I'm afraid blastall -d flag only receives custom-built or NCBI standard database, e.g. nr, refseq.
Raw fasta files must be built into a custom blast database in prior for blastp.
But in the line 77 of NCycProfiler.PL:
system("blastall -p blastp -d data/NCyc_100.faa -i $file -o $out -m 8 -e 1e-4 -b 1 -v 1")
attempts to directly assign the faa file to the -d flag. Has anyone made this successful?
BTW, the use of blastall is also discontinued from legacy blast suite. For users using newer versions of blast, modify the script to use blastp/blastn instead.
In addition, the error message of the above error is confusing and not documented. Since no return value checked after the system call, the fail of blastall is not caught. The script keeps execution and ended up in an error message from cp instead: no such file or directory of some_sample.blast (due to no output from blastall).
-m diamond has no this issue. Not checked with usearch mode.
Hi All,
I'm afraid
blastall -dflag only receives custom-built or NCBI standard database, e.g. nr, refseq. Raw fasta files must be built into a custom blast database in prior forblastp. But in the line 77 ofNCycProfiler.PL:system("blastall -p blastp -d data/NCyc_100.faa -i $file -o $out -m 8 -e 1e-4 -b 1 -v 1")attempts to directly assign the faa file to the-dflag. Has anyone made this successful? BTW, the use ofblastallis also discontinued from legacy blast suite. For users using newer versions of blast, modify the script to useblastp/blastninstead.In addition, the error message of the above error is confusing and not documented. Since no return value checked after the
systemcall, the fail ofblastallis not caught. The script keeps execution and ended up in an error message fromcpinstead: no such file or directory of some_sample.blast (due to no output from blastall).-m diamondhas no this issue. Not checked with usearch mode.