Starting /dee2/code/volunteer_pipeline.sh ERR6133534 current disk space = 1544506261504 free memory = 1600725040 ERR6133534 SRAfilesize f1b98d9599aca672b4e78f4e8d2c9237 ERR6133534.sra ERR6133534.sra file validated ERR6133534 is single end ERR6133534 is conventional basespace ERR6133534 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133534_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 47 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.7685 33.0 33.0 37.0 27.0 37.0 2 35.99075 37.0 37.0 37.0 33.0 37.0 3 35.191 37.0 33.0 37.0 33.0 37.0 4 35.29425 37.0 37.0 37.0 33.0 37.0 5 35.22825 37.0 37.0 37.0 33.0 37.0 6 35.615 37.0 37.0 37.0 33.0 37.0 7 37.4305 37.0 37.0 40.0 33.0 40.0 8 37.5 37.0 37.0 40.0 33.0 40.0 9 37.47925 37.0 37.0 40.0 33.0 40.0 10-11 37.494625 37.0 37.0 40.0 33.0 40.0 12-13 37.42425 37.0 37.0 40.0 33.0 40.0 14-15 37.412375 37.0 37.0 40.0 33.0 40.0 16-17 37.329125 37.0 37.0 40.0 33.0 40.0 18-19 37.280249999999995 37.0 37.0 40.0 33.0 40.0 20-21 37.22087500000001 37.0 37.0 40.0 33.0 40.0 22-23 37.055625 37.0 37.0 40.0 33.0 40.0 24-25 37.109875 37.0 37.0 40.0 33.0 40.0 26-27 37.100125 37.0 37.0 40.0 33.0 40.0 28-29 37.041875000000005 37.0 37.0 40.0 33.0 40.0 30-31 36.85925 37.0 37.0 40.0 33.0 40.0 32-33 36.770625 37.0 37.0 40.0 33.0 40.0 34-35 36.5415 37.0 37.0 40.0 33.0 40.0 36-37 36.296625 37.0 37.0 40.0 33.0 40.0 38-39 36.307125 37.0 37.0 40.0 33.0 40.0 40-41 36.051125 37.0 37.0 40.0 33.0 40.0 42-43 35.965625 37.0 37.0 40.0 33.0 40.0 44-45 35.705 37.0 33.0 38.5 33.0 40.0 46-47 35.36525 37.0 33.0 37.0 33.0 40.0 48-49 35.334875 37.0 33.0 37.0 33.0 40.0 50-51 35.309625 37.0 33.0 37.0 33.0 40.0 52-53 34.9925 37.0 33.0 37.0 27.0 40.0 54-55 34.932625 37.0 33.0 37.0 30.0 40.0 56-57 34.7855 37.0 33.0 37.0 30.0 37.0 58-59 34.14725 37.0 33.0 37.0 27.0 37.0 60-61 34.3515 37.0 33.0 37.0 27.0 37.0 62-63 34.345375000000004 37.0 33.0 37.0 27.0 37.0 64-65 34.322375 37.0 33.0 37.0 27.0 37.0 66-67 34.342625 37.0 33.0 37.0 27.0 37.0 68-69 33.46725 35.0 33.0 37.0 27.0 37.0 70-71 33.66120883383383 35.0 33.0 37.0 27.0 37.0 72-73 34.047516835731166 37.0 33.0 37.0 27.0 37.0 74-75 34.01656295490931 37.0 33.0 37.0 27.0 37.0 76-77 33.87029177452248 37.0 33.0 37.0 27.0 37.0 78-79 33.910938593941445 37.0 33.0 37.0 27.0 37.0 80-81 33.858805282372245 37.0 33.0 37.0 27.0 37.0 82-83 33.687570527462995 37.0 33.0 37.0 27.0 37.0 84-85 33.694184117557064 37.0 33.0 37.0 27.0 37.0 86-87 33.685616611800455 37.0 33.0 37.0 27.0 37.0 88-89 33.58533806026843 37.0 33.0 37.0 27.0 37.0 90-91 33.2680425424158 37.0 33.0 37.0 27.0 37.0 92-93 33.3503418586984 37.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 9.0 21 17.0 22 26.0 23 23.0 24 36.0 25 33.0 26 39.0 27 38.0 28 62.0 29 71.0 30 77.0 31 108.0 32 138.0 33 167.0 34 250.0 35 471.0 36 915.0 37 911.0 38 603.0 39 6.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 90.35 2.15 1.95 5.55 2 75.25 15.0 5.7250000000000005 4.025 3 37.55 38.824999999999996 11.95 11.675 4 35.275 28.7 18.725 17.299999999999997 5 25.374999999999996 31.624999999999996 23.625 19.375 6 21.325 38.1 23.95 16.625 7 38.45 27.700000000000003 18.825 15.024999999999999 8 31.8 30.3 21.55 16.35 9 27.375 28.875 25.174999999999997 18.575 10-11 27.2625 27.450000000000003 26.4125 18.875 12-13 30.525000000000002 25.025 25.5125 18.9375 14-15 22.225 30.049999999999997 28.462500000000002 19.2625 16-17 25.412499999999998 31.8125 24.075 18.7 18-19 24.349999999999998 27.250000000000004 25.95 22.45 20-21 25.912499999999998 26.525 26.6 20.962500000000002 22-23 27.325 23.799999999999997 26.375 22.5 24-25 27.525 23.7625 27.250000000000004 21.462500000000002 26-27 26.075 25.674999999999997 28.799999999999997 19.45 28-29 27.3375 25.8 25.55 21.3125 30-31 27.900000000000002 25.4375 25.362499999999997 21.3 32-33 24.762500000000003 26.7625 26.724999999999998 21.75 34-35 26.475737868934466 24.64982491245623 26.863431715857928 22.011005502751377 36-37 24.975 24.025 28.425 22.575 38-39 27.028378547318415 25.815726965870734 27.365920740092513 19.78997374671834 40-41 27.063531765882942 25.962981490745374 25.83791895947974 21.135567783891947 42-43 25.46933667083855 27.672090112640802 25.782227784730914 21.076345431789736 44-45 23.74937468734367 24.349674837418707 28.73936968484242 23.1615807903952 46-47 25.624999999999996 22.975 28.512500000000003 22.8875 48-49 26.334875578341876 24.096536201075402 28.698261848193074 20.87032637238965 50-51 26.9625 26.224999999999998 26.35 20.4625 52-53 26.345431789737173 26.12015018773467 26.245306633291616 21.289111389236545 54-55 24.525 26.787499999999998 27.250000000000004 21.4375 56-57 26.400000000000002 24.65 27.8625 21.087500000000002 58-59 24.9375 24.825 27.55 22.6875 60-61 24.9375 24.0 28.599999999999998 22.4625 62-63 23.4375 27.212500000000002 30.099999999999998 19.25 64-65 25.05 25.7875 28.9875 20.175 66-67 25.2 25.974999999999998 27.35 21.475 68-69 23.3 26.474999999999998 27.5625 22.662499999999998 70-71 25.78789394697349 25.350175087543768 27.213606803401703 21.64832416208104 72-73 25.899460950231916 23.968910618026825 27.66704274790021 22.464585683841044 74-75 23.65348399246704 26.390458254865035 29.001883239171374 20.954174513496547 76-77 23.067253299811437 25.66939032055311 28.62350722815839 22.63984915147706 78-79 24.452003023431594 24.817334341143866 28.92416225749559 21.80650037792895 80-81 24.640423921271765 27.794600050466816 28.28665152662125 19.27832450164017 82-83 24.709302325581394 24.835692618806878 29.24671385237614 21.20829120323559 84-85 24.29113924050633 22.797468354430382 30.77215189873418 22.139240506329113 86-87 22.955178526209167 25.43681944796151 31.76753608508483 19.840465940744494 88-89 22.689288427449988 28.108381868827554 29.779691061028107 19.422638642694352 90-91 26.095213978222336 25.46214231451 28.386933400860975 20.055710306406684 92-93 22.71461129399848 27.234742972904534 29.868321093947834 20.18232463914915 >>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 9.0 18 9.0 19 2.0 20 0.5 21 1.0 22 2.5 23 5.5 24 5.5 25 4.0 26 4.0 27 6.5 28 17.0 29 23.5 30 26.0 31 31.0 32 45.5 33 56.0 34 52.5 35 56.0 36 69.0 37 95.5 38 139.5 39 170.0 40 171.0 41 166.5 42 180.0 43 198.0 44 187.0 45 166.5 46 216.0 47 235.5 48 191.0 49 177.0 50 162.0 51 152.0 52 140.5 53 143.5 54 139.0 55 103.5 56 86.0 57 85.0 58 77.0 59 60.5 60 46.5 61 48.0 62 56.5 63 48.5 64 37.5 65 41.0 66 33.5 67 30.0 68 33.5 69 25.0 70 15.0 71 8.0 72 5.5 73 4.5 74 5.5 75 6.0 76 4.5 77 1.5 78 0.5 79 0.0 80 0.0 81 0.5 82 0.5 83 0.5 84 0.5 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 0.0125 40-41 0.05 42-43 0.125 44-45 0.05 46-47 0.0 48-49 0.0375 50-51 0.0 52-53 0.125 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 4.0 71 6.0 72 3.0 73 3.0 74 3.0 75 2.0 76 3.0 77 5.0 78 4.0 79 3.0 80 2.0 81 4.0 82 4.0 83 3.0 84 2.0 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 3949.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 81.925 #Duplication Level Percentage of deduplicated Percentage of total 1 93.28654256942325 76.425 2 4.11962160512664 6.75 3 0.7934086054317974 1.95 4 0.42722001830942935 1.4000000000000001 5 0.3051571559353067 1.25 6 0.183094293561184 0.8999999999999999 7 0.091547146780592 0.525 8 0.12206286237412267 0.8 9 0.091547146780592 0.675 >10 0.5797985962770826 9.325 >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 fail #Sequence Count Percentage Possible Source GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 50 1.25 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 35 0.8750000000000001 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 30 0.75 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 28 0.7000000000000001 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 25 0.625 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 24 0.6 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 20 0.5 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 17 0.42500000000000004 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 17 0.42500000000000004 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 16 0.4 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 16 0.4 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 15 0.375 No Hit GGGATGGAGATGGCCGCGGAGAACGGCGGCTGCGGCTGCAGCACCTGCAA 13 0.325 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 13 0.325 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 12 0.3 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 11 0.27499999999999997 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 11 0.27499999999999997 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 10 0.25 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 10 0.25 No Hit GGAGATGGCCGCGGAGAACGGCGGCTGCGGCTGCAGCACCTGCAAGTGCG 9 0.22499999999999998 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 9 0.22499999999999998 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 9 0.22499999999999998 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 8 0.2 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 8 0.2 No Hit GGGGAAGTACACCAGCGACGGCGAGGCCGCCGCCGCCAAGGAAGGCATGT 8 0.2 No Hit GGATTCTTCTTTTTTGTGGGCCATTTGTGGCATGCAGGAAGAGCCCGAGC 8 0.2 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 7 0.17500000000000002 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 7 0.17500000000000002 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 7 0.17500000000000002 No Hit GGATTTGAAGAAAAAAAAGACTTCGATTCATTTTCTATTTATTTCGTTAG 6 0.15 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 6 0.15 No Hit GGGGAAGAAGACCTCTTTCTGGGAGGCCGAAGCCACTTCGGCACCGGCAC 6 0.15 No Hit GGAGTAAACTAGCATAAATAATTTGTTTGATGCCAGTCATCAAGGTTGAG 6 0.15 No Hit GGGTGTGAGCTGGAGAGACGATCGGGTCTCTCAGCCGGCGTCTTCATCAG 6 0.15 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 6 0.15 No Hit GGGTGAGCATATATATTTATACGACGAATAAAAGGCTGCCACGTGGCGGG 5 0.125 No Hit GGAGAACGGCGGCTGCGGCTGCAGCACCTGCAAGTGCGGCACCAGCTGCG 5 0.125 No Hit GGAATAAGAATAAATCGCAACTCCTTTCCACTACACATAAAAATTGATTT 5 0.125 No Hit GGTGGGGCAATGGGCATTCCGTTGAGTTTGTATGGTGGGTGCTGTTTTGC 5 0.125 No Hit GGGACGACGGGGCTCCTGATCTGGGCCGTCACCCTGGCCGGCCTCCTCGG 5 0.125 No Hit GGGGATTGAGATGTCTGGCTGCAGTTTTAGTGTTTACTAAGTTTTGTCTA 5 0.125 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 5 0.125 No Hit GGGCGGCGGCATGTTCGGCGGCGGCAAGCACGGCCGCAAGTGGAAGTGAA 5 0.125 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 5 0.125 No Hit GGAAATGGTGAAGATGATACGAATATGCCGGCCGGGTGCTGATATTGTGA 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 GGGAGAG 20 0.0027549225 65.1 1 TTCAATT 25 0.006667318 52.079998 4 AATTTCA 25 0.006667318 52.079998 7 CAATTTC 25 0.006667318 52.079998 6 GGATTCA 25 0.006667318 52.079998 1 TTTCAAC 25 0.006667318 52.079998 9 TCAATTT 25 0.006667318 52.079998 5 GATTCAA 25 0.006667318 52.079998 2 ATTTCAA 25 0.006667318 52.079998 8 ATTCAAT 25 0.006667318 52.079998 3 AAAAAAA 25 0.0022271199 35.159492 86-87 TTGGGCT 30 0.0057907454 28.933334 54-55 TCTGTAG 30 0.0057907454 28.933334 18-19 >>END_MODULE Rejected 200850 READS because READLEN < 1 Read 200850 spots for ERR6133534.sra Written 200850 spots for ERR6133534.sra Rejected 200850 READS because READLEN < 1 Read 200850 spots for ERR6133534.sra Written 200850 spots for ERR6133534.sra Rejected 200850 READS because READLEN < 1 Read 200850 spots for ERR6133534.sra Written 200850 spots for ERR6133534.sra Rejected 200850 READS because READLEN < 1 Read 200850 spots for ERR6133534.sra Written 200850 spots for ERR6133534.sra Rejected 200850 READS because READLEN < 1 Read 200850 spots for ERR6133534.sra Written 200850 spots for ERR6133534.sra Rejected 200850 READS because READLEN < 1 Read 200850 spots for ERR6133534.sra Written 200850 spots for ERR6133534.sra Rejected 200850 READS because READLEN < 1 Read 200850 spots for ERR6133534.sra Written 200850 spots for ERR6133534.sra Rejected 200850 READS because READLEN < 1 Read 200850 spots for ERR6133534.sra Written 200850 spots for ERR6133534.sra Rejected 200850 READS because READLEN < 1 Read 200850 spots for ERR6133534.sra Written 200850 spots for ERR6133534.sra Rejected 200850 READS because READLEN < 1 Read 200850 spots for ERR6133534.sra Written 200850 spots for ERR6133534.sra Rejected 200850 READS because READLEN < 1 Read 200850 spots for ERR6133534.sra Written 200850 spots for ERR6133534.sra Rejected 200850 READS because READLEN < 1 Read 200850 spots for ERR6133534.sra Written 200850 spots for ERR6133534.sra Rejected 200850 READS because READLEN < 1 Read 200850 spots for ERR6133534.sra Written 200850 spots for ERR6133534.sra Rejected 200850 READS because READLEN < 1 Read 200850 spots for ERR6133534.sra Written 200850 spots for ERR6133534.sra Rejected 200850 READS because READLEN < 1 Read 200850 spots for ERR6133534.sra Written 200850 spots for ERR6133534.sra Rejected 200850 READS because READLEN < 1 Read 200850 spots for ERR6133534.sra Written 200850 spots for ERR6133534.sra Rejected 200850 READS because READLEN < 1 Read 200850 spots for ERR6133534.sra Written 200850 spots for ERR6133534.sra Rejected 200850 READS because READLEN < 1 Read 200850 spots for ERR6133534.sra Written 200850 spots for ERR6133534.sra Rejected 200850 READS because READLEN < 1 Read 200850 spots for ERR6133534.sra Written 200850 spots for ERR6133534.sra Rejected 200851 READS because READLEN < 1 Read 200851 spots for ERR6133534.sra Written 200851 spots for ERR6133534.sra SRR ids: ['ERR6133534.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_enyf1tk_ ERR6133534.sra spots: 4017001 blocks: [[1, 200850], [200851, 401700], [401701, 602550], [602551, 803400], [803401, 1004250], [1004251, 1205100], [1205101, 1405950], [1405951, 1606800], [1606801, 1807650], [1807651, 2008500], [2008501, 2209350], [2209351, 2410200], [2410201, 2611050], [2611051, 2811900], [2811901, 3012750], [3012751, 3213600], [3213601, 3414450], [3414451, 3615300], [3615301, 3816150], [3816151, 4017001]] ERR6133534 file size 890552 ERR6133534 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 ERR6133534 ERR6133534_1.fastq Input file: ERR6133534_1.fastq trimmed: ERR6133534-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 08:07:35 2024 >> started Sat Dec 7 08:07:37 2024 >> done (1.951s) 4017001 reads processed; of these: 36 ( 0.00%) short reads filtered out after trimming by size control 14 ( 0.00%) empty reads filtered out after trimming by size control 4016951 (100.00%) reads available; of these: 77616 ( 1.93%) trimmed reads available after processing 3939335 (98.07%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 5 0.00% 19 8 0.00% 20 5 0.00% 21 7 0.00% 22 7 0.00% 23 2 0.00% 24 1 0.00% 25 3 0.00% 26 5 0.00% 27 2 0.00% 28 5 0.00% 29 33 0.00% 30 6 0.00% 31 0 0.00% 32 5 0.00% 33 5 0.00% 34 7 0.00% 35 18 0.00% 36 347 0.01% 37 9 0.00% 38 10 0.00% 39 14 0.00% 40 20 0.00% 41 5 0.00% 42 9 0.00% 43 4 0.00% 44 1 0.00% 45 3 0.00% 46 6 0.00% 47 4 0.00% 48 7 0.00% 49 6 0.00% 50 3 0.00% 51 7 0.00% 52 4 0.00% 53 1 0.00% 54 4 0.00% 55 1 0.00% 56 2 0.00% 57 1 0.00% 58 1 0.00% 59 2 0.00% 60 6 0.00% 61 7 0.00% 62 2 0.00% 63 2 0.00% 64 10 0.00% 65 1 0.00% 66 10 0.00% 67 9 0.00% 68 24 0.00% 69 50 0.00% 70 3416 0.09% 71 3557 0.09% 72 3566 0.09% 73 3315 0.08% 74 3328 0.08% 75 3489 0.09% 76 3251 0.08% 77 3453 0.09% 78 3597 0.09% 79 4033 0.10% 80 3839 0.10% 81 3987 0.10% 82 4327 0.11% 83 4484 0.11% 84 3921 0.10% 85 210 0.01% 86 388 0.01% 87 662 0.02% 88 1143 0.03% 89 2043 0.05% 90 4405 0.11% 91 12846 0.32% 92 54053 1.35% 93 3884922 96.71% 4016951 reads passed initial QC criterion=sequence-density sequence-density=0.47 sequence-density-rank=1 fanout-score=7.09 fanout-score-rank=18 prefix-density=0.77 prefix-fanout=4.4 sequence=ATGCATGCATGC criterion=fanout-score sequence-density=0.01 sequence-density-rank=30 fanout-score=119.93 fanout-score-rank=1 prefix-density=0.18 prefix-fanout=7.8 sequence=AAAAGAAGGGGTGTTCCATCTCCGGACGACGATCCTGCCTGCAGAGGAAGACATGCCGGCGATCATGTCGAGCTTCAAGAAGTTCAACGACTCATTCATGGAGCAATACCAAGACTACTCCAGGCTGTGATGTGAAGAGGGAAACAACGAGGTCATCATCGACATGATATATTGCTGCTATTTTCCACCAGCGATTAAAAGTTAAAAAATTTAGCTGTAAGCTGTAACTATCTTGAAGAAACTAAACTGGTTGCTGTGCTTGATATGTAT Started job on | Dec 07 08:07:50 Started mapping on | Dec 07 08:07:50 Finished on | Dec 07 08:07:55 Mapping speed, Million of reads per hour | 2892.20 Number of input reads | 4016951 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 3144441 Uniquely mapped reads % | 78.28% Average mapped length | 92.44 Number of splices: Total | 211779 Number of splices: Annotated (sjdb) | 178654 Number of splices: GT/AG | 206308 Number of splices: GC/AG | 3683 Number of splices: AT/AC | 52 Number of splices: Non-canonical | 1736 Mismatch rate per base, % | 0.41% Deletion rate per base | 0.04% Deletion average length | 1.76 Insertion rate per base | 0.02% Insertion average length | 2.15 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 804565 % of reads mapped to multiple loci | 20.03% Number of reads mapped to too many loci | 16968 % of reads mapped to too many loci | 0.42% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.24% % of reads unmapped: other | 0.03% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 67945 67945 67945 N_multimapping 804565 804565 804565 N_noFeature 170995 198577 3011196 N_ambiguous 118485 12936 248 UnstrandedReadsAssigned:2854961 PositiveStrandReadsAssigned:2932928 NegativeStrandReadsAssigned:132997 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133534 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: ERR6133534-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 4,016,951 reads, 3,543,610 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,022 rounds 52973 ERR6133534.ke.tsv 35125 ERR6133534.se.tsv 88098 total ==> ERR6133534.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 109 29.041 PNS24243 293 194 0 0 KQK14069 1603 1504 187 45.45 KQK14071 474 375 0 0 ==> ERR6133534.se.tsv <== BRADI_1g14170v3 189 BRADI_1g53295v3 34 BRADI_1g59795v3 35 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 73 BRADI_1g74790v3 34 BRADI_1g09890v3 0 BRADI_1g77505v3 103 BRADI_1g48960v3 0 ERR6133534 completed mapping pipeline successfully