91 35.687250000000006 38.0 37.5 38.0 32.0 38.0 92-93 35.657875 38.0 38.0 38.0 32.5 38.0 94-95 35.010625 38.0 37.0 38.0 29.5 38.0 96-97 33.358125 38.0 36.0 38.0 14.5 38.0 98-99 31.19475 38.0 33.0 38.0 2.0 38.0 100-101 28.56975 38.0 24.5 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 15 1.0 16 0.0 17 0.0 18 1.0 19 0.0 20 0.0 21 1.0 22 0.0 23 3.0 24 11.0 25 21.0 26 20.0 27 19.0 28 24.0 29 31.0 30 49.0 31 68.0 32 78.0 33 117.0 34 197.0 35 404.0 36 761.0 37 2194.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 36.51093707804483 23.737510126924118 20.09181744531461 19.659735349716446 2 29.7 26.224999999999998 17.0 27.075 3 29.775000000000002 18.325 18.425 33.475 4 24.175 35.575 18.925 21.325 5 29.075 23.599999999999998 25.275 22.05 6 22.825 28.199999999999996 26.825 22.15 7 41.099999999999994 23.799999999999997 17.65 17.45 8 19.75 19.975 41.425 18.85 9 22.1 41.199999999999996 20.200000000000003 16.5 10-11 32.337500000000006 23.1125 26.6125 17.9375 12-13 20.175 21.525 24.5125 33.7875 14-15 21.3125 41.625 21.0 16.0625 16-17 23.200000000000003 26.3125 35.15 15.3375 18-19 35.1625 22.35 22.5625 19.925 20-21 19.787499999999998 29.562500000000004 28.325 22.325 22-23 28.1125 32.3125 25.8125 13.7625 24-25 28.6375 28.287499999999998 24.587500000000002 18.4875 26-27 29.212500000000002 29.425 22.75 18.6125 28-29 21.837500000000002 27.375 24.1375 26.650000000000002 30-31 26.424999999999997 19.5875 33.9875 20.0 32-33 23.6875 17.4 34.325 24.587500000000002 34-35 30.55 17.175 30.587500000000002 21.6875 36-37 34.225 18.3625 29.0875 18.325 38-39 32.05 19.375 29.5 19.075 40-41 29.475 17.4125 26.05 27.0625 42-43 32.1875 22.275 22.037499999999998 23.5 44-45 40.137499999999996 20.0375 16.475 23.35 46-47 33.6 26.487500000000004 16.425 23.4875 48-49 27.250000000000004 25.05 17.6625 30.0375 50-51 24.9375 26.025 14.899999999999999 34.137499999999996 52-53 26.200000000000003 32.4125 11.75 29.6375 54-55 21.475 32.0375 15.787499999999998 30.7 56-57 18.1375 30.425 15.862499999999999 35.575 58-59 14.524999999999999 32.7125 15.9125 36.85 60-61 16.0125 29.849999999999998 22.2125 31.924999999999997 62-63 13.4 31.0625 25.174999999999997 30.362499999999997 64-65 12.625 31.337500000000002 27.400000000000002 28.6375 66-67 12.1875 27.462500000000002 29.462500000000002 30.887500000000003 68-69 14.9625 25.724999999999998 30.3875 28.925 70-71 16.225 25.575 33.925 24.275 72-73 20.375 21.75 35.0875 22.787499999999998 74-75 15.25 17.8875 34.4625 32.4 76-77 19.3875 13.525 38.6125 28.475 78-79 19.2625 11.1125 38.824999999999996 30.8 80-81 20.575 10.225 38.737500000000004 30.4625 82-83 20.4875 9.112499999999999 42.262499999999996 28.1375 84-85 21.4875 8.9125 38.6875 30.912499999999998 86-87 20.549999999999997 14.399999999999999 37.6125 27.437499999999996 88-89 16.037499999999998 27.175 36.162499999999994 20.625 90-91 14.5375 35.85 31.887500000000003 17.724999999999998 92-93 14.2 44.925 24.325 16.55 94-95 12.2 55.275 21.625 10.9 96-97 8.5 67.3625 17.4875 6.65 98-99 6.937500000000001 77.51249999999999 10.5625 4.987500000000001 100-101 4.2625 84.275 7.387499999999999 4.075 >>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 1.5 32 3.0 33 5.0 34 8.0 35 8.5 36 7.0 37 11.5 38 32.5 39 53.0 40 102.5 41 163.5 42 210.0 43 313.5 44 362.5 45 388.5 46 403.5 47 331.0 48 302.0 49 347.5 50 314.5 51 184.0 52 104.0 53 87.5 54 117.0 55 87.5 56 22.0 57 8.0 58 4.5 59 5.0 60 5.0 61 3.5 62 1.5 63 0.5 64 0.0 65 0.0 66 0.5 67 0.5 68 0.0 69 0.0 70 0.0 71 0.0 72 0.0 73 0.0 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content warn #Base N-Count 1 7.425 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 51.775000000000006 #Duplication Level Percentage of deduplicated Percentage of total 1 83.96909705456301 43.475 2 6.518590053114437 6.75 3 2.897151134717528 4.5 4 1.6417189763399325 3.4000000000000004 5 0.6760019314340898 1.7500000000000002 6 0.9657170449058425 3.0 7 0.43457267020762913 1.575 8 0.3380009657170449 1.4000000000000001 9 0.24142926122646063 1.125 >10 1.979719942056977 18.75 >50 0.28971511347175277 10.95 >100 0.048285852245292124 3.325 >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 133 3.325 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 90 2.25 No Hit GGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 81 2.025 RNA PCR Primer, Index 1 (100% over 22bp) TCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 74 1.8499999999999999 No Hit CTCTGATGATGATCAAACTAATACTTTCGTTCTTCTGGAATTCTCGGGTG 69 1.725 No Hit AGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 68 1.7000000000000002 No Hit TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 56 1.4000000000000001 RNA PCR Primer, Index 1 (100% over 29bp) GACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 50 1.25 RNA PCR Primer, Index 1 (100% over 23bp) CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 43 1.075 No Hit GACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAAC 41 1.0250000000000001 RNA PCR Primer, Index 1 (100% over 24bp) GCACCAGTGGTCTAGTGGTAGAATAGTACCTGGAATTCTCGGGTGCCAAG 36 0.8999999999999999 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 34 0.8500000000000001 Illumina Small RNA Adapter 2 (100% over 21bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 32 0.8 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 32 0.8 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATATGGAATTCTCGGGTGCCAAGGAA 30 0.75 RNA PCR Primer, Index 1 (100% over 23bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTTGGAATTCT 27 0.675 No Hit CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTC 21 0.525 No Hit TCCTGTGGATGAGAAGGCATTTATATTCTGATGATATGGAATTCTCGGGT 20 0.5 No Hit GACACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACT 18 0.44999999999999996 RNA PCR Primer, Index 1 (100% over 25bp) GCCCACCCCAAGATGAGTGCTCTCTCTGGAATTCTCGGGTGCCAAGGAAC 18 0.44999999999999996 RNA PCR Primer, Index 1 (100% over 24bp) AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 18 0.44999999999999996 Illumina Small RNA Adapter 2 (100% over 21bp) GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 17 0.42500000000000004 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 16 0.4 Illumina Small RNA Adapter 2 (100% over 21bp) TTCGGACCAGGCTTCATTCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 16 0.4 RNA PCR Primer, Index 1 (100% over 29bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTTGGAATTCTCGGGTGCCA 16 0.4 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 15 0.375 No Hit ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGC 14 0.35000000000000003 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAATGGAATTCTCGGGTGCCA 13 0.325 No Hit CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGG 13 0.325 No Hit TCTCGGACCAGGCTTCATTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 13 0.325 RNA PCR Primer, Index 1 (100% over 29bp) AGGGCTATAGCTCAGTTCGGTAGAGCAACTCGTTTACACCGAGATGGAAT 13 0.325 No Hit ATATATTTCAAGTTATTTCGGATCTTGGAATTCTCGGGTGCCAAGGAACT 12 0.3 RNA PCR Primer, Index 1 (100% over 25bp) CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 12 0.3 RNA PCR Primer, Index 1 (100% over 28bp) CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 12 0.3 Illumina Small RNA Adapter 2 (100% over 21bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTCATGGAATTCTCGGGTG 12 0.3 No Hit NGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 11 0.27499999999999997 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGGAATTCTCGGGTGCCA 11 0.27499999999999997 No Hit TCTCGGGTGCCAAGGAACTCCAGTCACACTGATATCTCGTATGCCGTCTT 11 0.27499999999999997 RNA PCR Primer, Index 25 (100% over 50bp) CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 23bp) TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 11 0.27499999999999997 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTGGAATTCTCGGGTGCCA 11 0.27499999999999997 No Hit AGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGT 10 0.25 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCGTGGAATT 10 0.25 No Hit CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGGAATTCTCG 10 0.25 No Hit CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGG 10 0.25 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGATGGAATTCTC 10 0.25 No Hit NGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 10 0.25 No Hit GGGGATATAGCTCAGTTGGTAGATGGAATTCTCGGGTGCCAAGGAACTCC 10 0.25 RNA PCR Primer, Index 1 (100% over 27bp) AATTCTCGGGTGCCAAGGAACTCCAGTCACACTGATATCTCGTATGCCGT 9 0.22499999999999998 RNA PCR Primer, Index 25 (100% over 50bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTTGGAATTCTCGGGTGCC 9 0.22499999999999998 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGAATTCTCGGGTGCCAAGGAACTCCA 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 28bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGGAATTCTCGGGTGCCAA 9 0.22499999999999998 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTGGAATTCTC 9 0.22499999999999998 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGAGTGGAATTCT 8 0.2 No Hit GCACCAGTAGTCTAGTGGTAGAATAGTACCTGGAATTCTCGGGTGCCAAG 8 0.2 No Hit ATAACCGTAGTAATTCTAGAGCTAATACTGGAATTCTCGGGTGCCAAGGA 8 0.2 RNA PCR Primer, Index 1 (100% over 22bp) TTCTCGGGTGCCAAGGAACTCCAGTCACACTGATATCTCGTATGCCGTCT 8 0.2 RNA PCR Primer, Index 25 (100% over 50bp) TCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCG 8 0.2 No Hit NCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 8 0.2 RNA PCR Primer, Index 1 (100% over 29bp) CACGACTCTCGGCAACGGATATCTCGTGGAATTCTCGGGTGCCAAGGAAC 8 0.2 RNA PCR Primer, Index 1 (100% over 24bp) AGGGCTATAGCTCAGTTCGGTAGAGCAACTCGTTTACACTGGAATTCTCG 7 0.17500000000000002 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAAATGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit TCGGATAACCGTAGTAATTCTAGAGCTAATACGTGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit CTCGGGTGCCAAGGAACTCCAGTCACACTGATATCTCGTATGCCGTCTTC 7 0.17500000000000002 RNA PCR Primer, Index 25 (100% over 50bp) CGACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 22bp) GATAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAAC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 24bp) NTCTGATGATGATCAAACTAATACTTTCGTTCTTCTGGAATTCTCGGGTG 7 0.17500000000000002 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTAATCCTGGAATTC 7 0.17500000000000002 No Hit NACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 23bp) CACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAACT 6 0.15 RNA PCR Primer, Index 1 (100% over 25bp) TCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCG 6 0.15 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATACTCTGGAATTCTCGGGTGCCAAG 6 0.15 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGGTGGAATTC 6 0.15 No Hit GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTG 6 0.15 No Hit GAGAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGT 6 0.15 No Hit ACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) GGGATTGTAGTTCAATTGGTCAGAGCTGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) ATATATTTCAAGTTATTTCGGATCTGGAATTCTCGGGTGCCAAGGAACTC 6 0.15 RNA PCR Primer, Index 1 (100% over 26bp) CCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTG 6 0.15 No Hit GATAACCGTAGTAATTCTAGAGCTAATACTGGAATTCTCGGGTGCCAAGG 6 0.15 Illumina Small RNA Adapter 2 (100% over 21bp) GGGGATATGGCGAAATCGGTAGACGCTACGGACTTTGGAATTCTCGGGTG 6 0.15 No Hit GCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCC 6 0.15 No Hit AAGGGTGCTGAGAATACTTTGAATCTGACACTGGAATTCTCGGGTGCCAA 6 0.15 No Hit TAACCGTAGTAATTCTAGAGCTAATATGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGG 6 0.15 No Hit ACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTCT 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATGGAATTCTCGGGTG 6 0.15 No Hit TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTGGAATTCTCGGGTGC 6 0.15 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTTGGAATTCTCGGGTGC 6 0.15 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTAATCTGGAATTCT 5 0.125 No Hit GATAACCGTAGTAATTCTAGAGCTAATTGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) GATGAGCTCAACGAGAACAGAAATCTCGTGTGGAATTCTCGGGTGCCAAG 5 0.125 No Hit GGGGATATAGCTCAGTTGGTAGAGCTCCGCTCTTGCAATGGAATTCTCGG 5 0.125 No Hit AGAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTG 5 0.125 No Hit ATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGGTGCCA 5 0.125 No Hit NATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 5 0.125 No Hit TGCAAGTATGAACTAATTTGAACTGTGAAACTTGGAATTCTCGGGTGCCA 5 0.125 No Hit ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGGTGC 5 0.125 No Hit CTTAGCGGATACTATGATAGCACCTGGAATTCTCGGGTGCCAAGGAACTC 5 0.125 RNA PCR Primer, Index 1 (100% over 26bp) TGCCACGATCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAAT 5 0.125 No Hit NATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 5 0.125 No Hit NACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) TAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAACTC 5 0.125 RNA PCR Primer, Index 1 (100% over 26bp) >>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 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 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 0.16249999999999998 0.0 0.0 0.0 12-13 0.0 0.225 0.0 0.0 0.0 14-15 0.0 0.35 0.0 0.0 0.0 16-17 0.0 0.725 0.0 0.0 0.0 18-19 0.0 1.275 0.0 0.0 0.0 20-21 0.0 2.7375 0.0 0.0 0.0 22-23 0.0 9.275 0.0 0.0 0.0 24-25 0.0 18.2375 0.0 0.0 0.0 26-27 0.0 29.0875 0.0 0.0 0.0 28-29 0.0 38.8 0.0 0.0 0.0 30-31 0.0 48.8875 0.0 0.0 0.0 32-33 0.0 59.25 0.0 0.0 0.0 34-35 0.0 71.2375 0.0 0.0 0.0 36-37 0.0 81.25 0.0 0.0 0.0 38-39 0.0 86.225 0.0 0.0 0.0 40-41 0.0 89.2875 0.0 0.0 0.0 42-43 0.0 92.4875 0.0 0.0 0.0 44-45 0.0 94.375 0.0 0.0 0.0 46-47 0.0 95.0625 0.0 0.0 0.0 48-49 0.0 95.1375 0.0 0.0 0.0 50-51 0.0 95.175 0.0 0.0 0.0 52-53 0.0 95.175 0.0 0.0 0.0 54-55 0.0 95.175 0.0 0.0 0.0 56-57 0.0 95.175 0.0 0.0 0.0 58-59 0.0 95.175 0.0 0.0 0.0 60-61 0.0 95.175 0.0 0.0 0.0 62-63 0.0 95.175 0.0 0.0 0.0 64-65 0.0 95.175 0.0 0.0 0.0 66-67 0.0 95.175 0.0 0.0 0.0 68-69 0.0 95.175 0.0 0.0 0.0 70-71 0.0 95.175 0.0 0.0 0.0 72-73 0.0 95.175 0.0 0.0 0.0 74-75 0.0 95.175 0.0 0.0 0.0 76-77 0.0 95.175 0.0 0.0 0.0 78-79 0.0 95.175 0.0 0.0 0.0 80-81 0.0 95.19999999999999 0.0 0.0 0.0 82-83 0.0 95.225 0.0 0.0 0.0 84-85 0.0 95.225 0.0 0.0 0.0 86-87 0.0 95.225 0.0 0.0 0.0 88-89 0.0 95.225 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GCCTTGA 15 4.9992715E-4 99.947365 1 GGGATTG 20 1.1880853E-5 99.947365 1 CATCGAG 30 6.552E-9 99.947365 1 TAGTTCA 25 3.8410144E-7 94.950005 8 AGTTCAA 25 3.8410144E-7 94.950005 9 GTAGTTC 25 3.8410144E-7 94.950005 7 TGATGGT 15 6.1550457E-4 94.95 5 GTAGACC 30 9.493306E-9 94.95 7 GGTGAAA 15 6.1550457E-4 94.95 9 TTGTAGT 20 1.5432628E-5 94.95 5 AGTAGAC 30 9.493306E-9 94.95 6 ATGGTGA 15 6.1550457E-4 94.95 7 GGATTGT 20 1.5432628E-5 94.95 2 CCTTGAT 15 6.1550457E-4 94.95 2 GATTGTA 20 1.5432628E-5 94.95 3 GAGTAGA 30 9.493306E-9 94.95 5 TTGATGG 15 6.1550457E-4 94.95 4 CGAGTAG 30 9.493306E-9 94.95 4 AGACCTT 30 9.493306E-9 94.95 9 CTTGATG 15 6.1550457E-4 94.95 3 >>END_MODULE Rejected 938814 READS because READLEN < 1 Read 938814 spots for SRR8846513.sra Written 938814 spots for SRR8846513.sra Rejected 938814 READS because READLEN < 1 Read 938814 spots for SRR8846513.sra Written 938814 spots for SRR8846513.sra Rejected 938814 READS because READLEN < 1 Read 938814 spots for SRR8846513.sra Written 938814 spots for SRR8846513.sra Rejected 938814 READS because READLEN < 1 Read 938814 spots for SRR8846513.sra Written 938814 spots for SRR8846513.sra Rejected 938814 READS because READLEN < 1 Read 938814 spots for SRR8846513.sra Written 938814 spots for SRR8846513.sra Rejected 938814 READS because READLEN < 1 Read 938814 spots for SRR8846513.sra Written 938814 spots for SRR8846513.sra Rejected 938814 READS because READLEN < 1 Read 938814 spots for SRR8846513.sra Written 938814 spots for SRR8846513.sra Rejected 938814 READS because READLEN < 1 Read 938814 spots for SRR8846513.sra Written 938814 spots for SRR8846513.sra Rejected 938814 READS because READLEN < 1 Read 938814 spots for SRR8846513.sra Written 938814 spots for SRR8846513.sra Rejected 938814 READS because READLEN < 1 Read 938814 spots for SRR8846513.sra Written 938814 spots for SRR8846513.sra Rejected 938814 READS because READLEN < 1 Read 938814 spots for SRR8846513.sra Written 938814 spots for SRR8846513.sra Rejected 938814 READS because READLEN < 1 Read 938814 spots for SRR8846513.sra Written 938814 spots for SRR8846513.sra Rejected 938814 READS because READLEN < 1 Read 938814 spots for SRR8846513.sra Written 938814 spots for SRR8846513.sra Rejected 938814 READS because READLEN < 1 Read 938814 spots for SRR8846513.sra Written 938814 spots for SRR8846513.sra Rejected 938814 READS because READLEN < 1 Read 938814 spots for SRR8846513.sra Written 938814 spots for SRR8846513.sra Rejected 938824 READS because READLEN < 1 Read 938824 spots for SRR8846513.sra Written 938824 spots for SRR8846513.sra Rejected 938814 READS because READLEN < 1 Read 938814 spots for SRR8846513.sra Written 938814 spots for SRR8846513.sra Rejected 938814 READS because READLEN < 1 Read 938814 spots for SRR8846513.sra Written 938814 spots for SRR8846513.sra Rejected 938814 READS because READLEN < 1 Read 938814 spots for SRR8846513.sra Written 938814 spots for SRR8846513.sra Rejected 938814 READS because READLEN < 1 Read 938814 spots for SRR8846513.sra Written 938814 spots for SRR8846513.sra SRR ids: ['SRR8846513.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_oxyd0oe2 SRR8846513.sra spots: 18776290 blocks: [[1, 938814], [938815, 1877628], [1877629, 2816442], [2816443, 3755256], [3755257, 4694070], [4694071, 5632884], [5632885, 6571698], [6571699, 7510512], [7510513, 8449326], [8449327, 9388140], [9388141, 10326954], [10326955, 11265768], [11265769, 12204582], [12204583, 13143396], [13143397, 14082210], [14082211, 15021024], [15021025, 15959838], [15959839, 16898652], [16898653, 17837466], [17837467, 18776290]] SRR8846513 file size 4507346 SRR8846513 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 SRR8846513 SRR8846513_1.fastq Input file: SRR8846513_1.fastq trimmed: SRR8846513-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 Thu Dec 12 02:53:23 2024 >> started Thu Dec 12 02:53:33 2024 >> done (10.176s) 18776290 reads processed; of these: 309 ( 0.00%) short reads filtered out after trimming by size control 61 ( 0.00%) empty reads filtered out after trimming by size control 18775920 (100.00%) reads available; of these: 3325796 (17.71%) trimmed reads available after processing 15450124 (82.29%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 55 0.00% 19 47 0.00% 20 37 0.00% 21 53 0.00% 22 47 0.00% 23 56 0.00% 24 66 0.00% 25 91 0.00% 26 133 0.00% 27 259 0.00% 28 319 0.00% 29 416 0.00% 30 400 0.00% 31 383 0.00% 32 337 0.00% 33 277 0.00% 34 326 0.00% 35 220 0.00% 36 257 0.00% 37 170 0.00% 38 176 0.00% 39 162 0.00% 40 190 0.00% 41 193 0.00% 42 241 0.00% 43 269 0.00% 44 274 0.00% 45 326 0.00% 46 252 0.00% 47 232 0.00% 48 233 0.00% 49 215 0.00% 50 194 0.00% 51 200 0.00% 52 180 0.00% 53 205 0.00% 54 223 0.00% 55 205 0.00% 56 251 0.00% 57 247 0.00% 58 275 0.00% 59 489 0.00% 60 565 0.00% 61 934 0.00% 62 1211 0.01% 63 1596 0.01% 64 2572 0.01% 65 3128 0.02% 66 9056 0.05% 67 41397 0.22% 68 42944 0.23% 69 29465 0.16% 70 19968 0.11% 71 20988 0.11% 72 9556 0.05% 73 3508 0.02% 74 4365 0.02% 75 3055 0.02% 76 2808 0.01% 77 2840 0.02% 78 3295 0.02% 79 3475 0.02% 80 4172 0.02% 81 5531 0.03% 82 10451 0.06% 83 9452 0.05% 84 7963 0.04% 85 7615 0.04% 86 9639 0.05% 87 13349 0.07% 88 22352 0.12% 89 36187 0.19% 90 49616 0.26% 91 55860 0.30% 92 73913 0.39% 93 120161 0.64% 94 157015 0.84% 95 346989 1.85% 96 418887 2.23% 97 397225 2.12% 98 546518 2.91% 99 503744 2.68% 100 313250 1.67% 101 15450124 82.29% 18775920 reads passed initial QC criterion=sequence-density sequence-density=94.63 sequence-density-rank=1 fanout-score=32.17 fanout-score-rank=1 prefix-density=95.02 prefix-fanout=32.0 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTGATATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA criterion=fanout-score sequence-density=94.63 sequence-density-rank=1 fanout-score=32.17 fanout-score-rank=1 prefix-density=95.02 prefix-fanout=32.0 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTGATATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTGATATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA -o SRR8846513 - Input file: STDIN trimmed: SRR8846513-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTGATATCTCGTATGCCGTCTTCTGCTTGA -- 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 Thu Dec 12 02:54:22 2024 >> started Thu Dec 12 02:54:41 2024 >> done (19.122s) 18380638 reads processed; of these: 263219 ( 1.43%) short reads filtered out after trimming by size control 4562 ( 0.02%) empty reads filtered out after trimming by size control 18112857 (98.54%) reads available; of these: 17685376 (97.64%) trimmed reads available after processing 427481 ( 2.36%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 89480 0.49% 19 171549 0.95% 20 202969 1.12% 21 820446 4.53% 22 443281 2.45% 23 599987 3.31% 24 1642085 9.07% 25 723704 4.00% 26 882902 4.87% 27 983596 5.43% 28 913713 5.04% 29 801818 4.43% 30 1052858 5.81% 31 667594 3.69% 32 1384380 7.64% 33 1195572 6.60% 34 1065816 5.88% 35 985048 5.44% 36 822766 4.54% 37 382272 2.11% 38 308019 1.70% 39 278441 1.54% 40 300135 1.66% 41 354019 1.95% 42 295209 1.63% 43 117882 0.65% 44 106894 0.59% 45 41456 0.23% 46 18420 0.10% 47 8694 0.05% 48 6961 0.04% 49 3810 0.02% 50 2617 0.01% 51 2180 0.01% 52 1464 0.01% 53 1047 0.01% 54 1080 0.01% 55 365 0.00% 56 589 0.00% 57 255 0.00% 58 231 0.00% 59 406 0.00% 60 457 0.00% 61 822 0.00% 62 978 0.01% 63 1394 0.01% 64 2317 0.01% 65 2865 0.02% 66 8611 0.05% 67 40217 0.22% 68 41656 0.23% 69 28417 0.16% 70 19071 0.11% 71 20012 0.11% 72 8243 0.05% 73 2327 0.01% 74 2237 0.01% 75 1426 0.01% 76 1387 0.01% 77 1994 0.01% 78 1406 0.01% 79 1357 0.01% 80 2320 0.01% 81 1821 0.01% 82 1591 0.01% 83 2302 0.01% 84 1195 0.01% 85 1118 0.01% 86 989 0.01% 87 919 0.01% 88 819 0.00% 89 929 0.01% 90 866 0.00% 91 975 0.01% 92 1266 0.01% 93 1635 0.01% 94 1628 0.01% 95 2080 0.01% 96 3089 0.02% 97 3726 0.02% 98 5737 0.03% 99 5758 0.03% 100 7371 0.04% 101 195519 1.08% criterion=sequence-density sequence-density=5.71 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=13 prefix-density=0.00 prefix-fanout=1.0 sequence=CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATTCAAGA criterion=fanout-score sequence-density=0.30 sequence-density-rank=17 fanout-score=16.13 fanout-score-rank=1 prefix-density=4.86 prefix-fanout=1.0 sequence=TTGTGAGAATTAAAAA Started job on | Dec 12 02:55:06 Started mapping on | Dec 12 02:55:07 Finished on | Dec 12 02:56:06 Mapping speed, Million of reads per hour | 1129.31 Number of input reads | 18508139 Average input read length | 32 UNIQUE READS: Uniquely mapped reads number | 2944766 Uniquely mapped reads % | 15.91% Average mapped length | 28.06 Number of splices: Total | 34570 Number of splices: Annotated (sjdb) | 19713 Number of splices: GT/AG | 31067 Number of splices: GC/AG | 2746 Number of splices: AT/AC | 20 Number of splices: Non-canonical | 737 Mismatch rate per base, % | 0.14% Deletion rate per base | 0.00% Deletion average length | 1.35 Insertion rate per base | 0.00% Insertion average length | 1.02 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 7947479 % of reads mapped to multiple loci | 42.94% Number of reads mapped to too many loci | 6513386 % of reads mapped to too many loci | 35.19% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 5.51% % of reads unmapped: other | 0.44% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 7615894 7615894 7615894 N_multimapping 7947479 7947479 7947479 N_noFeature 1552648 1749276 2730943 N_ambiguous 53281 35707 521 UnstrandedReadsAssigned:1338837 PositiveStrandReadsAssigned:1159783 NegativeStrandReadsAssigned:213302 Dataset is classified positive stranded MeadianReadLen=30 20thPercentileLength=24 echo kmer=19 SRR8846513 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: SRR8846513-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 18,508,139 reads, 3,370,974 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,089 rounds 52973 SRR8846513.ke.tsv 35125 SRR8846513.se.tsv 88098 total ==> SRR8846513.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 0 0 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 2 0.545541 PNS24243 293 194 0 0 KQK14069 1603 1504 179.225 44.5966 KQK14071 474 375 5.36446 5.35361 ==> SRR8846513.se.tsv <== BRADI_1g14170v3 200 BRADI_1g53295v3 4 BRADI_1g59795v3 8 BRADI_1g07683v3 0 BRADI_1g00485v3 3 BRADI_1g20270v3 43 BRADI_1g74790v3 17 BRADI_1g09890v3 0 BRADI_1g77505v3 1 BRADI_1g48960v3 0 SRR8846513 completed mapping pipeline successfully