Open najouamghazli opened 2 years ago
Hi Najoua,
Apparently, something going on with the initial biom file ... Could you please share your three input files so I can check contents and reproduce the error?
regards
Maria
I sent them via e-mail, thank you.
Best regards,
Najoua
Hi Maria,
I am encountring a problem while trying to run the r_import_data.py. Bellow are the details:
(base) najoua@LAPTOP-NK0EB027:/mnt/e/Travail_Najoua_2021_2022/Odile$ /home/najoua/FROGS-3.1.0/app/r_import_data.py --biomfile 07-affiliation_Silva.biom --samplefile CompasMetadata.txt --treefile 13-tree-pynast.nwk --rdata 14-phylo_import.Rdata --html 14-phylo_import.html --log-file 14-phylo_import.log
This gives this error
When I run the Command
Rscript -e "rmarkdown::render('/home/najoua/FROGS-3.1.0/app/r_import_data.Rmd',output_file='/mnt/e/Travail_Najoua_2021_2022/Odile/14-phylo_import.html', params=list(biomfile='/mnt/e/Travail_Najoua_2021_2022/Odile/1654630328.4_83_07-affiliation_Silva.stdBiom', samplefile='/mnt/e/Travail_Najoua_2021_2022/Odile/CompasMetadata.txt', treefile='/mnt/e/Travail_Najoua_2021_2022/Odile/13-tree-pynast.nwk', normalization=FALSE, outputRdata='/mnt/e/Travail_Najoua_2021_2022/Odile/14-phylo_import.Rdata', ranks='Kingdom Phylum Class Order Family Genus Species', libdir ='/home/najoua/FROGS-3.1.0/lib/external-lib'), intermediates_dir='/mnt/e/Travail_Najoua_2021_2022/Odile')" 2> /mnt/e/Travail_Najoua_2021_2022/Odile/1654630328.4_83_rmarkdown.stderr
I get this in the 1654630328.4_83_rmarkdown.stderr file:
I am using FROGS-3.1.0 in Windows Subsystem Linux and also in a Server through putty, and in both cases I get the exact same error.
Could you please guide me in order to resolve this issue ?
Najoua