Starting /dee2/code/volunteer_pipeline.sh ERR6133544 current disk space = 1544497041408 free memory = 1600410948 ERR6133544 SRAfilesize 59cbbe36e5c33c75a11df22714be11d2 ERR6133544.sra ERR6133544.sra file validated ERR6133544 is single end ERR6133544 is conventional basespace ERR6133544 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133544_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 70-93 %GC 46 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.768 33.0 33.0 37.0 27.0 37.0 2 35.9185 37.0 37.0 37.0 33.0 37.0 3 35.07225 37.0 33.0 37.0 33.0 37.0 4 35.28725 37.0 37.0 37.0 33.0 37.0 5 35.1895 37.0 37.0 37.0 33.0 37.0 6 35.53775 37.0 37.0 37.0 33.0 37.0 7 37.31875 37.0 37.0 40.0 33.0 40.0 8 37.325 37.0 37.0 40.0 33.0 40.0 9 37.4825 37.0 37.0 40.0 33.0 40.0 10-11 37.451125000000005 37.0 37.0 40.0 33.0 40.0 12-13 37.470749999999995 37.0 37.0 40.0 33.0 40.0 14-15 37.467 37.0 37.0 40.0 33.0 40.0 16-17 37.221875 37.0 37.0 40.0 33.0 40.0 18-19 37.205375000000004 37.0 37.0 40.0 33.0 40.0 20-21 37.145250000000004 37.0 37.0 40.0 33.0 40.0 22-23 37.013374999999996 37.0 37.0 40.0 33.0 40.0 24-25 37.1715 37.0 37.0 40.0 33.0 40.0 26-27 37.109624999999994 37.0 37.0 40.0 33.0 40.0 28-29 37.01875 37.0 37.0 40.0 33.0 40.0 30-31 36.852125 37.0 37.0 40.0 33.0 40.0 32-33 36.685125 37.0 37.0 40.0 33.0 40.0 34-35 36.6445 37.0 37.0 40.0 33.0 40.0 36-37 36.404125 37.0 37.0 40.0 33.0 40.0 38-39 36.3915 37.0 37.0 40.0 33.0 40.0 40-41 36.148624999999996 37.0 37.0 40.0 33.0 40.0 42-43 35.964625 37.0 37.0 40.0 33.0 40.0 44-45 35.674375 37.0 35.0 37.0 33.0 40.0 46-47 35.373625000000004 37.0 33.0 37.0 30.0 40.0 48-49 35.302375 37.0 33.0 37.0 33.0 40.0 50-51 35.211375000000004 37.0 33.0 37.0 30.0 40.0 52-53 34.9345 37.0 33.0 37.0 27.0 40.0 54-55 34.857749999999996 37.0 33.0 37.0 27.0 37.0 56-57 34.737750000000005 37.0 33.0 37.0 27.0 37.0 58-59 34.121624999999995 37.0 33.0 37.0 27.0 37.0 60-61 34.243 37.0 33.0 37.0 27.0 37.0 62-63 34.301 37.0 33.0 37.0 27.0 37.0 64-65 34.319125 37.0 33.0 37.0 27.0 37.0 66-67 34.32725 37.0 33.0 37.0 27.0 37.0 68-69 33.439125000000004 35.0 33.0 37.0 27.0 37.0 70-71 33.474803204807216 35.0 33.0 37.0 27.0 37.0 72-73 33.84207999972803 37.0 33.0 37.0 27.0 37.0 74-75 33.830304001724926 37.0 33.0 37.0 27.0 37.0 76-77 33.79964199773205 37.0 33.0 37.0 27.0 37.0 78-79 33.826825829019576 37.0 33.0 37.0 27.0 37.0 80-81 33.8003603059076 37.0 33.0 37.0 27.0 37.0 82-83 33.64630789560121 37.0 33.0 37.0 27.0 37.0 84-85 33.77809117737106 37.0 33.0 37.0 27.0 37.0 86-87 33.511238825031924 37.0 33.0 37.0 27.0 37.0 88-89 33.675862068965515 37.0 33.0 37.0 27.0 37.0 90-91 33.384163473818646 37.0 33.0 37.0 27.0 37.0 92-93 33.1911877394636 37.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 11.0 21 14.0 22 17.0 23 23.0 24 29.0 25 32.0 26 45.0 27 45.0 28 70.0 29 74.0 30 83.0 31 120.0 32 137.0 33 188.0 34 228.0 35 447.0 36 921.0 37 939.0 38 570.0 39 7.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 89.5 1.925 2.325 6.25 2 75.47500000000001 14.325 6.4 3.8 3 36.525 39.074999999999996 13.325000000000001 11.075 4 34.0 28.125 16.625 21.25 5 25.4 32.4 24.75 17.45 6 20.9 36.75 25.8 16.55 7 36.325 28.549999999999997 18.7 16.425 8 29.375 29.625 24.525 16.475 9 26.125 29.775000000000002 26.625 17.474999999999998 10-11 25.55 26.75 26.825 20.875 12-13 27.800000000000004 25.7125 26.7625 19.725 14-15 21.987499999999997 30.175 28.675 19.162499999999998 16-17 24.975 30.862499999999997 24.4125 19.75 18-19 23.95 26.700000000000003 26.325 23.025000000000002 20-21 26.387500000000003 25.6125 27.450000000000003 20.549999999999997 22-23 27.9125 22.5125 26.6125 22.9625 24-25 26.674999999999997 23.8375 27.762500000000003 21.725 26-27 25.912499999999998 25.8625 29.75 18.475 28-29 26.137500000000003 27.5125 25.7625 20.5875 30-31 28.725 25.637500000000003 24.2875 21.349999999999998 32-33 24.9375 26.887499999999996 27.400000000000002 20.775 34-35 24.98436913842691 26.334875578341876 27.047642866074778 21.633112417156433 36-37 24.0625 24.975 27.9125 23.05 38-39 26.1 24.875 29.612500000000004 19.412499999999998 40-41 27.353419177397175 25.61570196274534 26.015751968996128 21.015126890861357 42-43 25.587793896948476 28.72686343171586 25.42521260630315 20.260130065032516 44-45 24.918729682420604 25.71892973243311 28.044511127781945 21.31782945736434 46-47 24.775 23.875 27.224999999999998 24.125 48-49 25.50318789848731 23.81547693461683 30.41630203775472 20.265033129141145 50-51 25.2 26.0 28.8625 19.9375 52-53 25.63781890945473 27.00100050025013 26.32566283141571 21.03551775887944 54-55 24.6625 29.099999999999998 26.487500000000004 19.75 56-57 26.700000000000003 25.887500000000003 26.950000000000003 20.4625 58-59 24.7375 24.675 28.212500000000002 22.375 60-61 25.0125 24.837500000000002 28.825 21.325 62-63 22.7625 27.025 31.5 18.712500000000002 64-65 24.3875 27.987499999999997 27.0 20.625 66-67 24.8625 28.212500000000002 26.25 20.674999999999997 68-69 23.150000000000002 27.200000000000003 27.1 22.55 70-71 26.832624468351263 25.31898924193145 26.007005253940456 21.841381035776834 72-73 26.759503199096724 24.21277129594781 27.085685610337475 21.94203989461799 74-75 24.338957441450514 27.851926466884912 27.663057164442208 20.146058927222363 76-77 23.690521267196768 26.088602801968953 27.931339139214945 22.289536791619334 78-79 24.709302325581394 24.595551061678464 29.73963599595551 20.955510616784633 80-81 24.82557402004313 28.567804135481417 28.085754154509708 18.52086768996575 82-83 24.720101781170484 25.025445292620862 28.816793893129773 21.43765903307888 84-85 24.489274770173648 23.557201225740553 29.80081716036772 22.15270684371808 86-87 22.758620689655174 26.909323116219667 31.213282247765008 19.118773946360154 88-89 21.826309067688378 28.467432950191572 29.59131545338442 20.114942528735632 90-91 27.369093231162196 25.644955300127712 28.27586206896552 18.71008939974457 92-93 23.205619412515965 29.22094508301405 27.816091954022987 19.757343550446997 >>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 0.5 17 4.5 18 5.0 19 1.0 20 1.0 21 2.0 22 2.0 23 2.5 24 3.5 25 4.5 26 9.0 27 10.0 28 9.5 29 12.5 30 16.0 31 23.0 32 36.5 33 51.0 34 57.5 35 73.0 36 99.0 37 128.5 38 155.0 39 148.0 40 157.0 41 194.5 42 204.5 43 201.5 44 192.0 45 180.0 46 229.5 47 229.0 48 156.5 49 155.5 50 180.0 51 181.0 52 163.0 53 168.5 54 165.0 55 110.5 56 72.0 57 66.0 58 63.5 59 54.5 60 42.5 61 31.5 62 31.0 63 31.5 64 28.5 65 24.5 66 23.5 67 26.5 68 24.0 69 21.0 70 13.0 71 7.0 72 6.0 73 5.0 74 5.5 75 5.0 76 2.5 77 1.0 78 1.0 79 1.0 80 0.5 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 0.0 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 0.0375 36-37 0.0 38-39 0.0 40-41 0.0125 42-43 0.05 44-45 0.025 46-47 0.0 48-49 0.0125 50-51 0.0 52-53 0.05 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 >>END_MODULE >>Sequence Length Distribution warn #Length Count 70 6.0 71 6.0 72 5.0 73 8.0 74 8.0 75 3.0 76 5.0 77 1.0 78 4.0 79 9.0 80 7.0 81 5.0 82 6.0 83 10.0 84 2.0 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 3915.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 78.375 #Duplication Level Percentage of deduplicated Percentage of total 1 92.91866028708135 72.82499999999999 2 3.7001594896331738 5.800000000000001 3 1.3078149920255184 3.075 4 0.4784688995215311 1.5 5 0.4784688995215311 1.875 6 0.2551834130781499 1.2 7 0.12759170653907495 0.7000000000000001 8 0.09569377990430622 0.6 9 0.03189792663476874 0.22499999999999998 >10 0.5422647527910686 9.049999999999999 >50 0.06379585326953748 3.15 >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 GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 70 1.7500000000000002 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 56 1.4000000000000001 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 40 1.0 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 35 0.8750000000000001 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 35 0.8750000000000001 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 34 0.8500000000000001 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 28 0.7000000000000001 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 26 0.65 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 22 0.5499999999999999 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 19 0.475 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 18 0.44999999999999996 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 15 0.375 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 15 0.375 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 15 0.375 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 14 0.35000000000000003 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 13 0.325 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 12 0.3 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 11 0.27499999999999997 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 10 0.25 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 9 0.22499999999999998 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 8 0.2 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 8 0.2 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 8 0.2 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 7 0.17500000000000002 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 7 0.17500000000000002 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 7 0.17500000000000002 No Hit GGGGAAGTACACCAGCGACGGCGAGGCCGCCGCCGCCAAGGAAGGCATGT 7 0.17500000000000002 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 6 0.15 No Hit GAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAAT 6 0.15 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 6 0.15 No Hit GGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGT 6 0.15 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 6 0.15 No Hit GTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCT 6 0.15 No Hit GGCATATGCCAGCTCTGACCGAAATCTTTGGGGATGATTCTGTATTACAA 6 0.15 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 6 0.15 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 5 0.125 No Hit GGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTT 5 0.125 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 5 0.125 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 5 0.125 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 5 0.125 No Hit GGGCAAGGAGAAGTACAAGTGCGGATCCAACGTCTTCTGGAAATGGTGAA 5 0.125 No Hit GGGAAACAACGAGGTCATCATCGACATGATATATTGCTGCTATTTTCCAC 5 0.125 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 5 0.125 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 5 0.125 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 5 0.125 No Hit GGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTAATAG 5 0.125 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 5 0.125 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 5 0.125 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 5 0.125 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 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 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.037500000000000006 0.0 0.0 0.0 0.0 26-27 0.05 0.0 0.0 0.0 0.0 28-29 0.05 0.0 0.0 0.0 0.0 30-31 0.05 0.0 0.0 0.0 0.0 32-33 0.05 0.0 0.0 0.0 0.0 34-35 0.05 0.0 0.0 0.0 0.0 36-37 0.0625 0.0 0.0 0.0 0.0 38-39 0.075 0.0 0.0 0.0 0.0 40-41 0.075 0.0 0.0 0.0 0.0 42-43 0.075 0.0 0.0 0.0 0.0 44-45 0.075 0.0 0.0 0.0 0.0 46-47 0.075 0.0 0.0 0.0 0.0 48-49 0.075 0.0 0.0 0.0 0.0 50-51 0.075 0.0 0.0 0.0 0.0 52-53 0.075 0.0 0.0 0.0 0.0 54-55 0.075 0.0 0.0 0.0 0.0 56-57 0.075 0.0 0.0 0.0 0.0 58-59 0.1 0.0 0.0 0.0 0.0 60-61 0.1 0.0 0.0 0.0 0.0 62-63 0.1 0.0 0.0 0.0 0.0 64-65 0.1 0.0 0.0 0.0 0.0 66-67 0.1 0.0 0.0 0.0 0.0 68-69 0.1 0.0 0.0 0.0 0.0 70-71 0.1 0.0 0.0 0.0 0.0 72-73 0.1 0.0 0.0 0.0 0.0 74-75 0.1 0.0 0.0 0.0 0.0 76-77 0.1 0.0 0.0 0.0 0.0 78-79 0.1 0.0 0.0 0.0 0.0 80-81 0.1 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGGATG 15 8.848908E-4 86.662506 1 GGGATGA 25 0.006709265 51.9975 2 AAGGGCG 25 4.4421693E-5 43.331253 66-67 GGGCGCG 25 4.4421693E-5 43.331253 68-69 GCTCGTG 30 1.11859095E-4 37.035255 80-81 TCTTGCT 30 1.11859095E-4 37.035255 76-77 GTGAAGG 30 1.11859095E-4 37.035255 84-85 TTGCTCG 30 1.11859095E-4 37.035255 78-79 GAAGGTA 30 1.11859095E-4 37.035255 86-87 GATCTTG 30 1.1621775E-4 36.799362 74-75 GCGATCT 30 1.3014468E-4 36.109375 72-73 TCGTGAA 35 2.7689303E-4 31.744507 82-83 TTAGAAG 35 3.219981E-4 30.950893 38-39 AACGAAG 35 3.219981E-4 30.950893 62-63 CGAAGGG 35 3.219981E-4 30.950893 64-65 GCGCGAT 35 3.219981E-4 30.950893 70-71 GTACAAG 35 3.219981E-4 30.950893 50-51 GCTCGTA 35 3.219981E-4 30.950893 56-57 TCGTAAC 35 3.219981E-4 30.950893 58-59 AAGCCTG 35 3.219981E-4 30.950893 42-43 >>END_MODULE Rejected 152293 READS because READLEN < 1 Read 152293 spots for ERR6133544.sra Written 152293 spots for ERR6133544.sra Rejected 152293 READS because READLEN < 1 Read 152293 spots for ERR6133544.sra Written 152293 spots for ERR6133544.sra Rejected 152293 READS because READLEN < 1 Read 152293 spots for ERR6133544.sra Written 152293 spots for ERR6133544.sra Rejected 152293 READS because READLEN < 1 Read 152293 spots for ERR6133544.sra Written 152293 spots for ERR6133544.sra Rejected 152293 READS because READLEN < 1 Read 152293 spots for ERR6133544.sra Written 152293 spots for ERR6133544.sra Rejected 152293 READS because READLEN < 1 Read 152293 spots for ERR6133544.sra Written 152293 spots for ERR6133544.sra Rejected 152293 READS because READLEN < 1 Read 152293 spots for ERR6133544.sra Written 152293 spots for ERR6133544.sra Rejected 152293 READS because READLEN < 1 Read 152293 spots for ERR6133544.sra Written 152293 spots for ERR6133544.sra Rejected 152293 READS because READLEN < 1 Read 152293 spots for ERR6133544.sra Written 152293 spots for ERR6133544.sra Rejected 152293 READS because READLEN < 1 Read 152293 spots for ERR6133544.sra Written 152293 spots for ERR6133544.sra Rejected 152293 READS because READLEN < 1 Read 152293 spots for ERR6133544.sra Written 152293 spots for ERR6133544.sra Rejected 152293 READS because READLEN < 1 Read 152293 spots for ERR6133544.sra Written 152293 spots for ERR6133544.sra Rejected 152293 READS because READLEN < 1 Read 152293 spots for ERR6133544.sra Written 152293 spots for ERR6133544.sra Rejected 152293 READS because READLEN < 1 Read 152293 spots for ERR6133544.sra Written 152293 spots for ERR6133544.sra Rejected 152293 READS because READLEN < 1 Read 152293 spots for ERR6133544.sra Written 152293 spots for ERR6133544.sra Rejected 152293 READS because READLEN < 1 Read 152293 spots for ERR6133544.sra Written 152293 spots for ERR6133544.sra Rejected 152293 READS because READLEN < 1 Read 152293 spots for ERR6133544.sra Written 152293 spots for ERR6133544.sra Rejected 152293 READS because READLEN < 1 Read 152293 spots for ERR6133544.sra Written 152293 spots for ERR6133544.sra Rejected 152304 READS because READLEN < 1 Read 152304 spots for ERR6133544.sra Written 152304 spots for ERR6133544.sra Rejected 152293 READS because READLEN < 1 Read 152293 spots for ERR6133544.sra Written 152293 spots for ERR6133544.sra SRR ids: ['ERR6133544.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_khb8t4gm ERR6133544.sra spots: 3045871 blocks: [[1, 152293], [152294, 304586], [304587, 456879], [456880, 609172], [609173, 761465], [761466, 913758], [913759, 1066051], [1066052, 1218344], [1218345, 1370637], [1370638, 1522930], [1522931, 1675223], [1675224, 1827516], [1827517, 1979809], [1979810, 2132102], [2132103, 2284395], [2284396, 2436688], [2436689, 2588981], [2588982, 2741274], [2741275, 2893567], [2893568, 3045871]] ERR6133544 file size 673759 ERR6133544 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 ERR6133544 ERR6133544_1.fastq Input file: ERR6133544_1.fastq trimmed: ERR6133544-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 08:20:18 2024 >> started Sat Dec 7 08:20:21 2024 >> done (2.485s) 3045871 reads processed; of these: 76 ( 0.00%) short reads filtered out after trimming by size control 20 ( 0.00%) empty reads filtered out after trimming by size control 3045775 (100.00%) reads available; of these: 60390 ( 1.98%) trimmed reads available after processing 2985385 (98.02%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 7 0.00% 19 29 0.00% 20 5 0.00% 21 9 0.00% 22 9 0.00% 23 6 0.00% 24 5 0.00% 25 1 0.00% 26 4 0.00% 27 5 0.00% 28 5 0.00% 29 5 0.00% 30 5 0.00% 31 9 0.00% 32 15 0.00% 33 12 0.00% 34 11 0.00% 35 40 0.00% 36 426 0.01% 37 13 0.00% 38 14 0.00% 39 29 0.00% 40 38 0.00% 41 10 0.00% 42 4 0.00% 43 7 0.00% 44 6 0.00% 45 7 0.00% 46 9 0.00% 47 8 0.00% 48 2 0.00% 49 7 0.00% 50 8 0.00% 51 23 0.00% 52 7 0.00% 53 10 0.00% 54 3 0.00% 55 5 0.00% 56 4 0.00% 57 8 0.00% 58 4 0.00% 59 9 0.00% 60 10 0.00% 61 7 0.00% 62 3 0.00% 63 4 0.00% 64 3 0.00% 65 3 0.00% 66 9 0.00% 67 8 0.00% 68 27 0.00% 69 65 0.00% 70 5065 0.17% 71 4746 0.16% 72 4899 0.16% 73 4283 0.14% 74 4541 0.15% 75 4704 0.15% 76 3991 0.13% 77 4228 0.14% 78 4536 0.15% 79 5344 0.18% 80 4828 0.16% 81 5418 0.18% 82 6058 0.20% 83 5758 0.19% 84 4916 0.16% 85 138 0.00% 86 244 0.01% 87 367 0.01% 88 813 0.03% 89 1548 0.05% 90 3493 0.11% 91 10338 0.34% 92 41301 1.36% 93 2913236 95.65% 3045775 reads passed initial QC criterion=sequence-density sequence-density=0.50 sequence-density-rank=1 fanout-score=5.55 fanout-score-rank=17 prefix-density=1.15 prefix-fanout=2.4 sequence=GCCGCCGCCGCCAAGGAAGGCATGTTCGTCAAGAACTACAGCTACTGATCCTAATCGCATCAAGCTTCAACGCCTGTGAGTGAAAACCAGTGATGAGAGTGCTGCTGCTAGCTAGCGCCGGCATTGATGAGCTTGAGAGGGCACTGTAGCCAGTGTGTCAGTCGTTGTTAAATTACAGGTTGAGATCATCAGCGTACTCCGATGGGAGGTGGACATCAGAAAGTATACTGTGTTTTACCACCCTAATTAAGTAAACAACTTTTGGAATGGTGATCATCTTACTGTTTTAAATAAATCTGTTTC criterion=fanout-score sequence-density=0.02 sequence-density-rank=25 fanout-score=53.66 fanout-score-rank=1 prefix-density=0.13 prefix-fanout=6.6 sequence=AAAAGAAGGGGTGTTCCATCTCCGGACGACGATCCTGCCTGCAGAGGAAGACATGCCGGCGATCATGTCGAGCTTCAAGAAGTTCAACGACTCATTCATGGAGCAATACCAAGACTACTCCAGGCTGTGATGTGAAGAGGGAAACAACGAGGTCATCATCGACATGATATATTGCTGCTATTTTCCACCAGCGATTAAAAGTTAAAAAATTTAGCTGTAAGCTGTAACTATCTTGAAGAAACTAAACTGGTTGCTGTGCTTGATATGTATAGGGAAAACATAATTTATGAGACAATCATACTGTGCAACTCTTGGCTCCATCGATTAATTAATACTCCTTGTTATTGCTTGCATGGTGG Started job on | Dec 07 08:20:34 Started mapping on | Dec 07 08:20:34 Finished on | Dec 07 08:20:40 Mapping speed, Million of reads per hour | 1827.47 Number of input reads | 3045775 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 2060485 Uniquely mapped reads % | 67.65% Average mapped length | 92.22 Number of splices: Total | 125966 Number of splices: Annotated (sjdb) | 106733 Number of splices: GT/AG | 122243 Number of splices: GC/AG | 2643 Number of splices: AT/AC | 51 Number of splices: Non-canonical | 1029 Mismatch rate per base, % | 0.42% Deletion rate per base | 0.04% Deletion average length | 1.81 Insertion rate per base | 0.02% Insertion average length | 1.78 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 914349 % of reads mapped to multiple loci | 30.02% Number of reads mapped to too many loci | 20326 % of reads mapped to too many loci | 0.67% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.61% % of reads unmapped: other | 0.05% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 70941 70941 70941 N_multimapping 914349 914349 914349 N_noFeature 131261 151470 1971282 N_ambiguous 78540 9525 267 UnstrandedReadsAssigned:1850684 PositiveStrandReadsAssigned:1899490 NegativeStrandReadsAssigned:88936 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133544 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: ERR6133544-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,045,775 reads, 2,567,286 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 970 rounds 52973 ERR6133544.ke.tsv 35125 ERR6133544.se.tsv 88098 total ==> ERR6133544.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 82 30.524 PNS24243 293 194 0 0 KQK14069 1603 1504 85.0787 28.8905 KQK14071 474 375 1 1.36192 ==> ERR6133544.se.tsv <== BRADI_1g14170v3 93 BRADI_1g53295v3 3 BRADI_1g59795v3 15 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 22 BRADI_1g74790v3 23 BRADI_1g09890v3 0 BRADI_1g77505v3 43 BRADI_1g48960v3 0 ERR6133544 completed mapping pipeline successfully