Starting /dee2/code/volunteer_pipeline.sh ERR6133364 current disk space = 1548113465344 free memory = 1601958636 ERR6133364 SRAfilesize ce0b808931644cf051c1c853a910860b ERR6133364.sra ERR6133364.sra file validated ERR6133364 is single end ERR6133364 is conventional basespace ERR6133364 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133364_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 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.39325 37.0 37.0 37.0 33.0 37.0 2 36.73125 37.0 37.0 37.0 37.0 37.0 3 36.653 37.0 37.0 37.0 37.0 37.0 4 36.424 37.0 37.0 37.0 37.0 37.0 5 36.4685 37.0 37.0 37.0 37.0 37.0 6 36.55 37.0 37.0 37.0 37.0 37.0 7 38.8125 40.0 37.0 40.0 37.0 40.0 8 38.8285 40.0 37.0 40.0 37.0 40.0 9 38.82575 40.0 37.0 40.0 37.0 40.0 10-11 38.827375 40.0 37.0 40.0 37.0 40.0 12-13 38.817375 40.0 37.0 40.0 37.0 40.0 14-15 38.844 40.0 37.0 40.0 37.0 40.0 16-17 38.78675 40.0 37.0 40.0 37.0 40.0 18-19 38.720124999999996 40.0 37.0 40.0 37.0 40.0 20-21 38.642250000000004 40.0 37.0 40.0 37.0 40.0 22-23 38.582625 40.0 37.0 40.0 37.0 40.0 24-25 38.483125 40.0 37.0 40.0 37.0 40.0 26-27 38.46075 40.0 37.0 40.0 37.0 40.0 28-29 38.51975 40.0 37.0 40.0 37.0 40.0 30-31 38.50425 40.0 37.0 40.0 37.0 40.0 32-33 38.362624999999994 40.0 37.0 40.0 37.0 40.0 34-35 38.283125 40.0 37.0 40.0 37.0 40.0 36-37 38.155375 40.0 37.0 40.0 37.0 40.0 38-39 38.1345 40.0 37.0 40.0 37.0 40.0 40-41 38.019999999999996 40.0 37.0 40.0 37.0 40.0 42-43 37.868875 37.0 37.0 40.0 37.0 40.0 44-45 37.73524999999999 37.0 37.0 40.0 37.0 40.0 46-47 37.6095 37.0 37.0 40.0 37.0 40.0 48-49 37.409000000000006 37.0 37.0 40.0 35.0 40.0 50-51 37.274625 37.0 37.0 40.0 33.0 40.0 52-53 37.13675 37.0 37.0 40.0 33.0 40.0 54-55 36.929 37.0 37.0 37.0 33.0 40.0 56-57 36.79925 37.0 37.0 37.0 33.0 40.0 58-59 36.56125 37.0 37.0 37.0 33.0 40.0 60-61 36.429125 37.0 37.0 37.0 33.0 40.0 62-63 36.28125 37.0 37.0 37.0 33.0 37.0 64-65 36.134625 37.0 37.0 37.0 33.0 37.0 66-67 36.076499999999996 37.0 37.0 37.0 33.0 37.0 68-69 35.257999999999996 37.0 35.0 37.0 33.0 37.0 70-71 35.41020898143502 37.0 35.0 37.0 33.0 37.0 72-73 35.8176736714974 37.0 37.0 37.0 33.0 37.0 74-75 35.65068638497325 37.0 37.0 37.0 33.0 37.0 76-77 35.70079772117609 37.0 37.0 37.0 33.0 37.0 78-79 35.77369095221108 37.0 37.0 37.0 33.0 37.0 80-81 35.69339118500423 37.0 37.0 37.0 33.0 37.0 82-83 35.60549583855523 37.0 37.0 37.0 33.0 37.0 84-85 35.57625603585802 37.0 37.0 37.0 33.0 37.0 86-87 35.53172690763052 37.0 37.0 37.0 33.0 37.0 88-89 35.6429718875502 37.0 37.0 37.0 33.0 37.0 90-91 35.53587684069612 37.0 37.0 37.0 33.0 37.0 92-93 35.40562248995984 37.0 33.0 37.0 33.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 2.0 21 2.0 22 2.0 23 9.0 24 8.0 25 5.0 26 15.0 27 10.0 28 16.0 29 15.0 30 37.0 31 30.0 32 47.0 33 62.0 34 89.0 35 164.0 36 668.0 37 1144.0 38 1627.0 39 48.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 65.9 8.125 7.7 18.275 2 49.85 26.400000000000002 14.625 9.125 3 27.675 40.150000000000006 18.275 13.900000000000002 4 31.275 25.624999999999996 21.375 21.725 5 25.974999999999998 25.6 27.800000000000004 20.625 6 20.775 32.675 27.400000000000002 19.15 7 33.800000000000004 26.6 21.5 18.099999999999998 8 26.5 28.425 28.075 17.0 9 23.799999999999997 27.875 30.125 18.2 10-11 24.375 27.1 29.849999999999998 18.675 12-13 25.137500000000003 27.8125 28.5875 18.462500000000002 14-15 20.3875 28.6875 31.0125 19.9125 16-17 23.549999999999997 31.0625 24.525 20.8625 18-19 22.7375 26.1625 30.45 20.65 20-21 25.2875 25.174999999999997 28.875 20.6625 22-23 27.5875 23.150000000000002 27.5625 21.7 24-25 24.0375 26.875 28.812500000000004 20.275000000000002 26-27 24.224999999999998 25.0625 29.625 21.087500000000002 28-29 24.962500000000002 27.175 28.225 19.6375 30-31 25.4625 27.175 27.537499999999998 19.825 32-33 24.0125 25.55 28.925 21.512500000000003 34-35 23.05 30.225 26.625 20.1 36-37 25.025 27.05 26.200000000000003 21.725 38-39 25.9407425928241 26.515814476809602 27.765970746343292 19.777472184023004 40-41 25.637500000000003 24.175 28.449999999999996 21.7375 42-43 25.424999999999997 28.9375 27.187499999999996 18.45 44-45 22.9375 26.85 29.75 20.4625 46-47 25.4 26.075 27.85 20.674999999999997 48-49 23.2625 26.0375 30.45 20.25 50-51 22.75 26.224999999999998 30.625000000000004 20.4 52-53 25.05 27.275 28.125 19.55 54-55 24.5625 26.2625 29.9 19.275000000000002 56-57 24.9 28.95 27.0625 19.0875 58-59 24.95 27.250000000000004 28.225 19.575 60-61 26.650000000000002 28.5625 26.75 18.0375 62-63 22.787499999999998 27.025 31.775 18.4125 64-65 22.468117029257314 30.89522380595149 27.59439859964991 19.042260565141287 66-67 24.25 28.475 27.750000000000004 19.525000000000002 68-69 21.0125 28.325 28.762500000000003 21.9 70-71 24.63060355622339 28.149261207112446 27.61081893313298 19.60931630353118 72-73 24.624889673433362 26.74315975286849 28.54621107048291 20.08573950321523 74-75 24.34871012835176 27.398652941924006 29.36840767568941 18.88422925403482 76-77 23.435897435897434 26.871794871794876 28.012820512820515 21.679487179487182 78-79 24.961260330578515 26.45919421487603 29.01601239669421 19.56353305785124 80-81 22.68041237113402 30.014354691374134 27.678454913219362 19.62677802427248 82-83 21.501255451301702 29.285053521871284 27.580282806924806 21.633408219902208 84-85 22.854091576558535 25.0166866906955 29.96929648912028 22.159925243625683 86-87 20.44176706827309 28.313253012048197 28.433734939759038 22.811244979919678 88-89 20.69611780455154 28.862115127175368 29.919678714859437 20.522088353413654 90-91 22.47657295850067 29.062918340026773 26.974564926372157 21.485943775100402 92-93 21.76706827309237 30.42838018741633 28.206157965194112 19.598393574297187 >>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 0.5 18 0.5 19 1.5 20 1.5 21 1.5 22 1.0 23 2.0 24 7.0 25 10.5 26 13.0 27 19.5 28 28.5 29 29.5 30 28.5 31 36.5 32 45.5 33 61.5 34 85.0 35 82.0 36 107.0 37 166.5 38 184.0 39 190.0 40 230.5 41 231.5 42 262.0 43 324.5 44 263.0 45 206.5 46 190.5 47 173.5 48 158.0 49 125.5 50 138.5 51 164.0 52 145.0 53 134.0 54 144.5 55 109.0 56 68.5 57 65.0 58 50.0 59 28.5 60 24.5 61 27.0 62 20.0 63 13.5 64 11.5 65 9.5 66 9.0 67 9.5 68 12.0 69 10.0 70 5.0 71 3.0 72 1.5 73 0.0 74 0.0 75 0.0 76 0.0 77 0.5 78 1.0 79 0.5 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 0.0 10-11 0.0 12-13 0.0 14-15 0.0 16-17 0.0 18-19 0.0 20-21 0.0 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.0 30-31 0.0 32-33 0.0 34-35 0.0 36-37 0.0 38-39 0.0125 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0 54-55 0.0 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.025 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 14.0 71 14.0 72 13.0 73 17.0 74 15.0 75 20.0 76 14.0 77 15.0 78 12.0 79 25.0 80 19.0 81 27.0 82 23.0 83 16.0 84 21.0 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 3735.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 74.45 #Duplication Level Percentage of deduplicated Percentage of total 1 91.57152451309604 68.175 2 4.029550033579583 6.0 3 1.3431833445265278 3.0 4 1.0073875083948958 3.0 5 0.4029550033579583 1.5 6 0.4029550033579583 1.7999999999999998 7 0.16789791806581597 0.8750000000000001 8 0.1343183344526528 0.8 9 0.0335795836131632 0.22499999999999998 >10 0.8059100067159166 10.15 >50 0.10073875083948958 4.475 >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 GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 67 1.675 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 59 1.4749999999999999 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 53 1.325 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 37 0.9249999999999999 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 32 0.8 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 32 0.8 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 30 0.75 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 27 0.675 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 20 0.5 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 19 0.475 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 16 0.4 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 15 0.375 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 15 0.375 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 15 0.375 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 14 0.35000000000000003 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 14 0.35000000000000003 No Hit GTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGT 13 0.325 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 12 0.3 No Hit GTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAA 12 0.3 No Hit GCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 11 0.27499999999999997 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 11 0.27499999999999997 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 11 0.27499999999999997 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 10 0.25 No Hit GCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATG 10 0.25 No Hit GGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCAT 10 0.25 No Hit AGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAA 10 0.25 No Hit CGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAG 10 0.25 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 9 0.22499999999999998 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 8 0.2 No Hit AACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCCC 8 0.2 No Hit AACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGA 8 0.2 No Hit GCACCCTAGATGGCTAAAGTCCAGTAGCCGAAAGCATCACTAGCTTACGC 8 0.2 No Hit CGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTAT 7 0.17500000000000002 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 7 0.17500000000000002 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 7 0.17500000000000002 No Hit CACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGT 7 0.17500000000000002 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 7 0.17500000000000002 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 6 0.15 No Hit GGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCATAGAT 6 0.15 No Hit GATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGC 6 0.15 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 6 0.15 No Hit GGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGA 6 0.15 No Hit TCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCAT 6 0.15 No Hit TATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAG 6 0.15 No Hit CGGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACC 6 0.15 No Hit GTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTC 6 0.15 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 6 0.15 No Hit GGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAA 6 0.15 No Hit TCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 6 0.15 No Hit GGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTA 5 0.125 No Hit GGTCAACCTTTTAAACTGCCTGCTGAATCCATGAGCAGGCAAGAGACAAC 5 0.125 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 5 0.125 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 5 0.125 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 5 0.125 No Hit GGGACGCATGCAACGACCATCTACATATAGCTACTCGATCTACCGCTACC 5 0.125 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 5 0.125 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 5 0.125 No Hit CGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAA 5 0.125 No Hit GGAAATTAACAGTTGGAAAGGGCGATCGGTCTTGATCCCTCTGTGTTTCC 5 0.125 No Hit GAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCC 5 0.125 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 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 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0125 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.025 0.0 0.0 0.0 0.0 68-69 0.025 0.0 0.0 0.0 0.0 70-71 0.025 0.0 0.0 0.0 0.0 72-73 0.025 0.0 0.0 0.0 0.0 74-75 0.025 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.025 0.0 0.0 0.0 0.0 80-81 0.025 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Rejected 305151 READS because READLEN < 1 Read 305151 spots for ERR6133364.sra Written 305151 spots for ERR6133364.sra Rejected 305151 READS because READLEN < 1 Read 305151 spots for ERR6133364.sra Written 305151 spots for ERR6133364.sra Rejected 305151 READS because READLEN < 1 Read 305151 spots for ERR6133364.sra Written 305151 spots for ERR6133364.sra Rejected 305151 READS because READLEN < 1 Read 305151 spots for ERR6133364.sra Written 305151 spots for ERR6133364.sra Rejected 305151 READS because READLEN < 1 Read 305151 spots for ERR6133364.sra Written 305151 spots for ERR6133364.sra Rejected 305151 READS because READLEN < 1 Read 305151 spots for ERR6133364.sra Written 305151 spots for ERR6133364.sra Rejected 305151 READS because READLEN < 1 Read 305151 spots for ERR6133364.sra Written 305151 spots for ERR6133364.sra Rejected 305151 READS because READLEN < 1 Read 305151 spots for ERR6133364.sra Written 305151 spots for ERR6133364.sra Rejected 305151 READS because READLEN < 1 Read 305151 spots for ERR6133364.sra Written 305151 spots for ERR6133364.sra Rejected 305151 READS because READLEN < 1 Read 305151 spots for ERR6133364.sra Written 305151 spots for ERR6133364.sra Rejected 305151 READS because READLEN < 1 Read 305151 spots for ERR6133364.sra Written 305151 spots for ERR6133364.sra Rejected 305151 READS because READLEN < 1 Read 305151 spots for ERR6133364.sra Written 305151 spots for ERR6133364.sra Rejected 305151 READS because READLEN < 1 Read 305151 spots for ERR6133364.sra Written 305151 spots for ERR6133364.sra Rejected 305151 READS because READLEN < 1 Read 305151 spots for ERR6133364.sra Written 305151 spots for ERR6133364.sra Rejected 305151 READS because READLEN < 1 Read 305151 spots for ERR6133364.sra Written 305151 spots for ERR6133364.sra Rejected 305169 READS because READLEN < 1 Read 305169 spots for ERR6133364.sra Written 305169 spots for ERR6133364.sra Rejected 305151 READS because READLEN < 1 Read 305151 spots for ERR6133364.sra Written 305151 spots for ERR6133364.sra Rejected 305151 READS because READLEN < 1 Read 305151 spots for ERR6133364.sra Written 305151 spots for ERR6133364.sra Rejected 305151 READS because READLEN < 1 Read 305151 spots for ERR6133364.sra Written 305151 spots for ERR6133364.sra Rejected 305151 READS because READLEN < 1 Read 305151 spots for ERR6133364.sra Written 305151 spots for ERR6133364.sra SRR ids: ['ERR6133364.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_r65zjc0e ERR6133364.sra spots: 6103038 blocks: [[1, 305151], [305152, 610302], [610303, 915453], [915454, 1220604], [1220605, 1525755], [1525756, 1830906], [1830907, 2136057], [2136058, 2441208], [2441209, 2746359], [2746360, 3051510], [3051511, 3356661], [3356662, 3661812], [3661813, 3966963], [3966964, 4272114], [4272115, 4577265], [4577266, 4882416], [4882417, 5187567], [5187568, 5492718], [5492719, 5797869], [5797870, 6103038]] ERR6133364 file size 1344333 ERR6133364 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 ERR6133364 ERR6133364_1.fastq Input file: ERR6133364_1.fastq trimmed: ERR6133364-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 01:29:47 2024 >> started Sat Dec 7 01:29:51 2024 >> done (3.444s) 6103038 reads processed; of these: 417 ( 0.01%) short reads filtered out after trimming by size control 11 ( 0.00%) empty reads filtered out after trimming by size control 6102610 (99.99%) reads available; of these: 37017 ( 0.61%) trimmed reads available after processing 6065593 (99.39%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 44 0.00% 19 83 0.00% 20 39 0.00% 21 33 0.00% 22 43 0.00% 23 39 0.00% 24 24 0.00% 25 16 0.00% 26 32 0.00% 27 33 0.00% 28 44 0.00% 29 354 0.01% 30 21 0.00% 31 37 0.00% 32 93 0.00% 33 776 0.01% 34 34 0.00% 35 85 0.00% 36 26 0.00% 37 31 0.00% 38 50 0.00% 39 128 0.00% 40 216 0.00% 41 62 0.00% 42 26 0.00% 43 45 0.00% 44 61 0.00% 45 37 0.00% 46 20 0.00% 47 19 0.00% 48 23 0.00% 49 19 0.00% 50 38 0.00% 51 258 0.00% 52 37 0.00% 53 27 0.00% 54 23 0.00% 55 15 0.00% 56 23 0.00% 57 74 0.00% 58 40 0.00% 59 19 0.00% 60 38 0.00% 61 39 0.00% 62 16 0.00% 63 23 0.00% 64 25 0.00% 65 33 0.00% 66 42 0.00% 67 53 0.00% 68 91 0.00% 69 186 0.00% 70 26638 0.44% 71 24914 0.41% 72 25730 0.42% 73 24675 0.40% 74 23710 0.39% 75 23189 0.38% 76 22476 0.37% 77 24525 0.40% 78 24545 0.40% 79 26175 0.43% 80 26446 0.43% 81 34579 0.57% 82 35487 0.58% 83 29071 0.48% 84 35851 0.59% 85 248 0.00% 86 344 0.01% 87 516 0.01% 88 774 0.01% 89 1318 0.02% 90 2367 0.04% 91 5536 0.09% 92 18755 0.31% 93 5661048 92.76% 6102610 reads passed initial QC criterion=sequence-density sequence-density=2.69 sequence-density-rank=1 fanout-score=2.03 fanout-score-rank=25 prefix-density=2.73 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=30 fanout-score=28.85 fanout-score-rank=1 prefix-density=0.04 prefix-fanout=4.5 sequence=GCTGCACCTGCGGCCACTGAAGCAGCAGCCTCTGATGCCTCTACCCGTACTACACTACTAGTAACCCCAGCTTAATTACGCTAACCCACGAGCACACGTGTCTGCTTGATGCGTGCGCACGTGGCGCGGCGTAAGCTATGACAATAAAAAGTGTGCTGTACCTGATGTGTCTGTGTGTCGATCTATGTCTGTCACGTACGTGGTCGTGCAAAAAACCCTGAAAGTTTAATTGGCTGGTTAATTTGTGCATAGGGAAATTAACAGTTGGAAAGGGCGATCGGTCTTGATCCCTCTGTGTTTCCCGTGTAACGGCTACTGATCCAGTGGTTAAGCTTCGGGTTGTATGTGAGTCCGTACGTGTTTGCATGGAATGAAATTTATCGTGTGGTCTTACTATC 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: 0 (0.00%) aligned 0 times 0 (0.00%) aligned exactly 1 time 1 (100.00%) aligned >1 times 100.00% overall alignment rate Potential adapter found in reference sequence. Continuing without clipping. Started job on | Dec 07 01:30:18 Started mapping on | Dec 07 01:30:18 Finished on | Dec 07 01:30:27 Mapping speed, Million of reads per hour | 2441.04 Number of input reads | 6102610 Average input read length | 91 UNIQUE READS: Uniquely mapped reads number | 3280235 Uniquely mapped reads % | 53.75% Average mapped length | 91.10 Number of splices: Total | 108151 Number of splices: Annotated (sjdb) | 86194 Number of splices: GT/AG | 103472 Number of splices: GC/AG | 2145 Number of splices: AT/AC | 115 Number of splices: Non-canonical | 2419 Mismatch rate per base, % | 0.40% Deletion rate per base | 0.05% Deletion average length | 1.72 Insertion rate per base | 0.02% Insertion average length | 1.70 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 2484873 % of reads mapped to multiple loci | 40.72% Number of reads mapped to too many loci | 199174 % of reads mapped to too many loci | 3.26% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.10% % of reads unmapped: other | 0.17% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 337502 337502 337502 N_multimapping 2484873 2484873 2484873 N_noFeature 288412 323523 3141509 N_ambiguous 120305 16752 508 UnstrandedReadsAssigned:2871518 PositiveStrandReadsAssigned:2939960 NegativeStrandReadsAssigned:138218 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133364 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: ERR6133364-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 6,102,610 reads, 4,345,099 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 988 rounds 52973 ERR6133364.ke.tsv 35125 ERR6133364.se.tsv 88098 total ==> ERR6133364.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 79 17.7444 PNS24243 293 194 0 0 KQK14069 1603 1504 194 39.7504 KQK14071 474 375 0 0 ==> ERR6133364.se.tsv <== BRADI_1g14170v3 194 BRADI_1g53295v3 14 BRADI_1g59795v3 27 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 19 BRADI_1g74790v3 46 BRADI_1g09890v3 0 BRADI_1g77505v3 69 BRADI_1g48960v3 0 ERR6133364 completed mapping pipeline successfully