Starting /dee2/code/volunteer_pipeline.sh SRR7472589 current disk space = 3088373911552 free memory = 1450132244 SRR7472589 SRAfilesize 9197b62deac8ee98e08cb74e6b98989e SRR7472589.sra SRR7472589.sra file validated SRR7472589 is single end SRR7472589 is conventional basespace SRR7472589 read1 length is 51 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7472589_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 51 %GC 52 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.1325 34.0 33.0 34.0 32.0 34.0 2 33.19975 34.0 33.0 34.0 33.0 34.0 3 33.2585 34.0 34.0 34.0 33.0 34.0 4 33.2445 34.0 34.0 34.0 33.0 34.0 5 33.225 34.0 34.0 34.0 33.0 34.0 6 36.97975 38.0 38.0 38.0 36.0 38.0 7 37.1425 38.0 38.0 38.0 37.0 38.0 8 37.3195 38.0 38.0 38.0 37.0 38.0 9 37.2475 38.0 38.0 38.0 37.0 38.0 10 36.57175 38.0 38.0 38.0 35.0 38.0 11 37.136 38.0 38.0 38.0 37.0 38.0 12 37.26325 38.0 38.0 38.0 37.0 38.0 13 37.20475 38.0 38.0 38.0 37.0 38.0 14 37.271 38.0 38.0 38.0 38.0 38.0 15 37.1675 38.0 38.0 38.0 38.0 38.0 16 37.1645 38.0 38.0 38.0 37.0 38.0 17 37.1605 38.0 38.0 38.0 37.0 38.0 18 37.2475 38.0 38.0 38.0 37.0 38.0 19 37.2705 38.0 38.0 38.0 38.0 38.0 20 37.21225 38.0 38.0 38.0 37.0 38.0 21 37.201 38.0 38.0 38.0 37.0 38.0 22 37.08425 38.0 38.0 38.0 37.0 38.0 23 37.232 38.0 38.0 38.0 38.0 38.0 24 37.0925 38.0 38.0 38.0 37.0 38.0 25 37.279 38.0 38.0 38.0 38.0 38.0 26 37.27675 38.0 38.0 38.0 38.0 38.0 27 37.207 38.0 38.0 38.0 38.0 38.0 28 37.20575 38.0 38.0 38.0 37.0 38.0 29 37.2875 38.0 38.0 38.0 38.0 38.0 30 37.28275 38.0 38.0 38.0 38.0 38.0 31 37.17675 38.0 38.0 38.0 37.0 38.0 32 37.1625 38.0 38.0 38.0 37.0 38.0 33 37.286 38.0 38.0 38.0 37.0 38.0 34 37.38875 38.0 38.0 38.0 38.0 38.0 35 37.36325 38.0 38.0 38.0 38.0 38.0 36 37.0465 38.0 38.0 38.0 37.0 38.0 37 37.296 38.0 38.0 38.0 38.0 38.0 38 37.36725 38.0 38.0 38.0 38.0 38.0 39 37.34175 38.0 38.0 38.0 38.0 38.0 40 37.32275 38.0 38.0 38.0 38.0 38.0 41 37.24875 38.0 38.0 38.0 38.0 38.0 42 37.2745 38.0 38.0 38.0 38.0 38.0 43 37.37 38.0 38.0 38.0 38.0 38.0 44 37.27375 38.0 38.0 38.0 38.0 38.0 45 37.297 38.0 38.0 38.0 38.0 38.0 46 37.3105 38.0 38.0 38.0 38.0 38.0 47 37.27175 38.0 38.0 38.0 38.0 38.0 48 37.29625 38.0 38.0 38.0 38.0 38.0 49 37.33225 38.0 38.0 38.0 38.0 38.0 50 37.31275 38.0 38.0 38.0 38.0 38.0 51 37.25825 38.0 38.0 38.0 38.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 19.0 3 0.0 4 1.0 5 1.0 6 3.0 7 1.0 8 1.0 9 2.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 2.0 18 0.0 19 0.0 20 0.0 21 4.0 22 1.0 23 0.0 24 4.0 25 6.0 26 8.0 27 5.0 28 10.0 29 8.0 30 14.0 31 22.0 32 35.0 33 48.0 34 75.0 35 109.0 36 257.0 37 3364.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 33.425 24.975 24.525 17.075000000000003 2 29.575000000000003 19.925 26.575 23.925 3 25.650000000000002 21.099999999999998 21.85 31.4 4 42.675000000000004 22.125 15.75 19.45 5 31.724999999999998 25.5 22.5 20.275000000000002 6 23.0 27.0 26.75 23.25 7 34.925 20.95 26.8 17.325 8 27.525 23.1 33.15 16.225 9 23.055763940985248 35.83395848962241 22.58064516129032 18.529632408102024 10 39.25 27.825 16.05 16.875 11 31.75 20.3 26.3 21.65 12 25.1 23.3 28.775000000000002 22.825 13 21.775 19.625 29.475 29.125 14 19.15 40.925 21.8 18.125 15 35.25 32.425 18.0 14.325 16 28.075 23.45 28.849999999999998 19.625 17 29.75 20.349999999999998 32.05 17.849999999999998 18 39.675 17.375 22.225 20.724999999999998 19 29.65 19.900000000000002 32.7 17.75 20 26.400000000000002 29.275000000000002 26.55 17.775 21 25.074999999999996 34.449999999999996 22.925 17.549999999999997 22 26.25 28.725 25.6 19.425 23 30.525000000000002 25.4 25.825 18.25 24 24.75 32.525 23.65 19.075 25 24.675 27.3 36.0 12.025 26 32.13303325831458 23.78094523630908 30.182545636409102 13.903475868967242 27 27.55 20.025000000000002 28.625 23.799999999999997 28 17.65 30.425 26.450000000000003 25.474999999999998 29 23.275000000000002 21.95 25.074999999999996 29.7 30 27.0 17.05 41.775 14.174999999999999 31 25.4 12.825000000000001 29.775000000000002 32.0 32 32.6081520380095 10.777694423605903 22.83070767691923 33.78344586146537 33 27.250000000000004 14.575 40.225 17.95 34 33.175 14.95 30.599999999999998 21.275 35 44.9 11.75 29.175 14.174999999999999 36 48.15 12.85 24.425 14.575 37 38.074999999999996 20.45 18.95 22.525000000000002 38 26.05 24.875 28.9 20.175 39 30.575000000000003 24.9 22.5 22.025 40 25.3 24.099999999999998 21.9 28.7 41 28.325 19.35 21.65 30.675 42 29.897423067300476 26.720040030022517 22.191643732799598 21.19089316987741 43 26.025 29.349999999999998 18.224999999999998 26.400000000000002 44 43.375 22.45 13.025 21.15 45 41.55 19.15 11.4 27.900000000000002 46 30.75768942235559 26.78169542385596 17.65441360340085 24.8062015503876 47 25.75 30.349999999999998 17.175 26.724999999999998 48 28.1 21.65 14.05 36.199999999999996 49 24.825 21.575 21.175 32.425 50 26.55 21.275 11.025 41.15 51 17.05 33.625 14.6 34.725 >>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 0.5 33 1.0 34 3.0 35 5.0 36 9.5 37 14.0 38 23.0 39 32.0 40 53.5 41 75.0 42 120.5 43 166.0 44 184.5 45 203.0 46 237.0 47 271.0 48 349.0 49 427.0 50 620.0 51 813.0 52 683.5 53 554.0 54 507.5 55 461.0 56 514.5 57 568.0 58 372.0 59 176.0 60 141.0 61 106.0 62 94.5 63 83.0 64 52.5 65 22.0 66 15.5 67 9.0 68 9.5 69 10.0 70 5.5 71 1.0 72 2.0 73 3.0 74 1.5 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 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.025 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 0.025 27 0.0 28 0.0 29 0.0 30 0.0 31 0.0 32 0.025 33 0.0 34 0.0 35 0.0 36 0.0 37 0.0 38 0.0 39 0.0 40 0.0 41 0.0 42 0.075 43 0.0 44 0.0 45 0.0 46 0.025 47 0.0 48 0.0 49 0.0 50 0.0 51 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 51 4000.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 57.35 #Duplication Level Percentage of deduplicated Percentage of total 1 89.27637314734089 51.2 2 4.489973844812554 5.1499999999999995 3 1.8308631211857016 3.15 4 1.046207497820401 2.4 5 0.7410636442894507 2.125 6 0.13077593722755013 0.44999999999999996 7 0.2179598953792502 0.8750000000000001 8 0.2179598953792502 1.0 9 0.08718395815170009 0.44999999999999996 >10 1.6564952048823016 17.65 >50 0.2179598953792502 8.774999999999999 >100 0.08718395815170009 6.775 >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 GTCGTTGTAGTATAGTGGTGAGTATTCCCGCCTTGGAATTCTCGGGTGCCA 139 3.4750000000000005 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGGA 132 3.3000000000000003 RNA PCR Primer, Index 1 (100% over 22bp) CTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 79 1.975 RNA PCR Primer, Index 1 (100% over 28bp) TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT 75 1.875 RNA PCR Primer, Index 1 (100% over 30bp) GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTTGGAATTCTCGGGTGCC 73 1.825 No Hit GTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTTGGAATTCTCGGGTGCCA 65 1.625 No Hit TCTCGGACCAGGCTTCATTCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT 59 1.4749999999999999 RNA PCR Primer, Index 1 (100% over 30bp) TTTGGATTGAAGGGAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 40 1.0 RNA PCR Primer, Index 1 (100% over 31bp) GGGCCTGTAGCTCAGAGGATGGAATTCTCGGGTGCCAAGGAACTCCAGTCA 32 0.8 RNA PCR Primer, Index 1 (100% over 32bp) TCCTCAGTAGCTCAGTGGTAGAGCGGTCGGCTTGGAATTCTCGGGTGCCAA 31 0.775 No Hit AGTTACTAATTCATGATCTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG 30 0.75 RNA PCR Primer, Index 1 (100% over 29bp) ATCCGGTTAGGATCGATCTAAACCAGCCCTGGAATTCTCGGGTGCCAAGGA 28 0.7000000000000001 RNA PCR Primer, Index 1 (100% over 22bp) GTCGGGATAGCTCAGCAGGTAGAGCAGAGGACTGATGGAATTCTCGGGTGC 27 0.675 No Hit AGCGTGGAGGTTCGAGTCCTCTTCAAGGCACCATGGAATTCTCGGGTGCCA 25 0.625 No Hit TCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTC 22 0.5499999999999999 RNA PCR Primer, Index 1 (100% over 26bp) GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGTGGAATTCTCGGGTGC 22 0.5499999999999999 No Hit TGAGGCATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAA 22 0.5499999999999999 No Hit GCGGATATAGTCGAATGGTAAAATTTCTCTTTGCCTGGAATTCTCGGGTGC 22 0.5499999999999999 No Hit TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTAGAGATCTCGTATGCC 21 0.525 RNA PCR Primer, Index 17 (100% over 51bp) TCCGTTGTCGTCCAGCGGTTAGGATATCTGGCTTGGAATTCTCGGGTGCCA 20 0.5 No Hit GGGGATGTAGCTCAAATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGT 20 0.5 RNA PCR Primer, Index 1 (97% over 35bp) ACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 19 0.475 RNA PCR Primer, Index 1 (100% over 31bp) GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGTTGGAATTCTCGGGTG 19 0.475 No Hit CCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCC 19 0.475 RNA PCR Primer, Index 1 (100% over 27bp) CATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAAC 19 0.475 RNA PCR Primer, Index 1 (100% over 24bp) TAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAG 19 0.475 RNA PCR Primer, Index 1 (100% over 29bp) CGATTGGGGGAGTAAGAATAGTATTTAATTGCTGGAATTCTCGGGTGCCAA 19 0.475 No Hit ATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACT 17 0.42500000000000004 RNA PCR Primer, Index 1 (100% over 25bp) AACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGT 17 0.42500000000000004 RNA PCR Primer, Index 1 (100% over 30bp) CGCGGGGTAGAGCAGCTTGGTAGCTCGCAAGGCTCTGGAATTCTCGGGTGC 16 0.4 No Hit GGTGGCTGTAGTTTAGTGGTAAGAATTCCACGTTTGGAATTCTCGGGTGCC 16 0.4 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCCA 15 0.375 No Hit GAGGCATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAG 14 0.35000000000000003 No Hit GAGCGTGGAGGTTCGAGTCCTCTTCAAGGCACCATGGAATTCTCGGGTGCC 13 0.325 No Hit CAGCTGAGGCATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTG 12 0.3 No Hit GCGGATATAGTCGAATGGTAAAATTTCTCTTTTGGAATTCTCGGGTGCCAA 12 0.3 No Hit GCCGCCATGGTGAAATCGGTAGACACGCTGCTCTTATGGAATTCTCGGGTG 12 0.3 No Hit CGCGGGGTAGAGCAGCTTGGTAGCTCGCAAGGCTCATGGAATTCTCGGGTG 12 0.3 No Hit GGGGATGTAGCTCATATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGT 11 0.27499999999999997 RNA PCR Primer, Index 1 (97% over 35bp) GCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGGAA 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 23bp) CAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCA 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 32bp) GCGCCTGTAGCTCAGTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGTCA 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 32bp) TCCTCAGTAGCTCAGTGGTAGAGCGGTCGGCTGTGGAATTCTCGGGTGCCA 10 0.25 No Hit GCCCCATGTCGCTCCGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCCAG 10 0.25 RNA PCR Primer, Index 1 (100% over 29bp) AGGCATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGG 10 0.25 Illumina Small RNA Adapter 2 (100% over 21bp) TTTGGATTGAAGGGAGCTCTATGGAATTCTCGGGTGCCAAGGAACTCCAGT 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 30bp) GGGGATGTAGCTCAGATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGT 9 0.22499999999999998 RNA PCR Primer, Index 1 (97% over 35bp) GGTGGCTGTAGTTTAGTGGTAAGAATTCCACGTTGTTGGAATTCTCGGGTG 8 0.2 No Hit GCATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAA 8 0.2 RNA PCR Primer, Index 1 (100% over 23bp) TCAGCCCCATGTCGCTCCGATTCGTTGGAATTCTCGGGTGCCAAGGAACTC 8 0.2 RNA PCR Primer, Index 1 (100% over 26bp) AGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC 8 0.2 RNA PCR Primer, Index 1 (100% over 33bp) GCGACCCCAGGTCAGGCGGGACTTGGAATTCTCGGGTGCCAAGGAACTCCA 8 0.2 RNA PCR Primer, Index 1 (100% over 28bp) CACGTCTGCCTGGGTGTCACGCTGGAATTCTCGGGTGCCAAGGAACTCCAG 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 29bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTTGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit GGGGTTGTAGCTCATATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGT 7 0.17500000000000002 RNA PCR Primer, Index 1 (97% over 35bp) GTGGGAATGAACATTATGAGATGGAATTCTCGGGTGCCAAGGAACTCCAGT 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 30bp) TCCGTTGTCGTCCAGCGGTTAGGATATCTGGCTGGAATTCTCGGGTGCCAA 7 0.17500000000000002 No Hit GGCATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGA 6 0.15 RNA PCR Primer, Index 1 (100% over 22bp) CCCATGTCGCTCCGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 6 0.15 RNA PCR Primer, Index 1 (100% over 31bp) GCCTTGGTGGTGAAATGGTAGACACGCGAGACTCATGGAATTCTCGGGTGC 6 0.15 No Hit TGCAGCTGAGGCATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGG 5 0.125 No Hit AGGGATGTAGCGCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACG 5 0.125 RNA PCR Primer, Index 6 (100% over 34bp) GAAAAATAGCTCGACGCCAGGATGTGGAATTCTCGGGTGCCAAGGAACTCC 5 0.125 RNA PCR Primer, Index 1 (100% over 27bp) GTCGGGATAGCTCAGCATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACG 5 0.125 RNA PCR Primer, Index 6 (100% over 34bp) GCCGCCATGGTGAAATCGGTAGACACGCTGCTCTTTGGAATTCTCGGGTGC 5 0.125 No Hit CCTCCTGGGAAGTCCTCGTGTTGCACCCCTTGGAATTCTCGGGTGCCAAGG 5 0.125 Illumina Small RNA Adapter 2 (100% over 21bp) ATCCGGTTAGGATCGATCTAAACCAGCCTGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) AACGACTCTCGGCAACGGATATCTCGGCTTGGAATTCTCGGGTGCCAAGGA 5 0.125 RNA PCR Primer, Index 1 (100% over 22bp) GCGGATGTAGCCAAGTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGTCA 5 0.125 RNA PCR Primer, Index 1 (100% over 32bp) ATTCAGCCCCATGTCGCTCCGATTCGTTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) GCGGATATAGTCGAATGGTAAAATTTCTCTTTGCTGGAATTCTCGGGTGCC 5 0.125 No Hit CAGCCCCATGTCGCTCCGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCC 5 0.125 RNA PCR Primer, Index 1 (100% over 27bp) GTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGGAATTCTCGGGTGCCAA 5 0.125 No Hit GGCGGATGTAGCCAAGTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGTC 5 0.125 RNA PCR Primer, Index 1 (100% over 31bp) TTGGACTGAAGGGAGCTCCCTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 5 0.125 RNA PCR Primer, Index 1 (100% over 31bp) AGTTACTAATTCATGATCTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA 5 0.125 RNA PCR Primer, Index 1 (100% over 28bp) CTGAGGCATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCA 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 0.6 0.0 0.0 0.0 2 0.0 0.6 0.0 0.0 0.0 3 0.0 0.6 0.0 0.0 0.0 4 0.0 0.6 0.0 0.0 0.0 5 0.0 0.6 0.0 0.0 0.0 6 0.0 0.6 0.0 0.0 0.0 7 0.0 0.625 0.0 0.0 0.0 8 0.0 0.65 0.0 0.0 0.0 9 0.0 0.725 0.0 0.0 0.0 10 0.0 0.775 0.0 0.0 0.0 11 0.0 0.85 0.0 0.0 0.0 12 0.0 0.9 0.0 0.0 0.0 13 0.0 0.975 0.0 0.0 0.0 14 0.0 1.075 0.0 0.0 0.0 15 0.0 1.325 0.0 0.0 0.0 16 0.0 1.7 0.0 0.0 0.0 17 0.0 3.525 0.0 0.0 0.0 18 0.0 4.525 0.0 0.0 0.0 19 0.0 5.475 0.0 0.0 0.0 20 0.0 8.2 0.0 0.0 0.0 21 0.0 11.475 0.0 0.0 0.0 22 0.0 19.5 0.0 0.0 0.0 23 0.0 24.45 0.0 0.0 0.0 24 0.0 30.275 0.0 0.0 0.0 25 0.0 42.675 0.0 0.0 0.0 26 0.0 46.25 0.0 0.0 0.0 27 0.0 49.025 0.0 0.0 0.0 28 0.0 52.275 0.0 0.0 0.0 29 0.0 55.4 0.0 0.0 0.0 30 0.0 61.9 0.0 0.0 0.0 31 0.0 64.525 0.0 0.0 0.0 32 0.0 67.525 0.0 0.0 0.0 33 0.0 72.425 0.0 0.0 0.0 34 0.0 81.85 0.0 0.0 0.0 35 0.0 87.175 0.0 0.0 0.0 36 0.0 91.8 0.0 0.0 0.0 37 0.0 94.7 0.0 0.0 0.0 38 0.0 95.75 0.0 0.0 0.0 39 0.0 96.475 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AAACCAG 20 6.085455E-4 45.189873 20 CGCCTTG 20 6.085455E-4 45.189873 29 TTGTAGT 20 6.085455E-4 45.189873 5 CCGCCTT 20 6.085455E-4 45.189873 28 GTATTCC 20 6.085455E-4 45.189873 22 AGTATTC 20 6.085455E-4 45.189873 21 AGTATAG 20 6.085455E-4 45.189873 9 TTCCCGC 20 6.085455E-4 45.189873 25 CCCGCCT 20 6.085455E-4 45.189873 27 AACCAGC 20 6.085455E-4 45.189873 21 TAGTATA 20 6.085455E-4 45.189873 8 TGTAGTA 20 6.085455E-4 45.189873 6 TATTCCC 20 6.085455E-4 45.189873 23 TCCCGCC 20 6.085455E-4 45.189873 26 CGTTGTA 20 6.085455E-4 45.189873 3 ATTCCCG 20 6.085455E-4 45.189873 24 GTAGTAT 20 6.085455E-4 45.189873 7 CCGGTTA 20 6.085455E-4 45.189873 3 GTTGTAG 20 6.085455E-4 45.189873 4 ACCAGCC 20 6.085455E-4 45.189873 22 >>END_MODULE Rejected 512430 READS because READLEN < 1 Read 512430 spots for SRR7472589.sra Written 512430 spots for SRR7472589.sra Rejected 512430 READS because READLEN < 1 Read 512430 spots for SRR7472589.sra Written 512430 spots for SRR7472589.sra Rejected 512430 READS because READLEN < 1 Read 512430 spots for SRR7472589.sra Written 512430 spots for SRR7472589.sra Rejected 512430 READS because READLEN < 1 Read 512430 spots for SRR7472589.sra Written 512430 spots for SRR7472589.sra Rejected 512430 READS because READLEN < 1 Read 512430 spots for SRR7472589.sra Written 512430 spots for SRR7472589.sra Rejected 512430 READS because READLEN < 1 Read 512430 spots for SRR7472589.sra Written 512430 spots for SRR7472589.sra Rejected 512430 READS because READLEN < 1 Read 512430 spots for SRR7472589.sra Written 512430 spots for SRR7472589.sra Rejected 512430 READS because READLEN < 1 Read 512430 spots for SRR7472589.sra Written 512430 spots for SRR7472589.sra Rejected 512430 READS because READLEN < 1 Read 512430 spots for SRR7472589.sra Written 512430 spots for SRR7472589.sra Rejected 512430 READS because READLEN < 1 Read 512430 spots for SRR7472589.sra Written 512430 spots for SRR7472589.sra Rejected 512430 READS because READLEN < 1 Read 512430 spots for SRR7472589.sra Written 512430 spots for SRR7472589.sra Rejected 512430 READS because READLEN < 1 Read 512430 spots for SRR7472589.sra Written 512430 spots for SRR7472589.sra Rejected 512430 READS because READLEN < 1 Read 512430 spots for SRR7472589.sra Written 512430 spots for SRR7472589.sra Rejected 512434 READS because READLEN < 1 Read 512434 spots for SRR7472589.sra Written 512434 spots for SRR7472589.sra Rejected 512430 READS because READLEN < 1 Read 512430 spots for SRR7472589.sra Written 512430 spots for SRR7472589.sra Rejected 512430 READS because READLEN < 1 Read 512430 spots for SRR7472589.sra Written 512430 spots for SRR7472589.sra Rejected 512430 READS because READLEN < 1 Read 512430 spots for SRR7472589.sra Written 512430 spots for SRR7472589.sra Rejected 512430 READS because READLEN < 1 Read 512430 spots for SRR7472589.sra Written 512430 spots for SRR7472589.sra Rejected 512430 READS because READLEN < 1 Read 512430 spots for SRR7472589.sra Written 512430 spots for SRR7472589.sra Rejected 512430 READS because READLEN < 1 Read 512430 spots for SRR7472589.sra Written 512430 spots for SRR7472589.sra SRR ids: ['SRR7472589.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_x4l8qbg0 SRR7472589.sra spots: 10248604 blocks: [[1, 512430], [512431, 1024860], [1024861, 1537290], [1537291, 2049720], [2049721, 2562150], [2562151, 3074580], [3074581, 3587010], [3587011, 4099440], [4099441, 4611870], [4611871, 5124300], [5124301, 5636730], [5636731, 6149160], [6149161, 6661590], [6661591, 7174020], [7174021, 7686450], [7686451, 8198880], [8198881, 8711310], [8711311, 9223740], [9223741, 9736170], [9736171, 10248604]] SRR7472589 file size 1439526 SRR7472589 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 SRR7472589 SRR7472589_1.fastq Input file: SRR7472589_1.fastq trimmed: SRR7472589-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 Feb 13 18:11:35 2025 >> started Thu Feb 13 18:11:39 2025 >> done (4.059s) 10248604 reads processed; of these: 6782 ( 0.07%) short reads filtered out after trimming by size control 12710 ( 0.12%) empty reads filtered out after trimming by size control 10229112 (99.81%) reads available; of these: 36006 ( 0.35%) trimmed reads available after processing 10193106 (99.65%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 206 0.00% 19 284 0.00% 20 216 0.00% 21 264 0.00% 22 234 0.00% 23 203 0.00% 24 211 0.00% 25 276 0.00% 26 312 0.00% 27 257 0.00% 28 249 0.00% 29 317 0.00% 30 243 0.00% 31 261 0.00% 32 210 0.00% 33 252 0.00% 34 285 0.00% 35 439 0.00% 36 399 0.00% 37 387 0.00% 38 456 0.00% 39 608 0.01% 40 726 0.01% 41 671 0.01% 42 1012 0.01% 43 1354 0.01% 44 1216 0.01% 45 1649 0.02% 46 1764 0.02% 47 2663 0.03% 48 3265 0.03% 49 4096 0.04% 50 11021 0.11% 51 10193106 99.65% 10229112 reads passed initial QC criterion=sequence-density sequence-density=96.69 sequence-density-rank=1 fanout-score=28.74 fanout-score-rank=1 prefix-density=97.60 prefix-fanout=28.5 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTAGAGATCTCGTATGCCG criterion=fanout-score sequence-density=96.69 sequence-density-rank=1 fanout-score=28.74 fanout-score-rank=1 prefix-density=97.60 prefix-fanout=28.5 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTAGAGATCTCGTATGCCG 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTAGAGATCTCGTATGCCG -o SRR7472589 - Input file: STDIN trimmed: SRR7472589-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTAGAGATCTCGTATGCCG -- 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 Feb 13 18:11:54 2025 >> started Thu Feb 13 18:12:01 2025 >> done (7.197s) 10018203 reads processed; of these: 410674 ( 4.10%) short reads filtered out after trimming by size control 48848 ( 0.49%) empty reads filtered out after trimming by size control 9558681 (95.41%) reads available; of these: 9456292 (98.93%) trimmed reads available after processing 102389 ( 1.07%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 117816 1.23% 19 285355 2.99% 20 312962 3.27% 21 879746 9.20% 22 542359 5.67% 23 532224 5.57% 24 1181749 12.36% 25 417640 4.37% 26 307157 3.21% 27 315572 3.30% 28 291820 3.05% 29 722107 7.55% 30 256273 2.68% 31 284290 2.97% 32 476238 4.98% 33 952122 9.96% 34 527171 5.52% 35 447335 4.68% 36 290387 3.04% 37 115197 1.21% 38 76190 0.80% 39 41982 0.44% 40 31262 0.33% 41 19162 0.20% 42 16271 0.17% 43 7545 0.08% 44 4643 0.05% 45 3003 0.03% 46 2140 0.02% 47 1582 0.02% 48 2015 0.02% 49 373 0.00% 50 595 0.01% 51 96398 1.01% criterion=sequence-density sequence-density=5.77 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=16 prefix-density=0.00 prefix-fanout=1.0 sequence=GTCGTTGTAGTATAGTGGTGAGTATTCCCGCCTGTCA criterion=fanout-score sequence-density=0.23 sequence-density-rank=21 fanout-score=9.36 fanout-score-rank=1 prefix-density=1.64 prefix-fanout=1.3 sequence=GAAGGGAGCTCCCTT Started job on | Feb 13 18:12:14 Started mapping on | Feb 13 18:12:14 Finished on | Feb 13 18:12:33 Mapping speed, Million of reads per hour | 1851.08 Number of input reads | 9769590 Average input read length | 28 UNIQUE READS: Uniquely mapped reads number | 3733324 Uniquely mapped reads % | 38.21% Average mapped length | 27.34 Number of splices: Total | 26767 Number of splices: Annotated (sjdb) | 15078 Number of splices: GT/AG | 24500 Number of splices: GC/AG | 323 Number of splices: AT/AC | 81 Number of splices: Non-canonical | 1863 Mismatch rate per base, % | 0.26% Deletion rate per base | 0.01% Deletion average length | 1.12 Insertion rate per base | 0.00% Insertion average length | 1.08 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 2984245 % of reads mapped to multiple loci | 30.55% Number of reads mapped to too many loci | 2649851 % of reads mapped to too many loci | 27.12% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.99% % of reads unmapped: other | 1.12% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 3052021 3052021 3052021 N_multimapping 2984245 2984245 2984245 N_noFeature 2186235 2244200 3112825 N_ambiguous 564564 1682 359 UnstrandedReadsAssigned:982525 PositiveStrandReadsAssigned:1487442 NegativeStrandReadsAssigned:620140 Dataset is classified unstranded MeadianReadLen=27 20thPercentileLength=22 echo kmer=19 SRR7472589 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: 52,400 [index] number of k-mers: 59,590,899 [index] number of equivalence classes: 293,668 [quant] running in single-end mode [quant] will process file 1: SRR7472589-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 9,769,590 reads, 3,492,117 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,128 rounds 52401 SRR7472589.ke.tsv 34699 SRR7472589.se.tsv 87100 total ==> SRR7472589.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 29.2889 3.43388 Potri.005G024800.1.v4.1 1035 936 4.01215 0.964402 Potri.004G059700.1.v4.1 961 862 0 0 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 7.40181 0.585552 Potri.016G087400.1.v4.1 270 171 7 9.20998 Potri.015G069301.1.v4.1 564 465 1 0.483842 Potri.010G195200.1.v4.1 1773 1674 0 0 Potri.012G127500.1.v4.1 977 878 21 5.38123 ==> SRR7472589.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 0 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 3 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 1 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 0 SRR7472589 completed mapping pipeline successfully