"cannot create directory" and "no such file or directory" errors

[sjfleck]

Hello,
I'm running the default RepeatOBserver command and I got these errors:

There were 50 or more warnings (use warnings() to see the first 50)
rm: cannot remove 'Centromere_summary.txt': No such file or directory
rm: cannot remove 'Centromere_summary_Shannon.txt': No such file or directory
grep: Centromere_summary_Shannon_35_no_telo.txt: No such file or directory
cp: cannot stat '/full/path/to/RepeatObserver/Salb/input_chromosomes//isochore/.png': No such file or directory
cp: cannot stat '/full/path/to/RepeatObserver/Salb/output_chromosomes/Salb_H0-AT/Chr/histograms/histogram_POWER_SUM_seqvals_0.5std_1.pdf': No such file or directory
mkdir: cannot create directory ‘Summary_output’: File exists
mkdir: cannot create directory ‘spectra’: File exists
mkdir: cannot create directory ‘spectra_parts_35-2000’: File exists
mkdir: cannot create directory ‘spectra_parts_15-35’: File exists
mkdir: cannot create directory ‘spectra_parts_2-8’: File exists
mkdir: cannot create directory ‘spectra_total_merged’: File exists
mkdir: cannot create directory ‘histograms’: File exists
rm: cannot remove 'Centromere_summary.txt': No such file or directory
mkdir: cannot create directory ‘DNAwalks’: File exists
mkdir: cannot create directory ‘2D’: File exists
mkdir: cannot create directory ‘1D’: File exists
mkdir: cannot create directory ‘Shannon_div’: File exists
mkdir: cannot create directory ‘Shannon_div_5kbp’: File exists
mkdir: cannot create directory ‘Shannon_div_500kbp’: File exists
mkdir: cannot create directory ‘Shannon_div_5Mbp’: File exists
mkdir: cannot create directory ‘Shannon_div_1.25Mbp’: File exists
mkdir: cannot create directory ‘Shannon_div_2.5Mbp’: File exists
rm: cannot remove 'Centromere_summary_Shannon.txt': No such file or directory
grep: Centromere_summary_Shannon_35_no_telo.txt: No such file or directory
mkdir: cannot create directory ‘Shannon_div_window’: File exists
mkdir: cannot create directory ‘output_data’: File exists
mkdir: cannot create directory ‘isochores’: File exists
cp: cannot stat '/full/path/to/RepeatObserver/Salb/input_chromosomes//isochore/.png': No such file or directory
mkdir: cannot create directory ‘pdfs’: File exists
mkdir: cannot create directory ‘histograms’: File exists
cp: cannot stat '/full/path/to/RepeatObserver/Salb/output_chromosomes/Salb_H0-AT/Chr*/histograms/*histogram_POWER_SUM_seqvals_0.5std_1.pdf': No such file or directory
mkdir: cannot create directory ‘DNAwalks’: File exists
mkdir: cannot create directory ‘Shannon_div’: File exists
Warning messages:
1: In ggplot2::geom_histogram(stat = "count", bins = 10, position = "stack", :
Ignoring unknown parameters: binwidth, bins, and pad
2: In ggplot2::geom_histogram(stat = "count", bins = 10, position = "stack", :
Ignoring unknown parameters: binwidth, bins, and pad
Error in data.frame(beg.freq = d1, end.freq = d2, size = NA, beg.indx = d1i, :
arguments imply differing number of rows: 1, 0
Calls: calculate_ranges -> -> data.frame
Execution halted

If it helps, here are my commands. I don't think anything is wrong with them:
REF_FULL_PATH="/full/path/to/Salb.renamed.fasta"
SP_CODE="Salb"
REF=$SP_CODE # I just use the species code for the genome fastas
THREADS="40"
MEM="187000"

mkdir $SP_CODE && cd $SP_CODE
ln -s $REF_FULL_PATH $REF.fasta

wget https://raw.githubusercontent.com/celphin/RepeatOBserverV1/main/Setup_Run_Repeats.sh
chmod +x Setup_Run_Repeats.sh
dos2unix Setup_Run_Repeats.sh

module load miniconda3/22.11.1-1
eval "$(/projects/academic/tkrabben/modules_KrabLab/easybuild/2023.01/software/Core/miniconda3/22.11.1-1/bin/conda shell.bash hook)"
conda activate RepeatOBserver-v1
module load seqkit/2.3.1

sh Setup_Run_Repeats.sh -i $SP_CODE -f $REF.fasta -h H0 -c $THREADS -m $MEM -g FALSE

[celphin]

Sorry for the slow response - I have been away traveling. I'm just looking through these issues now. I don't see anything obviously wrong with your commands. I noticed you use miniconda. Do you need this for R on your server? Have you installed the R package somewhere? The symbolic link should be fine.

# install the R package in an interactive R session first
R
install.packages("devtools")
library(devtools)
install_github("celphin/RepeatOBserverV1") #to install the package
# Select 1:All to install all the required packages
library(RepeatOBserverV1) # to load the package
q() # to quit
n

If you are still having issues with the program, could you send me the whole output from the program (maybe as a text file) and I can check for errors earlier in the code?