ParallelStructure in R - error upon completion

[Filip Varga]

I am currently migrating all practical exercises from our course on Molecular diversity and evolution to R, and I have stumbled upon your package for running structure analysis in R.

After reading the manual and several tutorials, I have compiled a script for running the analysis on our example data, but after the function finishes running, no results are written in the folder, and I receive an error:

Error in file(file, "rt") : cannot open the connection In addition: Warning message: In file(file, "rt") : cannot open file 'F:/Dropbox/01_Work/Nastava/MRE/MRE 2023_2024/vježba 4 - R/structure calculations/0_results/results_job_run1_q': No such file or directory

The code I'm running is:

parallel_structure(joblist= "joblist.txt", n_cpu=1, structure_path="C:/Program Files (x86)/Structure2.3.4/bin/",
                 infile="So_Structure.txt", outpath="F:/Dropbox/01_Work/Nastava/MRE/MRE 2023_2024/vježba 4 - R/structure calculations/0_results/",
                   numinds=709, numloci=8, plot_output=1, label=1,
                   popdata=1, popflag=0, phenotypes=0, markernames=0, mapdist=0, onerowperind=0, phaseinfo=0,
                   extracol=0, missing=-9, ploidy=2, usepopinfo=0, revert_convert=0, printqhat=0, locdata=0,
                   recessivealleles=0, phased=0, noadmix=0, linkage=0, locprior=0, inferalpha=1)

In my working directory I can see generation of temporary files, but nothing gets written in the results folder.
I have tried running R as an Administrator, as suggested by people on google group dedicated to this topic with no luck.
I am attaching both joblist and infile here.

Any help would be much appreciated.

Thank you in advance,

[Vikram Chhatre]

In general, it's a bad idea to include spaces in either file or folder names. I would fix that first and try again.

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