Starting /dee2/code/volunteer_pipeline.sh ERR6133413 current disk space = 1547263324160 free memory = 1594885432 ERR6133413 SRAfilesize e9983cdad5d40d7fc4c718112b42bebc ERR6133413.sra ERR6133413.sra file validated ERR6133413 is single end ERR6133413 is conventional basespace ERR6133413 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133413_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 35.457 37.0 33.0 37.0 33.0 37.0 2 36.411 37.0 37.0 37.0 37.0 37.0 3 36.08875 37.0 37.0 37.0 33.0 37.0 4 35.712 37.0 37.0 37.0 33.0 37.0 5 35.4825 37.0 37.0 37.0 33.0 37.0 6 35.77425 37.0 37.0 37.0 33.0 37.0 7 37.75475 40.0 37.0 40.0 33.0 40.0 8 37.768 40.0 37.0 40.0 33.0 40.0 9 37.87975 40.0 37.0 40.0 33.0 40.0 10-11 37.82425 40.0 37.0 40.0 33.0 40.0 12-13 37.735 40.0 37.0 40.0 33.0 40.0 14-15 37.68625 40.0 37.0 40.0 33.0 40.0 16-17 37.661875 40.0 37.0 40.0 33.0 40.0 18-19 37.6 40.0 37.0 40.0 33.0 40.0 20-21 37.511875 40.0 37.0 40.0 33.0 40.0 22-23 37.452875 40.0 37.0 40.0 33.0 40.0 24-25 37.545249999999996 40.0 37.0 40.0 33.0 40.0 26-27 37.575874999999996 40.0 37.0 40.0 33.0 40.0 28-29 37.5105 40.0 37.0 40.0 33.0 40.0 30-31 37.319625 38.5 37.0 40.0 33.0 40.0 32-33 37.15775 37.0 37.0 40.0 33.0 40.0 34-35 37.127125 37.0 37.0 40.0 33.0 40.0 36-37 37.023875000000004 37.0 37.0 40.0 33.0 40.0 38-39 36.712 37.0 37.0 40.0 33.0 40.0 40-41 36.447375 37.0 37.0 40.0 33.0 40.0 42-43 36.277875 37.0 37.0 40.0 33.0 40.0 44-45 35.966375 37.0 35.0 40.0 33.0 40.0 46-47 35.7365 37.0 33.0 38.5 33.0 40.0 48-49 35.732375000000005 37.0 33.0 37.0 33.0 40.0 50-51 35.594125 37.0 33.0 37.0 33.0 40.0 52-53 35.242000000000004 37.0 33.0 37.0 33.0 40.0 54-55 35.199375 37.0 33.0 37.0 33.0 40.0 56-57 34.88 37.0 33.0 37.0 30.0 38.5 58-59 33.538250000000005 35.0 33.0 37.0 27.0 37.0 60-61 34.394 37.0 33.0 37.0 27.0 37.0 62-63 34.511250000000004 37.0 33.0 37.0 27.0 37.0 64-65 34.3785 37.0 33.0 37.0 27.0 37.0 66-67 34.5115 37.0 33.0 37.0 27.0 37.0 68-69 33.7815 35.0 33.0 37.0 30.0 37.0 70-71 33.89575932882545 35.0 33.0 37.0 27.0 37.0 72-73 34.305312909079746 37.0 33.0 37.0 30.0 37.0 74-75 33.99980606293525 37.0 33.0 37.0 27.0 37.0 76-77 34.03681940915717 37.0 33.0 37.0 27.0 37.0 78-79 34.09677916164457 37.0 33.0 37.0 27.0 37.0 80-81 33.972890487289874 37.0 33.0 37.0 27.0 37.0 82-83 33.84360281239023 37.0 33.0 37.0 27.0 37.0 84-85 33.810569011313575 37.0 33.0 37.0 27.0 37.0 86-87 33.686412055079245 37.0 33.0 37.0 27.0 37.0 88-89 33.87100545596259 37.0 33.0 37.0 27.0 37.0 90-91 33.62120031176929 37.0 33.0 37.0 27.0 37.0 92-93 33.40958690568979 37.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 9.0 21 12.0 22 19.0 23 26.0 24 17.0 25 25.0 26 25.0 27 44.0 28 47.0 29 73.0 30 74.0 31 97.0 32 130.0 33 172.0 34 235.0 35 387.0 36 816.0 37 1083.0 38 684.0 39 25.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 80.10000000000001 4.125 9.25 6.525 2 60.199999999999996 24.525 8.95 6.325 3 30.7 34.575 17.275 17.45 4 28.725 27.55 20.424999999999997 23.3 5 23.150000000000002 27.3 31.125000000000004 18.425 6 18.099999999999998 39.800000000000004 25.275 16.825000000000003 7 37.325 27.500000000000004 20.474999999999998 14.7 8 30.15 28.749999999999996 24.05 17.05 9 22.35 26.0 28.1 23.549999999999997 10-11 22.3125 28.425 28.287499999999998 20.974999999999998 12-13 24.45 25.6125 27.1625 22.775000000000002 14-15 22.3625 30.9625 27.325 19.35 16-17 25.25 31.7375 23.8875 19.125 18-19 22.25 28.537499999999998 27.1125 22.1 20-21 26.625 27.1375 27.0125 19.225 22-23 31.3125 22.037499999999998 26.5 20.150000000000002 24-25 24.087500000000002 28.812500000000004 27.85 19.25 26-27 28.675 25.124999999999996 27.975 18.224999999999998 28-29 25.275 26.5625 26.424999999999997 21.7375 30-31 27.450000000000003 25.1 28.449999999999996 19.0 32-33 24.425 27.325 27.700000000000003 20.549999999999997 34-35 21.85 29.5375 26.525 22.0875 36-37 26.337500000000002 26.337500000000002 25.837500000000002 21.4875 38-39 27.494678853136346 24.214348316013524 28.158257167897833 20.132715662952297 40-41 24.307730860794386 27.314872822954516 25.47299837113144 22.90439794511966 42-43 25.753595997498437 29.305816135084427 25.90368980612883 19.036898061288305 44-45 22.6125 29.062500000000004 29.2 19.125 46-47 25.874999999999996 24.175 28.349999999999998 21.6 48-49 23.2625 25.724999999999998 30.162499999999998 20.849999999999998 50-51 21.525 26.3125 30.45 21.712500000000002 52-53 27.147335423197493 25.9435736677116 26.545454545454543 20.363636363636363 54-55 28.075 25.687500000000004 28.175 18.0625 56-57 27.250000000000004 26.75 28.075 17.925 58-59 23.425 24.05 32.2125 20.3125 60-61 25.912499999999998 26.937499999999996 28.9375 18.212500000000002 62-63 20.8125 32.574999999999996 29.325000000000003 17.2875 64-65 22.3625 30.099999999999998 29.675 17.8625 66-67 22.95286910863858 31.428928616077012 26.67833479184898 18.939867483435428 68-69 21.625 26.8 27.175 24.4 70-71 23.095208307268862 27.686725885149503 29.163017640435378 20.055048167146253 72-73 26.528562460765855 27.106089139987443 27.645951035781547 18.71939736346516 74-75 22.828690281104247 28.06000252111433 30.228160847094415 18.883146350687003 76-77 21.582278481012658 25.278481012658226 27.139240506329116 26.0 78-79 27.052524222335546 24.630290668026518 29.21978582355941 19.09739928607853 80-81 23.90745501285347 29.652956298200518 28.483290488431876 17.95629820051414 82-83 22.57272139625081 28.312863606981253 29.631544925662574 19.482870071105367 84-85 21.472153706348177 23.484356744125666 33.35064260677658 21.692846942749576 86-87 20.355936606910884 26.643283969862303 29.72200571577033 23.278773707456484 88-89 19.08287866978436 33.07352559106261 27.669524551831643 20.17407118732138 90-91 24.35697583787997 28.487918939984414 29.579111457521435 17.575993764614186 92-93 23.629514159521953 31.060015588464534 26.786178228111197 18.524292023902312 >>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 11.0 18 13.5 19 3.5 20 1.5 21 5.0 22 5.5 23 5.0 24 6.0 25 5.0 26 9.0 27 13.0 28 23.0 29 33.5 30 34.5 31 41.5 32 56.0 33 76.0 34 94.0 35 97.0 36 102.5 37 122.0 38 162.0 39 186.5 40 178.5 41 192.0 42 222.5 43 238.0 44 198.0 45 171.0 46 199.0 47 188.0 48 152.0 49 167.5 50 257.0 51 247.5 52 145.0 53 122.0 54 121.5 55 81.5 56 50.0 57 50.0 58 42.5 59 33.5 60 28.0 61 26.5 62 25.5 63 20.5 64 18.0 65 15.0 66 12.0 67 9.5 68 8.5 69 10.5 70 11.0 71 9.0 72 6.5 73 4.5 74 4.0 75 3.0 76 2.5 77 1.0 78 0.5 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 0.1625 40-41 0.2375 42-43 0.0625 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.3125 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 0.0125 68-69 0.0 70-71 0.0 72-73 0.0 74-75 0.012603982858583314 76-77 0.0 78-79 0.0 80-81 0.012851818532322323 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 7.0 71 7.0 72 7.0 73 7.0 74 10.0 75 9.0 76 6.0 77 17.0 78 16.0 79 18.0 80 11.0 81 12.0 82 11.0 83 8.0 84 5.0 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 3849.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 74.575 #Duplication Level Percentage of deduplicated Percentage of total 1 92.45725779416695 68.95 2 4.022795843110962 6.0 3 1.2068387529332887 2.7 4 0.5028494803888702 1.5 5 0.30170968823332217 1.125 6 0.23466309084813944 1.05 7 0.2011397921555481 1.05 8 0.16761649346295676 1.0 9 0.0670465973851827 0.44999999999999996 >10 0.771035869929601 10.375 >50 0.03352329869259135 1.375 >100 0.03352329869259135 4.425 >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 177 4.425 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 55 1.375 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 45 1.125 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 37 0.9249999999999999 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 25 0.625 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 23 0.575 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 23 0.575 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 21 0.525 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 21 0.525 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 20 0.5 No Hit GATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGC 20 0.5 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 18 0.44999999999999996 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 15 0.375 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 15 0.375 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 15 0.375 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 15 0.375 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 13 0.325 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 13 0.325 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 13 0.325 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 11 0.27499999999999997 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 11 0.27499999999999997 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 11 0.27499999999999997 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 10 0.25 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 10 0.25 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 10 0.25 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 9 0.22499999999999998 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 9 0.22499999999999998 No Hit GACCACAGCGCATTCCCAATTAGCATCTAAGCTCTCGTTGACATTTCCTT 8 0.2 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 8 0.2 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 8 0.2 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 8 0.2 No Hit GAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGA 8 0.2 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 7 0.17500000000000002 No Hit CAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGG 7 0.17500000000000002 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 7 0.17500000000000002 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 7 0.17500000000000002 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 7 0.17500000000000002 No Hit GGGCCATTTGTGGCATGCAGGAAGAGCCCGAGCTGCTGCAGCAGGTTTTG 7 0.17500000000000002 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 6 0.15 No Hit GATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAAT 6 0.15 No Hit GAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAAT 6 0.15 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 6 0.15 No Hit GGCATATGCCAGCTCTGACCGAAATCTTTGGGGATGATTCTGTATTACAA 6 0.15 No Hit GGGGTACTCTTTCTACACCTATATTAGTATTAGTACCGAAATGCTTTAAA 6 0.15 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 6 0.15 No Hit GGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGT 5 0.125 No Hit GCAACATAGGTCATCGAAAAGATCTCGGACGACTCACCAAAGCACGAAAG 5 0.125 No Hit GGAGTGGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGAG 5 0.125 No Hit GGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTA 5 0.125 No Hit GGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACTA 5 0.125 No Hit GGGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGC 5 0.125 No Hit CGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAG 5 0.125 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 5 0.125 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 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 0.05 0.0 0.0 0.0 0.0 34-35 0.05 0.0 0.0 0.0 0.0 36-37 0.05 0.0 0.0 0.0 0.0 38-39 0.05 0.0 0.0 0.0 0.0 40-41 0.05 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 0.075 0.0 0.0 0.0 0.0 60-61 0.075 0.0 0.0 0.0 0.0 62-63 0.075 0.0 0.0 0.0125 0.0 64-65 0.075 0.0 0.0 0.025 0.0 66-67 0.075 0.0 0.0 0.025 0.0 68-69 0.075 0.0 0.0 0.025 0.0 70-71 0.075 0.0 0.0 0.025 0.0 72-73 0.125 0.0 0.0 0.025 0.0 74-75 0.125 0.0 0.0 0.025 0.0 76-77 0.125 0.0 0.0 0.025 0.0 78-79 0.125 0.0 0.0 0.025 0.0 80-81 0.125 0.0 0.0 0.025 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGCACCC 40 7.60462E-4 43.20625 7 CTAGGCA 40 7.60462E-4 43.20625 4 CACCCAG 40 7.60462E-4 43.20625 9 AGGCACC 40 7.60462E-4 43.20625 6 GCACCCA 40 7.60462E-4 43.20625 8 ACCTAGG 40 7.60462E-4 43.20625 2 CCTAGGC 40 7.60462E-4 43.20625 3 TAGGCAC 40 7.60462E-4 43.20625 5 TACCTAG 45 0.001358058 38.405556 1 CAAATAG 25 0.002004083 35.911686 86-87 CCAAATA 30 0.0048982208 29.926405 86-87 GCATAGA 30 0.005737972 28.985323 68-69 GTGCTGC 30 0.0059187976 28.804165 20-21 >>END_MODULE Rejected 179484 READS because READLEN < 1 Read 179484 spots for ERR6133413.sra Written 179484 spots for ERR6133413.sra Rejected 179484 READS because READLEN < 1 Read 179484 spots for ERR6133413.sra Written 179484 spots for ERR6133413.sra Rejected 179484 READS because READLEN < 1 Read 179484 spots for ERR6133413.sra Written 179484 spots for ERR6133413.sra Rejected 179484 READS because READLEN < 1 Read 179484 spots for ERR6133413.sra Written 179484 spots for ERR6133413.sra Rejected 179484 READS because READLEN < 1 Read 179484 spots for ERR6133413.sra Written 179484 spots for ERR6133413.sra Rejected 179484 READS because READLEN < 1 Read 179484 spots for ERR6133413.sra Written 179484 spots for ERR6133413.sra Rejected 179484 READS because READLEN < 1 Read 179484 spots for ERR6133413.sra Written 179484 spots for ERR6133413.sra Rejected 179484 READS because READLEN < 1 Read 179484 spots for ERR6133413.sra Written 179484 spots for ERR6133413.sra Rejected 179484 READS because READLEN < 1 Read 179484 spots for ERR6133413.sra Written 179484 spots for ERR6133413.sra Rejected 179484 READS because READLEN < 1 Read 179484 spots for ERR6133413.sra Written 179484 spots for ERR6133413.sra Rejected 179484 READS because READLEN < 1 Read 179484 spots for ERR6133413.sra Written 179484 spots for ERR6133413.sra Rejected 179484 READS because READLEN < 1 Read 179484 spots for ERR6133413.sra Written 179484 spots for ERR6133413.sra Rejected 179484 READS because READLEN < 1 Read 179484 spots for ERR6133413.sra Written 179484 spots for ERR6133413.sra Rejected 179484 READS because READLEN < 1 Read 179484 spots for ERR6133413.sra Written 179484 spots for ERR6133413.sra Rejected 179484 READS because READLEN < 1 Read 179484 spots for ERR6133413.sra Written 179484 spots for ERR6133413.sra Rejected 179484 READS because READLEN < 1 Read 179484 spots for ERR6133413.sra Written 179484 spots for ERR6133413.sra Rejected 179489 READS because READLEN < 1 Read 179489 spots for ERR6133413.sra Written 179489 spots for ERR6133413.sra Rejected 179484 READS because READLEN < 1 Read 179484 spots for ERR6133413.sra Written 179484 spots for ERR6133413.sra Rejected 179484 READS because READLEN < 1 Read 179484 spots for ERR6133413.sra Written 179484 spots for ERR6133413.sra Rejected 179484 READS because READLEN < 1 Read 179484 spots for ERR6133413.sra Written 179484 spots for ERR6133413.sra SRR ids: ['ERR6133413.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_hv_u7ghp ERR6133413.sra spots: 3589685 blocks: [[1, 179484], [179485, 358968], [358969, 538452], [538453, 717936], [717937, 897420], [897421, 1076904], [1076905, 1256388], [1256389, 1435872], [1435873, 1615356], [1615357, 1794840], [1794841, 1974324], [1974325, 2153808], [2153809, 2333292], [2333293, 2512776], [2512777, 2692260], [2692261, 2871744], [2871745, 3051228], [3051229, 3230712], [3230713, 3410196], [3410197, 3589685]] ERR6133413 file size 792311 ERR6133413 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 ERR6133413 ERR6133413_1.fastq Input file: ERR6133413_1.fastq trimmed: ERR6133413-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 03:56:15 2024 >> started Sat Dec 7 03:56:17 2024 >> done (2.080s) 3589685 reads processed; of these: 370 ( 0.01%) short reads filtered out after trimming by size control 77 ( 0.00%) empty reads filtered out after trimming by size control 3589238 (99.99%) reads available; of these: 69864 ( 1.95%) trimmed reads available after processing 3519374 (98.05%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 40 0.00% 19 90 0.00% 20 77 0.00% 21 83 0.00% 22 94 0.00% 23 24 0.00% 24 30 0.00% 25 15 0.00% 26 15 0.00% 27 33 0.00% 28 105 0.00% 29 61 0.00% 30 38 0.00% 31 86 0.00% 32 37 0.00% 33 34 0.00% 34 54 0.00% 35 494 0.01% 36 521 0.01% 37 63 0.00% 38 63 0.00% 39 289 0.01% 40 111 0.00% 41 104 0.00% 42 22 0.00% 43 20 0.00% 44 10 0.00% 45 14 0.00% 46 7 0.00% 47 6 0.00% 48 10 0.00% 49 15 0.00% 50 17 0.00% 51 46 0.00% 52 18 0.00% 53 8 0.00% 54 6 0.00% 55 11 0.00% 56 12 0.00% 57 11 0.00% 58 23 0.00% 59 12 0.00% 60 15 0.00% 61 6 0.00% 62 3 0.00% 63 3 0.00% 64 2 0.00% 65 4 0.00% 66 15 0.00% 67 27 0.00% 68 22 0.00% 69 137 0.00% 70 10218 0.28% 71 9572 0.27% 72 11072 0.31% 73 9504 0.26% 74 9685 0.27% 75 9908 0.28% 76 8777 0.24% 77 8935 0.25% 78 9834 0.27% 79 11007 0.31% 80 10072 0.28% 81 10847 0.30% 82 12847 0.36% 83 12558 0.35% 84 10428 0.29% 85 123 0.00% 86 275 0.01% 87 415 0.01% 88 780 0.02% 89 1494 0.04% 90 2951 0.08% 91 9136 0.25% 92 50044 1.39% 93 3365693 93.77% 3589238 reads passed initial QC criterion=sequence-density sequence-density=0.49 sequence-density-rank=1 fanout-score=1.56 fanout-score-rank=31 prefix-density=0.03 prefix-fanout=1.6 sequence=GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAAAAATTCTTCCTGGGTCGATGCCCGAGCGGTTAATGGGGACGGACTGTAAATTCGTTGACAAAATGTCTACGCTGGTTCAAATCCAGCTCGGCCCAAAAATCTGGGGCTTCGTGAATATGAACTAAATCTTTTTATTT criterion=fanout-score sequence-density=0.01 sequence-density-rank=34 fanout-score=85.74 fanout-score-rank=1 prefix-density=0.09 prefix-fanout=7.2 sequence=AAAAGAAGGGGTGTTCCATCTCCGGACGACGATCCTGCCTGCAGAGGAAGACATGCCGGCGATCATGTCGAGCTTCAAGAAGTTCAACGACTCATTCATGGAGCAATACCAAGACTACTCCAGGCTGTGATGTGAAGAGGGAAACAACGAGGTCATCATCGACATGATATATTGCTGCTATTTTCCACCAGCGATTAAAAGTTAAAAAATTTAGCTGTAAGCTGTAACTATCTTGAAGAAACTAAACTGGTTGCTGTGCTTGATATGTATAGGGAAAACATAATTTATGAGACAATCATACTGTGCAACTCTTGGCTCCATCGATTAATTAATACTCCTTGTTATTGCTTGC Started job on | Dec 07 03:56:28 Started mapping on | Dec 07 03:56:28 Finished on | Dec 07 03:56:33 Mapping speed, Million of reads per hour | 2584.25 Number of input reads | 3589238 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 2167147 Uniquely mapped reads % | 60.38% Average mapped length | 91.68 Number of splices: Total | 98053 Number of splices: Annotated (sjdb) | 81143 Number of splices: GT/AG | 94459 Number of splices: GC/AG | 1963 Number of splices: AT/AC | 55 Number of splices: Non-canonical | 1576 Mismatch rate per base, % | 0.43% Deletion rate per base | 0.05% Deletion average length | 1.73 Insertion rate per base | 0.02% Insertion average length | 1.78 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1328967 % of reads mapped to multiple loci | 37.03% Number of reads mapped to too many loci | 34463 % of reads mapped to too many loci | 0.96% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.56% % of reads unmapped: other | 0.07% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 93124 93124 93124 N_multimapping 1328967 1328967 1328967 N_noFeature 159912 182582 2068910 N_ambiguous 85756 10003 460 UnstrandedReadsAssigned:1921479 PositiveStrandReadsAssigned:1974562 NegativeStrandReadsAssigned:97777 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133413 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: ERR6133413-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,589,238 reads, 2,735,672 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,017 rounds 52973 ERR6133413.ke.tsv 35125 ERR6133413.se.tsv 88098 total ==> ERR6133413.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 58 20.5569 PNS24243 293 194 0 0 KQK14069 1603 1504 68 21.986 KQK14071 474 375 0 0 ==> ERR6133413.se.tsv <== BRADI_1g14170v3 68 BRADI_1g53295v3 27 BRADI_1g59795v3 23 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 27 BRADI_1g74790v3 13 BRADI_1g09890v3 0 BRADI_1g77505v3 67 BRADI_1g48960v3 0 ERR6133413 completed mapping pipeline successfully