error on Rscript_Markerlength_develop_Color.R

[amandaamelo]

Hello there!

First of all I'd like to congratulate you and your team for gathering such a well descriptive and detailed pipeline and scripts.

I'm trying to run script #3 to generate the histograms and I've created all the folders that are required for this step, the directory to store the PDFs, the matrices and the allele table.

When I try to run the following code: Rscript --vanilla Rscript_Markerlength_develop_Color.R \ /media/lgbio-nas1/amandamelo/SSR-GBS-Bra-Piloto/SSR-GBS-Bra-Piloto-27-10-23-401900626/Tibihika-Pipeline/contagem-output/ \ 30 \ /media/lgbio-nas1/amandamelo/SSR-GBS-Bra-Piloto/SSR-GBS-Bra-Piloto-27-10-23-401900626/Tibihika-Pipeline/BarPiloto-histogramas/ \ 0.7 \ /media/lgbio-nas1/amandamelo/SSR-GBS-Bra-Piloto/SSR-GBS-Bra-Piloto-27-10-23-401900626/Tibihika-Pipeline/output-matriz/ \ /media/lgbio-nas1/amandamelo/SSR-GBS-Bra-Piloto/SSR-GBS-Bra-Piloto-27-10-23-401900626/Tibihika-Pipeline/alelo-output/ \ 100 \ 450

I get the following error message: Error in pdf(file = pathPDF, width = 7, height = 18) : cannot open file '/media/lgbio-nas1/amandamelo/SSR-GBS-Bra-Piloto/SSR-GBS-Bra-Piloto-27-10-23-401900626/Tibihika-Pipeline/BarPiloto-histogramas'

Indeed, it is a folder and it will not open as a file.

I checked the code and it asks to open the pathPDF as a file pdf(file=pathPDF,width=7,height=18)

However, it is rather a directory.

Am I typing anything wrong on the code? I've tried several things and cannot seem to have success.

I thank the help in advance!

[mcurto]

Thank you for given the pipeline a try. I just realized it is not clear in the description but for arguments 3, 5 and 6 you should provided path to files and not directories. I will correct it in the description. In your case the code should be something like this:

Rscript --vanilla Rscript_Markerlength_develop_Color.R /media/lgbio-nas1/amandamelo/SSR-GBS-Bra-Piloto/SSR-GBS-Bra-Piloto-27-10-23-401900626/Tibihika-Pipeline/contagem-output/ 30 /media/lgbio-nas1/amandamelo/SSR-GBS-Bra-Piloto/SSR-GBS-Bra-Piloto-27-10-23-401900626/Tibihika-Pipeline/BarPiloto-histogramas.pdf 0.7 /media/lgbio-nas1/amandamelo/SSR-GBS-Bra-Piloto/SSR-GBS-Bra-Piloto-27-10-23-401900626/Tibihika-Pipeline/output-matriz.csv /media/lgbio-nas1/amandamelo/SSR-GBS-Bra-Piloto/SSR-GBS-Bra-Piloto-27-10-23-401900626/Tibihika-Pipeline/alelo-output.csv 100 450

Let me know if it works. Best, Manuel

[amandaamelo]

Hi Manuel!

That worked perfectly fine now!

I'm sorry, from the description I thought you wanted a directory. Thank you so much! I'll keep using the pipeline and I'll get in touch if needed.

Anyway, congratulations again on the complete and detailed pipeline, it is helping me a lot! I wish all developers had the care and thought of explaining the pipeline in so many detail like you guys!

Thanks again!

Em sáb., 4 de nov. de 2023 às 15:30, mcurto @.***> escreveu:

Thank you for given the pipeline a try. I just realized it is not clear in the description but for arguments 3, 5 and 6 you should provided path to files and not directories. I will correct it in the description. In your case the code should be something like this:

Rscript --vanilla Rscript_Markerlength_develop_Color.R

/media/lgbio-nas1/amandamelo/SSR-GBS-Bra-Piloto/SSR-GBS-Bra-Piloto-27-10-23-401900626/Tibihika-Pipeline/contagem-output/ 30

/media/lgbio-nas1/amandamelo/SSR-GBS-Bra-Piloto/SSR-GBS-Bra-Piloto-27-10-23-401900626/Tibihika-Pipeline/BarPiloto-histogramas.pdf 0.7

/media/lgbio-nas1/amandamelo/SSR-GBS-Bra-Piloto/SSR-GBS-Bra-Piloto-27-10-23-401900626/Tibihika-Pipeline/output-matriz.csv

/media/lgbio-nas1/amandamelo/SSR-GBS-Bra-Piloto/SSR-GBS-Bra-Piloto-27-10-23-401900626/Tibihika-Pipeline/alelo-output.csv 100 450

Let me know if it works. Best, Manuel

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-- Msc. Amanda Alves de Melo Ximenes CRBio: 117330/04-D Doutoranda no PPG em Genética e Biologia Molecular - UFG Laboratório de Genética e Biodiversidade - ICB/UFG