Kmergenie：could find the best K value

Question

[805251959]

When I run the code

"kmergenie fastq_list.txt -o ./result_haploid/haploid -l 15 -k 105 -s 10 -t 1"

There are some problem:

running histogram estimation File fastq_list.txt starts with character "/", hence is interpreted as a list of file names Reading 2 read files Linear estimation: ~41 M distinct 63-mers are in the reads K-mer sampling: 1/7 | processing | [going to estimate histograms for values of k: 105 95 85 75 65 55 45 35 25 15 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Total time Wallclock 1198.75 s fitting model to histograms to estimate best k could not fit ./result_haploid/haploid-k105.histo could not fit ./result_haploid/haploid-k15.histo could not fit ./result_haploid/haploid-k25.histo could not fit ./result_haploid/haploid-k35.histo could not fit ./result_haploid/haploid-k45.histo could not fit ./result_haploid/haploid-k55.histo could not fit ./result_haploid/haploid-k65.histo could not fit ./result_haploid/haploid-k75.histo could not fit ./result_haploid/haploid-k85.histo could not fit ./result_haploid/haploid-k95.histo cannot generate histogram for file ./result_haploid/haploid-k105.histo stdout: ; stderr: dyld: Library not loaded: @rpath/libreadline.6.2.dylib Referenced from: /Users/nio/miniconda3/envs/py27/lib/R/lib/libR.dylib Reason: image not found cannot generate histogram for file ./result_haploid/haploid-k15.histo stdout: ; stderr: dyld: Library not loaded: @rpath/libreadline.6.2.dylib Referenced from: /Users/nio/miniconda3/envs/py27/lib/R/lib/libR.dylib Reason: image not found cannot generate histogram for file ./result_haploid/haploid-k25.histo stdout: ; stderr: dyld: Library not loaded: @rpath/libreadline.6.2.dylib Referenced from: /Users/nio/miniconda3/envs/py27/lib/R/lib/libR.dylib Reason: image not found ............ ............ could not predict a best k value No best k found

Does anyone have idea to fix it? Many thanks!

Answer 1

[Alex Reynolds]

This error seems to show up a couple times:

dyld: Library not loaded: @rpath/libreadline.6.2.dylib

Probably check your setup and ensure that you have necessary libraries installed.

[805251959]

Thanks for your quick reply. I use brew install kmergenie. So the libraries may be completely installed, right?

[805251959]

That would be the R problem. Thanks for your help!

[shaileshdesai76]

How did you solve this, i have already installed r in root do I need to install in the same directory, where my kmergenie is ??