Starting /dee2/code/volunteer_pipeline.sh ERR6133529 current disk space = 1544512647168 free memory = 1601448924 ERR6133529 SRAfilesize 39a85835e54075a8ceb297feefefa69c ERR6133529.sra ERR6133529.sra file validated ERR6133529 is single end ERR6133529 is conventional basespace ERR6133529 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133529_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 34.01475 37.0 33.0 37.0 33.0 37.0 2 36.0985 37.0 37.0 37.0 33.0 37.0 3 35.1145 37.0 33.0 37.0 33.0 37.0 4 35.248 37.0 37.0 37.0 33.0 37.0 5 35.1555 37.0 37.0 37.0 33.0 37.0 6 35.59875 37.0 37.0 37.0 33.0 37.0 7 37.313 37.0 37.0 40.0 33.0 40.0 8 37.2825 37.0 37.0 40.0 33.0 40.0 9 37.304 37.0 37.0 40.0 33.0 40.0 10-11 37.2755 37.0 37.0 40.0 33.0 40.0 12-13 37.2535 37.0 37.0 40.0 33.0 40.0 14-15 37.332875 37.0 37.0 40.0 33.0 40.0 16-17 37.234125000000006 37.0 37.0 40.0 33.0 40.0 18-19 37.196749999999994 37.0 37.0 40.0 33.0 40.0 20-21 37.01525 37.0 37.0 40.0 33.0 40.0 22-23 37.031125 37.0 37.0 40.0 33.0 40.0 24-25 37.09075 37.0 37.0 40.0 33.0 40.0 26-27 37.064875 37.0 37.0 40.0 33.0 40.0 28-29 37.010374999999996 37.0 37.0 40.0 33.0 40.0 30-31 36.98975 37.0 37.0 40.0 33.0 40.0 32-33 36.853375 37.0 37.0 40.0 33.0 40.0 34-35 36.673249999999996 37.0 37.0 40.0 33.0 40.0 36-37 36.4955 37.0 37.0 40.0 33.0 40.0 38-39 36.491625 37.0 37.0 40.0 33.0 40.0 40-41 36.271625 37.0 37.0 40.0 33.0 40.0 42-43 36.241875 37.0 37.0 40.0 33.0 40.0 44-45 35.983000000000004 37.0 37.0 38.5 33.0 40.0 46-47 35.59325 37.0 33.0 37.0 33.0 40.0 48-49 35.54375 37.0 33.0 37.0 33.0 40.0 50-51 35.518 37.0 33.0 37.0 33.0 40.0 52-53 35.069 37.0 33.0 37.0 30.0 40.0 54-55 35.010875 37.0 33.0 37.0 33.0 38.5 56-57 34.894375 37.0 33.0 37.0 33.0 37.0 58-59 34.438874999999996 37.0 33.0 37.0 27.0 37.0 60-61 34.592124999999996 37.0 33.0 37.0 27.0 37.0 62-63 34.46525 37.0 33.0 37.0 27.0 37.0 64-65 34.422625 37.0 33.0 37.0 27.0 37.0 66-67 34.505375 37.0 33.0 37.0 27.0 37.0 68-69 33.680125000000004 35.0 33.0 37.0 27.0 37.0 70-71 33.7661359759157 35.0 33.0 37.0 27.0 37.0 72-73 34.22237120488607 37.0 33.0 37.0 27.0 37.0 74-75 34.18768716838645 37.0 33.0 37.0 27.0 37.0 76-77 34.145141908837815 37.0 33.0 37.0 27.0 37.0 78-79 34.16410305503861 37.0 33.0 37.0 27.0 37.0 80-81 34.11265038426595 37.0 33.0 37.0 27.0 37.0 82-83 33.99847026428286 37.0 33.0 37.0 27.0 37.0 84-85 33.96381487955459 37.0 33.0 37.0 27.0 37.0 86-87 33.92613927291347 37.0 33.0 37.0 27.0 37.0 88-89 34.02227342549923 37.0 33.0 37.0 27.0 37.0 90-91 33.662954429083456 37.0 33.0 37.0 27.0 37.0 92-93 33.61277521761393 37.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 12.0 21 15.0 22 18.0 23 16.0 24 33.0 25 27.0 26 31.0 27 49.0 28 63.0 29 55.0 30 87.0 31 100.0 32 151.0 33 150.0 34 225.0 35 401.0 36 1010.0 37 925.0 38 624.0 39 8.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 90.025 2.5250000000000004 3.225 4.2250000000000005 2 79.57499999999999 11.85 4.9 3.675 3 38.3 39.65 12.875 9.175 4 33.675 30.5 17.525 18.3 5 25.45 34.9 23.150000000000002 16.5 6 22.05 41.099999999999994 23.125 13.725000000000001 7 40.65 28.7 16.875 13.775 8 34.1 30.725 21.575 13.600000000000001 9 28.475 28.525 26.25 16.75 10-11 28.262500000000003 27.8375 26.950000000000003 16.950000000000003 12-13 30.2875 25.8 28.549999999999997 15.3625 14-15 22.1875 30.099999999999998 30.075000000000003 17.6375 16-17 23.4375 33.825 25.900000000000002 16.8375 18-19 23.95 28.1125 26.9125 21.025 20-21 25.2125 26.087500000000002 27.900000000000002 20.8 22-23 27.224999999999998 23.575 28.8875 20.3125 24-25 26.174999999999997 24.575 29.0875 20.1625 26-27 25.912499999999998 25.2 30.0 18.8875 28-29 25.8625 26.337500000000002 28.249999999999996 19.55 30-31 26.6125 24.75 28.6125 20.025000000000002 32-33 23.4125 27.425 28.1875 20.974999999999998 34-35 25.012506253126567 24.73736868434217 28.339169584792394 21.91095547773887 36-37 24.975 24.224999999999998 29.6875 21.1125 38-39 27.0125 25.025 28.9125 19.05 40-41 26.747530323871448 25.497061398024258 27.32274602976116 20.432662248343128 42-43 24.337168584292147 25.78789394697349 29.277138569284645 20.597798899449725 44-45 23.67137676628736 25.984744279104667 29.486057271476806 20.857821683131174 46-47 24.05 24.4 29.862499999999997 21.6875 48-49 25.54069258657332 24.765595699462434 30.316289536192027 19.37742217777222 50-51 25.85 25.324999999999996 29.349999999999998 19.475 52-53 25.196948855820935 26.297361510566464 28.79829936226085 19.70739027135176 54-55 25.05 28.0875 28.462500000000002 18.4 56-57 24.887500000000003 25.05 30.662499999999998 19.400000000000002 58-59 24.9 25.4625 29.2375 20.4 60-61 23.5625 24.9 31.3 20.2375 62-63 22.95 26.437500000000004 31.574999999999996 19.037499999999998 64-65 25.2375 24.9125 31.25 18.6 66-67 25.05 26.150000000000002 29.299999999999997 19.5 68-69 22.625 25.887500000000003 30.225 21.2625 70-71 23.741547708489858 23.829201101928373 30.540946656649137 21.888304532932633 72-73 26.160231417431767 24.701295434536537 29.568607722299085 19.569865425732612 74-75 23.234997478567827 26.588502269288956 30.307614725163894 19.868885526979323 76-77 22.31070661104791 26.78548856023259 30.65352041461257 20.25028441410694 78-79 23.779327837666457 24.5149017121116 32.03551046290425 19.670259987317692 80-81 23.78893833439288 26.99300699300699 30.46408137317228 18.753973299427845 82-83 23.72276723149446 25.570136323098485 30.71728882660211 19.989807618804946 84-85 23.79491113668329 23.51361718450326 32.39994885564506 20.291522823168393 86-87 21.32616487455197 25.627240143369175 33.99897593445981 19.047619047619047 88-89 21.940604198668716 27.227342549923193 32.84690220174091 17.985151049667177 90-91 24.795186891961084 26.0752688172043 30.798771121351763 18.330773169482846 92-93 22.91346646185356 27.112135176651304 31.336405529953915 18.63799283154122 >>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 6.0 18 6.5 19 0.5 20 0.0 21 2.0 22 4.5 23 5.0 24 4.0 25 2.5 26 5.0 27 11.0 28 20.0 29 26.0 30 26.5 31 32.0 32 48.0 33 75.0 34 80.0 35 98.0 36 117.0 37 133.0 38 171.5 39 180.0 40 199.0 41 221.0 42 232.0 43 244.5 44 218.5 45 190.0 46 218.0 47 216.5 48 164.0 49 159.5 50 172.5 51 158.0 52 132.0 53 110.5 54 96.0 55 81.5 56 58.5 57 41.5 58 48.0 59 45.5 60 36.5 61 33.5 62 26.0 63 23.0 64 29.5 65 27.0 66 20.0 67 18.5 68 16.5 69 13.5 70 8.0 71 6.0 72 5.0 73 3.5 74 3.0 75 1.5 76 0.0 77 0.5 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 0.05 36-37 0.0 38-39 0.0 40-41 0.0375 42-43 0.05 44-45 0.0375 46-47 0.0 48-49 0.0125 50-51 0.0 52-53 0.0375 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 9.0 72 3.0 73 6.0 74 4.0 75 4.0 76 9.0 77 8.0 78 1.0 79 7.0 80 5.0 81 1.0 82 9.0 83 5.0 84 9.0 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 3906.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 83.22500000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 91.88945629318114 76.47500000000001 2 4.92640432562331 8.200000000000001 3 1.3517572844698107 3.375 4 0.6007810153199159 2.0 5 0.3604686091919495 1.5 6 0.21027335536197056 1.05 7 0.09011715229798738 0.525 8 0.09011715229798738 0.6 9 0.06007810153199159 0.44999999999999996 >10 0.39050765995794534 4.55 >50 0.030039050765995796 1.275 >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 GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 51 1.275 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 17 0.42500000000000004 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 17 0.42500000000000004 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 16 0.4 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 15 0.375 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 15 0.375 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 15 0.375 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 15 0.375 No Hit GGTGGGGCAATGGGCATTCCGTTGAGTTTGTATGGTGGGTGCTGTTTTGC 14 0.35000000000000003 No Hit GGGGAAGAAGAATGCTGGCGAAATTAATTTGCTTTTTTTGGGGAGAATGG 12 0.3 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 12 0.3 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 12 0.3 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 11 0.27499999999999997 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 11 0.27499999999999997 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 9 0.22499999999999998 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 9 0.22499999999999998 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 8 0.2 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 8 0.2 No Hit GGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCAAGT 8 0.2 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 7 0.17500000000000002 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 7 0.17500000000000002 No Hit GGGCAAGTTCATGTAAACATAGATCGATATATGGCGGAGCGCCATTTTAT 7 0.17500000000000002 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 6 0.15 No Hit GGCAAGGAGAAGTACAAGTGCGGATCCAACGTCTTCTGGAAATGGTGAAG 6 0.15 No Hit GGGCAAGGAGAAGTACAAGTGCGGATCCAACGTCTTCTGGAAATGGTGAA 6 0.15 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 6 0.15 No Hit GGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 6 0.15 No Hit GGAAACAACGAGGTCATCATCGACATGATATATTGCTGCTATTTTCCACC 6 0.15 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 6 0.15 No Hit GGGGGAGAAGTCTTATGTTATATATGGTAATCGCCTTGCCTATAGTGCCC 5 0.125 No Hit GGAGGAGAGCGGCGGCGGTCTGTTCAAGATGGCTCAGGGCTTCATGAAGT 5 0.125 No Hit TCATCGTTCGTCCCCGACATATACATGCATAGAAGATGCAAAGACTAAAA 5 0.125 No Hit GGAGATGGCCGCGGAGAACGGCGGCTGCGGCTGCAGCACCTGCAAGTGCG 5 0.125 No Hit CTGAGCCGTGCTCTCTTCTGTGTACATCTTCATGTCATTTTAGCGATTCT 5 0.125 No Hit GGAGTGGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGAG 5 0.125 No Hit GGCATTGATGAGCTTGAGAGGGCACTGTAGCCAGTGTGTCAGTCGTTGTT 5 0.125 No Hit GGGCTCGAGGAGCATATGTACATTTGAACCCTGACTACACATTTACACAC 5 0.125 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 5 0.125 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 5 0.125 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 5 0.125 No Hit GGGTGTCAATATATGATGATGTGTTGTTATAATGTACGCGCCTGCAAACT 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 0.0125 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 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 139406 READS because READLEN < 1 Read 139406 spots for ERR6133529.sra Written 139406 spots for ERR6133529.sra Rejected 139406 READS because READLEN < 1 Read 139406 spots for ERR6133529.sra Written 139406 spots for ERR6133529.sra Rejected 139406 READS because READLEN < 1 Read 139406 spots for ERR6133529.sra Written 139406 spots for ERR6133529.sra Rejected 139406 READS because READLEN < 1 Read 139406 spots for ERR6133529.sra Written 139406 spots for ERR6133529.sra Rejected 139406 READS because READLEN < 1 Read 139406 spots for ERR6133529.sra Written 139406 spots for ERR6133529.sra Rejected 139406 READS because READLEN < 1 Read 139406 spots for ERR6133529.sra Written 139406 spots for ERR6133529.sra Rejected 139406 READS because READLEN < 1 Read 139406 spots for ERR6133529.sra Written 139406 spots for ERR6133529.sra Rejected 139406 READS because READLEN < 1 Read 139406 spots for ERR6133529.sra Written 139406 spots for ERR6133529.sra Rejected 139406 READS because READLEN < 1 Read 139406 spots for ERR6133529.sra Written 139406 spots for ERR6133529.sra Rejected 139406 READS because READLEN < 1 Read 139406 spots for ERR6133529.sra Written 139406 spots for ERR6133529.sra Rejected 139406 READS because READLEN < 1 Read 139406 spots for ERR6133529.sra Written 139406 spots for ERR6133529.sra Rejected 139406 READS because READLEN < 1 Read 139406 spots for ERR6133529.sra Written 139406 spots for ERR6133529.sra Rejected 139406 READS because READLEN < 1 Read 139406 spots for ERR6133529.sra Written 139406 spots for ERR6133529.sra Rejected 139406 READS because READLEN < 1 Read 139406 spots for ERR6133529.sra Written 139406 spots for ERR6133529.sra Rejected 139406 READS because READLEN < 1 Read 139406 spots for ERR6133529.sra Written 139406 spots for ERR6133529.sra Rejected 139415 READS because READLEN < 1 Read 139415 spots for ERR6133529.sra Written 139415 spots for ERR6133529.sra Rejected 139406 READS because READLEN < 1 Read 139406 spots for ERR6133529.sra Written 139406 spots for ERR6133529.sra Rejected 139406 READS because READLEN < 1 Read 139406 spots for ERR6133529.sra Written 139406 spots for ERR6133529.sra Rejected 139406 READS because READLEN < 1 Read 139406 spots for ERR6133529.sra Written 139406 spots for ERR6133529.sra Rejected 139406 READS because READLEN < 1 Read 139406 spots for ERR6133529.sra Written 139406 spots for ERR6133529.sra SRR ids: ['ERR6133529.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_qmr0h59u ERR6133529.sra spots: 2788129 blocks: [[1, 139406], [139407, 278812], [278813, 418218], [418219, 557624], [557625, 697030], [697031, 836436], [836437, 975842], [975843, 1115248], [1115249, 1254654], [1254655, 1394060], [1394061, 1533466], [1533467, 1672872], [1672873, 1812278], [1812279, 1951684], [1951685, 2091090], [2091091, 2230496], [2230497, 2369902], [2369903, 2509308], [2509309, 2648714], [2648715, 2788129]] ERR6133529 file size 616726 ERR6133529 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 ERR6133529 ERR6133529_1.fastq Input file: ERR6133529_1.fastq trimmed: ERR6133529-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 07:59:11 2024 >> started Sat Dec 7 07:59:13 2024 >> done (1.827s) 2788129 reads processed; of these: 70 ( 0.00%) short reads filtered out after trimming by size control 15 ( 0.00%) empty reads filtered out after trimming by size control 2788044 (100.00%) reads available; of these: 43935 ( 1.58%) trimmed reads available after processing 2744109 (98.42%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 11 0.00% 19 18 0.00% 20 7 0.00% 21 7 0.00% 22 24 0.00% 23 5 0.00% 24 4 0.00% 25 1 0.00% 26 1 0.00% 27 9 0.00% 28 9 0.00% 29 37 0.00% 30 5 0.00% 31 16 0.00% 32 4 0.00% 33 5 0.00% 34 10 0.00% 35 58 0.00% 36 217 0.01% 37 18 0.00% 38 14 0.00% 39 54 0.00% 40 34 0.00% 41 22 0.00% 42 1 0.00% 43 3 0.00% 44 6 0.00% 45 5 0.00% 46 5 0.00% 47 3 0.00% 48 2 0.00% 49 2 0.00% 50 4 0.00% 51 13 0.00% 52 2 0.00% 53 3 0.00% 54 1 0.00% 55 0 0.00% 56 4 0.00% 57 2 0.00% 58 3 0.00% 59 4 0.00% 60 5 0.00% 61 2 0.00% 62 4 0.00% 63 0 0.00% 64 2 0.00% 65 5 0.00% 66 8 0.00% 67 12 0.00% 68 11 0.00% 69 51 0.00% 70 4817 0.17% 71 3918 0.14% 72 3781 0.14% 73 3498 0.13% 74 3870 0.14% 75 3670 0.13% 76 3432 0.12% 77 3528 0.13% 78 3989 0.14% 79 4323 0.16% 80 4061 0.15% 81 4408 0.16% 82 5094 0.18% 83 5138 0.18% 84 4301 0.15% 85 107 0.00% 86 193 0.01% 87 335 0.01% 88 559 0.02% 89 1115 0.04% 90 2413 0.09% 91 6981 0.25% 92 30670 1.10% 93 2683090 96.24% 2788044 reads passed initial QC criterion=sequence-density sequence-density=0.46 sequence-density-rank=1 fanout-score=3.53 fanout-score-rank=31 prefix-density=0.55 prefix-fanout=3.0 sequence=GTGTTGTGTTGT criterion=fanout-score sequence-density=0.05 sequence-density-rank=18 fanout-score=68.71 fanout-score-rank=1 prefix-density=0.29 prefix-fanout=11.1 sequence=TTTTTTTTTTAAGAATCCTCCATTTTTGTTCTTCCACCCATGCAATAGAGAGCAAATGGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTGAAATCGGAGTCATGGAATAATGGTGAATTCAAATGTTTAGTTCTTTAGTATAAGAAGTATAAGAA Started job on | Dec 07 07:59:27 Started mapping on | Dec 07 07:59:28 Finished on | Dec 07 07:59:33 Mapping speed, Million of reads per hour | 2007.39 Number of input reads | 2788044 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 2275882 Uniquely mapped reads % | 81.63% Average mapped length | 92.22 Number of splices: Total | 82365 Number of splices: Annotated (sjdb) | 67812 Number of splices: GT/AG | 78453 Number of splices: GC/AG | 2421 Number of splices: AT/AC | 26 Number of splices: Non-canonical | 1465 Mismatch rate per base, % | 0.49% Deletion rate per base | 0.05% Deletion average length | 1.81 Insertion rate per base | 0.02% Insertion average length | 1.84 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 459719 % of reads mapped to multiple loci | 16.49% Number of reads mapped to too many loci | 8788 % of reads mapped to too many loci | 0.32% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.54% % of reads unmapped: other | 0.02% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 52443 52443 52443 N_multimapping 459719 459719 459719 N_noFeature 135088 158026 2167193 N_ambiguous 93743 8118 211 UnstrandedReadsAssigned:2047051 PositiveStrandReadsAssigned:2109738 NegativeStrandReadsAssigned:108478 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133529 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: ERR6133529-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 2,788,044 reads, 2,408,351 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,043 rounds 52973 ERR6133529.ke.tsv 35125 ERR6133529.se.tsv 88098 total ==> ERR6133529.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 74 30.9716 PNS24243 293 194 0 0 KQK14069 1603 1504 263 100.414 KQK14071 474 375 0 0 ==> ERR6133529.se.tsv <== BRADI_1g14170v3 262 BRADI_1g53295v3 46 BRADI_1g59795v3 23 BRADI_1g07683v3 2 BRADI_1g00485v3 4 BRADI_1g20270v3 30 BRADI_1g74790v3 39 BRADI_1g09890v3 0 BRADI_1g77505v3 40 BRADI_1g48960v3 5 ERR6133529 completed mapping pipeline successfully