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wu-lab-uva / RasperGade16S

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predict_16SGCN_from_sequences #4

Open avportal opened 1 month ago

avportal commented 1 month ago

Hi there,

I am trying to run pred.GCN = predict_16SGCN_from_sequences(), following the information provided @ https://github.com/wu-lab-uva/RasperGade16S

However, I get the following:

No FASTA file supplied, running prediction using demo sequences in /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RasperGade16S/extdata/Demo/demo.SILVA.fasta

[1] "hmmalign --trim --dna -o RasperGade16S_align//seq.align --mapali /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RasperGade16S/extdata/aligned_remove_dot.fasta /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RasperGade16S/extdata/16S_core_gg.hmm /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RasperGade16S/extdata/Demo/demo.SILVA.fasta" [1] "esl-reformat -o RasperGade16S_align//seq.afa -u --gapsym=- afa RasperGade16S_align//seq.align" sh: esl-reformat: command not found Error in system(command = cmd, intern = TRUE) : error in running command

Any assistance will be highly appreciated.

Angel

TomZhang1018 commented 1 month ago

My condition is similar to yours.It shows: [1] "hmmalign --trim --dna -o RasperGade16S_align//seq.align --mapali /home/tom/R/x86_64-pc-linux-gnu-library/3.6/RasperGade16S/extdata/aligned_remove_dot.fasta /home/tom/R/x86_64-pc-linux-gnu-library/3.6/RasperGade16S/extdata/16S_core_gg.hmm /home/tom/R/x86_64-pc-linux-gnu-library/3.6/RasperGade16S/extdata/Demo/demo.SILVA.fasta" sh: 1: hmmalign: not found Error in system(command = cmd, intern = TRUE) : error in running command And I don't know why it doesn't work...