When I ran 00.run.sh, I got the following error info: wrong format at /home/shu/Downloads/WGDdetector/config/software.config: Error in file(file, "rt") : cannot open the connection Calls: read.table -> file In addition: Warning message: In file(file, "rt") : cannot open file 'output/04.final_paralogs_ks/final.ks.distribution.list': No such file or directory Execution halted ln: failed to create symbolic link './final.ks.distribution.list.pdf': File exists

I changed the software.config file according my own software locations as following:

multithread

parallel = /home/shu/bin/parallel

clustering

mmseqs2 = /home/shu/Anaconda3/bin/mmseqs makeblastdb = /home/shu/Music/ncbi-blast-2.8.0+/bin/makeblastdb blastp = /home/shu/Music/ncbi-blast-2.8.0+/bin/blastp blast2graphs = /home/shu/Music/BlastGraphMetrics/blast2graphs.py

the python script from the pipeline of BlastGraphMetrics

mcl = /usr/local/bin/mcl

ks value estimated

codeml = /home/share/software/PAML/paml4.8/bin/codeml

mafft = /home/share/users/yangyongzhi2012//tools/mafft/mafft-7.402-without-extensions-build/bin/mafft

muscle = /home/shu/Anaconda3/bin/muscle pal2nal = /usr/share/lintian/overrides/pal2nal Rscript = /usr/bin/Rscript

protdist = /home/share/software/phylip/phylip-3.696/exe/protdist

fastme = /usr/local/bin/fastme

I am not sure what does wrong format mean? Could you help me with this issue? Thank you very much! Shu

yongzhiyang2012 / WGDdetector

error while running 00.run.sh #5