Starting /dee2/code/volunteer_pipeline.sh ERR1942999 current disk space = 1523691929600 free memory = 1601589836 ERR1942999 SRAfilesize 4c7292444934b304b6abb92fc54bb557 ERR1942999.sra ERR1942999.sra file validated ERR1942999 is single end ERR1942999 is conventional basespace ERR1942999 read1 length is 25-250 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR1942999_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 25-250 %GC 61 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 24.7545 26.0 23.0 27.0 20.0 28.0 2 24.3105 25.0 22.0 27.0 19.0 29.0 3 20.8675 22.0 18.0 24.0 14.0 27.0 4 24.57575 26.0 23.0 28.0 14.0 29.0 5 21.46075 23.0 19.0 24.0 14.0 27.0 6 24.197 26.0 23.0 27.0 14.0 28.0 7 24.79125 26.0 23.0 27.0 20.0 29.0 8 24.46575 26.0 23.0 27.0 20.0 28.0 9 24.4945 26.0 22.0 28.0 18.0 29.0 10-14 24.402449999999998 25.4 22.6 27.0 18.8 28.8 15-19 25.535899999999998 27.0 23.8 28.0 19.4 29.4 20-24 24.751399999999997 26.0 22.8 27.8 19.2 28.2 25-29 23.741421343003903 25.0 21.6 27.0 17.8 28.4 30-34 23.57584883653167 25.2 21.6 26.6 17.2 28.2 35-39 24.386650271401646 25.6 22.4 27.2 19.4 28.2 40-44 24.31883097946353 25.6 22.6 27.2 19.0 28.0 45-49 24.104559680725252 25.4 22.2 27.0 19.0 27.8 50-54 23.734824246817674 24.8 21.8 26.6 18.4 28.0 55-59 24.259736542205616 25.6 22.6 27.0 18.8 28.0 60-64 23.91240692635123 25.2 22.2 26.6 18.4 27.8 65-69 22.121767178582516 23.4 18.6 26.0 14.4 27.6 70-74 19.12840251113376 20.4 13.0 24.4 10.6 27.0 75-79 21.055868809794994 22.2 18.2 24.8 13.0 27.0 80-84 18.793952422460773 20.4 14.0 24.0 9.2 26.8 85-89 19.301115357485912 20.4 14.0 23.8 11.6 26.0 90-94 18.841593343645172 19.8 14.0 22.8 10.6 25.4 95-99 20.323259727477765 21.8 16.6 24.0 12.0 26.0 100-104 19.454647162077457 20.2 14.0 23.8 11.2 26.0 105-109 20.032925644235554 21.0 16.4 24.0 12.8 26.4 110-114 19.8488733264125 21.0 15.8 24.0 12.0 26.0 115-119 18.581281878847015 19.4 13.4 23.0 10.0 25.4 120-124 19.10214356307298 20.2 13.8 23.0 11.2 25.0 125-129 18.181146766397653 19.4 14.0 22.4 10.8 24.8 130-134 18.654381410825867 20.0 14.0 23.0 10.6 25.0 135-139 19.02839449905264 20.0 14.0 23.0 10.8 25.0 140-144 18.425786894284506 20.0 14.0 22.6 11.0 24.6 145-149 18.802845023414612 20.0 14.0 22.8 11.4 24.6 150-154 18.867370368764846 20.0 14.0 23.0 11.0 25.0 155-159 18.744826591470012 20.0 14.0 22.8 11.4 25.0 160-164 17.959677156456273 19.6 14.0 22.0 10.6 24.0 165-169 17.82478820515926 19.0 13.8 22.0 10.6 24.2 170-174 18.46359197912244 19.6 14.0 22.0 12.0 24.0 175-179 18.603290231717686 19.6 14.0 22.0 12.2 24.2 180-184 18.524264160751237 19.6 14.0 22.6 11.8 24.4 185-189 18.326100699361223 19.6 14.0 22.0 11.0 24.4 190-194 18.789267660635613 20.0 14.0 22.6 12.0 24.8 195-199 18.678772193989584 20.0 14.0 22.6 11.6 25.0 200-204 18.855296092406554 19.6 14.2 23.0 11.2 24.8 205-209 18.837087531654767 20.0 14.0 23.0 12.0 25.0 210-214 17.540967131310786 NaN NaN NaN NaN NaN 215-219 17.774735751462156 NaN NaN NaN NaN NaN 220-224 17.32361479516652 NaN NaN NaN NaN NaN 225-229 16.6003663003663 NaN NaN NaN NaN NaN 230-234 20.07171717171717 NaN NaN NaN NaN NaN 235-239 18.823333333333334 NaN NaN NaN NaN NaN 240-244 16.96666666666667 NaN NaN NaN NaN NaN 245-249 19.06666666666667 NaN NaN NaN NaN NaN 250 19.0 NaN NaN NaN NaN NaN >>END_MODULE >>Per sequence quality scores warn #Quality Count 15 1.0 16 13.0 17 55.0 18 144.0 19 323.0 20 522.0 21 621.0 22 583.0 23 538.0 24 435.0 25 257.0 26 273.0 27 228.0 28 7.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 4.2 86.75 0.8 8.25 2 7.3 18.775 0.575 73.35000000000001 3 6.7250000000000005 5.525 2.1 85.65 4 20.375 70.075 0.525 9.025 5 8.5 82.15 0.1 9.25 6 7.5 8.7 2.5749999999999997 81.22500000000001 7 5.925 71.05 11.05 11.975 8 7.9 13.05 62.55 16.5 9 2.1999999999999997 70.075 6.825 20.9 10-14 34.13 36.17 2.905 26.795 15-19 35.675000000000004 9.9 15.68 38.745000000000005 20-24 33.035 22.64 17.845 26.479999999999997 25-29 24.831776639550064 48.1771617957216 2.30993271065582 24.68112885407251 30-34 49.61228446076931 10.208142026323845 3.994490358126722 36.18508315478012 35-39 27.289215940301602 20.925532466186453 28.045810229569362 23.739441363942582 40-44 11.614939505523408 49.17937927406628 4.765912677538138 34.43976854287217 45-49 22.992505353319057 23.008565310492504 28.37259100642398 25.626338329764454 50-54 31.613720200407418 13.973462533722403 16.874965589385013 37.53785167648516 55-59 23.03655554892957 13.035959210447851 26.554952591090704 37.37253264953188 60-64 29.155196672172263 13.708937419710038 33.35780265492139 23.778063253196304 65-69 24.8424730176555 18.853328342379438 8.615634163079418 47.688564476885645 70-74 40.92132029660739 5.800905571231708 20.33598005118446 32.94179408097644 75-79 34.58735336988964 8.759630735059346 7.6351773443464985 49.01783855070452 80-84 14.898097315183875 30.69865383169136 12.032789350981425 42.37045950214334 85-89 26.466275659824046 23.36265884652981 14.345063538611926 35.826001955034215 90-94 12.42043847241867 34.839108910891085 6.4268033946251775 46.31364922206506 95-99 18.403181994567326 23.932867675591773 17.9860302677532 39.6779200620877 100-104 16.469310157523083 32.243346007604565 11.591526344378057 39.69581749049429 105-109 15.616974440503853 18.124006359300477 12.596306713953773 53.662712486241894 110-114 34.557689611664095 25.220804710500488 8.551801486050751 31.669704191784664 115-119 37.34639912894696 14.947892362731373 10.981490122880697 36.72421838544097 120-124 27.567760342368047 18.170470756062766 12.28601997146933 41.97574893009986 125-129 41.356628982528264 9.188078108941419 21.04830421377184 28.40698869475848 130-134 30.417991821899136 9.495683780099954 13.448432530667878 46.63789186733303 135-139 26.551189245087905 21.406411582213032 5.118924508790072 46.923474663909 140-144 31.32118451025057 28.75854214123007 6.06492027334852 33.85535307517084 145-149 29.26457125419591 15.746109246261824 14.739090631675314 40.25022886786695 150-154 25.745257452574528 22.188346883468835 15.074525745257453 36.99186991869919 155-159 30.503380916604055 16.416228399699474 13.148009015777612 39.93238166791886 160-164 32.57355988396187 9.573145462080399 17.861583091587235 39.99171156237049 165-169 34.38679245283019 13.773584905660377 11.179245283018869 40.66037735849057 170-174 26.064648537711648 18.88147768086198 12.570548999486917 42.48332478193946 175-179 20.461095100864554 18.55907780979827 22.13256484149856 38.847262247838614 180-184 25.064267352185087 9.768637532133676 26.47814910025707 38.688946015424165 185-189 29.822064056939503 15.373665480427047 19.00355871886121 35.80071174377224 190-194 23.809523809523807 24.084249084249084 14.102564102564102 38.003663003663 195-199 24.728260869565215 19.021739130434785 17.527173913043477 38.72282608695652 200-204 25.97402597402597 20.941558441558442 19.155844155844157 33.92857142857143 205-209 26.252505010020037 21.8436873747495 14.629258517034069 37.27454909819639 210-214 28.869047619047617 17.559523809523807 23.511904761904763 30.059523809523807 215-219 30.120481927710845 25.301204819277107 12.048192771084338 32.53012048192771 220-224 33.33333333333333 11.805555555555555 18.055555555555554 36.80555555555556 225-229 32.3943661971831 16.901408450704224 18.30985915492958 32.3943661971831 230-234 21.052631578947366 15.789473684210526 23.684210526315788 39.473684210526315 235-239 34.61538461538461 3.8461538461538463 26.923076923076923 34.61538461538461 240-244 22.22222222222222 22.22222222222222 22.22222222222222 33.33333333333333 245-249 55.55555555555556 22.22222222222222 0.0 22.22222222222222 250 0.0 0.0 100.0 0.0 >>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 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 0.0 27 0.5 28 2.0 29 3.5 30 4.0 31 7.0 32 9.0 33 6.0 34 7.5 35 10.5 36 9.0 37 9.5 38 8.5 39 9.0 40 11.5 41 9.0 42 4.0 43 2.5 44 4.5 45 20.0 46 36.5 47 22.5 48 8.5 49 10.5 50 18.0 51 31.0 52 63.5 53 127.0 54 268.0 55 365.0 56 289.5 57 183.0 58 172.5 59 287.0 60 699.5 61 822.5 62 522.1666666666667 63 385.0000000000001 64 251.6666666666672 65 122.8333333333332 66 65.66666666666671 67 32.16666666666666 68 28.5 69 33.0 70 26.5 71 21.0 72 27.0 73 23.5 74 20.0 75 19.5 76 11.0 77 5.5 78 1.5 79 1.0 80 1.0 81 0.5 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 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150-154 0.0 155-159 0.0 160-164 0.0 165-169 0.0 170-174 0.0 175-179 0.0 180-184 0.0 185-189 0.0 190-194 0.0 195-199 0.0 200-204 0.0 205-209 0.0 210-214 0.0 215-219 0.0 220-224 0.0 225-229 0.0 230-234 0.0 235-239 0.0 240-244 0.0 245-249 0.0 250 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 25-29 42.0 30-34 86.0 35-39 48.0 40-44 59.0 45-49 48.0 50-54 338.0 55-59 73.0 60-64 75.0 65-69 89.0 70-74 186.0 75-79 197.0 80-84 233.0 85-89 186.0 90-94 206.0 95-99 189.0 100-104 220.0 105-109 221.0 110-114 181.0 115-119 111.0 120-124 186.0 125-129 111.0 130-134 84.0 135-139 112.0 140-144 42.0 145-149 63.0 150-154 59.0 155-159 54.0 160-164 53.0 165-169 46.0 170-174 36.0 175-179 47.0 180-184 22.0 185-189 45.0 190-194 84.0 195-199 40.0 200-204 18.0 205-209 34.0 210-214 19.0 215-219 18.0 220-224 24.0 225-229 4.0 230-234 5.0 235-239 2.0 240-244 1.0 245-249 2.0 250-251 1.0 >>END_MODULE >>Sequence Duplication Levels fail #Total Deduplicated Percentage 20.599999999999998 #Duplication Level Percentage of deduplicated Percentage of total 1 79.12621359223301 16.3 2 7.281553398058252 3.0 3 2.7912621359223304 1.725 4 1.3349514563106795 1.0999999999999999 5 0.9708737864077669 1.0 6 0.7281553398058253 0.8999999999999999 7 0.9708737864077669 1.4000000000000001 8 0.3640776699029126 0.6 9 0.48543689320388345 0.8999999999999999 >10 5.097087378640777 20.3 >50 0.3640776699029126 4.5 >100 0.3640776699029126 12.875 >500 0.0 0.0 >1k 0.12135922330097086 35.4 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences fail #Sequence Count Percentage Possible Source ACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAACACGTTCAT 1416 35.4 No Hit AACGACTCCAGCCCCAGCGGCTCCGGCACCGGCAGCCGGAACGACCAAGA 230 5.75 No Hit ACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAACACGTTCATCCG 174 4.35 No Hit ACCGGCAGCCGGAACGACCAAGACGACCAACATAACAGGCGTGCTAGCGA 111 2.775 No Hit AACGACCAAGACGACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAGT 73 1.825 No Hit CAGCCGGAACGACCAAGACGACCAACATAACAGGCGTGCTAGCGAAAGCC 56 1.4000000000000001 No Hit ACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAACACGTTCATCCGGCTGCTGCGTTCCACGG 51 1.275 No Hit GGAACGACCAAGACGACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCA 46 1.15 No Hit CCCAAAAATTCTAGGTTTAGATCGGAGTTCGCGCTTGCTGGATCGGCTCC 44 1.0999999999999999 No Hit ACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAACACGTTCATCC 36 0.8999999999999999 No Hit AGTGCTGCTCGTGATCTCAGCGGCGATCACGGCGTCGGCGCAGGGCCCAA 35 0.8750000000000001 No Hit GAACGACCAAGACGACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAG 32 0.8 No Hit AGCCCCAGCGGCTCCGGCACCGGCAGCCGGAACGACCAAGACGACCAACA 27 0.675 No Hit AAGACGACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAACAC 27 0.675 No Hit CGGAACGACCAAGACGACCAACATAACAGGCGTGCTAGCGAAAGCCGGGC 25 0.625 No Hit ACCACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAACACGTTCATC 25 0.625 No Hit ACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAACACG 24 0.6 No Hit CACCGGCAGCCGGAACGACCAAGACGACCAACATAACAGGCGTGCTAGCG 22 0.5499999999999999 No Hit ACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAAC 22 0.5499999999999999 No Hit ACCAACATAACAGGCGTGCTAGCGAAAGCCG 21 0.525 No Hit ACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAACACGTTCATC 21 0.525 No Hit ACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAACACGTTCATCCGG 21 0.525 No Hit TGGCGACTTTGTTTATTTGGTCAACCCGAGCTGATAAGCTTTGACCGTGA 20 0.5 No Hit CCGGAACGACCAAGACGACCAACATAACAGGCGTGCTAGCGAAAGCCGGG 19 0.475 No Hit CCAACGACTCCAGCCCCAGCGGCTCCGGCACCGGCAGCCGGAACGACCAAGACGACCAACA 19 0.475 No Hit CCCCAGCGGCTCCGGCACCGGCAGCCGGAACGACCAAGACGACCAACATA 19 0.475 No Hit ACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAACACGTTCATCCGGCTGCTGCATTCCACG 19 0.475 No Hit ACCAACATAACAGGCGTGCTAGCGAAGCCGGGCAGTTCAACACGTTCATC 17 0.42500000000000004 No Hit ATAGATCACTCTCGCATTTGTCCTCGCTGATAGCTAGAGTTTCACGATTACACCACCAG 17 0.42500000000000004 No Hit ACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAACACGTTCATCCGGCTGCTGCGTTCCACGGG 16 0.4 No Hit ACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCACACGTTCATC 16 0.4 No Hit CGGCACCGGCAGCCGGAACGACCAAGACGACCAACATAACAGGCGTGCTA 15 0.375 No Hit ACCAACATAAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAACACGTTCA 15 0.375 No Hit GACGACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAACACGT 15 0.375 No Hit ACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCGTTCAACACGTTCATC 14 0.35000000000000003 No Hit AGATAGATCACTCTCGCATTTGTCCTCGCTGATAGCTAGAGTTTCACGATTACACCACCAG 14 0.35000000000000003 No Hit ACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTTC 13 0.325 No Hit ACCAACATAACAGGCGTGCTAGCGAAAGCC 13 0.325 No Hit AACGACTCCAGCCCCCAGCGGCTCCGGCACCGGCAGCCGGAACGACCAAG 13 0.325 No Hit ACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAACACGTTCTC 12 0.3 No Hit ACCAAACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAACACGTTCA 12 0.3 No Hit ACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAACACGTTGAT 12 0.3 No Hit ACCAACATAACAGGCGTGCTAGCGAAAGCCGGGC 11 0.27499999999999997 No Hit ACCCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAACACGTTCA 11 0.27499999999999997 No Hit ACCAACATAACAGGCGTGCTGGCTTCCGGCACGCTCAACTCGCTTTCGGACAGC 11 0.27499999999999997 No Hit AAAAAAGGAGCGTGAGAGCCAAATGAATCGAAAGATTCATGTTTGGTTCG 11 0.27499999999999997 No Hit ACGACTCCAGCCCCAGCGGCTCCGGCACCGGCAGCCGGAACGACCAAGAC 10 0.25 No Hit ACCAACATAACAGGCGTGCTAGCGAAAGCCGGG 10 0.25 No Hit ACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAACACGTTCATCCGGCTGCTGCGTTCCACGGC 10 0.25 No Hit ACCAACATAACAGGCGTGCTAGCGAAAAGCCGGGCAGTTCAACACGTTCA 9 0.22499999999999998 No Hit ACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTT 9 0.22499999999999998 No Hit ACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAACACGTTCATCCGGCTGCTGCGTTCCACGGCGT 9 0.22499999999999998 No Hit ACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAACACGTTCATCCGGCTGCTGCGTTCCACGGCGTC 9 0.22499999999999998 No Hit AACGACTCCAGCCCCAGCGGCTCCGGCACCGGCAGCCGGAACGACCAGAC 8 0.2 No Hit ACTCCAGCCCCAGCGGCTCCGGCACCGGCAGCCGGAACGACCAAGACGAC 8 0.2 No Hit ACCAACATAACAGGCGTGCTAGCGAAAGC 8 0.2 No Hit ACCAACATAACAGGCGTGCTAGCGAAAGCCAGTGCTGCTCGTGATCTCAGCGGCG 7 0.17500000000000002 No Hit CCGCATTGCTGAAGCGGCAGCTGCGCCAACGACTCCAGCCCCAGCGGCTC 7 0.17500000000000002 No Hit ACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAACACGTTTCA 7 0.17500000000000002 No Hit ACCAACATAACAGGCGTGCTAGCGAAAGCCGGCAGTTCAACACGTTCATC 7 0.17500000000000002 No Hit ACCGGCAGCCGGAACGACCAAGACGACCAACATAACAGGCGTCTAGCGAA 7 0.17500000000000002 No Hit CAGCGGCTCCGGCACCGGCAGCCGGAACGACCAAGACGACCAACATAACA 7 0.17500000000000002 No Hit ACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAACACGTTCATCCGGCTGCTGCGTTCC 7 0.17500000000000002 No Hit ACCAACAATAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAACACGTTCA 7 0.17500000000000002 No Hit ACCGGCAGCCGGAACGACCAAGACGCCAACATAACAGGCGTGCTAGCGAA 6 0.15 No Hit ACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAACACGTTCATCCGGCTGCTGCGTTCCACGGCGTCG 6 0.15 No Hit ACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAACACGTTCATCCGGCTGCTGCGTTCCACGGCG 6 0.15 No Hit ACCAACGTAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAACACGTTCATCCG 6 0.15 No Hit AGCCCCCAGCGGCTCCGGCACCGGCAGCCGGAACGACCAAGACGACCAAC 6 0.15 No Hit CCCAGCGGCTCCGGCACCGGCAGCCGGAACGACCAAGACGACCAACATAA 6 0.15 No Hit GCTCCGGCACCGGCAGCCGGAACGACCAAGACGACCAACATAACAGGCGT 5 0.125 No Hit ACCAACATAACAGGCGTGCTAGCGGAAGCCGGGCAGTTCAACACGTTCATCCGG 5 0.125 No Hit ACCAACATAACAGGCGTGCTAGCGAAGCCGGGCAGTTCAACACGTTCATCCG 5 0.125 No Hit ACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAACACGTTCATCCGGCTGCTGCGTTCCACGGCGCGC 5 0.125 No Hit ACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAACACGTTCATCCGGCTGCTGCGTTCCACGGCGC 5 0.125 No Hit ACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAACAC 5 0.125 No Hit ACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAACACGTTCATCCGGCTGCTGCGTTCCA 5 0.125 No Hit ACCGGCAGCCGGAACGACCAAGACGACCAACATAACAGGCGTCTAGCTAA 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 10-14 0.0 0.0 0.0 0.0 0.0 15-19 0.0 0.0 0.0 0.0 0.0 20-24 0.0 0.0 0.0 0.0 0.0 25-29 0.0 0.0 0.0 0.0 0.0 30-34 0.0 0.0 0.0 0.0 0.0 35-39 0.0 0.0 0.0 0.0 0.0 40-44 0.0 0.0 0.0 0.0 0.0 45-49 0.0 0.0 0.0 0.0 0.0 50-54 0.0 0.0 0.0 0.0 0.0 55-59 0.0 0.0 0.0 0.0 0.0 60-64 0.0 0.0 0.0 0.0 0.0 65-69 0.0 0.0 0.0 0.0 0.0 70-74 0.0 0.0 0.0 0.0 0.0 75-79 0.0 0.0 0.0 0.0 0.0 80-84 0.0 0.0 0.0 0.0 0.0 85-89 0.0 0.0 0.0 0.0 0.0 90-94 0.0 0.0 0.0 0.0 0.0 95-99 0.0 0.0 0.0 0.0 0.0 100-104 0.0 0.0 0.0 0.0 0.0 105-109 0.0 0.0 0.0 0.0 0.0 110-114 0.0 0.0 0.0 0.0 0.0 115-119 0.0 0.0 0.0 0.0 0.0 120-124 0.0 0.0 0.0 0.0 0.0 125-129 0.0 0.0 0.0 0.0 0.0 130-134 0.0 0.0 0.0 0.0 0.0 135-139 0.0 0.0 0.0 0.0 0.0 140-144 0.0 0.0 0.0 0.0 0.0 145-149 0.0 0.0 0.0 0.0 0.0 150-154 0.0 0.0 0.0 0.0 0.0 155-159 0.0 0.0 0.0 0.0 0.0 160-164 0.0 0.0 0.0 0.0 0.0 165-169 0.0 0.0 0.0 0.0 0.0 170-174 0.0 0.0 0.0 0.0 0.0 175-179 0.0 0.0 0.0 0.0 0.0 180-184 0.0 0.0 0.0 0.0 0.0 185-189 0.0 0.0 0.0 0.0 0.0 190-194 0.0 0.0 0.0 0.0 0.0 195-199 0.0 0.0 0.0 0.0 0.0 200-204 0.0 0.0 0.0 0.0 0.0 205-209 0.0 0.0 0.0 0.0 0.0 210-214 0.0 0.0 0.0 0.0 0.0 215-219 0.0 0.0 0.0 0.0 0.0 220-224 0.0 0.0 0.0 0.0 0.0 225-229 0.0 0.0 0.0 0.0 0.0 230-234 0.0 0.0 0.0 0.0 0.0 235-238 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 CGCTTTC 15 0.008493179 801.7778 210-212 GCTTTCG 15 0.008493179 801.7778 210-212 CTTTCGG 15 0.008493179 801.7778 210-212 GCGGACT 10 0.0022679917 206.17143 115-119 CGCGCCA 25 3.9688854E-5 180.40001 130-134 CGGACTC 10 0.0071923863 141.4902 115-119 CTGGCTC 25 3.3833503E-4 108.24 155-159 CACGCGT 20 4.4324828E-4 102.113205 140-144 GTCACGA 25 5.500688E-4 96.21334 145-149 CGCCACG 20 5.968665E-4 94.94737 130-134 GCGCCAC 20 5.968665E-4 94.94737 130-134 GCCACGG 20 5.968665E-4 94.94737 130-134 ACGCGTC 30 1.8075287E-5 90.76729 140-144 GTGTTCG 40 2.4805558E-8 82.0 125-129 CGTCACG 30 0.0011354522 80.17777 145-149 TGTTCGC 35 1.1801349E-6 78.09524 125-129 ACGGACA 45 1.6966387E-6 72.888885 135-139 CACGGAC 45 1.6966387E-6 72.888885 135-139 CGGTGTT 40 6.266782E-8 72.159996 120-124 CAGCCCC 45 2.568413E-9 70.15556 9 >>END_MODULE Read 951679 spots for ERR1942999.sra Written 951679 spots for ERR1942999.sra Read 951679 spots for ERR1942999.sra Written 951679 spots for ERR1942999.sra Read 951679 spots for ERR1942999.sra Written 951679 spots for ERR1942999.sra Read 951679 spots for ERR1942999.sra Written 951679 spots for ERR1942999.sra Read 951679 spots for ERR1942999.sra Written 951679 spots for ERR1942999.sra Read 951679 spots for ERR1942999.sra Written 951679 spots for ERR1942999.sra Read 951679 spots for ERR1942999.sra Written 951679 spots for ERR1942999.sra Read 951679 spots for ERR1942999.sra Written 951679 spots for ERR1942999.sra Read 951679 spots for ERR1942999.sra Written 951679 spots for ERR1942999.sra Read 951679 spots for ERR1942999.sra Written 951679 spots for ERR1942999.sra Read 951687 spots for ERR1942999.sra Written 951687 spots for ERR1942999.sra Read 951679 spots for ERR1942999.sra Written 951679 spots for ERR1942999.sra Read 951679 spots for ERR1942999.sra Written 951679 spots for ERR1942999.sra Read 951679 spots for ERR1942999.sra Written 951679 spots for ERR1942999.sra Read 951679 spots for ERR1942999.sra Written 951679 spots for ERR1942999.sra Read 951679 spots for ERR1942999.sra Written 951679 spots for ERR1942999.sra Read 951679 spots for ERR1942999.sra Written 951679 spots for ERR1942999.sra Read 951679 spots for ERR1942999.sra Written 951679 spots for ERR1942999.sra Read 951679 spots for ERR1942999.sra Written 951679 spots for ERR1942999.sra Read 951679 spots for ERR1942999.sra Written 951679 spots for ERR1942999.sra SRR ids: ['ERR1942999.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_zuggtce_ ERR1942999.sra spots: 19033588 blocks: [[1, 951679], [951680, 1903358], [1903359, 2855037], [2855038, 3806716], [3806717, 4758395], [4758396, 5710074], [5710075, 6661753], [6661754, 7613432], [7613433, 8565111], [8565112, 9516790], [9516791, 10468469], [10468470, 11420148], [11420149, 12371827], [12371828, 13323506], [13323507, 14275185], [14275186, 15226864], [15226865, 16178543], [16178544, 17130222], [17130223, 18081901], [18081902, 19033588]] ERR1942999 file size 4977816 ERR1942999 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 ERR1942999 ERR1942999_1.fastq Input file: ERR1942999_1.fastq trimmed: ERR1942999-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 Tue Dec 10 00:55:46 2024 >> started Tue Dec 10 00:55:57 2024 >> done (11.214s) 19033588 reads processed; of these: 388 ( 0.00%) short reads filtered out after trimming by size control 0 ( 0.00%) empty reads filtered out after trimming by size control 19033200 (100.00%) reads available; of these: 1623314 ( 8.53%) trimmed reads available after processing 17409886 (91.47%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 422 0.00% 19 572 0.00% 20 1030 0.01% 21 1667 0.01% 22 2927 0.02% 23 3878 0.02% 24 8347 0.04% 25 45540 0.24% 26 46693 0.25% 27 48516 0.25% 28 49484 0.26% 29 51538 0.27% 30 53192 0.28% 31 54227 0.28% 32 55562 0.29% 33 58093 0.31% 34 59660 0.31% 35 61168 0.32% 36 63526 0.33% 37 66169 0.35% 38 68269 0.36% 39 73211 0.38% 40 73713 0.39% 41 76206 0.40% 42 78219 0.41% 43 80694 0.42% 44 81807 0.43% 45 84234 0.44% 46 88175 0.46% 47 86071 0.45% 48 90347 0.47% 49 94029 0.49% 50 97721 0.51% 51 101551 0.53% 52 99586 0.52% 53 101726 0.53% 54 101672 0.53% 55 103152 0.54% 56 106443 0.56% 57 110308 0.58% 58 114174 0.60% 59 114806 0.60% 60 116681 0.61% 61 115339 0.61% 62 119866 0.63% 63 122794 0.65% 64 120036 0.63% 65 119712 0.63% 66 120094 0.63% 67 121080 0.64% 68 122589 0.64% 69 123721 0.65% 70 123586 0.65% 71 124509 0.65% 72 124995 0.66% 73 125710 0.66% 74 128438 0.67% 75 127754 0.67% 76 129551 0.68% 77 132206 0.69% 78 130897 0.69% 79 131076 0.69% 80 131431 0.69% 81 133173 0.70% 82 135735 0.71% 83 134674 0.71% 84 135186 0.71% 85 135296 0.71% 86 141618 0.74% 87 138927 0.73% 88 139803 0.73% 89 138617 0.73% 90 142662 0.75% 91 142607 0.75% 92 140817 0.74% 93 141483 0.74% 94 140684 0.74% 95 143159 0.75% 96 143504 0.75% 97 143612 0.75% 98 147421 0.77% 99 143738 0.76% 100 140691 0.74% 101 143965 0.76% 102 141925 0.75% 103 142696 0.75% 104 144285 0.76% 105 144241 0.76% 106 143347 0.75% 107 142969 0.75% 108 145709 0.77% 109 144049 0.76% 110 144138 0.76% 111 146248 0.77% 112 148524 0.78% 113 138031 0.73% 114 140805 0.74% 115 140689 0.74% 116 141519 0.74% 117 142209 0.75% 118 141850 0.75% 119 139650 0.73% 120 146917 0.77% 121 139671 0.73% 122 138404 0.73% 123 137966 0.72% 124 139025 0.73% 125 135662 0.71% 126 135624 0.71% 127 134784 0.71% 128 132768 0.70% 129 134230 0.71% 130 132299 0.70% 131 131256 0.69% 132 128950 0.68% 133 127037 0.67% 134 128253 0.67% 135 125878 0.66% 136 126818 0.67% 137 126171 0.66% 138 128328 0.67% 139 123809 0.65% 140 128077 0.67% 141 128054 0.67% 142 120746 0.63% 143 117933 0.62% 144 119171 0.63% 145 117489 0.62% 146 121574 0.64% 147 116277 0.61% 148 115393 0.61% 149 111942 0.59% 150 110168 0.58% 151 106842 0.56% 152 108030 0.57% 153 110220 0.58% 154 108737 0.57% 155 107234 0.56% 156 103227 0.54% 157 101327 0.53% 158 98500 0.52% 159 100155 0.53% 160 97724 0.51% 161 96667 0.51% 162 100052 0.53% 163 98990 0.52% 164 93732 0.49% 165 90548 0.48% 166 87758 0.46% 167 86117 0.45% 168 82577 0.43% 169 80479 0.42% 170 78822 0.41% 171 79460 0.42% 172 79008 0.42% 173 75792 0.40% 174 73096 0.38% 175 70891 0.37% 176 70583 0.37% 177 70820 0.37% 178 70402 0.37% 179 66097 0.35% 180 63034 0.33% 181 61042 0.32% 182 57876 0.30% 183 57794 0.30% 184 57213 0.30% 185 54637 0.29% 186 54450 0.29% 187 52271 0.27% 188 50435 0.26% 189 48650 0.26% 190 45233 0.24% 191 43956 0.23% 192 42743 0.22% 193 41712 0.22% 194 40857 0.21% 195 39412 0.21% 196 37692 0.20% 197 36110 0.19% 198 34777 0.18% 199 33227 0.17% 200 32006 0.17% 201 30804 0.16% 202 29707 0.16% 203 28820 0.15% 204 28125 0.15% 205 27257 0.14% 206 25792 0.14% 207 25094 0.13% 208 23746 0.12% 209 22555 0.12% 210 21134 0.11% 211 20460 0.11% 212 20364 0.11% 213 19993 0.11% 214 19263 0.10% 215 18105 0.10% 216 16925 0.09% 217 15585 0.08% 218 14717 0.08% 219 13799 0.07% 220 12971 0.07% 221 12146 0.06% 222 11371 0.06% 223 10786 0.06% 224 10183 0.05% 225 9451 0.05% 226 8959 0.05% 227 8210 0.04% 228 7696 0.04% 229 7244 0.04% 230 6704 0.04% 231 6292 0.03% 232 5913 0.03% 233 5584 0.03% 234 5063 0.03% 235 4802 0.03% 236 4510 0.02% 237 4257 0.02% 238 3834 0.02% 239 3578 0.02% 240 3126 0.02% 241 2910 0.02% 242 2577 0.01% 243 2368 0.01% 244 2183 0.01% 245 1909 0.01% 246 1822 0.01% 247 1643 0.01% 248 1366 0.01% 249 1229 0.01% 250 1146 0.01% 251 1010 0.01% 252 914 0.00% 253 800 0.00% 254 692 0.00% 255 644 0.00% 256 564 0.00% 257 497 0.00% 258 456 0.00% 259 394 0.00% 260 352 0.00% 261 328 0.00% 262 265 0.00% 263 253 0.00% 264 215 0.00% 265 202 0.00% 266 164 0.00% 267 141 0.00% 268 123 0.00% 269 117 0.00% 270 106 0.00% 271 77 0.00% 272 75 0.00% 273 74 0.00% 274 50 0.00% 275 48 0.00% 276 34 0.00% 277 40 0.00% 278 20 0.00% 279 20 0.00% 280 10 0.00% 281 14 0.00% 282 5 0.00% 283 12 0.00% 284 13 0.00% 285 6 0.00% 286 11 0.00% 287 5 0.00% 288 4 0.00% 289 4 0.00% 290 3 0.00% 291 0 0.00% 292 3 0.00% 293 2 0.00% 294 2 0.00% 295 1 0.00% 296 1 0.00% 297 1 0.00% 298 1 0.00% 299 1 0.00% 300 1 0.00% 301 0 0.00% 302 1 0.00% 303 1 0.00% 304 0 0.00% 305 1 0.00% 306 0 0.00% 307 0 0.00% 308 0 0.00% 309 0 0.00% 310 0 0.00% 311 0 0.00% 312 0 0.00% 313 0 0.00% 314 0 0.00% 315 0 0.00% 316 0 0.00% 317 0 0.00% 318 0 0.00% 319 0 0.00% 320 0 0.00% 321 0 0.00% 322 1 0.00% 323 0 0.00% 324 0 0.00% 325 0 0.00% 326 0 0.00% 327 0 0.00% 328 0 0.00% 329 0 0.00% 330 0 0.00% 331 0 0.00% 332 1 0.00% 333 0 0.00% 334 0 0.00% 335 1 0.00% 336 0 0.00% 337 0 0.00% 338 0 0.00% 339 0 0.00% 340 0 0.00% 341 0 0.00% 342 0 0.00% 343 0 0.00% 344 0 0.00% 345 1 0.00% 346 0 0.00% 347 0 0.00% 348 0 0.00% 349 0 0.00% 350 0 0.00% 351 0 0.00% 352 0 0.00% 353 0 0.00% 354 0 0.00% 355 0 0.00% 356 0 0.00% 357 1 0.00% 358 1 0.00% 359 0 0.00% 360 0 0.00% 361 0 0.00% 362 0 0.00% 363 1 0.00% 364 0 0.00% 365 1 0.00% 366 0 0.00% 367 1 0.00% 368 0 0.00% 369 0 0.00% 370 1 0.00% 19033200 reads passed initial QC criterion=sequence-density sequence-density=1.51 sequence-density-rank=1 fanout-score=1.00 fanout-score-rank=39 prefix-density=0.01 prefix-fanout=1.0 sequence=ACAGCTATCACACACAGGCAAAACACAGCTGATTCGTGTACTCGATCTCCCCAGCAAGTTAAGGCCACCATGTCGAGCGGCTGCGGCAACTGCGACTGCGCTGACAAGACCCAGTGTGTGAAGAAGGGAAACGGCTACGGCATCGTCATGGTTGACACCGAGAAGAGCCACTTCGAGGTGCAGGAGTCCGCGGCGGAGAACGACGGCAAGTGCAAGTGCGGCA criterion=fanout-score sequence-density=0.04 sequence-density-rank=30 fanout-score=47.72 fanout-score-rank=1 prefix-density=0.43 prefix-fanout=4.9 sequence=CTGCTGCTGGATGTATCTCTGATTAATGAGTTGCTGCTCTTTAGAAGGAAGAAGGGGTTTGATATCGCCGCGGACACGCTGCATTGGCGTCTAGTGAGTGGTATTTTGGTGTGGCAGACAGAGTTACGTGCTGAGTTTATACTAGTCGGGTCTTTTGTTATCTTTTGTGGTTTTCCTTCGTTTTCGAGTCTAAAACTGCAATAGCTGTGCAGTTTGCTCTATCAGTCGTCCTGTTATTTTTTAGTATGCTGAAACTGCATCAGTAATACCATATGTGATATTCGTACCCTGTTAAAAA Started job on | Dec 10 00:56:25 Started mapping on | Dec 10 00:56:25 Finished on | Dec 10 00:57:11 Mapping speed, Million of reads per hour | 1489.55 Number of input reads | 19033200 Average input read length | 112 UNIQUE READS: Uniquely mapped reads number | 15886769 Uniquely mapped reads % | 83.47% Average mapped length | 108.04 Number of splices: Total | 4055215 Number of splices: Annotated (sjdb) | 3560660 Number of splices: GT/AG | 3753227 Number of splices: GC/AG | 57095 Number of splices: AT/AC | 3016 Number of splices: Non-canonical | 241877 Mismatch rate per base, % | 0.48% Deletion rate per base | 0.31% Deletion average length | 1.17 Insertion rate per base | 0.23% Insertion average length | 1.15 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 804062 % of reads mapped to multiple loci | 4.22% Number of reads mapped to too many loci | 363040 % of reads mapped to too many loci | 1.91% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 9.09% % of reads unmapped: other | 1.31% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 2342369 2342369 2342369 N_multimapping 804062 804062 804062 N_noFeature 607993 727950 15412938 N_ambiguous 404135 54550 2119 UnstrandedReadsAssigned:14874641 PositiveStrandReadsAssigned:15104269 NegativeStrandReadsAssigned:471712 Dataset is classified positive stranded MeadianReadLen=109 20thPercentileLength=71 echo kmer=67 ERR1942999 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: ERR1942999-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 19,033,200 reads, 15,050,213 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,171 rounds 52973 ERR1942999.ke.tsv 35125 ERR1942999.se.tsv 88098 total ==> ERR1942999.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 86.615 9.39614 PNS24247 1044 945 0 0 PNS24249 1928 1829 0 0 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 174.385 11.5408 PNS24243 293 194 0 0 KQK14069 1603 1504 6082.54 367.214 KQK14071 474 375 67.3493 16.3074 ==> ERR1942999.se.tsv <== BRADI_1g14170v3 5946 BRADI_1g53295v3 13 BRADI_1g59795v3 228 BRADI_1g07683v3 0 BRADI_1g00485v3 18 BRADI_1g20270v3 675 BRADI_1g74790v3 239 BRADI_1g09890v3 0 BRADI_1g77505v3 303 BRADI_1g48960v3 0 ERR1942999 completed mapping pipeline successfully