Starting /dee2/code/volunteer_pipeline.sh SRR1850671 current disk space = 1545917054976 free memory = 1598399012 SRR1850671 SRAfilesize 177c3231ee3d843971e6ca84252f15f0 SRR1850671.sra SRR1850671.sra file validated SRR1850671 is single end SRR1850671 is conventional basespace SRR1850671 read1 length is 50 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR1850671_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 50 %GC 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.76125 34.0 31.0 34.0 31.0 34.0 2 33.06175 34.0 33.0 34.0 31.0 34.0 3 33.05575 34.0 33.0 34.0 31.0 34.0 4 36.45925 37.0 37.0 37.0 35.0 37.0 5 36.42075 37.0 37.0 37.0 35.0 37.0 6 36.32625 37.0 37.0 37.0 35.0 37.0 7 36.3695 37.0 37.0 37.0 35.0 37.0 8 36.3645 37.0 37.0 37.0 35.0 37.0 9 38.15625 39.0 39.0 39.0 37.0 39.0 10 38.204 39.0 39.0 39.0 37.0 39.0 11 38.152 39.0 39.0 39.0 37.0 39.0 12 38.07625 39.0 38.0 39.0 37.0 39.0 13 38.08 39.0 39.0 39.0 35.0 39.0 14 39.60675 41.0 40.0 41.0 37.0 41.0 15 39.549 41.0 40.0 41.0 37.0 41.0 16 39.56375 41.0 40.0 41.0 37.0 41.0 17 39.5905 41.0 40.0 41.0 37.0 41.0 18 39.5575 41.0 40.0 41.0 37.0 41.0 19 39.429 41.0 40.0 41.0 36.0 41.0 20 39.37625 41.0 39.0 41.0 36.0 41.0 21 39.308 41.0 39.0 41.0 36.0 41.0 22 39.329 41.0 39.0 41.0 36.0 41.0 23 39.2675 41.0 39.0 41.0 36.0 41.0 24 39.25975 41.0 39.0 41.0 36.0 41.0 25 39.12175 41.0 39.0 41.0 36.0 41.0 26 38.99425 41.0 39.0 41.0 36.0 41.0 27 38.84825 40.0 39.0 41.0 35.0 41.0 28 38.7375 40.0 39.0 41.0 35.0 41.0 29 38.6765 40.0 39.0 41.0 35.0 41.0 30 38.5345 40.0 38.0 41.0 35.0 41.0 31 38.44025 40.0 38.0 41.0 35.0 41.0 32 38.2785 40.0 38.0 41.0 34.0 41.0 33 38.14975 40.0 38.0 41.0 34.0 41.0 34 38.09025 40.0 38.0 41.0 34.0 41.0 35 38.35575 40.0 38.0 41.0 34.0 41.0 36 38.2225 40.0 38.0 41.0 34.0 41.0 37 38.1965 40.0 38.0 41.0 34.0 41.0 38 38.0025 40.0 38.0 41.0 34.0 41.0 39 37.78825 40.0 38.0 41.0 33.0 41.0 40 37.79675 40.0 38.0 41.0 33.0 41.0 41 37.8155 40.0 38.0 41.0 33.0 41.0 42 37.8905 40.0 38.0 41.0 34.0 41.0 43 37.795 40.0 38.0 41.0 33.0 41.0 44 37.6715 40.0 38.0 41.0 33.0 41.0 45 37.3125 40.0 38.0 41.0 32.0 41.0 46 37.40575 40.0 38.0 41.0 33.0 41.0 47 37.16475 40.0 38.0 41.0 32.0 41.0 48 36.99425 40.0 38.0 41.0 32.0 41.0 49 36.9335 40.0 37.0 41.0 31.0 41.0 50 36.56025 40.0 37.0 41.0 30.0 41.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 1101 1 0.0 1101 2 0.0 1101 3 0.0 1101 4 0.0 1101 5 0.0 1101 6 0.0 1101 7 0.0 1101 8 0.0 1101 9 0.0 1101 10 0.0 1101 11 0.0 1101 12 0.0 1101 13 0.0 1101 14 0.0 1101 15 0.0 1101 16 0.0 1101 17 0.0 1101 18 0.0 1101 19 0.0 1101 20 0.0 1101 21 0.0 1101 22 0.0 1101 23 0.0 1101 24 0.0 1101 25 0.0 1101 26 0.0 1101 27 0.0 1101 28 0.0 1101 29 0.0 1101 30 0.0 1101 31 0.0 1101 32 0.0 1101 33 0.0 1101 34 0.0 1101 35 0.0 1101 36 0.0 1101 37 0.0 1101 38 0.0 1101 39 0.0 1101 40 0.0 1101 41 0.0 1101 42 0.0 1101 43 0.0 1101 44 0.0 1101 45 0.0 1101 46 0.0 1101 47 0.0 1101 48 0.0 1101 49 0.0 1101 50 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 2.0 14 2.0 15 6.0 16 4.0 17 6.0 18 4.0 19 5.0 20 6.0 21 6.0 22 9.0 23 18.0 24 14.0 25 13.0 26 12.0 27 13.0 28 29.0 29 21.0 30 36.0 31 50.0 32 60.0 33 65.0 34 98.0 35 147.0 36 204.0 37 263.0 38 551.0 39 2356.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 39.7 11.675 13.725000000000001 34.9 2 27.625 12.65 28.275 31.45 3 36.15211408556417 14.010507880910684 20.01501125844383 29.82236677508131 4 33.275 22.0 15.6 29.125 5 34.425 27.800000000000004 18.925 18.85 6 27.0 31.85 17.675 23.474999999999998 7 11.35 38.35 32.85 17.45 8 19.375 30.349999999999998 29.075 21.2 9 22.375 19.8 35.55 22.275 10 16.2 41.75 25.75 16.3 11 27.05 31.55 18.95 22.45 12 24.275 29.25 22.825 23.65 13 18.65 38.45 22.625 20.275000000000002 14 23.400000000000002 31.374999999999996 25.650000000000002 19.575 15 20.025000000000002 37.9 21.0 21.075 16 21.975 33.7 22.075 22.25 17 23.849999999999998 34.300000000000004 20.275000000000002 21.575 18 18.05 36.1 24.75 21.099999999999998 19 19.900000000000002 31.924999999999997 24.25 23.925 20 15.65 31.95 29.275000000000002 23.125 21 20.200000000000003 28.7 28.050000000000004 23.05 22 15.1 41.199999999999996 22.625 21.075 23 18.5 36.75 23.849999999999998 20.9 24 17.65 34.8 21.65 25.900000000000002 25 18.025 33.275 28.7 20.0 26 17.925 34.55 23.3 24.224999999999998 27 21.375 30.325000000000003 26.174999999999997 22.125 28 24.125 38.875 21.625 15.375 29 29.15 31.75 21.425 17.675 30 24.05 30.55 25.874999999999996 19.525000000000002 31 28.849999999999998 26.0 22.25 22.900000000000002 32 24.956239059764943 31.707926981745437 23.355838959739934 19.979994998749685 33 26.331582895723933 32.733183295823956 19.05476369092273 21.880470117529384 34 21.705426356589147 39.68492123030758 19.254813703425857 19.35483870967742 35 25.85 35.525 20.349999999999998 18.275 36 19.979994998749685 27.93198299574894 27.85696424106027 24.23105776444111 37 26.070623591284747 27.973954420235415 29.351364888554972 16.60405709992487 38 19.925 26.75 33.1 20.225 39 22.900000000000002 29.525000000000002 27.675 19.900000000000002 40 22.05 32.35 25.650000000000002 19.950000000000003 41 21.0 26.075 27.6 25.324999999999996 42 19.41941941941942 33.233233233233236 25.325325325325327 22.02202202202202 43 20.375 30.575000000000003 26.424999999999997 22.625 44 20.030007501875467 28.032008002000502 26.331582895723933 25.6064016004001 45 18.220551378446114 29.273182957393484 32.13032581453634 20.37593984962406 46 17.271589486858574 27.584480600750936 33.46683354192741 21.67709637046308 47 20.235411970949162 31.755572251440018 29.10092662158778 18.90808915602304 48 21.53576788394197 32.3911955977989 27.163581790895446 18.90945472736368 49 23.200000000000003 34.599999999999994 21.925 20.275000000000002 50 25.756439109777446 27.106776694173547 27.53188297074269 19.604901225306325 >>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 0.5 18 1.0 19 2.0 20 3.0 21 4.0 22 5.0 23 9.0 24 13.0 25 24.5 26 36.0 27 35.0 28 34.0 29 43.0 30 52.0 31 58.0 32 64.0 33 111.0 34 158.0 35 257.0 36 356.0 37 443.5 38 531.0 39 407.5 40 284.0 41 301.0 42 318.0 43 386.0 44 454.0 45 422.5 46 391.0 47 319.0 48 247.0 49 282.5 50 318.0 51 289.5 52 261.0 53 179.0 54 97.0 55 77.0 56 57.0 57 53.0 58 49.0 59 49.0 60 49.0 61 40.0 62 31.0 63 30.0 64 29.0 65 22.5 66 16.0 67 26.5 68 37.0 69 36.5 70 36.0 71 35.0 72 34.0 73 24.0 74 14.0 75 11.0 76 8.0 77 6.5 78 5.0 79 5.5 80 6.0 81 5.0 82 4.0 83 2.0 84 0.0 85 0.5 86 1.0 87 1.0 88 1.0 89 0.5 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 0.075 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 0.025 33 0.025 34 0.025 35 0.0 36 0.025 37 0.17500000000000002 38 0.0 39 0.0 40 0.0 41 0.0 42 0.1 43 0.0 44 0.025 45 0.25 46 0.125 47 0.17500000000000002 48 0.05 49 0.0 50 0.025 >>END_MODULE >>Sequence Length Distribution pass #Length Count 50 4000.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 50.14999999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 84.64606181455633 42.449999999999996 2 6.331006979062812 6.35 3 2.642073778664008 3.975 4 1.5453639082751744 3.1 5 0.897308075772682 2.25 6 0.5982053838484547 1.7999999999999998 7 0.3489531405782652 1.225 8 0.19940179461615154 0.8 9 0.24925224327018944 1.125 >10 2.243270189431705 22.525000000000002 >50 0.19940179461615154 7.025 >100 0.09970089730807577 7.375 >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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGCGTAGCATCTCGTAT 152 3.8 TruSeq Adapter, Index 1 (97% over 36bp) GCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACG 143 3.5749999999999997 No Hit CTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGG 89 2.225 No Hit GTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTA 69 1.725 No Hit GGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTT 62 1.55 No Hit GCGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAG 61 1.525 No Hit CGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGT 47 1.175 No Hit TCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGG 47 1.175 No Hit ACGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAG 46 1.15 No Hit CGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGG 41 1.0250000000000001 No Hit GTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTC 37 0.9249999999999999 No Hit CTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAG 34 0.8500000000000001 No Hit GCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGGT 33 0.8250000000000001 No Hit GCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGCAT 33 0.8250000000000001 No Hit CGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGA 29 0.7250000000000001 No Hit GCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAA 28 0.7000000000000001 No Hit CTCGCGAATACCATCAATATCTACTGGAGGGGCTGCGATGAAGGCGATAA 28 0.7000000000000001 No Hit CTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGCATAC 26 0.65 No Hit GCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGAT 25 0.625 No Hit GGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGAC 25 0.625 No Hit GCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGG 25 0.625 No Hit ATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACC 22 0.5499999999999999 No Hit GGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAA 21 0.525 No Hit GGCCAAAATAACCATGAGCAGCCACAATATTATAAGTCTCTTCCTCTTGA 20 0.5 No Hit CGGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATCT 19 0.475 No Hit CGCAGAAGTAGGAATAATAGCACCAGAGATAATATTGTTTCCATAAAGTA 18 0.44999999999999996 No Hit GTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACG 17 0.42500000000000004 No Hit TGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCT 16 0.4 No Hit CGCTGGAGTAGGCTGCGAGGCCCAAGCGGCCAAGGAGTGCAGCGGCCCGT 15 0.375 No Hit GGAGGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAA 13 0.325 No Hit TTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCC 13 0.325 No Hit GCGGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATC 13 0.325 No Hit CGCGAATACCATCAATATCTACTGGAGGGGCTGCGATGAAGGCGATAATA 12 0.3 No Hit CAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACGAT 12 0.3 No Hit CGCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTAC 12 0.3 No Hit TTTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCATT 12 0.3 No Hit CCACCATTGTATAACCATTCATCAACGGATGCAGCTTCCCAAATTGGGTA 12 0.3 No Hit CCCAAGTATTAATAACGCGACCTTGACTATCAACTACAGATTGGTTGAAA 12 0.3 No Hit TTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTTCGTGCA 11 0.27499999999999997 No Hit TGCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTAC 11 0.27499999999999997 No Hit GCGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAG 11 0.27499999999999997 No Hit AGCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTAC 11 0.27499999999999997 No Hit CTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGC 11 0.27499999999999997 No Hit CTTTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCAT 11 0.27499999999999997 No Hit GGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGT 11 0.27499999999999997 No Hit AGGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGG 11 0.27499999999999997 No Hit GCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAAC 10 0.25 No Hit CCGCAGAAGTAGGAATAATAGCACCAGAGATAATATTGTTTCCATAAAGT 10 0.25 No Hit ATGCATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAG 10 0.25 No Hit TGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATT 10 0.25 No Hit TGCGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAA 10 0.25 No Hit CGCGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAA 9 0.22499999999999998 No Hit TGATGATATCAGCCCAAGTATTAATAACGCGACCTTGACTATCAACTACA 9 0.22499999999999998 No Hit GCTAGTTATCCAGTTGCAGAAGCGACCCCACAGGCTTGTACTTTCGCGTC 9 0.22499999999999998 No Hit CTCATAAGGACCACCATTGTATAACCATTCATCAACGGATGCAGCTTCCC 9 0.22499999999999998 No Hit CTCATTAGCAGATTCATTTTCAGTAGTTTCCCTGATCAAACTAGAGGTTA 9 0.22499999999999998 No Hit CCCCAGTTAAGTAGTCATGCATTACAATAGGAACACCTAATTCTCTCGCA 8 0.2 No Hit GGATGCATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAA 8 0.2 No Hit GTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACGATTTTCAGT 8 0.2 No Hit GTTCGCTGGAGTAGGCTGCGAGGCCCAAGCGGCCAAGGAGTGCAGCGGCC 8 0.2 No Hit TCGCGAATACCATCAATATCTACTGGAGGGGCTGCGATGAAGGCGATAAT 7 0.17500000000000002 No Hit GCATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTA 7 0.17500000000000002 No Hit GGCTAGTTCAGGACTCCATTTGCAAGCTGCTCGGATAATTTCATTACCTT 7 0.17500000000000002 No Hit AGCAGCCACAATATTATAAGTCTCTTCCTCTTGACCAAATTTGTAACCCT 7 0.17500000000000002 No Hit CACCATTGTATAACCATTCATCAACGGATGCAGCTTCCCAAATTGGGTAA 7 0.17500000000000002 No Hit CGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATC 7 0.17500000000000002 No Hit TAGTTATCCAGTTGCAGAAGCGACCCCACAGGCTTGTACTTTCGCGTCTC 7 0.17500000000000002 No Hit TGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAA 6 0.15 No Hit CTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGGTTGAAC 6 0.15 No Hit CCGGGGTGTAGTAAGTCAATCTATAATCTTTAACACCAGCTTTAAATCCA 6 0.15 No Hit CGTCTCTCTAAAATTGCAGTCATGGTAAGATCTTGGTTTATTCAAATTGC 6 0.15 No Hit GGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTA 6 0.15 No Hit CGCATACCCAAACGGAAACTAAGTTCCCACTCACGACCCATATAACAAGC 6 0.15 No Hit GCGAATACCATCAATATCTACTGGAGGGGCTGCGATGAAGGCGATAATAA 6 0.15 No Hit CCAAGTATTAATAACGCGACCTTGACTATCAACTACAGATTGGTTGAAAT 6 0.15 No Hit AACGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTA 6 0.15 No Hit AATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAACACCGA 6 0.15 No Hit GCCAAAATAACCATGAGCAGCCACAATATTATAAGTCTCTTCCTCTTGAC 6 0.15 No Hit TGCTAGTTATCCAGTTGCAGAAGCGACCCCACAGGCTTGTACTTTCGCGT 6 0.15 No Hit CGCCATAGTACTAATACCTAAAGCAGTGAACCAGATTCCTACTACAGGCC 5 0.125 No Hit CCGCCGAAAACACCAGCTACACCTAACATGTGAAATGGATGCATAAGGAT 5 0.125 No Hit GCCGAAAACACCAGCTACACCTAACATGTGAAATGGATGCATAAGGATGT 5 0.125 No Hit ACCAGATATTCCTAAAGGCATACCATCAGAGAAGCTTCCTTGACCAATAG 5 0.125 No Hit CTGTGCCTGCCAACATTATGGGCCGCGAAGCCTAGCTTTCGCTTAAGCTC 5 0.125 No Hit CGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAA 5 0.125 No Hit GGCGCATACCCAAACGGAAACTAAGTTCCCACTCACGACCCATATAACAA 5 0.125 No Hit GACCACCATTGTATAACCATTCATCAACGGATGCAGCTTCCCAAATTGGG 5 0.125 No Hit ATAAGGACCACCATTGTATAACCATTCATCAACGGATGCAGCTTCCCAAA 5 0.125 No Hit TTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCATTA 5 0.125 No Hit GTGAGCATTACGTTCGTGCATTACTTCCATACCAAGATTAGCACGGTTGA 5 0.125 No Hit ATGCATTACAATAGGAACACCTAATTCTCTCGCAAAAACAGCTCTCTTCA 5 0.125 No Hit GCCACAATATTATAAGTCTCTTCCTCTTGACCAAATTTGTAACCCTCATT 5 0.125 No Hit GCTTTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCA 5 0.125 No Hit CATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTAC 5 0.125 No Hit CACGGTTGATGATATCAGCCCAAGTATTAATAACGCGACCTTGACTATCA 5 0.125 No Hit TGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGA 5 0.125 No Hit CGGCCAAAATAACCATGAGCAGCCACAATATTATAAGTCTCTTCCTCTTG 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #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 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10 0.0 0.0 0.0 0.0 0.0 11 0.0 0.0 0.0 0.0 0.0 12 0.0 0.0 0.0 0.0 0.0 13 0.0 0.0 0.0 0.0 0.0 14 0.0 0.0 0.0 0.0 0.0 15 0.0 0.0 0.0 0.0 0.0 16 0.0 0.0 0.0 0.0 0.0 17 0.0 0.0 0.0 0.0 0.0 18 0.0 0.0 0.0 0.0 0.0 19 0.0 0.0 0.0 0.0 0.0 20 0.0 0.0 0.0 0.0 0.0 21 0.0 0.0 0.0 0.0 0.0 22 0.0 0.0 0.0 0.0 0.0 23 0.0 0.0 0.0 0.0 0.0 24 0.0 0.0 0.0 0.0 0.0 25 0.0 0.0 0.0 0.0 0.0 26 0.0 0.0 0.0 0.0 0.0 27 0.0 0.0 0.0 0.0 0.0 28 0.0 0.0 0.0 0.0 0.0 29 0.0 0.0 0.0 0.0 0.0 30 0.0 0.0 0.0 0.0 0.0 31 0.0 0.0 0.0 0.0 0.0 32 0.0 0.0 0.0 0.0 0.0 33 0.0 0.0 0.0 0.0 0.0 34 0.0 0.0 0.0 0.0 0.0 35 0.0 0.0 0.0 0.0 0.0 36 0.0 0.0 0.0 0.0 0.0 37 0.0 0.0 0.0 0.0 0.0 38 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 973612 spots for SRR1850671.sra Written 973612 spots for SRR1850671.sra Read 973612 spots for SRR1850671.sra Written 973612 spots for SRR1850671.sra Read 973612 spots for SRR1850671.sra Written 973612 spots for SRR1850671.sra Read 973612 spots for SRR1850671.sra Written 973612 spots for SRR1850671.sra Read 973612 spots for SRR1850671.sra Written 973612 spots for SRR1850671.sra Read 973612 spots for SRR1850671.sra Written 973612 spots for SRR1850671.sra Read 973612 spots for SRR1850671.sra Written 973612 spots for SRR1850671.sra Read 973615 spots for SRR1850671.sra Written 973615 spots for SRR1850671.sra Read 973612 spots for SRR1850671.sra Written 973612 spots for SRR1850671.sra Read 973612 spots for SRR1850671.sra Written 973612 spots for SRR1850671.sra Read 973612 spots for SRR1850671.sra Written 973612 spots for SRR1850671.sra Read 973612 spots for SRR1850671.sra Written 973612 spots for SRR1850671.sra Read 973612 spots for SRR1850671.sra Written 973612 spots for SRR1850671.sra Read 973612 spots for SRR1850671.sra Written 973612 spots for SRR1850671.sra Read 973612 spots for SRR1850671.sra Written 973612 spots for SRR1850671.sra Read 973612 spots for SRR1850671.sra Written 973612 spots for SRR1850671.sra Read 973612 spots for SRR1850671.sra Written 973612 spots for SRR1850671.sra Read 973612 spots for SRR1850671.sra Written 973612 spots for SRR1850671.sra Read 973612 spots for SRR1850671.sra Written 973612 spots for SRR1850671.sra Read 973612 spots for SRR1850671.sra Written 973612 spots for SRR1850671.sra SRR ids: ['SRR1850671.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_gk61y_hf SRR1850671.sra spots: 19472243 blocks: [[1, 973612], [973613, 1947224], [1947225, 2920836], [2920837, 3894448], [3894449, 4868060], [4868061, 5841672], [5841673, 6815284], [6815285, 7788896], [7788897, 8762508], [8762509, 9736120], [9736121, 10709732], [10709733, 11683344], [11683345, 12656956], [12656957, 13630568], [13630569, 14604180], [14604181, 15577792], [15577793, 16551404], [16551405, 17525016], [17525017, 18498628], [18498629, 19472243]] SRR1850671 file size 3364041 SRR1850671 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 SRR1850671 SRR1850671_1.fastq Input file: SRR1850671_1.fastq trimmed: SRR1850671-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 Sat Dec 7 06:16:56 2024 >> started Sat Dec 7 06:17:09 2024 >> done (12.582s) 19472243 reads processed; of these: 2541 ( 0.01%) short reads filtered out after trimming by size control 619601 ( 3.18%) empty reads filtered out after trimming by size control 18850101 (96.80%) reads available; of these: 913592 ( 4.85%) trimmed reads available after processing 17936509 (95.15%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 1379 0.01% 19 2180 0.01% 20 5233 0.03% 21 4936 0.03% 22 5549 0.03% 23 6047 0.03% 24 7621 0.04% 25 8225 0.04% 26 8235 0.04% 27 9440 0.05% 28 8837 0.05% 29 17959 0.10% 30 17996 0.10% 31 13598 0.07% 32 23532 0.12% 33 15171 0.08% 34 16373 0.09% 35 16717 0.09% 36 17459 0.09% 37 27021 0.14% 38 18663 0.10% 39 20545 0.11% 40 28128 0.15% 41 25029 0.13% 42 41812 0.22% 43 44340 0.24% 44 71148 0.38% 45 66481 0.35% 46 80724 0.43% 47 93658 0.50% 48 103711 0.55% 49 85845 0.46% 50 17936509 95.15% 18850101 reads passed initial QC criterion=sequence-density sequence-density=0.32 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=15 prefix-density=0.00 prefix-fanout=1.0 sequence=TGCGGGAACTTC criterion=fanout-score sequence-density=0.01 sequence-density-rank=36 fanout-score=25.78 fanout-score-rank=1 prefix-density=0.04 prefix-fanout=3.8 sequence=TTTATTTTGTTTCTTTTTATTTAGACCTTCTTCATATTTAGTTTTATCTATTAATCGATAGTATCTACCGGCGCGAACTCGAATTTGATCGCCTTCCATACTTCACAAGCTGCGGCTAGTTCAGGACTCCATTTGCAAGCTGCTCGGATAATTTCATTACCTTCACGAGCAAGATCGCGCCCTTCGTTACGAGCTTGTACACAGGCTTCTAAAGCCACTCGATTAGCTGCTGCACCAGGTGCATTTCCCCAAGGATGTCCTAAAGTTCCTCCACCAAATTGTAATACAGAATCATCCCCAAAGATTTCGGTCAGAGCTGGCATATGCCAAACATGAATACCACCTGAAGCTACTGGTATAACACCTGGCATGGATACCCAGTCCTGAGTGAAAAAGATACCGCGAGCACGATCTTTTTCAATAAAATCGTCGCGCAATAAATCAACAAAACCTAAAGTGATTTCGCGTTCCCCTTCTAACTTACCTACTACTGTACCGGCGTGGATATGAT Started job on | Dec 07 06:17:18 Started mapping on | Dec 07 06:17:19 Finished on | Dec 07 06:17:34 Mapping speed, Million of reads per hour | 4524.02 Number of input reads | 18850101 Average input read length | 49 UNIQUE READS: Uniquely mapped reads number | 4285074 Uniquely mapped reads % | 22.73% Average mapped length | 49.41 Number of splices: Total | 273006 Number of splices: Annotated (sjdb) | 257335 Number of splices: GT/AG | 267847 Number of splices: GC/AG | 3275 Number of splices: AT/AC | 150 Number of splices: Non-canonical | 1734 Mismatch rate per base, % | 0.27% Deletion rate per base | 0.01% Deletion average length | 1.47 Insertion rate per base | 0.01% Insertion average length | 1.34 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 14261330 % of reads mapped to multiple loci | 75.66% Number of reads mapped to too many loci | 56726 % of reads mapped to too many loci | 0.30% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.30% % of reads unmapped: other | 0.01% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 303697 303697 303697 N_multimapping 14261330 14261330 14261330 N_noFeature 881384 4152491 947311 N_ambiguous 100746 794 34263 UnstrandedReadsAssigned:3302944 PositiveStrandReadsAssigned:131789 NegativeStrandReadsAssigned:3303500 Dataset is classified negative stranded MeadianReadLen=50 20thPercentileLength=50 echo kmer=45 SRR1850671 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=31 [quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20 [index] k-mer length: 31 [index] number of targets: 52,972 [index] number of k-mers: 66,720,672 [index] number of equivalence classes: 111,837 [quant] running in single-end mode [quant] will process file 1: SRR1850671-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 18,850,101 reads, 16,162,796 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 966 rounds 52973 SRR1850671.ke.tsv 35125 SRR1850671.se.tsv 88098 total ==> SRR1850671.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 16.7188 1.37252 PNS24247 1044 945 1.16708e-08 8.48611e-10 PNS24249 1928 1829 20.2812 0.761943 PNS24246 1044 945 1.16708e-08 8.48611e-10 PNS24248 1044 945 1.16708e-08 8.48611e-10 PNS24244 1471 1372 0 0 PNS24243 293 194 0 0 KQK14069 1603 1504 29.7175 1.3577 KQK14071 474 375 17.2907 3.16827 ==> SRR1850671.se.tsv <== BRADI_1g14170v3 74 BRADI_1g53295v3 0 BRADI_1g59795v3 20 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 33 BRADI_1g74790v3 4 BRADI_1g09890v3 0 BRADI_1g77505v3 33 BRADI_1g48960v3 0 SRR1850671 completed mapping pipeline successfully