I am new to bioinformatics and am working on VLP-enriched viral metagenomic datasets and so would like to use Demovir for getting taxonomic annotation on my viral contigs.
However, I got an error as follows:
sort: No such file or directory,
rm: trembl_ublast.viral.txt: No such file or directory,
Error in read.table(file = file, header = header, sep = sep, quote = quote, :
no lines available in input,
Calls: read.delim -> read.table,
My steps were:
1) I downloaded/installed required components in macOS 11.5.2;
2) I downloaded Usearch-32 bit and put it into the user’s directory then ran gunzip to decompress the tool, followed by using chmod +x to execute it;
3) I downloaded nr.95.fasta.bz2 database from FigShare then put it in the Demovir directory, followed by using chmod 777 * to execute all files in the Demovir directory, and then performed bash format_db.sh (note: I found a message showed “format_db.sh: line 2: usearch: command not found” in the usearch_database.log, not sure if this is the case?);
4) Finally, I tried to run my samples placed in a folder at my desktop: bash /path_to_demovir/demovir.sh input.fasta threads.
If there’s anything wrong or I misunderstand it, can someone guide me to correct it please? Many thanks in advance.
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