Starting /dee2/code/volunteer_pipeline.sh ERR6133392 current disk space = 1547402530816 free memory = 1363134868 ERR6133392 SRAfilesize 1032a474fe89dae53ef8aa7dbbf4d22b ERR6133392.sra ERR6133392.sra file validated ERR6133392 is single end ERR6133392 is conventional basespace ERR6133392 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133392_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 36.91025 37.0 37.0 37.0 37.0 37.0 2 36.7995 37.0 37.0 37.0 37.0 37.0 3 36.60525 37.0 37.0 37.0 37.0 37.0 4 36.05625 37.0 37.0 37.0 33.0 37.0 5 36.0735 37.0 37.0 37.0 33.0 37.0 6 36.25375 37.0 37.0 37.0 33.0 37.0 7 38.148 40.0 37.0 40.0 37.0 40.0 8 38.12075 40.0 37.0 40.0 37.0 40.0 9 38.22625 40.0 37.0 40.0 37.0 40.0 10-11 38.19225 40.0 37.0 40.0 37.0 40.0 12-13 38.13875 40.0 37.0 40.0 37.0 40.0 14-15 38.111875 40.0 37.0 40.0 37.0 40.0 16-17 38.061875 40.0 37.0 40.0 35.0 40.0 18-19 37.882125 40.0 37.0 40.0 33.0 40.0 20-21 37.872749999999996 40.0 37.0 40.0 33.0 40.0 22-23 37.784375 40.0 37.0 40.0 33.0 40.0 24-25 37.57575 40.0 37.0 40.0 33.0 40.0 26-27 37.4825 40.0 37.0 40.0 33.0 40.0 28-29 37.3735 37.0 37.0 40.0 33.0 40.0 30-31 37.210499999999996 37.0 37.0 40.0 33.0 40.0 32-33 37.063874999999996 37.0 37.0 40.0 33.0 40.0 34-35 36.863 37.0 37.0 40.0 33.0 40.0 36-37 36.95175 37.0 37.0 40.0 33.0 40.0 38-39 36.992625000000004 37.0 37.0 40.0 33.0 40.0 40-41 37.281875 37.0 37.0 40.0 33.0 40.0 42-43 37.236375 37.0 37.0 40.0 33.0 40.0 44-45 37.084875 37.0 37.0 40.0 33.0 40.0 46-47 36.769625 37.0 37.0 40.0 33.0 40.0 48-49 36.698750000000004 37.0 37.0 40.0 33.0 40.0 50-51 36.622375 37.0 37.0 40.0 33.0 40.0 52-53 36.477000000000004 37.0 37.0 37.0 33.0 40.0 54-55 36.225750000000005 37.0 37.0 37.0 33.0 40.0 56-57 35.996125 37.0 37.0 37.0 33.0 40.0 58-59 35.940125 37.0 37.0 37.0 33.0 40.0 60-61 35.791375 37.0 37.0 37.0 33.0 37.0 62-63 35.50175 37.0 35.0 37.0 33.0 37.0 64-65 35.27525 37.0 33.0 37.0 33.0 37.0 66-67 35.25475 37.0 33.0 37.0 33.0 37.0 68-69 34.353 35.0 33.0 37.0 30.0 37.0 70-71 34.54308239135895 37.0 33.0 37.0 33.0 37.0 72-73 34.946124707519616 37.0 33.0 37.0 33.0 37.0 74-75 35.00921414648328 37.0 33.0 37.0 33.0 37.0 76-77 34.898059425801435 37.0 33.0 37.0 33.0 37.0 78-79 35.00499530155045 37.0 33.0 37.0 33.0 37.0 80-81 34.92475566667214 37.0 33.0 37.0 33.0 37.0 82-83 34.514081749448195 37.0 33.0 37.0 33.0 37.0 84-85 34.58214071213554 37.0 33.0 37.0 33.0 37.0 86-87 34.63249800053319 37.0 33.0 37.0 33.0 37.0 88-89 34.497867235403895 37.0 33.0 37.0 33.0 37.0 90-91 34.01079712076779 37.0 33.0 37.0 30.0 37.0 92-93 33.82298053852306 37.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 5.0 21 6.0 22 4.0 23 9.0 24 12.0 25 17.0 26 22.0 27 31.0 28 34.0 29 44.0 30 54.0 31 65.0 32 86.0 33 106.0 34 200.0 35 384.0 36 851.0 37 1059.0 38 964.0 39 47.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 81.875 4.025 4.475 9.625 2 61.12499999999999 23.125 10.05 5.7 3 34.725 36.6 16.650000000000002 12.025 4 32.5 27.500000000000004 18.75 21.25 5 21.7 33.225 27.500000000000004 17.575 6 20.0 38.95 26.05 15.0 7 34.35 30.55 20.125 14.975 8 29.7 30.775000000000002 24.2 15.325 9 26.1 26.924999999999997 28.325 18.65 10-11 25.1875 27.85 27.462500000000002 19.5 12-13 27.1 24.875 29.575000000000003 18.45 14-15 21.45 26.5875 32.875 19.0875 16-17 24.462500000000002 31.525 27.0125 17.0 18-19 22.8875 27.025 28.287499999999998 21.8 20-21 24.9375 27.3125 27.700000000000003 20.05 22-23 26.9125 23.974999999999998 28.8375 20.275000000000002 24-25 25.5 25.025 29.25 20.225 26-27 25.2625 25.362499999999997 30.7375 18.637500000000003 28-29 25.993998499624904 25.23130782695674 28.08202050512628 20.69267316829207 30-31 26.400000000000002 24.625 29.1875 19.787499999999998 32-33 23.8625 27.287499999999998 29.1625 19.6875 34-35 25.087500000000002 24.2 29.3375 21.375 36-37 24.15 25.724999999999998 29.262500000000003 20.8625 38-39 24.753094136767096 25.603200400050007 32.016502062757844 17.627203400425053 40-41 25.14064258032254 25.828228528566072 28.066008251031377 20.96512064008001 42-43 23.8625 28.262500000000003 27.625 20.25 44-45 22.85 26.087500000000002 30.7125 20.349999999999998 46-47 24.55 24.5625 28.9375 21.95 48-49 23.6125 26.337500000000002 30.85 19.2 50-51 23.875 26.3625 29.9 19.8625 52-53 25.0125 27.200000000000003 28.1375 19.650000000000002 54-55 24.1625 28.3125 28.7 18.825 56-57 24.6625 25.887500000000003 29.9875 19.4625 58-59 22.275 26.187500000000004 30.6875 20.849999999999998 60-61 24.3125 24.925 29.475 21.2875 62-63 21.975 28.812500000000004 31.175000000000004 18.0375 64-65 23.9875 26.474999999999998 30.0375 19.5 66-67 24.0625 27.2625 29.675 19.0 68-69 23.6125 26.85 28.95 20.5875 70-71 23.74389174288936 25.64841498559078 29.80829469991229 20.79939857160757 72-73 25.81174984207201 25.192672141503476 29.38723941882502 19.608338597599495 74-75 21.907183725365545 26.853146853146853 30.781945327399875 20.45772409408773 76-77 22.525991528686948 27.018354511615968 31.279681683994355 19.175972275702733 78-79 23.804587274847737 25.6576389788778 30.478165090060905 20.059608656213555 80-81 24.32644520010463 27.975411980120324 29.42715145173947 18.270991368035574 82-83 23.96890235867703 25.550138358149955 31.532481222822504 18.948478060350507 84-85 23.50905218317359 24.90681576144835 31.12353567625133 20.46059637912673 86-87 22.967208744334844 26.55291922154092 31.27166089042922 19.208211143695014 88-89 21.154358837643294 29.072247400693147 31.298320447880567 18.475073313782993 90-91 24.00693148493735 27.779258864302854 29.432151426286325 18.781658224473475 92-93 22.10077312716609 29.138896294321516 30.35190615835777 18.408424420154628 >>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 1.0 16 1.5 17 9.5 18 9.5 19 1.0 20 1.0 21 2.0 22 2.0 23 4.5 24 9.0 25 8.5 26 9.5 27 10.0 28 18.5 29 31.5 30 35.0 31 49.0 32 73.0 33 86.5 34 98.0 35 119.0 36 140.5 37 171.0 38 193.0 39 189.0 40 185.0 41 188.5 42 195.0 43 194.5 44 185.0 45 175.5 46 192.0 47 209.0 48 193.5 49 174.5 50 165.0 51 154.5 52 133.5 53 128.0 54 112.0 55 71.0 56 53.5 57 54.0 58 61.5 59 50.0 60 30.5 61 28.5 62 26.0 63 19.5 64 16.5 65 18.5 66 14.5 67 10.0 68 8.0 69 5.0 70 2.5 71 2.0 72 1.5 73 0.5 74 0.5 75 1.0 76 1.0 77 0.5 78 0.0 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 0.0 22-23 0.0 24-25 0.0 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 0.0125 40-41 0.0125 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 0.0 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 19.0 71 15.0 72 17.0 73 12.0 74 9.0 75 27.0 76 11.0 77 20.0 78 23.0 79 17.0 80 14.0 81 12.0 82 19.0 83 24.0 84 10.0 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 3751.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 83.025 #Duplication Level Percentage of deduplicated Percentage of total 1 93.61638060825052 77.725 2 3.4929238181270703 5.800000000000001 3 1.1743450767841013 2.9250000000000003 4 0.45167118337850043 1.5 5 0.36133694670280037 1.5 6 0.06022282445046673 0.3 7 0.09033423667570009 0.525 8 0.12044564890093346 0.8 9 0.09033423667570009 0.675 >10 0.5420054200542005 8.25 >50 0.0 0.0 >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 warn #Sequence Count Percentage Possible Source GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 35 0.8750000000000001 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 34 0.8500000000000001 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 26 0.65 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 23 0.575 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 19 0.475 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 19 0.475 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 19 0.475 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 18 0.44999999999999996 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 18 0.44999999999999996 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 18 0.44999999999999996 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 17 0.42500000000000004 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 14 0.35000000000000003 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 13 0.325 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 13 0.325 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 12 0.3 No Hit GGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAGA 11 0.27499999999999997 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 11 0.27499999999999997 No Hit GAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTG 10 0.25 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 9 0.22499999999999998 No Hit GTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCA 9 0.22499999999999998 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 9 0.22499999999999998 No Hit GGGAAATTAACAGTTGGAAAGGGCGATCGGTCTTGATCCCTCTGTGTTTC 8 0.2 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 8 0.2 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 8 0.2 No Hit GGGGAAGTACACCAGCGACGGCGAGGCCGCCGCCGCCAAGGAAGGCATGT 8 0.2 No Hit GGGCCTGTTATCTCTATCAATATGATTCTAATTCGTCAGATATTATTTAT 7 0.17500000000000002 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 7 0.17500000000000002 No Hit GGCATATGCCAGCTCTGACCGAAATCTTTGGGGATGATTCTGTATTACAA 7 0.17500000000000002 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 6 0.15 No Hit TAGTTTCCACCGCCTGTCCAGGGTTGAGCCCTGGGATTTGACGGCGGACT 6 0.15 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 5 0.125 No Hit GAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAAT 5 0.125 No Hit GGGATGATGATGATCGATCGATGGACTACTTGTAATTTTAAAGTTTCAAC 5 0.125 No Hit GGGAAACAACGAGGTCATCATCGACATGATATATTGCTGCTATTTTCCAC 5 0.125 No Hit GGAGAAGTACAAGTGCGGATCCAACGTCTTCTGGAAATGGTGAAGATGAT 5 0.125 No Hit GGGACAGTCGGGGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGA 5 0.125 No Hit GGAGTGGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGAG 5 0.125 No Hit GTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGCA 5 0.125 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 5 0.125 No Hit AACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGC 5 0.125 No Hit GGAGATCGAGTTGTTACTTGAGAGTTTGTAACCCTTTATCATGCCATGTC 5 0.125 No Hit GATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAG 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 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGATGAT 15 8.848908E-4 86.662506 2 GGGATGA 15 8.848908E-4 86.662506 1 >>END_MODULE Rejected 239720 READS because READLEN < 1 Read 239720 spots for ERR6133392.sra Written 239720 spots for ERR6133392.sra Rejected 239720 READS because READLEN < 1 Read 239720 spots for ERR6133392.sra Written 239720 spots for ERR6133392.sra Rejected 239720 READS because READLEN < 1 Read 239720 spots for ERR6133392.sra Written 239720 spots for ERR6133392.sra Rejected 239720 READS because READLEN < 1 Read 239720 spots for ERR6133392.sra Written 239720 spots for ERR6133392.sra Rejected 239720 READS because READLEN < 1 Read 239720 spots for ERR6133392.sra Written 239720 spots for ERR6133392.sra Rejected 239720 READS because READLEN < 1 Read 239720 spots for ERR6133392.sra Written 239720 spots for ERR6133392.sra Rejected 239720 READS because READLEN < 1 Read 239720 spots for ERR6133392.sra Written 239720 spots for ERR6133392.sra Rejected 239720 READS because READLEN < 1 Read 239720 spots for ERR6133392.sra Written 239720 spots for ERR6133392.sra Rejected 239720 READS because READLEN < 1 Read 239720 spots for ERR6133392.sra Written 239720 spots for ERR6133392.sra Rejected 239720 READS because READLEN < 1 Read 239720 spots for ERR6133392.sra Written 239720 spots for ERR6133392.sra Rejected 239737 READS because READLEN < 1 Read 239737 spots for ERR6133392.sra Written 239737 spots for ERR6133392.sra Rejected 239720 READS because READLEN < 1 Read 239720 spots for ERR6133392.sra Written 239720 spots for ERR6133392.sra Rejected 239720 READS because READLEN < 1 Read 239720 spots for ERR6133392.sra Written 239720 spots for ERR6133392.sra Rejected 239720 READS because READLEN < 1 Read 239720 spots for ERR6133392.sra Written 239720 spots for ERR6133392.sra Rejected 239720 READS because READLEN < 1 Read 239720 spots for ERR6133392.sra Written 239720 spots for ERR6133392.sra Rejected 239720 READS because READLEN < 1 Read 239720 spots for ERR6133392.sra Written 239720 spots for ERR6133392.sra Rejected 239720 READS because READLEN < 1 Read 239720 spots for ERR6133392.sra Written 239720 spots for ERR6133392.sra Rejected 239720 READS because READLEN < 1 Read 239720 spots for ERR6133392.sra Written 239720 spots for ERR6133392.sra Rejected 239720 READS because READLEN < 1 Read 239720 spots for ERR6133392.sra Written 239720 spots for ERR6133392.sra Rejected 239720 READS because READLEN < 1 Read 239720 spots for ERR6133392.sra Written 239720 spots for ERR6133392.sra SRR ids: ['ERR6133392.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_848wypfq ERR6133392.sra spots: 4794417 blocks: [[1, 239720], [239721, 479440], [479441, 719160], [719161, 958880], [958881, 1198600], [1198601, 1438320], [1438321, 1678040], [1678041, 1917760], [1917761, 2157480], [2157481, 2397200], [2397201, 2636920], [2636921, 2876640], [2876641, 3116360], [3116361, 3356080], [3356081, 3595800], [3595801, 3835520], [3835521, 4075240], [4075241, 4314960], [4314961, 4554680], [4554681, 4794417]] ERR6133392 file size 1055419 ERR6133392 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 ERR6133392 ERR6133392_1.fastq Input file: ERR6133392_1.fastq trimmed: ERR6133392-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 02:52:58 2024 >> started Sat Dec 7 02:53:01 2024 >> done (2.884s) 4794417 reads processed; of these: 360 ( 0.01%) short reads filtered out after trimming by size control 7 ( 0.00%) empty reads filtered out after trimming by size control 4794050 (99.99%) reads available; of these: 179022 ( 3.73%) trimmed reads available after processing 4615028 (96.27%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 42 0.00% 19 69 0.00% 20 29 0.00% 21 10 0.00% 22 24 0.00% 23 15 0.00% 24 8 0.00% 25 12 0.00% 26 16 0.00% 27 15 0.00% 28 13 0.00% 29 19 0.00% 30 14 0.00% 31 18 0.00% 32 52 0.00% 33 16 0.00% 34 12 0.00% 35 12 0.00% 36 14 0.00% 37 22 0.00% 38 67 0.00% 39 90 0.00% 40 218 0.00% 41 46 0.00% 42 34 0.00% 43 40 0.00% 44 56 0.00% 45 47 0.00% 46 83 0.00% 47 117 0.00% 48 261 0.01% 49 1607 0.03% 50 404 0.01% 51 460 0.01% 52 449 0.01% 53 518 0.01% 54 573 0.01% 55 699 0.01% 56 742 0.02% 57 886 0.02% 58 905 0.02% 59 1049 0.02% 60 1349 0.03% 61 1084 0.02% 62 1043 0.02% 63 1648 0.03% 64 1354 0.03% 65 1455 0.03% 66 1644 0.03% 67 1845 0.04% 68 2370 0.05% 69 1110 0.02% 70 20326 0.42% 71 20885 0.44% 72 26161 0.55% 73 22053 0.46% 74 23080 0.48% 75 24645 0.51% 76 20582 0.43% 77 20564 0.43% 78 24867 0.52% 79 26592 0.55% 80 23696 0.49% 81 23026 0.48% 82 27867 0.58% 83 35064 0.73% 84 25361 0.53% 85 6952 0.15% 86 7995 0.17% 87 9620 0.20% 88 12066 0.25% 89 11689 0.24% 90 16182 0.34% 91 18673 0.39% 92 19857 0.41% 93 4301562 89.73% 4794050 reads passed initial QC criterion=sequence-density sequence-density=0.36 sequence-density-rank=1 fanout-score=8.68 fanout-score-rank=17 prefix-density=0.59 prefix-fanout=5.3 sequence=ATGCATGCATGC criterion=fanout-score sequence-density=0.01 sequence-density-rank=27 fanout-score=288.89 fanout-score-rank=1 prefix-density=0.47 prefix-fanout=7.2 sequence=GAAGAAGAAAAGTTTTCTCAACATGGGGAGGAAGTCCCTCCGAAATTTGATTTGTTATTGTATTGTAAGGGGCTTTTTTAGTATTTATCTAAAGGAAGGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCAAGTGGGATATATGGCATACTATTCTTTCCATTTTCATCTTTTTTTCTATTCCACTCCATCTAGATATAAGAAAGAACCCAATGCAATGAAATTCCACTAATATACAATACAAAAAAGAAGAATAGATACAGGGTCTCAAACCTTGCTATAGAGTTTTTGCTT Started job on | Dec 07 02:53:17 Started mapping on | Dec 07 02:53:18 Finished on | Dec 07 02:53:26 Mapping speed, Million of reads per hour | 2157.32 Number of input reads | 4794050 Average input read length | 91 UNIQUE READS: Uniquely mapped reads number | 3545050 Uniquely mapped reads % | 73.95% Average mapped length | 91.10 Number of splices: Total | 129682 Number of splices: Annotated (sjdb) | 105582 Number of splices: GT/AG | 123418 Number of splices: GC/AG | 3594 Number of splices: AT/AC | 29 Number of splices: Non-canonical | 2641 Mismatch rate per base, % | 0.46% Deletion rate per base | 0.03% Deletion average length | 1.77 Insertion rate per base | 0.01% Insertion average length | 1.77 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1097835 % of reads mapped to multiple loci | 22.90% Number of reads mapped to too many loci | 48050 % of reads mapped to too many loci | 1.00% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.02% % of reads unmapped: other | 0.13% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 151165 151165 151165 N_multimapping 1097835 1097835 1097835 N_noFeature 185936 218657 3373589 N_ambiguous 152745 13912 599 UnstrandedReadsAssigned:3206369 PositiveStrandReadsAssigned:3312481 NegativeStrandReadsAssigned:170862 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133392 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: ERR6133392-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 4,794,050 reads, 4,032,689 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,050 rounds 52973 ERR6133392.ke.tsv 35125 ERR6133392.se.tsv 88098 total ==> ERR6133392.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 106 26.6364 PNS24243 293 194 0 0 KQK14069 1603 1504 119 27.2786 KQK14071 474 375 0 0 ==> ERR6133392.se.tsv <== BRADI_1g14170v3 119 BRADI_1g53295v3 72 BRADI_1g59795v3 33 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 32 BRADI_1g74790v3 41 BRADI_1g09890v3 0 BRADI_1g77505v3 110 BRADI_1g48960v3 0 ERR6133392 completed mapping pipeline successfully