Starting /dee2/code/volunteer_pipeline.sh ERR3959307 current disk space = 1547620118528 free memory = 1598340988 ERR3959307 SRAfilesize d134babc368d20bb95d275561d68be1e ERR3959307.sra ERR3959307.sra file validated ERR3959307 is paired end ERR3959307 is conventional basespace ERR3959307 read1 length is 20-140 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3959307_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 20-140 %GC 53 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.624 37.0 37.0 37.0 37.0 37.0 2 36.508 37.0 37.0 37.0 37.0 37.0 3 36.5945 37.0 37.0 37.0 37.0 37.0 4 36.5195 37.0 37.0 37.0 37.0 37.0 5 36.568 37.0 37.0 37.0 37.0 37.0 6 36.6175 37.0 37.0 37.0 37.0 37.0 7 36.604 37.0 37.0 37.0 37.0 37.0 8 36.507 37.0 37.0 37.0 37.0 37.0 9 36.4805 37.0 37.0 37.0 37.0 37.0 10-14 36.5272 37.0 37.0 37.0 37.0 37.0 15-19 36.4653 37.0 37.0 37.0 37.0 37.0 20-24 36.45508277757527 37.0 37.0 37.0 37.0 37.0 25-29 36.48513357739947 37.0 37.0 37.0 37.0 37.0 30-34 36.47594629704669 37.0 37.0 37.0 37.0 37.0 35-39 36.46078582113333 37.0 37.0 37.0 37.0 37.0 40-44 36.43581449729736 37.0 37.0 37.0 37.0 37.0 45-49 36.44802047552927 37.0 37.0 37.0 37.0 37.0 50-54 36.43269940380783 37.0 37.0 37.0 37.0 37.0 55-59 36.47247897585801 37.0 37.0 37.0 37.0 37.0 60-64 36.41211393573491 37.0 37.0 37.0 37.0 37.0 65-69 36.43866921682019 37.0 37.0 37.0 37.0 37.0 70-74 36.36504790463404 37.0 37.0 37.0 37.0 37.0 75-79 36.4071019577036 37.0 37.0 37.0 37.0 37.0 80-84 36.338257303322635 37.0 37.0 37.0 37.0 37.0 85-89 36.334204242267774 37.0 37.0 37.0 37.0 37.0 90-94 36.3561064547642 37.0 37.0 37.0 37.0 37.0 95-99 36.347780592882366 37.0 37.0 37.0 37.0 37.0 100-104 36.30938134690692 37.0 37.0 37.0 37.0 37.0 105-109 36.31619934061888 37.0 37.0 37.0 37.0 37.0 110-114 36.3359905045023 37.0 37.0 37.0 37.0 37.0 115-119 36.342156020998274 37.0 37.0 37.0 37.0 37.0 120-124 36.27688251760839 37.0 37.0 37.0 37.0 37.0 125-129 36.27985150613282 37.0 37.0 37.0 37.0 37.0 130-134 36.209989449363334 37.0 37.0 37.0 37.0 37.0 135-139 36.16859169110607 37.0 37.0 37.0 37.0 37.0 140 36.61199294532628 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 27 1.0 28 3.0 29 9.0 30 21.0 31 28.0 32 48.0 33 80.0 34 135.0 35 317.0 36 2862.0 37 496.0 >>END_MODULE >>Per base sequence content pass #Base G A T C 1 27.200000000000003 24.425 20.474999999999998 27.900000000000002 2 26.625 20.025000000000002 24.4 28.95 3 25.55 22.725 24.7 27.025 4 25.05 23.65 25.775 25.525 5 23.9 23.849999999999998 24.474999999999998 27.775 6 25.025 23.400000000000002 24.474999999999998 27.1 7 24.45 24.224999999999998 23.775 27.55 8 24.325 23.425 24.7 27.55 9 25.674999999999997 24.0 23.175 27.150000000000002 10-14 24.505 23.735 24.445 27.315 15-19 25.790000000000003 23.69 23.79 26.729999999999997 20-24 24.779911964785914 24.009603841536613 24.079631852741095 27.13085234093637 25-29 25.313220406935955 23.032975844442216 24.521399218201864 27.13240453041997 30-34 25.61435248002412 24.347957183778078 22.840343735866124 27.197346600331674 35-39 25.547114755747852 23.45927453841123 23.484429239824923 27.509181466015995 40-44 25.49869030828128 23.710457384646382 23.614749143663108 27.176103163409227 45-49 25.67812846627004 23.08661893717858 24.165574266411213 27.069678330140164 50-54 25.795213571644954 23.230334242148846 23.609007371503584 27.365444814702617 55-59 25.31472774154406 23.580565245967946 23.76763233732747 27.337074675160522 60-64 26.18914948584165 22.52672103743478 23.90962970467555 27.374499772048022 65-69 25.629441624365484 23.101522842639593 23.96446700507614 27.304568527918782 70-74 25.925360215874953 23.094547120818696 23.532406700269846 27.447685963036506 75-79 25.946360153256702 23.381864623243935 23.43295019157088 27.23882503192848 80-84 25.59010673234811 23.132183908045977 24.122536945812808 27.155172413793103 85-89 25.777502707720874 23.61648357316004 22.956315436587758 27.649698282531332 90-94 25.84030339238402 23.154449581796456 23.08171853083277 27.923528494986755 95-99 25.892716690262702 23.31288343558282 23.019243878139584 27.775155996014895 100-104 25.440779372054852 23.910626356753323 23.471170646476413 27.177423624715413 105-109 26.150638798310794 23.386967445341316 24.124659218474367 26.337734537873526 110-114 26.27215086977727 23.210318105457105 23.37831246951715 27.13921855524847 115-119 26.313764291996485 23.14204045734389 22.88368513632366 27.660510114335974 120-124 26.111700050214807 23.05417619818111 23.494950622105673 27.339173129498413 125-129 25.72241183162685 23.754266211604094 23.037542662116042 27.485779294653014 130-134 26.4955792857963 22.98771385922609 22.740842806292342 27.775864048685268 135-139 27.019241848139185 22.58900795022468 23.038368475630833 27.3533817260053 140 26.807760141093475 24.485596707818928 22.692533803644917 26.014109347442684 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 1.0 1 0.5 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 1.0 26 1.0 27 1.0 28 3.0 29 5.0 30 5.5 31 8.5 32 12.0 33 14.0 34 20.5 35 30.0 36 42.0 37 54.5 38 60.0 39 76.5 40 105.0 41 113.5 42 129.0 43 144.0 44 154.5 45 174.0 46 185.5 47 193.5 48 171.0 49 141.0 50 150.0 51 141.0 52 104.5 53 88.5 54 95.5 55 108.5 56 102.0 57 88.0 58 91.0 59 87.5 60 76.5 61 80.0 62 75.5 63 74.0 64 73.5 65 67.0 66 74.0 67 72.0 68 61.5 69 68.0 70 63.5 71 62.0 72 68.5 73 56.0 74 40.5 75 35.5 76 32.0 77 29.0 78 24.0 79 21.5 80 19.0 81 12.0 82 11.0 83 7.0 84 2.5 85 1.0 86 1.5 87 1.5 88 1.0 89 0.0 90 0.0 91 0.0 92 0.5 93 1.0 94 1.0 95 0.5 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 0.01152073732718894 140 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 20-24 6.0 25-29 9.0 30-34 8.0 35-39 4.0 40-44 6.0 45-49 4.0 50-54 6.0 55-59 7.0 60-64 6.0 65-69 10.0 70-74 13.0 75-79 18.0 80-84 18.0 85-89 19.0 90-94 41.0 95-99 36.0 100-104 28.0 105-109 47.0 110-114 52.0 115-119 54.0 120-124 62.0 125-129 58.0 130-134 12.0 135-139 74.0 140-141 3402.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 94.95 #Duplication Level Percentage of deduplicated Percentage of total 1 94.91837809373355 90.125 2 4.844655081621906 9.2 3 0.23696682464454977 0.675 4 0.0 0.0 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >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 pass >>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 82-83 0.0 0.0 0.0 0.0 0.0 84-85 0.0 0.0 0.0 0.0 0.0 86-87 0.0 0.0 0.0 0.0 0.0 88-89 0.0 0.0 0.0 0.0 0.0 90-91 0.0 0.0 0.0 0.0 0.0 92-93 0.0 0.0 0.0 0.0 0.0 94-95 0.0 0.0 0.0 0.0 0.0 96-97 0.0 0.0 0.0 0.0 0.0 98-99 0.0 0.0 0.0 0.0 0.0 100-101 0.0 0.0 0.0 0.0 0.0 102-103 0.0 0.0 0.0 0.0 0.0 104-105 0.0 0.0 0.0 0.0 0.0 106-107 0.0 0.0 0.0 0.0 0.0 108-109 0.0 0.0 0.0 0.0 0.0 110-111 0.0 0.0 0.0 0.0 0.0 112-113 0.0 0.0 0.0 0.0 0.0 114-115 0.0 0.0 0.0 0.0 0.0 116-117 0.0 0.0 0.0 0.0 0.0 118-119 0.0 0.0 0.0 0.0 0.0 120-121 0.0 0.0 0.0 0.0 0.0 122-123 0.0 0.0 0.0 0.0 0.0 124-125 0.0 0.0 0.0 0.0 0.0 126-127 0.0 0.0 0.0 0.0 0.0 128 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 AAATACA 10 0.009083958 131.8125 1 GCGCCGA 10 0.009083958 131.8125 3 AATACAC 10 0.009083958 131.8125 2 >>END_MODULE ERR3959307 read2 length is 20-140 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3959307_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 20-140 %GC 54 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.4875 37.0 37.0 37.0 37.0 37.0 2 36.5115 37.0 37.0 37.0 37.0 37.0 3 36.493 37.0 37.0 37.0 37.0 37.0 4 36.422 37.0 37.0 37.0 37.0 37.0 5 36.4915 37.0 37.0 37.0 37.0 37.0 6 36.4055 37.0 37.0 37.0 37.0 37.0 7 36.404 37.0 37.0 37.0 37.0 37.0 8 36.467 37.0 37.0 37.0 37.0 37.0 9 36.3925 37.0 37.0 37.0 37.0 37.0 10-14 36.4341 37.0 37.0 37.0 37.0 37.0 15-19 36.3662 37.0 37.0 37.0 37.0 37.0 20-24 36.27076382108502 37.0 37.0 37.0 37.0 37.0 25-29 36.30051073142977 37.0 37.0 37.0 37.0 37.0 30-34 36.32502397135471 37.0 37.0 37.0 37.0 37.0 35-39 36.32036914434498 37.0 37.0 37.0 37.0 37.0 40-44 36.30627366836863 37.0 37.0 37.0 37.0 37.0 45-49 36.22832670779408 37.0 37.0 37.0 37.0 37.0 50-54 36.21615096498874 37.0 37.0 37.0 37.0 37.0 55-59 36.246330126514586 37.0 37.0 37.0 37.0 37.0 60-64 36.28271159698288 37.0 37.0 37.0 37.0 37.0 65-69 36.20331596094552 37.0 37.0 37.0 37.0 37.0 70-74 36.21110727605129 37.0 37.0 37.0 37.0 37.0 75-79 36.26178580181745 37.0 37.0 37.0 37.0 37.0 80-84 36.19513925692261 37.0 37.0 37.0 37.0 37.0 85-89 36.21923721547505 37.0 37.0 37.0 37.0 37.0 90-94 36.23949658988316 37.0 37.0 37.0 37.0 37.0 95-99 36.181912315821776 37.0 37.0 37.0 37.0 37.0 100-104 36.13905881863833 37.0 37.0 37.0 37.0 37.0 105-109 36.14751513944301 37.0 37.0 37.0 37.0 37.0 110-114 36.147400395549504 37.0 37.0 37.0 37.0 37.0 115-119 36.0406920555864 37.0 37.0 37.0 37.0 37.0 120-124 36.00220690363224 37.0 37.0 37.0 37.0 37.0 125-129 35.920043240693886 37.0 37.0 37.0 37.0 37.0 130-134 36.03563915807873 37.0 37.0 37.0 37.0 37.0 135-139 35.896580070142186 37.0 37.0 37.0 37.0 37.0 140 36.45349158156224 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 26 2.0 27 3.0 28 4.0 29 10.0 30 15.0 31 24.0 32 55.0 33 101.0 34 196.0 35 573.0 36 2715.0 37 302.0 >>END_MODULE >>Per base sequence content pass #Base G A T C 1 28.475 22.400000000000002 18.5 30.625000000000004 2 29.275000000000002 19.0 21.975 29.75 3 25.85 22.375 24.425 27.35 4 27.3 23.724999999999998 23.3 25.674999999999997 5 27.925 24.05 22.425 25.6 6 26.974999999999998 23.175 23.35 26.5 7 27.400000000000002 23.674999999999997 22.7 26.224999999999998 8 24.975 24.05 23.575 27.400000000000002 9 26.474999999999998 22.575 23.075000000000003 27.875 10-14 27.534999999999997 23.425 22.525000000000002 26.515 15-19 27.150000000000002 23.685000000000002 22.125 27.04 20-24 26.77981375788525 23.85601281666166 22.634424752177832 26.729748673275257 25-29 26.947791164658636 23.775100401606426 22.555220883534137 26.7218875502008 30-34 27.501760032183448 23.187166851050993 22.654128532636026 26.656944584129537 35-39 27.39767406736143 23.68725771535015 22.45380858883351 26.461259628454915 40-44 27.510344131597535 24.12453325259865 22.05066101523867 26.314461600565142 45-49 27.83083219645293 23.13677934414633 22.363700672022638 26.668687787378104 50-54 28.07959090678953 23.011493088957522 22.743152245455928 26.165763758797024 55-59 27.526521496370744 23.744987564083043 22.963301355261155 25.765189584285064 60-64 27.609170860657823 23.130496670225202 22.6017996034772 26.65853286563977 65-69 27.590244895881067 23.140369634947305 22.941805407056666 26.327580062114965 70-74 28.042004383952694 23.38278024162716 22.449915889279705 26.12529948514044 75-79 28.172537008677896 22.84328739152629 22.71567126084737 26.268504338948446 80-84 27.53119247289834 22.954591941092247 23.000613622417674 26.51360196359174 85-89 27.90292852754454 23.42822035633832 22.347941839033382 26.32090927708376 90-94 27.724802624833384 23.76191940941249 22.17779144878499 26.335486516969137 95-99 28.020737090647778 23.760394210040037 22.477158402628067 25.74171029668412 100-104 27.97533401849949 24.06474820143885 22.3792394655704 25.580678314491262 105-109 28.441264284978896 23.69504787398332 21.7903840214146 26.073303819623185 110-114 27.846598534117888 24.021885000516153 22.349540621451432 25.781975843914523 115-119 28.510110151522987 23.804106117805244 22.23716191756736 25.44862181310441 120-124 29.11241375732738 23.162317788037555 22.851066037246458 24.874202417388595 125-129 28.628147528993836 24.036150872427122 22.103228502768783 25.23247309581026 130-134 28.953335090957026 24.281571315581335 21.940416556815187 24.824677036646452 135-139 28.730453220249142 23.408428306387492 22.79883381924198 25.062284654121385 140 29.671542920231854 24.56527739442451 21.501518078940105 24.261661606403536 >>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 1.0 26 1.0 27 0.0 28 2.5 29 4.0 30 4.5 31 6.5 32 6.5 33 8.0 34 16.0 35 25.5 36 30.0 37 37.0 38 55.0 39 66.0 40 84.5 41 106.5 42 116.0 43 140.0 44 164.5 45 159.5 46 153.5 47 156.0 48 146.0 49 146.0 50 147.5 51 138.5 52 127.0 53 114.0 54 107.0 55 100.5 56 87.0 57 82.5 58 87.5 59 92.5 60 84.0 61 75.5 62 93.5 63 100.0 64 82.0 65 86.0 66 89.5 67 87.5 68 84.5 69 78.0 70 78.5 71 76.0 72 70.5 73 55.5 74 51.0 75 44.5 76 32.5 77 26.5 78 23.0 79 20.5 80 14.5 81 9.5 82 11.0 83 8.5 84 4.0 85 5.0 86 5.0 87 4.5 88 4.0 89 3.0 90 1.5 91 1.0 92 1.0 93 0.5 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.5 >>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 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 20-24 13.0 25-29 7.0 30-34 5.0 35-39 7.0 40-44 9.0 45-49 5.0 50-54 12.0 55-59 3.0 60-64 9.0 65-69 5.0 70-74 3.0 75-79 9.0 80-84 5.0 85-89 5.0 90-94 5.0 95-99 3.0 100-104 8.0 105-109 8.0 110-114 8.0 115-119 10.0 120-124 13.0 125-129 47.0 130-134 17.0 135-139 161.0 140-141 3623.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 94.75 #Duplication Level Percentage of deduplicated Percentage of total 1 94.67018469656992 89.7 2 5.118733509234828 9.700000000000001 3 0.21108179419525064 0.6 4 0.0 0.0 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >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 pass >>END_MODULE >>Adapter Content warn #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 0.0125 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 0.05 0.0 0.0 0.0 0.0 60-61 0.0875 0.0 0.0 0.0 0.0 62-63 0.1 0.0 0.0 0.0 0.0 64-65 0.1125 0.0 0.0 0.0 0.0 66-67 0.15 0.0 0.0 0.0 0.0 68-69 0.1875 0.0 0.0 0.0 0.0 70-71 0.23750000000000002 0.0 0.0 0.0 0.0 72-73 0.4125 0.0 0.0 0.0 0.0 74-75 0.44999999999999996 0.0 0.0 0.0 0.0 76-77 0.6125 0.0 0.0 0.0 0.0 78-79 0.75 0.0 0.0 0.0 0.0 80-81 0.85 0.0 0.0 0.0 0.0 82-83 1.0 0.0 0.0 0.0 0.0 84-85 1.075 0.0 0.0 0.0 0.0 86-87 1.225 0.0 0.0 0.0 0.0 88-89 1.3375 0.0 0.0 0.0 0.0 90-91 1.6749999999999998 0.0 0.0 0.0 0.0 92-93 1.9749999999999999 0.0 0.0 0.0 0.0 94-95 2.2875 0.0 0.0 0.0 0.0 96-97 2.4625 0.0 0.0 0.0 0.0 98-99 2.75 0.0 0.0 0.0 0.0 100-101 3.0875000000000004 0.0 0.0 0.0 0.0 102-103 3.3625 0.0 0.0 0.0 0.0 104-105 3.55 0.0 0.0 0.0 0.0 106-107 3.9875 0.0 0.0 0.0 0.0 108-109 4.4 0.0 0.0 0.0 0.0 110-111 4.825 0.0 0.0 0.0 0.0 112-113 5.387499999999999 0.0 0.0 0.0 0.0 114-115 5.7625 0.0 0.0 0.0 0.0 116-117 6.35 0.0 0.0 0.0 0.0 118-119 6.75 0.0 0.0 0.0 0.0 120-121 7.275 0.0 0.0 0.0 0.0 122-123 7.8125 0.0 0.0 0.0 0.0 124-125 8.4875 0.0 0.0 0.0 0.0 126-127 8.675 0.0 0.0 0.0 0.0 128 8.675 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CAAAACT 10 0.00888854 132.77501 7 >>END_MODULE Read 2337176 spots for ERR3959307.sra Written 2337176 spots for ERR3959307.sra Read 2337176 spots for ERR3959307.sra Written 2337176 spots for ERR3959307.sra Read 2337176 spots for ERR3959307.sra Written 2337176 spots for ERR3959307.sra Read 2337176 spots for ERR3959307.sra Written 2337176 spots for ERR3959307.sra Read 2337176 spots for ERR3959307.sra Written 2337176 spots for ERR3959307.sra Read 2337176 spots for ERR3959307.sra Written 2337176 spots for ERR3959307.sra Read 2337176 spots for ERR3959307.sra Written 2337176 spots for ERR3959307.sra Read 2337188 spots for ERR3959307.sra Written 2337188 spots for ERR3959307.sra Read 2337176 spots for ERR3959307.sra Written 2337176 spots for ERR3959307.sra Read 2337176 spots for ERR3959307.sra Written 2337176 spots for ERR3959307.sra Read 2337176 spots for ERR3959307.sra Written 2337176 spots for ERR3959307.sra Read 2337176 spots for ERR3959307.sra Written 2337176 spots for ERR3959307.sra Read 2337176 spots for ERR3959307.sra Written 2337176 spots for ERR3959307.sra Read 2337176 spots for ERR3959307.sra Written 2337176 spots for ERR3959307.sra Read 2337176 spots for ERR3959307.sra Written 2337176 spots for ERR3959307.sra Read 2337176 spots for ERR3959307.sra Written 2337176 spots for ERR3959307.sra Read 2337176 spots for ERR3959307.sra Written 2337176 spots for ERR3959307.sra Read 2337176 spots for ERR3959307.sra Written 2337176 spots for ERR3959307.sra Read 2337176 spots for ERR3959307.sra Written 2337176 spots for ERR3959307.sra Read 2337176 spots for ERR3959307.sra Written 2337176 spots for ERR3959307.sra SRR ids: ['ERR3959307.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_198dnqgq ERR3959307.sra spots: 46743532 blocks: [[1, 2337176], [2337177, 4674352], [4674353, 7011528], [7011529, 9348704], [9348705, 11685880], [11685881, 14023056], [14023057, 16360232], [16360233, 18697408], [18697409, 21034584], [21034585, 23371760], [23371761, 25708936], [25708937, 28046112], [28046113, 30383288], [30383289, 32720464], [32720465, 35057640], [35057641, 37394816], [37394817, 39731992], [39731993, 42069168], [42069169, 44406344], [44406345, 46743532]] ERR3959307 file size 14355613 ERR3959307 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 ERR3959307 ERR3959307_1.fastq ERR3959307_2.fastq Input file: ERR3959307_1.fastq Paired file: ERR3959307_2.fastq trimmed: ERR3959307-trimmed-pair1.fastq, ERR3959307-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA -- 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 -- number of concurrent threads (-t): 20 Sat Dec 7 02:35:22 2024 >> started Sat Dec 7 02:36:11 2024 >> done (48.509s) 46743532 read pairs processed; of these: 0 ( 0.00%) short read pairs filtered out after trimming by size control 0 ( 0.00%) empty read pairs filtered out after trimming by size control 46743532 (100.00%) read pairs available; of these: 107265 ( 0.23%) trimmed read pairs available after processing 46636267 (99.77%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 1 0.00% 19 0 0.00% 20 408 0.00% 21 880 0.00% 22 1423 0.00% 23 1682 0.00% 24 2067 0.00% 25 2392 0.01% 26 2683 0.01% 27 3040 0.01% 28 3237 0.01% 29 3364 0.01% 30 3553 0.01% 31 3758 0.01% 32 3975 0.01% 33 4101 0.01% 34 4255 0.01% 35 4291 0.01% 36 4490 0.01% 37 4665 0.01% 38 4707 0.01% 39 4865 0.01% 40 4914 0.01% 41 4974 0.01% 42 5074 0.01% 43 5059 0.01% 44 5144 0.01% 45 5236 0.01% 46 5281 0.01% 47 5549 0.01% 48 5700 0.01% 49 5463 0.01% 50 5712 0.01% 51 5783 0.01% 52 5867 0.01% 53 5956 0.01% 54 6067 0.01% 55 6185 0.01% 56 6254 0.01% 57 6375 0.01% 58 6478 0.01% 59 6631 0.01% 60 6585 0.01% 61 6741 0.01% 62 6891 0.01% 63 6948 0.01% 64 7090 0.02% 65 7312 0.02% 66 7202 0.02% 67 7450 0.02% 68 7477 0.02% 69 7634 0.02% 70 7794 0.02% 71 8036 0.02% 72 8175 0.02% 73 8594 0.02% 74 8893 0.02% 75 9051 0.02% 76 8990 0.02% 77 9160 0.02% 78 9361 0.02% 79 11965 0.03% 80 44667 0.10% 81 45484 0.10% 82 44907 0.10% 83 44107 0.09% 84 43352 0.09% 85 43813 0.09% 86 43855 0.09% 87 44297 0.09% 88 44684 0.10% 89 45036 0.10% 90 43984 0.09% 91 44843 0.10% 92 44721 0.10% 93 45601 0.10% 94 45621 0.10% 95 45574 0.10% 96 44998 0.10% 97 46109 0.10% 98 47853 0.10% 99 47709 0.10% 100 49354 0.11% 101 49356 0.11% 102 51942 0.11% 103 53850 0.12% 104 56568 0.12% 105 58337 0.12% 106 60570 0.13% 107 63966 0.14% 108 65835 0.14% 109 74326 0.16% 110 84937 0.18% 111 81578 0.17% 112 105264 0.23% 113 97745 0.21% 114 115028 0.25% 115 124920 0.27% 116 136352 0.29% 117 151060 0.32% 118 169498 0.36% 119 176445 0.38% 120 190628 0.41% 121 200828 0.43% 122 208137 0.45% 123 223298 0.48% 124 235136 0.50% 125 249248 0.53% 126 383824 0.82% 127 395026 0.85% 128 401933 0.86% 129 281140 0.60% 130 290025 0.62% 131 298891 0.64% 132 303147 0.65% 133 58271 0.12% 134 47400 0.10% 135 36331 0.08% 136 37722 0.08% 137 45873 0.10% 138 79147 0.17% 139 1559861 3.34% 140 38150632 81.62% 46743532 reads passed initial QC criterion=sequence-density sequence-density=0.17 sequence-density-rank=1 fanout-score=2.78 fanout-score-rank=26 prefix-density=0.20 prefix-fanout=2.4 sequence=TAGGCGTCCGGGTACTCCTTCTTGACCTCCTCCAGCTCCTTGAGCACCTG criterion=fanout-score sequence-density=0.04 sequence-density-rank=37 fanout-score=423.36 fanout-score-rank=1 prefix-density=0.93 prefix-fanout=18.5 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=7.56 sequence-density-rank=1 fanout-score=45.89 fanout-score-rank=2 prefix-density=8.63 prefix-fanout=40.2 sequence=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTCTTCACCAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAA criterion=fanout-score sequence-density=0.17 sequence-density-rank=6 fanout-score=131.80 fanout-score-rank=1 prefix-density=1.12 prefix-fanout=19.4 sequence=CCGCCGCCGCCG Potential 3prime adapter identified. Now checking if in reference sequence /dee2/code/volunteer_pipeline.sh: line 905: -f: command not found /dee2/code/volunteer_pipeline.sh: line 906: -f: command not found Adapter seq not found in reference. Now shuffling file before clipping skewer v0.2.2 [April 4, 2016] COMMAND LINE: skewer -f sanger -l 18 -t 20 -x TAGGCGTCCGGGTACTCCTTCTTGACCTCCTCCAGCTCCTTGAGCACCTG -y AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTCTTCACCAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAA -o ERR3959307 ERR3959307_1.fastq ERR3959307_2.fastq Input file: ERR3959307_1.fastq Paired file: ERR3959307_2.fastq trimmed: ERR3959307-trimmed-pair1.fastq, ERR3959307-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): TAGGCGTCCGGGTACTCCTTCTTGACCTCCTCCAGCTCCTTGAGCACCTG -- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTCTTCACCAGTGTAGATCTCGGTGGTCGCCGT -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- number of concurrent threads (-t): 20 Sat Dec 7 02:39:40 2024 >> started Sat Dec 7 02:40:12 2024 >> done (32.424s) 28046119 read pairs processed; of these: 16 ( 0.00%) short read pairs filtered out after trimming by size control 630 ( 0.00%) empty read pairs filtered out after trimming by size control 28045473 (100.00%) read pairs available; of these: 35852 ( 0.13%) trimmed read pairs available after processing 28009621 (99.87%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 19 1 0.00% 20 249 0.00% 21 527 0.00% 22 858 0.00% 23 1017 0.00% 24 1223 0.00% 25 1435 0.01% 26 1587 0.01% 27 1779 0.01% 28 1944 0.01% 29 2014 0.01% 30 2099 0.01% 31 2312 0.01% 32 2427 0.01% 33 2478 0.01% 34 2518 0.01% 35 2558 0.01% 36 2672 0.01% 37 2792 0.01% 38 2838 0.01% 39 2929 0.01% 40 2960 0.01% 41 2955 0.01% 42 3061 0.01% 43 3041 0.01% 44 3052 0.01% 45 3117 0.01% 46 3190 0.01% 47 3295 0.01% 48 3436 0.01% 49 3305 0.01% 50 3445 0.01% 51 3476 0.01% 52 3502 0.01% 53 3646 0.01% 54 3629 0.01% 55 3712 0.01% 56 3859 0.01% 57 3782 0.01% 58 3831 0.01% 59 3937 0.01% 60 3961 0.01% 61 3989 0.01% 62 4191 0.01% 63 4063 0.01% 64 4238 0.02% 65 4353 0.02% 66 4325 0.02% 67 4395 0.02% 68 4381 0.02% 69 4572 0.02% 70 4677 0.02% 71 4890 0.02% 72 4980 0.02% 73 5151 0.02% 74 5384 0.02% 75 5423 0.02% 76 5372 0.02% 77 5572 0.02% 78 5644 0.02% 79 7149 0.03% 80 26719 0.10% 81 27235 0.10% 82 26777 0.10% 83 26498 0.09% 84 26026 0.09% 85 26222 0.09% 86 26269 0.09% 87 26591 0.09% 88 26805 0.10% 89 27071 0.10% 90 26412 0.09% 91 26799 0.10% 92 26727 0.10% 93 27509 0.10% 94 27336 0.10% 95 27631 0.10% 96 27052 0.10% 97 27600 0.10% 98 28799 0.10% 99 28627 0.10% 100 29665 0.11% 101 29691 0.11% 102 31083 0.11% 103 32255 0.12% 104 33916 0.12% 105 35014 0.12% 106 36244 0.13% 107 38624 0.14% 108 39612 0.14% 109 44656 0.16% 110 51296 0.18% 111 48968 0.17% 112 63021 0.22% 113 58841 0.21% 114 68844 0.25% 115 74941 0.27% 116 81898 0.29% 117 90583 0.32% 118 101855 0.36% 119 106139 0.38% 120 114167 0.41% 121 120499 0.43% 122 124934 0.45% 123 134047 0.48% 124 141237 0.50% 125 149681 0.53% 126 230536 0.82% 127 237212 0.85% 128 240887 0.86% 129 168343 0.60% 130 174060 0.62% 131 179445 0.64% 132 182013 0.65% 133 34804 0.12% 134 28537 0.10% 135 21887 0.08% 136 23117 0.08% 137 29125 0.10% 138 52984 0.19% 139 960767 3.43% 140 22856142 81.50% criterion=sequence-density sequence-density=0.17 sequence-density-rank=1 fanout-score=2.74 fanout-score-rank=24 prefix-density=0.20 prefix-fanout=2.4 sequence=TAGGCGTCCGGGTACTCCTTCTTGACCTCCTCCAGCTCCTTGAGCACCTG criterion=fanout-score sequence-density=0.04 sequence-density-rank=34 fanout-score=384.01 fanout-score-rank=1 prefix-density=0.92 prefix-fanout=18.4 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=7.81 sequence-density-rank=1 fanout-score=45.99 fanout-score-rank=1 prefix-density=8.90 prefix-fanout=40.3 sequence=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTCTTCACCAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAA criterion=fanout-score sequence-density=7.81 sequence-density-rank=1 fanout-score=45.99 fanout-score-rank=1 prefix-density=8.90 prefix-fanout=40.3 sequence=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTCTTCACCAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAA ERR3959307 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 02:41:20 Started mapping on | Dec 07 02:41:21 Finished on | Dec 07 02:44:02 Mapping speed, Million of reads per hour | 1045.18 Number of input reads | 46742886 Average input read length | 272 UNIQUE READS: Uniquely mapped reads number | 37861187 Uniquely mapped reads % | 81.00% Average mapped length | 274.07 Number of splices: Total | 35081302 Number of splices: Annotated (sjdb) | 33152908 Number of splices: GT/AG | 34503031 Number of splices: GC/AG | 529152 Number of splices: AT/AC | 17874 Number of splices: Non-canonical | 31245 Mismatch rate per base, % | 0.07% Deletion rate per base | 0.00% Deletion average length | 1.49 Insertion rate per base | 0.00% Insertion average length | 1.16 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 496675 % of reads mapped to multiple loci | 1.06% Number of reads mapped to too many loci | 187732 % of reads mapped to too many loci | 0.40% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 16.09% % of reads unmapped: other | 1.44% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 8489348 8489348 8489348 N_multimapping 496675 496675 496675 N_noFeature 1204004 36869554 1556938 N_ambiguous 881457 6749 249930 UnstrandedReadsAssigned:35775726 PositiveStrandReadsAssigned:984884 NegativeStrandReadsAssigned:36054319 Dataset is classified negative stranded MeadianReadLen=140 20thPercentileLength=140 echo kmer=135 ERR3959307 Starting Kallisto paired end mapping to ensembl reference transcriptome [quant] fragment length distribution will be estimated from the data [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 paired-end mode [quant] will process pair 1: ERR3959307-trimmed-pair1.fastq ERR3959307-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 46,742,886 reads, 43,294,034 reads pseudoaligned [quant] estimated average fragment length: 224.617 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,214 rounds 52973 ERR3959307.ke.tsv 35125 ERR3959307.se.tsv 88098 total ==> ERR3959307.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 712.694 0 0 PNS24247 1044 820.383 84.9168 3.45407 PNS24249 1928 1704.38 830.579 16.2618 PNS24246 1044 820.383 84.9168 3.45407 PNS24248 1044 820.383 84.9168 3.45407 PNS24244 1471 1247.38 72.6708 1.94408 PNS24243 293 111.602 0 0 KQK14069 1603 1379.38 50077.7 1211.47 KQK14071 474 261.729 2169.83 276.648 ==> ERR3959307.se.tsv <== BRADI_1g14170v3 45085 BRADI_1g53295v3 614 BRADI_1g59795v3 545 BRADI_1g07683v3 0 BRADI_1g00485v3 23 BRADI_1g20270v3 1329 BRADI_1g74790v3 1432 BRADI_1g09890v3 4 BRADI_1g77505v3 473 BRADI_1g48960v3 0 ERR3959307 completed mapping pipeline successfully