I am new to R and command line softwares as well. I am using Win7 and R studio. Whenever I call
hmmerScan.exe from R, it gives me this error. Kindly guide me about the problem and solution.
hmmerScan: Scanning D:/R-files/Micropan/prepped/NIH1_GID1.fasta ... Failed to parse command line: Arg looks like option? Use --domtblout=--cpu if you really mean it. Usage: hmmscan [-options] <hmm database> <query seqfile> where most common options are: -h : show brief help on version and usage To see more help on available options, do /Genomes/hmmscan -h Warning messages: 1: running command 'hmmscan -o hmmer3.txt --cut_ga --noali --domtblout --cpu 0 D:/R-files/Micropan/pfam/GID1_vs_Pfam-A.hmm.txt D:/R-files/Micropan/Pfam-A.hmm D:/R-files/Micropan/prepped/NIH1_GID1.fasta' had status 1