Starting /dee2/code/volunteer_pipeline.sh ERR6133490 current disk space = 1544558161920 free memory = 1476865908 ERR6133490 SRAfilesize ec118fa09ada903f720ed1b0cf857678 ERR6133490.sra ERR6133490.sra file validated ERR6133490 is single end ERR6133490 is conventional basespace ERR6133490 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133490_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.521 37.0 33.0 37.0 33.0 37.0 2 36.53525 37.0 37.0 37.0 37.0 37.0 3 36.0485 37.0 37.0 37.0 33.0 37.0 4 35.4905 37.0 37.0 37.0 33.0 37.0 5 35.31575 37.0 37.0 37.0 33.0 37.0 6 35.692 37.0 37.0 37.0 33.0 37.0 7 37.627 40.0 37.0 40.0 33.0 40.0 8 37.72575 40.0 37.0 40.0 33.0 40.0 9 37.73975 40.0 37.0 40.0 33.0 40.0 10-11 37.63175 40.0 37.0 40.0 33.0 40.0 12-13 37.548 40.0 37.0 40.0 33.0 40.0 14-15 37.544624999999996 37.0 37.0 40.0 33.0 40.0 16-17 37.432874999999996 38.5 37.0 40.0 33.0 40.0 18-19 37.445625 37.0 37.0 40.0 33.0 40.0 20-21 37.29675 37.0 37.0 40.0 33.0 40.0 22-23 37.2595 37.0 37.0 40.0 33.0 40.0 24-25 37.376875 37.0 37.0 40.0 33.0 40.0 26-27 37.3025 37.0 37.0 40.0 33.0 40.0 28-29 37.258250000000004 37.0 37.0 40.0 33.0 40.0 30-31 37.121624999999995 37.0 37.0 40.0 33.0 40.0 32-33 36.973875 37.0 37.0 40.0 33.0 40.0 34-35 36.843 37.0 37.0 40.0 33.0 40.0 36-37 36.6805 37.0 37.0 40.0 33.0 40.0 38-39 36.432375 37.0 37.0 40.0 33.0 40.0 40-41 36.2285 37.0 37.0 40.0 33.0 40.0 42-43 36.0985 37.0 37.0 40.0 33.0 40.0 44-45 35.8315 37.0 35.0 40.0 33.0 40.0 46-47 35.591 37.0 33.0 37.0 33.0 40.0 48-49 35.435125 37.0 33.0 37.0 33.0 40.0 50-51 35.385374999999996 37.0 33.0 37.0 33.0 40.0 52-53 35.02975 37.0 33.0 37.0 27.0 40.0 54-55 35.01825 37.0 33.0 37.0 27.0 40.0 56-57 34.786500000000004 37.0 33.0 37.0 27.0 38.5 58-59 33.57825 35.0 33.0 37.0 27.0 37.0 60-61 34.255624999999995 37.0 33.0 37.0 27.0 37.0 62-63 34.29675 37.0 33.0 37.0 27.0 37.0 64-65 34.18725 37.0 33.0 37.0 27.0 37.0 66-67 34.238125 37.0 33.0 37.0 27.0 37.0 68-69 33.536249999999995 35.0 33.0 37.0 27.0 37.0 70-71 33.65354848218766 35.0 33.0 37.0 27.0 37.0 72-73 33.93954028203525 37.0 33.0 37.0 27.0 37.0 74-75 33.684552244318795 37.0 33.0 37.0 27.0 37.0 76-77 33.81807157452782 37.0 33.0 37.0 27.0 37.0 78-79 33.87722332386795 37.0 33.0 37.0 27.0 37.0 80-81 33.78026879636821 37.0 33.0 37.0 27.0 37.0 82-83 33.68987243081608 37.0 33.0 37.0 27.0 37.0 84-85 33.72282934875065 37.0 33.0 37.0 27.0 37.0 86-87 33.51469823100936 37.0 33.0 37.0 27.0 37.0 88-89 33.731789802289285 37.0 33.0 37.0 27.0 37.0 90-91 33.46266909469303 37.0 33.0 37.0 27.0 37.0 92-93 33.30762226847034 37.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 12.0 21 18.0 22 14.0 23 26.0 24 23.0 25 33.0 26 42.0 27 39.0 28 79.0 29 61.0 30 69.0 31 115.0 32 131.0 33 134.0 34 256.0 35 412.0 36 888.0 37 1000.0 38 633.0 39 15.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 83.525 3.9 6.225 6.35 2 65.77499999999999 21.05 8.35 4.825 3 32.925 36.8 15.4 14.875 4 30.2 26.150000000000002 19.900000000000002 23.75 5 23.125 31.025000000000002 28.675 17.175 6 18.025 37.0 27.900000000000002 17.075000000000003 7 36.35 27.474999999999998 19.875 16.3 8 30.049999999999997 28.299999999999997 24.375 17.275 9 23.175 27.05 28.375 21.4 10-11 23.35 28.3375 27.85 20.4625 12-13 24.637500000000003 26.5 27.9375 20.925 14-15 21.275 31.362499999999997 28.999999999999996 18.3625 16-17 23.825 32.3625 24.0625 19.75 18-19 22.6125 27.625 27.675 22.0875 20-21 26.378297287160894 26.065758219777475 27.65345668208526 19.90248781097637 22-23 30.049999999999997 22.025 27.525 20.4 24-25 24.915614451806476 26.978372296537067 27.665958244780597 20.44005500687586 26-27 27.3625 24.9125 29.9375 17.7875 28-29 25.6064016004001 26.39409852463116 27.969492373093274 20.030007501875467 30-31 27.9125 25.137500000000003 27.1 19.85 32-33 23.9125 27.075 27.725 21.2875 34-35 23.925 28.512500000000003 25.837500000000002 21.725 36-37 24.925 26.05 26.8625 22.162499999999998 38-39 28.19614711033275 23.892919689767325 29.97247935951964 17.938453840380287 40-41 26.68918918918919 25.425425425425423 26.126126126126124 21.75925925925926 42-43 25.381345336334082 29.332333083270818 26.63165791447862 18.65466366591648 44-45 22.85 28.050000000000004 28.4 20.7 46-47 25.275 24.712500000000002 27.950000000000003 22.0625 48-49 23.724999999999998 25.35 30.7125 20.2125 50-51 23.225 25.3 30.575000000000003 20.9 52-53 27.134986225895318 26.383671424993736 25.66992236413724 20.811419984973703 54-55 26.424999999999997 27.224999999999998 28.375 17.974999999999998 56-57 26.950000000000003 26.974999999999998 27.725 18.35 58-59 22.9375 24.8 31.275 20.9875 60-61 25.0375 26.8375 28.487499999999997 19.6375 62-63 20.6625 31.125000000000004 30.875000000000004 17.3375 64-65 21.575 29.8875 29.062500000000004 19.475 66-67 23.9375 30.375000000000004 27.0125 18.675 68-69 22.3 26.4625 27.712500000000002 23.525 70-71 23.491109441522664 27.38542449286251 28.149261207112446 20.97420485850238 72-73 26.29190824300479 25.40962944290396 28.258129568943787 20.040332745147467 74-75 23.056469992403137 28.564193466700434 29.50113952899468 18.878197011901747 76-77 22.294289711306117 25.931578278010935 27.57217347068549 24.201958539997456 78-79 25.693113581193305 24.594352881052767 30.126485243388274 19.586048294365657 80-81 23.23699421965318 31.085420680796403 27.24470134874759 18.432883750802826 82-83 23.029286543671784 27.028770481228225 29.815507676428847 20.12643529867114 84-85 22.363636363636363 23.42857142857143 32.857142857142854 21.350649350649352 86-87 20.889698231009366 26.716961498439122 30.072840790842868 22.320499479708637 88-89 19.523933402705516 30.515088449531735 30.293964620187303 19.667013527575442 90-91 24.661810613943807 27.79656607700312 29.09729448491155 18.44432882414152 92-93 23.23100936524454 29.5525494276795 28.616024973985432 18.60041623309053 >>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 1.5 17 9.5 18 8.5 19 1.0 20 1.0 21 0.5 22 1.0 23 3.5 24 7.5 25 10.5 26 11.5 27 15.0 28 22.0 29 25.0 30 26.5 31 42.5 32 61.0 33 75.5 34 83.0 35 87.5 36 116.0 37 149.0 38 163.0 39 166.0 40 177.0 41 191.5 42 226.0 43 255.5 44 227.0 45 193.5 46 206.5 47 189.5 48 149.0 49 161.0 50 207.0 51 193.0 52 140.5 53 128.5 54 124.5 55 96.5 56 61.0 57 53.0 58 46.0 59 33.5 60 25.0 61 24.5 62 25.5 63 20.5 64 19.0 65 20.0 66 19.5 67 18.5 68 13.5 69 10.0 70 9.5 71 9.0 72 7.0 73 5.5 74 4.5 75 2.5 76 2.0 77 1.5 78 0.5 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-11 0.0 12-13 0.0 14-15 0.0 16-17 0.0 18-19 0.0 20-21 0.0125 22-23 0.0 24-25 0.0125 26-27 0.0 28-29 0.025 30-31 0.0 32-33 0.0 34-35 0.0 36-37 0.0 38-39 0.075 40-41 0.1 42-43 0.025 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.17500000000000002 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 14.0 71 12.0 72 14.0 73 6.0 74 10.0 75 8.0 76 9.0 77 10.0 78 7.0 79 14.0 80 7.0 81 7.0 82 13.0 83 13.0 84 12.0 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 3844.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 73.825 #Duplication Level Percentage of deduplicated Percentage of total 1 91.53403318658991 67.575 2 4.53775821198781 6.7 3 1.2529630883846934 2.775 4 0.6772773450728073 2.0 5 0.4063664070436844 1.5 6 0.37250253979004405 1.6500000000000001 7 0.23704707077548257 1.225 8 0.033863867253640365 0.2 9 0.06772773450728073 0.44999999999999996 >10 0.7788689468337284 10.299999999999999 >50 0.06772773450728073 2.9250000000000003 >100 0.033863867253640365 2.7 >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 TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 108 2.7 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 66 1.6500000000000001 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 51 1.275 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 36 0.8999999999999999 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 34 0.8500000000000001 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 29 0.7250000000000001 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 26 0.65 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 26 0.65 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 25 0.625 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 23 0.575 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 19 0.475 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 17 0.42500000000000004 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 16 0.4 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 15 0.375 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 15 0.375 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 14 0.35000000000000003 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 13 0.325 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 13 0.325 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 13 0.325 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 13 0.325 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 13 0.325 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 11 0.27499999999999997 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 11 0.27499999999999997 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 10 0.25 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 10 0.25 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 10 0.25 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 9 0.22499999999999998 No Hit GCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAA 9 0.22499999999999998 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 8 0.2 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 7 0.17500000000000002 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 7 0.17500000000000002 No Hit GAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGG 7 0.17500000000000002 No Hit GGAGTCCCATATATATATGTATAAGATGCCAGCCCGGTTTCGTCAACCAT 7 0.17500000000000002 No Hit GGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTACCTGCT 7 0.17500000000000002 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 7 0.17500000000000002 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 7 0.17500000000000002 No Hit GGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTC 6 0.15 No Hit GGAGTGGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGAG 6 0.15 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 6 0.15 No Hit GTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCA 6 0.15 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 6 0.15 No Hit GATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAAT 6 0.15 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 6 0.15 No Hit GAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAAT 6 0.15 No Hit GAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTG 6 0.15 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 6 0.15 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 6 0.15 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 5 0.125 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 5 0.125 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 5 0.125 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 5 0.125 No Hit GGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTA 5 0.125 No Hit GGATATCGTGTGTGTACATTTGAATGTACCGACATGGGCTCGAGGAGCAT 5 0.125 No Hit GGAGATGACCCTACAGATCGATCCATTGATGTGGATGCGATGCCATGGAG 5 0.125 No Hit GATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGC 5 0.125 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 5 0.125 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 5 0.125 No Hit GGGGAAGTACACCAGCGACGGCGAGGCCGCCGCCGCCAAGGAAGGCATGT 5 0.125 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 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 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.05 0.0 0.0 0.0 0.0 74-75 0.05 0.0 0.0 0.0 0.0 76-77 0.0625 0.0 0.0 0.0 0.0 78-79 0.075 0.0 0.0 0.0 0.0 80-81 0.075 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 8.8337105E-4 86.700005 1 GGGATGA 25 0.0066977916 52.020004 1 AATTTGG 30 1.2981374E-4 36.125 18-19 TTACAAT 30 1.2981374E-4 36.125 14-15 TTTGGTG 30 1.2981374E-4 36.125 20-21 TGTATTA 30 1.2981374E-4 36.125 10-11 TGGTGGA 30 1.2981374E-4 36.125 22-23 ACAATTT 30 1.2981374E-4 36.125 16-17 TAGGACA 35 3.211819E-4 30.964285 36-37 AGGAACT 35 3.211819E-4 30.964285 28-29 CCTTGGG 35 3.211819E-4 30.964285 44-45 ACATCCT 35 3.211819E-4 30.964285 40-41 TTGGGGA 35 3.211819E-4 30.964285 46-47 TTTAGGA 35 3.211819E-4 30.964285 34-35 TATTACA 35 3.211819E-4 30.964285 12-13 GTGGAGG 35 3.211819E-4 30.964285 24-25 GTATTAC 30 0.0058234707 28.9 12-13 ATTACAA 30 0.0058234707 28.9 14-15 TACAATT 30 0.0058234707 28.9 16-17 ATTTGGT 30 0.0058234707 28.9 20-21 >>END_MODULE Rejected 185760 READS because READLEN < 1 Read 185760 spots for ERR6133490.sra Written 185760 spots for ERR6133490.sra Rejected 185760 READS because READLEN < 1 Read 185760 spots for ERR6133490.sra Written 185760 spots for ERR6133490.sra Rejected 185760 READS because READLEN < 1 Read 185760 spots for ERR6133490.sra Written 185760 spots for ERR6133490.sra Rejected 185760 READS because READLEN < 1 Read 185760 spots for ERR6133490.sra Written 185760 spots for ERR6133490.sra Rejected 185760 READS because READLEN < 1 Read 185760 spots for ERR6133490.sra Written 185760 spots for ERR6133490.sra Rejected 185760 READS because READLEN < 1 Read 185760 spots for ERR6133490.sra Written 185760 spots for ERR6133490.sra Rejected 185760 READS because READLEN < 1 Read 185760 spots for ERR6133490.sra Written 185760 spots for ERR6133490.sra Rejected 185760 READS because READLEN < 1 Read 185760 spots for ERR6133490.sra Written 185760 spots for ERR6133490.sra Rejected 185760 READS because READLEN < 1 Read 185760 spots for ERR6133490.sra Written 185760 spots for ERR6133490.sra Rejected 185760 READS because READLEN < 1 Read 185760 spots for ERR6133490.sra Written 185760 spots for ERR6133490.sra Rejected 185760 READS because READLEN < 1 Read 185760 spots for ERR6133490.sra Written 185760 spots for ERR6133490.sra Rejected 185760 READS because READLEN < 1 Read 185760 spots for ERR6133490.sra Written 185760 spots for ERR6133490.sra Rejected 185760 READS because READLEN < 1 Read 185760 spots for ERR6133490.sra Written 185760 spots for ERR6133490.sra Rejected 185760 READS because READLEN < 1 Read 185760 spots for ERR6133490.sra Written 185760 spots for ERR6133490.sra Rejected 185760 READS because READLEN < 1 Read 185760 spots for ERR6133490.sra Written 185760 spots for ERR6133490.sra Rejected 185760 READS because READLEN < 1 Read 185760 spots for ERR6133490.sra Written 185760 spots for ERR6133490.sra Rejected 185760 READS because READLEN < 1 Read 185760 spots for ERR6133490.sra Written 185760 spots for ERR6133490.sra Rejected 185760 READS because READLEN < 1 Read 185760 spots for ERR6133490.sra Written 185760 spots for ERR6133490.sra Rejected 185760 READS because READLEN < 1 Read 185760 spots for ERR6133490.sra Written 185760 spots for ERR6133490.sra Rejected 185779 READS because READLEN < 1 Read 185779 spots for ERR6133490.sra Written 185779 spots for ERR6133490.sra SRR ids: ['ERR6133490.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_kgflf0br ERR6133490.sra spots: 3715219 blocks: [[1, 185760], [185761, 371520], [371521, 557280], [557281, 743040], [743041, 928800], [928801, 1114560], [1114561, 1300320], [1300321, 1486080], [1486081, 1671840], [1671841, 1857600], [1857601, 2043360], [2043361, 2229120], [2229121, 2414880], [2414881, 2600640], [2600641, 2786400], [2786401, 2972160], [2972161, 3157920], [3157921, 3343680], [3343681, 3529440], [3529441, 3715219]] ERR6133490 file size 819980 ERR6133490 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 ERR6133490 ERR6133490_1.fastq Input file: ERR6133490_1.fastq trimmed: ERR6133490-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 07:12:44 2024 >> started Sat Dec 7 07:12:51 2024 >> done (7.539s) 3715219 reads processed; of these: 266 ( 0.01%) short reads filtered out after trimming by size control 30 ( 0.00%) empty reads filtered out after trimming by size control 3714923 (99.99%) reads available; of these: 69794 ( 1.88%) trimmed reads available after processing 3645129 (98.12%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 35 0.00% 19 79 0.00% 20 56 0.00% 21 65 0.00% 22 62 0.00% 23 19 0.00% 24 16 0.00% 25 9 0.00% 26 10 0.00% 27 23 0.00% 28 52 0.00% 29 51 0.00% 30 25 0.00% 31 43 0.00% 32 35 0.00% 33 30 0.00% 34 33 0.00% 35 276 0.01% 36 391 0.01% 37 29 0.00% 38 45 0.00% 39 231 0.01% 40 113 0.00% 41 85 0.00% 42 10 0.00% 43 14 0.00% 44 11 0.00% 45 15 0.00% 46 11 0.00% 47 6 0.00% 48 7 0.00% 49 4 0.00% 50 8 0.00% 51 32 0.00% 52 10 0.00% 53 7 0.00% 54 9 0.00% 55 4 0.00% 56 10 0.00% 57 7 0.00% 58 8 0.00% 59 14 0.00% 60 10 0.00% 61 14 0.00% 62 1 0.00% 63 2 0.00% 64 4 0.00% 65 6 0.00% 66 10 0.00% 67 17 0.00% 68 33 0.00% 69 114 0.00% 70 12008 0.32% 71 10204 0.27% 72 11574 0.31% 73 9541 0.26% 74 10205 0.27% 75 10352 0.28% 76 8549 0.23% 77 8989 0.24% 78 10696 0.29% 79 12599 0.34% 80 10752 0.29% 81 11248 0.30% 82 13172 0.35% 83 13323 0.36% 84 10997 0.30% 85 124 0.00% 86 250 0.01% 87 406 0.01% 88 752 0.02% 89 1439 0.04% 90 3101 0.08% 91 9126 0.25% 92 50787 1.37% 93 3482518 93.74% 3714923 reads passed initial QC criterion=sequence-density sequence-density=0.75 sequence-density-rank=1 fanout-score=2.38 fanout-score-rank=29 prefix-density=0.85 prefix-fanout=2.1 sequence=TGTACATTTGAACCCTGACTACACATATACACACATATACATGTAATATTATACAATCTGTCGAGTATGTGTTGGTTCATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=28 fanout-score=58.19 fanout-score-rank=1 prefix-density=0.11 prefix-fanout=5.7 sequence=AAAAGAAGGGGTGTTCCATCTCCGGACGACGATCCTGCCTGCAGAGGAAGACATGCCGGCGATCATGTCGAGCTTCAAGAAGTTCAACGACTCATTCATGGAGCAATACCAAGACTACTCCAGGCTGTGATGTGAAGAGGGAAACAACGAGGTCATCATCGACATGATATATTGCTGCTATTTTCCACCAGCGATTAAAAGTTAAAAAATTTAGCTGTAAGCTGTAACTATCTTGAAGAAACTAAACTGGTTGCTGTGCTTGATATGTATAGGGAAAACATAATTTATGAGACAATCATACTGTGCAACTCTTGGCTCCATCGATTAATTAATACTCCTTGTTATTGCTTGCATGGTGG Started job on | Dec 07 07:13:12 Started mapping on | Dec 07 07:13:12 Finished on | Dec 07 07:13:28 Mapping speed, Million of reads per hour | 835.86 Number of input reads | 3714923 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 2212042 Uniquely mapped reads % | 59.54% Average mapped length | 91.63 Number of splices: Total | 87098 Number of splices: Annotated (sjdb) | 70379 Number of splices: GT/AG | 82746 Number of splices: GC/AG | 1796 Number of splices: AT/AC | 92 Number of splices: Non-canonical | 2464 Mismatch rate per base, % | 0.51% Deletion rate per base | 0.07% Deletion average length | 1.82 Insertion rate per base | 0.03% Insertion average length | 1.84 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1415709 % of reads mapped to multiple loci | 38.11% Number of reads mapped to too many loci | 31403 % of reads mapped to too many loci | 0.85% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.44% % of reads unmapped: other | 0.06% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 87172 87172 87172 N_multimapping 1415709 1415709 1415709 N_noFeature 181237 206772 2113617 N_ambiguous 84100 11147 597 UnstrandedReadsAssigned:1946705 PositiveStrandReadsAssigned:1994123 NegativeStrandReadsAssigned:97828 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133490 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: ERR6133490-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,714,923 reads, 2,916,528 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 960 rounds 52973 ERR6133490.ke.tsv 35125 ERR6133490.se.tsv 88098 total ==> ERR6133490.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 42 14.0817 PNS24243 293 194 0 0 KQK14069 1603 1504 41 12.5399 KQK14071 474 375 0 0 ==> ERR6133490.se.tsv <== BRADI_1g14170v3 41 BRADI_1g53295v3 28 BRADI_1g59795v3 6 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 22 BRADI_1g74790v3 15 BRADI_1g09890v3 0 BRADI_1g77505v3 47 BRADI_1g48960v3 0 ERR6133490 completed mapping pipeline successfully