Starting /dee2/code/volunteer_pipeline.sh SRR7472591 current disk space = 3087846604800 free memory = 1542196064 SRR7472591 SRAfilesize f35d47af8e9bf1b176060db60ece821f SRR7472591.sra SRR7472591.sra file validated SRR7472591 is single end SRR7472591 is conventional basespace SRR7472591 read1 length is 51 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7472591_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 30.657 32.0 32.0 32.0 27.0 32.0 2 31.366 32.0 32.0 32.0 32.0 32.0 3 31.336 32.0 32.0 32.0 32.0 32.0 4 31.48825 32.0 32.0 32.0 32.0 32.0 5 31.42425 32.0 32.0 32.0 32.0 32.0 6 35.319 37.0 37.0 37.0 32.0 37.0 7 35.5715 37.0 37.0 37.0 32.0 37.0 8 35.49925 37.0 37.0 37.0 32.0 37.0 9 35.201 37.0 37.0 37.0 32.0 37.0 10 35.639 37.0 37.0 37.0 32.0 37.0 11 35.4515 37.0 37.0 37.0 32.0 37.0 12 35.66125 37.0 37.0 37.0 32.0 37.0 13 35.52375 37.0 37.0 37.0 32.0 37.0 14 35.17825 37.0 37.0 37.0 32.0 37.0 15 35.71825 37.0 37.0 37.0 32.0 37.0 16 35.57775 37.0 37.0 37.0 32.0 37.0 17 35.72875 37.0 37.0 37.0 32.0 37.0 18 35.425 37.0 37.0 37.0 32.0 37.0 19 35.09925 37.0 37.0 37.0 32.0 37.0 20 35.0625 37.0 37.0 37.0 32.0 37.0 21 34.94525 37.0 37.0 37.0 32.0 37.0 22 35.113 37.0 37.0 37.0 32.0 37.0 23 35.46 37.0 37.0 37.0 32.0 37.0 24 35.31225 37.0 37.0 37.0 32.0 37.0 25 35.2775 37.0 37.0 37.0 32.0 37.0 26 35.60325 37.0 37.0 37.0 32.0 37.0 27 35.7915 37.0 37.0 37.0 37.0 37.0 28 35.46825 37.0 37.0 37.0 32.0 37.0 29 35.477 37.0 37.0 37.0 32.0 37.0 30 35.70625 37.0 37.0 37.0 32.0 37.0 31 35.53 37.0 37.0 37.0 32.0 37.0 32 35.533 37.0 37.0 37.0 32.0 37.0 33 35.54875 37.0 37.0 37.0 32.0 37.0 34 35.70325 37.0 37.0 37.0 37.0 37.0 35 35.6545 37.0 37.0 37.0 37.0 37.0 36 35.7165 37.0 37.0 37.0 37.0 37.0 37 35.71875 37.0 37.0 37.0 37.0 37.0 38 35.51925 37.0 37.0 37.0 32.0 37.0 39 35.153 37.0 37.0 37.0 32.0 37.0 40 35.3295 37.0 37.0 37.0 32.0 37.0 41 35.491 37.0 37.0 37.0 32.0 37.0 42 35.2395 37.0 37.0 37.0 32.0 37.0 43 35.475 37.0 37.0 37.0 32.0 37.0 44 35.6425 37.0 37.0 37.0 32.0 37.0 45 35.513 37.0 37.0 37.0 32.0 37.0 46 35.297 37.0 37.0 37.0 32.0 37.0 47 35.298 37.0 37.0 37.0 32.0 37.0 48 35.495 37.0 37.0 37.0 32.0 37.0 49 35.19325 37.0 37.0 37.0 32.0 37.0 50 35.4435 37.0 37.0 37.0 32.0 37.0 51 34.86625 37.0 37.0 37.0 32.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 17 2.0 18 0.0 19 0.0 20 3.0 21 1.0 22 11.0 23 10.0 24 11.0 25 15.0 26 28.0 27 22.0 28 41.0 29 44.0 30 57.0 31 77.0 32 120.0 33 185.0 34 414.0 35 1288.0 36 1671.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 32.925 28.249999999999996 24.15 14.674999999999999 2 29.925 22.5 24.4 23.175 3 29.725 22.225 19.15 28.9 4 43.175000000000004 22.225 14.424999999999999 20.175 5 30.0 29.925 21.975 18.099999999999998 6 24.36740890688259 27.327935222672068 29.630566801619434 18.67408906882591 7 38.525 24.95 21.475 15.049999999999999 8 23.5 25.8 36.375 14.325 9 25.825 39.675 17.625 16.875 10 41.425 25.7 16.35 16.525000000000002 11 27.075 20.724999999999998 25.874999999999996 26.325 12 28.925 21.75 27.200000000000003 22.125 13 26.875 18.55 24.075 30.5 14 23.0 42.975 17.45 16.575 15 38.05 31.324999999999996 16.6 14.025000000000002 16 24.7 29.775000000000002 25.025 20.5 17 30.425 24.175 28.499999999999996 16.900000000000002 18 40.0 20.599999999999998 23.200000000000003 16.2 19 30.575000000000003 27.125 26.275 16.025 20 27.325 31.974999999999998 24.775 15.925 21 23.5 36.65 22.400000000000002 17.45 22 28.475 28.575 26.775 16.175 23 29.925 23.575 29.475 17.025000000000002 24 23.525 31.075000000000003 24.625 20.775 25 22.680670167541887 26.78169542385596 37.634408602150536 12.903225806451612 26 26.825 24.025 32.225 16.925 27 30.55763940985246 19.854963740935233 27.906976744186046 21.680420105026258 28 26.43821910955478 24.387193596798397 28.4392196098049 20.735367683841922 29 26.988494247123562 22.11105552776388 26.43821910955478 24.462231115557778 30 28.95723930982746 17.104276069017253 37.7344336084021 16.204051012753187 31 28.75718929732433 13.528382095523881 31.357839459864966 26.356589147286826 32 31.45786446611653 11.852963240810203 24.50612653163291 32.18304576144036 33 28.80720180045011 11.677919479869967 35.23380845211303 24.281070267566893 34 33.50837709427357 14.628657164291074 28.557139284821204 23.305826456614152 35 41.86046511627907 15.603900975243812 23.355838959739934 19.179794948737182 36 47.398699349674835 13.556778389194598 19.484742371185593 19.559779889944974 37 41.74587293646824 19.834917458729365 15.682841420710355 22.736368184092047 38 30.107526881720432 27.831957989497376 21.180295073768445 20.880220055013755 39 32.032032032032035 28.653653653653656 18.06806806806807 21.246246246246248 40 28.32832832832833 24.1991991991992 18.243243243243242 29.22922922922923 41 27.402402402402405 22.44744744744745 19.01901901901902 31.131131131131127 42 27.2022022022022 29.77977977977978 16.866866866866868 26.151151151151154 43 24.312156078039017 32.36618309154578 11.255627813906953 32.06603301650826 44 34.50950950950951 31.056056056056057 10.885885885885886 23.54854854854855 45 37.05926481620405 26.106526631657918 11.377844461115279 25.456364091022753 46 28.182045511377847 28.232058014503625 17.95448862215554 25.63140785196299 47 21.155288822205552 30.732683170792697 16.504126031507877 31.607901975493874 48 23.53088272068017 27.70692673168292 13.028257064266066 35.73393348337085 49 18.95473868467117 25.131282820705174 20.130032508127034 35.783945986496626 50 22.67267267267267 21.746746746746748 15.465465465465467 40.11511511511511 51 15.950000000000001 28.050000000000004 21.45 34.55 >>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 0.5 20 1.0 21 0.5 22 0.0 23 0.5 24 1.0 25 0.5 26 0.5 27 1.0 28 1.5 29 2.0 30 1.0 31 0.0 32 0.5 33 1.0 34 4.0 35 7.0 36 12.0 37 17.0 38 22.0 39 27.0 40 47.0 41 67.0 42 95.0 43 123.0 44 152.5 45 182.0 46 218.5 47 255.0 48 345.0 49 435.0 50 669.0 51 903.0 52 772.5 53 642.0 54 559.0 55 476.0 56 497.0 57 518.0 58 321.5 59 125.0 60 114.0 61 103.0 62 89.0 63 75.0 64 52.5 65 30.0 66 17.5 67 5.0 68 4.0 69 3.0 70 1.5 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 0.5 94 1.0 95 0.5 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 1.2 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 0.025 26 0.0 27 0.025 28 0.05 29 0.05 30 0.025 31 0.025 32 0.025 33 0.025 34 0.025 35 0.025 36 0.05 37 0.05 38 0.025 39 0.1 40 0.1 41 0.1 42 0.1 43 0.05 44 0.1 45 0.025 46 0.025 47 0.025 48 0.025 49 0.025 50 0.1 51 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 51 4000.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 60.9 #Duplication Level Percentage of deduplicated Percentage of total 1 88.91625615763546 54.15 2 5.377668308702791 6.550000000000001 3 1.3957307060755337 2.55 4 0.9031198686371099 2.1999999999999997 5 0.41050903119868637 1.25 6 0.49261083743842365 1.7999999999999998 7 0.20525451559934318 0.8750000000000001 8 0.08210180623973727 0.4 9 0.24630541871921183 1.35 >10 1.7651888341543513 21.0 >50 0.20525451559934318 7.875 >100 0.0 0.0 >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 76 1.9 No Hit CTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 66 1.6500000000000001 RNA PCR Primer, Index 1 (100% over 28bp) GGGGATGTAGCTCAAATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGT 64 1.6 RNA PCR Primer, Index 1 (97% over 35bp) TTTGGATTGAAGGGAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 55 1.375 RNA PCR Primer, Index 1 (100% over 31bp) GGGCCTGTAGCTCAGAGGATGGAATTCTCGGGTGCCAAGGAACTCCAGTCA 54 1.35 RNA PCR Primer, Index 1 (100% over 32bp) GTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTTGGAATTCTCGGGTGCCA 40 1.0 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGGA 39 0.975 RNA PCR Primer, Index 1 (100% over 22bp) GCGCCTGTAGCTCAGTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGTCA 32 0.8 RNA PCR Primer, Index 1 (100% over 32bp) CGCGGGGTAGAGCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACG 31 0.775 RNA PCR Primer, Index 6 (100% over 34bp) AACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGT 29 0.7250000000000001 RNA PCR Primer, Index 1 (100% over 30bp) ACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 28 0.7000000000000001 RNA PCR Primer, Index 1 (100% over 31bp) TGCGTAGAGATCGGAAAGAACACCAACTGGAATTCTCGGGTGCCAAGGAAC 26 0.65 RNA PCR Primer, Index 1 (100% over 24bp) CATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAAC 26 0.65 RNA PCR Primer, Index 1 (100% over 24bp) AGTTACTAATTCATGATCTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG 25 0.625 RNA PCR Primer, Index 1 (100% over 29bp) TCTCGGACCAGGCTTCATTCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT 25 0.625 RNA PCR Primer, Index 1 (100% over 30bp) GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTTGGAATTCTCGGGTGCC 24 0.6 No Hit GTCGGGATAGCTCAGCATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACG 24 0.6 RNA PCR Primer, Index 6 (100% over 34bp) TAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAG 24 0.6 RNA PCR Primer, Index 1 (100% over 29bp) GTCGGGATAGCTCAGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGT 24 0.6 RNA PCR Primer, Index 1 (97% over 35bp) TCCGTTGTCGTCCAGCGGTTAGGATATCTGGCTTGGAATTCTCGGGTGCCA 23 0.575 No Hit TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT 23 0.575 RNA PCR Primer, Index 1 (100% over 30bp) TCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTC 22 0.5499999999999999 RNA PCR Primer, Index 1 (100% over 26bp) GGGGATGTAGCTCATATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGT 20 0.5 RNA PCR Primer, Index 1 (97% over 35bp) AGGGATGTAGCGCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACG 20 0.5 RNA PCR Primer, Index 6 (100% over 34bp) GGGGATGTAGCTCAGATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGT 20 0.5 RNA PCR Primer, Index 1 (97% over 35bp) TCCTCAGTAGCTCAGTGGTAGAGCGGTCGGCTTGGAATTCTCGGGTGCCAA 20 0.5 No Hit GCGGATATAGTCGAATGGTAAAATTTCTCTTTGCCTGGAATTCTCGGGTGC 19 0.475 No Hit TGCGTAGAGATCGGAAAGAACACCATGGAATTCTCGGGTGCCAAGGAACTC 19 0.475 RNA PCR Primer, Index 1 (100% over 26bp) ATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACT 18 0.44999999999999996 RNA PCR Primer, Index 1 (100% over 25bp) GCGTAGAGATCGGAAAGAACACCAACTGGAATTCTCGGGTGCCAAGGAACT 17 0.42500000000000004 RNA PCR Primer, Index 1 (100% over 25bp) CGCGGGGTAGAGCAGCTTGGTAGCTCGCAAGGCTCTGGAATTCTCGGGTGC 17 0.42500000000000004 No Hit AGCGTGGAGGTTCGAGTCCTCTTCAAGGCACCATGGAATTCTCGGGTGCCA 16 0.4 No Hit TCTCATGGAGAGTTCGATCCTGGCTTGGAATTCTCGGGTGCCAAGGAACTC 15 0.375 RNA PCR Primer, Index 1 (100% over 26bp) CCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCC 14 0.35000000000000003 RNA PCR Primer, Index 1 (100% over 27bp) TGAGGCATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAA 14 0.35000000000000003 No Hit CGATGGATACTGGGCGCTGTGCGTATGGAATTCTCGGGTGCCAAGGAACTC 13 0.325 RNA PCR Primer, Index 1 (100% over 26bp) ATCCGGTTAGGATCGATCTAAACCAGCCCTGGAATTCTCGGGTGCCAAGGA 13 0.325 RNA PCR Primer, Index 1 (100% over 22bp) GCATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAA 12 0.3 RNA PCR Primer, Index 1 (100% over 23bp) TGCGTAGAGATCGGAAAGATGGAATTCTCGGGTGCCAAGGAACTCCAGTCA 12 0.3 RNA PCR Primer, Index 1 (100% over 32bp) GAGGCATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAG 12 0.3 No Hit TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTTTCGATCTCGTATGCC 12 0.3 RNA PCR Primer, Index 21 (100% over 51bp) GCGGATATAGTCGAATGGTAAAATTTCTCTTTTGGAATTCTCGGGTGCCAA 11 0.27499999999999997 No Hit ATGCGTAGAGATCGGAAAGAACACCAACTGGAATTCTCGGGTGCCAAGGAA 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 23bp) GGGGTTGTAGCTCATATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGT 10 0.25 RNA PCR Primer, Index 1 (97% over 35bp) GACCGCATAGCGCAGTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGTCA 10 0.25 RNA PCR Primer, Index 1 (100% over 32bp) CCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTT 10 0.25 RNA PCR Primer, Index 9 (97% over 36bp) GCGTAGAGATCGGAAAGAACACCATGGAATTCTCGGGTGCCAAGGAACTCC 10 0.25 RNA PCR Primer, Index 1 (100% over 27bp) AGGCATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGG 10 0.25 Illumina Small RNA Adapter 2 (100% over 21bp) TAAACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGT 9 0.22499999999999998 No Hit TTTGGATTGAAGGGAGCTCTATGGAATTCTCGGGTGCCAAGGAACTCCAGT 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 30bp) GGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTTTC 9 0.22499999999999998 RNA PCR Primer, Index 21 (100% over 38bp) ACGATGGATACTGGGCGCTGTGCGTATGGAATTCTCGGGTGCCAAGGAACT 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 25bp) GCGGATATAGTCGAATGGTAAAATTTCTCTTTGCTGGAATTCTCGGGTGCC 9 0.22499999999999998 No Hit GGCGGATGTAGCCAAGTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGTC 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 31bp) GGGGATGTAGCTCAATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTT 8 0.2 RNA PCR Primer, Index 9 (97% over 36bp) CGCGGGGTAGAGCAGCTTGGTAGCTCGCAAGGCTCATGGAATTCTCGGGTG 8 0.2 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCCA 7 0.17500000000000002 No Hit GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGTGGAATTCTCGGGTGC 7 0.17500000000000002 No Hit GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGTTGGAATTCTCGGGTG 7 0.17500000000000002 No Hit AAAGGATTGAGCCGAATTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACG 7 0.17500000000000002 RNA PCR Primer, Index 6 (100% over 34bp) GTCGGGATAGCTCAGCAGGTAGAGCAGAGGACTGATGGAATTCTCGGGTGC 7 0.17500000000000002 No Hit GGTCGAGGGCACGTCTGCCTGGGTGTCACGCTGGAATTCTCGGGTGCCAAG 6 0.15 No Hit TGTGTTCTCAGGTCGCCCCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT 6 0.15 RNA PCR Primer, Index 1 (100% over 30bp) TGCGTAGAGATCGGAAAGAACATGGAATTCTCGGGTGCCAAGGAACTCCAG 6 0.15 RNA PCR Primer, Index 1 (100% over 29bp) CCCGTGCAGTGCTGTAGCTATGGAATTCTCGGGTGCCAAGGAACTCCAGTC 6 0.15 RNA PCR Primer, Index 1 (100% over 31bp) AATGCGTAGAGATCGGAAAGATGGAATTCTCGGGTGCCAAGGAACTCCAGT 6 0.15 RNA PCR Primer, Index 1 (100% over 30bp) ATGCGTAGAGATCGGAAAGAACACCATGGAATTCTCGGGTGCCAAGGAACT 6 0.15 RNA PCR Primer, Index 1 (100% over 25bp) GCCGCCATGGTGAAATCGGTAGACACGCTGCTCTTTGGAATTCTCGGGTGC 6 0.15 No Hit AATGCGTAGAGATCGGAAAGAACACCAACTGGAATTCTCGGGTGCCAAGGA 6 0.15 RNA PCR Primer, Index 1 (100% over 22bp) GAGCGTGGAGGTTCGAGTCCTCTTCAAGGCACCATGGAATTCTCGGGTGCC 6 0.15 No Hit GGTGGCTGTAGTTTAGTGGTAAGAATTCCACGTTTGGAATTCTCGGGTGCC 6 0.15 No Hit TCGACCCGTGCAGTGCTGTAGCTATGGAATTCTCGGGTGCCAAGGAACTCC 6 0.15 RNA PCR Primer, Index 1 (100% over 27bp) AATCATGTGGGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTT 6 0.15 RNA PCR Primer, Index 9 (97% over 36bp) TGCGATGATGATAGAACAGTAGGTTATGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) ATGCGATGATGATAGAACAGTAGGTTATGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) AACGATGGATACTGGGCGCTGTGCGTATGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) GTTTGGAACCCTGAACAGACTGCCGGTGATGGAATTCTCGGGTGCCAAGGA 5 0.125 RNA PCR Primer, Index 1 (100% over 22bp) AGGGATGTAGCGCAGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGT 5 0.125 RNA PCR Primer, Index 1 (97% over 35bp) GCCGCCATGGTGAAATCGGTAGACACGCTGCTCTTATGGAATTCTCGGGTG 5 0.125 No Hit ACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGT 5 0.125 RNA PCR Primer, Index 1 (97% over 35bp) GCGTAGAGATCGGAAAGATGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC 5 0.125 RNA PCR Primer, Index 1 (100% over 33bp) AAGCTGTGAGGAAATCTGTGCTCATTGGAATTCTCGGGTGCCAAGGAACTC 5 0.125 RNA PCR Primer, Index 1 (100% over 26bp) GTCGGGATAGCTCAGCAGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCCA 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 0.35 0.0 0.0 0.0 2 0.0 0.35 0.0 0.0 0.0 3 0.0 0.35 0.0 0.0 0.0 4 0.0 0.35 0.0 0.0 0.0 5 0.0 0.35 0.0 0.0 0.0 6 0.0 0.35 0.0 0.0 0.0 7 0.0 0.35 0.0 0.0 0.0 8 0.0 0.375 0.0 0.0 0.0 9 0.0 0.4 0.0 0.0 0.0 10 0.0 0.425 0.0 0.0 0.0 11 0.0 0.575 0.0 0.0 0.0 12 0.0 0.675 0.0 0.0 0.0 13 0.0 0.875 0.0 0.0 0.0 14 0.0 1.4 0.0 0.0 0.0 15 0.0 2.175 0.0 0.0 0.0 16 0.0 3.5 0.0 0.0 0.0 17 0.0 8.8 0.0 0.0 0.0 18 0.0 12.225 0.0 0.0 0.0 19 0.0 13.95 0.0 0.0 0.0 20 0.0 19.025 0.0 0.0 0.0 21 0.0 24.425 0.0 0.0 0.0 22 0.0 31.85 0.0 0.0 0.0 23 0.0 37.7 0.0 0.0 0.0 24 0.0 43.475 0.0 0.0 0.0 25 0.0 53.85 0.0 0.0 0.0 26 0.0 59.275 0.0 0.0 0.0 27 0.0 63.675 0.0 0.0 0.0 28 0.0 67.85 0.0 0.0 0.0 29 0.0 70.775 0.0 0.0 0.0 30 0.0 74.15 0.0 0.0 0.0 31 0.0 75.975 0.0 0.0 0.0 32 0.0 78.325 0.0 0.0 0.0 33 0.0 81.275 0.0 0.0 0.0 34 0.0 87.3 0.0 0.0 0.0 35 0.0 90.175 0.0 0.0 0.0 36 0.0 92.55 0.0 0.0 0.0 37 0.0 93.7 0.0 0.0 0.0 38 0.0 94.125 0.0 0.0 0.0 39 0.0 94.275 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AGCTCAG 35 8.797542E-8 44.850002 9 TAGCTCA 60 0.0 44.850002 8 GGGATGT 35 8.797542E-8 44.850002 2 AAATGGA 30 1.7104339E-6 44.850002 14 AAGTATT 20 6.3262763E-4 44.85 20 GCCTTGG 25 3.3006167E-5 44.85 30 AGCTCAA 25 3.3006167E-5 44.85 9 CGCCTTG 25 3.3006167E-5 44.85 29 TTGTAGT 20 6.3262763E-4 44.85 5 GTCGTTG 20 6.3262763E-4 44.85 1 TGGTAAG 20 6.3262763E-4 44.85 16 CCTGTAG 20 6.3262763E-4 44.85 4 TAAGTAT 20 6.3262763E-4 44.85 19 CCGCCTT 25 3.3006167E-5 44.85 28 AGTGGTA 20 6.3262763E-4 44.85 14 GTATTCC 25 3.3006167E-5 44.85 22 AGTATTC 25 3.3006167E-5 44.85 21 GTATAGT 25 3.3006167E-5 44.85 10 AGTATAG 25 3.3006167E-5 44.85 9 TTCCCGC 25 3.3006167E-5 44.85 25 >>END_MODULE Rejected 913203 READS because READLEN < 1 Read 913203 spots for SRR7472591.sra Written 913203 spots for SRR7472591.sra Rejected 913203 READS because READLEN < 1 Read 913203 spots for SRR7472591.sra Written 913203 spots for SRR7472591.sra Rejected 913203 READS because READLEN < 1 Read 913203 spots for SRR7472591.sra Written 913203 spots for SRR7472591.sra Rejected 913203 READS because READLEN < 1 Read 913203 spots for SRR7472591.sra Written 913203 spots for SRR7472591.sra Rejected 913203 READS because READLEN < 1 Read 913203 spots for SRR7472591.sra Written 913203 spots for SRR7472591.sra Rejected 913203 READS because READLEN < 1 Read 913203 spots for SRR7472591.sra Written 913203 spots for SRR7472591.sra Rejected 913215 READS because READLEN < 1 Read 913215 spots for SRR7472591.sra Written 913215 spots for SRR7472591.sra Rejected 913203 READS because READLEN < 1 Read 913203 spots for SRR7472591.sra Written 913203 spots for SRR7472591.sra Rejected 913203 READS because READLEN < 1 Read 913203 spots for SRR7472591.sra Written 913203 spots for SRR7472591.sra Rejected 913203 READS because READLEN < 1 Read 913203 spots for SRR7472591.sra Written 913203 spots for SRR7472591.sra Rejected 913203 READS because READLEN < 1 Read 913203 spots for SRR7472591.sra Written 913203 spots for SRR7472591.sra Rejected 913203 READS because READLEN < 1 Read 913203 spots for SRR7472591.sra Written 913203 spots for SRR7472591.sra Rejected 913203 READS because READLEN < 1 Read 913203 spots for SRR7472591.sra Written 913203 spots for SRR7472591.sra Rejected 913203 READS because READLEN < 1 Read 913203 spots for SRR7472591.sra Written 913203 spots for SRR7472591.sra Rejected 913203 READS because READLEN < 1 Read 913203 spots for SRR7472591.sra Written 913203 spots for SRR7472591.sra Rejected 913203 READS because READLEN < 1 Read 913203 spots for SRR7472591.sra Written 913203 spots for SRR7472591.sra Rejected 913203 READS because READLEN < 1 Read 913203 spots for SRR7472591.sra Written 913203 spots for SRR7472591.sra Rejected 913203 READS because READLEN < 1 Read 913203 spots for SRR7472591.sra Written 913203 spots for SRR7472591.sra Rejected 913203 READS because READLEN < 1 Read 913203 spots for SRR7472591.sra Written 913203 spots for SRR7472591.sra Rejected 913203 READS because READLEN < 1 Read 913203 spots for SRR7472591.sra Written 913203 spots for SRR7472591.sra SRR ids: ['SRR7472591.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_dbcxazkd SRR7472591.sra spots: 18264072 blocks: [[1, 913203], [913204, 1826406], [1826407, 2739609], [2739610, 3652812], [3652813, 4566015], [4566016, 5479218], [5479219, 6392421], [6392422, 7305624], [7305625, 8218827], [8218828, 9132030], [9132031, 10045233], [10045234, 10958436], [10958437, 11871639], [11871640, 12784842], [12784843, 13698045], [13698046, 14611248], [14611249, 15524451], [15524452, 16437654], [16437655, 17350857], [17350858, 18264072]] SRR7472591 file size 2582356 SRR7472591 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 SRR7472591 SRR7472591_1.fastq Input file: SRR7472591_1.fastq trimmed: SRR7472591-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 18:33:03 2025 >> started Thu Feb 13 18:33:12 2025 >> done (9.770s) 18264072 reads processed; of these: 0 ( 0.00%) short reads filtered out after trimming by size control 0 ( 0.00%) empty reads filtered out after trimming by size control 18264072 (100.00%) reads available; of these: 234831 ( 1.29%) trimmed reads available after processing 18029241 (98.71%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 37 1 0.00% 38 0 0.00% 39 0 0.00% 40 3 0.00% 41 6 0.00% 42 12 0.00% 43 34 0.00% 44 87 0.00% 45 241 0.00% 46 708 0.00% 47 2294 0.01% 48 7670 0.04% 49 28449 0.16% 50 195326 1.07% 51 18029241 98.71% 18264072 reads passed initial QC criterion=sequence-density sequence-density=94.86 sequence-density-rank=1 fanout-score=27.29 fanout-score-rank=1 prefix-density=94.88 prefix-fanout=27.3 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTTTCGATCTCGTATGCCG criterion=fanout-score sequence-density=94.86 sequence-density-rank=1 fanout-score=27.29 fanout-score-rank=1 prefix-density=94.88 prefix-fanout=27.3 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTTTCGATCTCGTATGCCG 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTTTCGATCTCGTATGCCG -o SRR7472591 - Input file: STDIN trimmed: SRR7472591-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTTTCGATCTCGTATGCCG -- 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 18:33:37 2025 >> started Thu Feb 13 18:33:55 2025 >> done (17.723s) 17879565 reads processed; of these: 2301791 (12.87%) short reads filtered out after trimming by size control 130334 ( 0.73%) empty reads filtered out after trimming by size control 15447440 (86.40%) reads available; of these: 15140376 (98.01%) trimmed reads available after processing 307064 ( 1.99%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 455150 2.95% 19 1126639 7.29% 20 931577 6.03% 21 1624357 10.52% 22 1110574 7.19% 23 1070805 6.93% 24 1840304 11.91% 25 957055 6.20% 26 712672 4.61% 27 721377 4.67% 28 495301 3.21% 29 664631 4.30% 30 365412 2.37% 31 349919 2.27% 32 518225 3.35% 33 918888 5.95% 34 475583 3.08% 35 420963 2.73% 36 195273 1.26% 37 72865 0.47% 38 43116 0.28% 39 20313 0.13% 40 14943 0.10% 41 11289 0.07% 42 7620 0.05% 43 4070 0.03% 44 3352 0.02% 45 2589 0.02% 46 2496 0.02% 47 3043 0.02% 48 5724 0.04% 49 9857 0.06% 50 27288 0.18% 51 264170 1.71% criterion=sequence-density sequence-density=3.15 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=17 prefix-density=0.00 prefix-fanout=1.0 sequence=GTCGTTGTAGTATAGTGGTGAGTATTCCCGCCTGTCA criterion=fanout-score sequence-density=0.01 sequence-density-rank=37 fanout-score=27.19 fanout-score-rank=1 prefix-density=0.14 prefix-fanout=1.3 sequence=TGCCAAGGATGTTTTCATTAATCAAGAACGAAAGTTGGGGGCTCGAAGACGATCAGATACCGTCCTAGTCTCAACCATAAACGATGCCGACCAGGGATTGGCGGATGTTGCTTTTAGGACTCCGCCAGCACCTTATGAGAAATCAAAGT Started job on | Feb 13 18:34:09 Started mapping on | Feb 13 18:34:10 Finished on | Feb 13 18:34:47 Mapping speed, Million of reads per hour | 1540.41 Number of input reads | 15831947 Average input read length | 26 UNIQUE READS: Uniquely mapped reads number | 6751281 Uniquely mapped reads % | 42.64% Average mapped length | 25.17 Number of splices: Total | 56801 Number of splices: Annotated (sjdb) | 27101 Number of splices: GT/AG | 53126 Number of splices: GC/AG | 683 Number of splices: AT/AC | 177 Number of splices: Non-canonical | 2815 Mismatch rate per base, % | 0.54% Deletion rate per base | 0.00% Deletion average length | 1.17 Insertion rate per base | 0.00% Insertion average length | 1.06 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 4599755 % of reads mapped to multiple loci | 29.05% Number of reads mapped to too many loci | 3639237 % of reads mapped to too many loci | 22.99% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.25% % of reads unmapped: other | 1.07% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 4480911 4480911 4480911 N_multimapping 4599755 4599755 4599755 N_noFeature 4134522 4325876 5912665 N_ambiguous 651323 3381 699 UnstrandedReadsAssigned:1965436 PositiveStrandReadsAssigned:2422024 NegativeStrandReadsAssigned:837917 Dataset is classified unstranded MeadianReadLen=24 20thPercentileLength=21 echo kmer=19 SRR7472591 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: SRR7472591-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 15,831,947 reads, 4,948,267 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,140 rounds 52401 SRR7472591.ke.tsv 34699 SRR7472591.se.tsv 87100 total ==> SRR7472591.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 55 4.58404 Potri.005G024800.1.v4.1 1035 936 7.01374 1.19849 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 12.7021 0.714344 Potri.016G087400.1.v4.1 270 171 2.21884 2.07535 Potri.015G069301.1.v4.1 564 465 10 3.4396 Potri.010G195200.1.v4.1 1773 1674 1 0.0955444 Potri.012G127500.1.v4.1 977 878 45.7916 8.34164 ==> SRR7472591.se.tsv <== Potri.001G166300.v4.1 1 Potri.001G448400.v4.1 3 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 5 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 3 Potri.001G416900.v4.1 4 Potri.001G452600.v4.1 0 SRR7472591 completed mapping pipeline successfully