I am experiencing constant crashes with MelonnPan Predict on my input files. The processing ends with the following result:
Error in ztransform(formula, data, family) :
formula argument must be a formula or one of (numeric, integer, double)
Calls: → apply → FUN → ztransform
I am attaching a fairly simple example, but similar behavior happens on larger files as well.
melonnpan_test1.txt (184 Bytes)
When I run MelonnPan with the demo file from its tutorial web site
everything works okay, so I assume that my MelonnPan installation is also okay.
I cannot see any structural differences between my files and the demo one. I have checked with the hexdump utility that my as well as the demo files have the same use of tab and newline characters, and they are both strictly ASCII coded.
MelonnPan is installed in a separate Conda environment. I am uploading a file with package list in the environment, as well as R packages.
conda_package_list.txt (12.3 KB)
R_packages.txt (186.7 KB)
MelonnPan installation was done by the following commands:
conda create -y --name melonnpan_env r-base=3.6.3 r-devtools=2.3.2
conda run --name melonnpan_env Rscript -e ‘devtools::install_version(“GenABEL.data”, version = “1.0.0”, repos = “http://cran.us.r-project.org”)’
conda run --name melonnpan_env Rscript -e ‘devtools::install_version(“GenABEL”, version = “1.8-0”, repos = “http://cran.us.r-project.org”)’
conda run --name melonnpan_env Rscript -e ‘devtools::install_github(“biobakery/melonnpan”)’
After these steps MelonnPan successfully processes the demo input file. However, with some of my files the above mentioned crash occurs. With some other files the processing ends with the message that there is no overlap between IDs.
I am trying to input results of Humann2 and Humann3 to MelonnPan. I am restructuring the HumannX output files with my programs to be suitable for MelonnPan, since I was unable to find any utility or instructions for making the conversion. However, many MelonnPan users do the same, and I suspect that there is some utility for the task. I would appreciate any information about it.
Thank you and best regards,