I have seen two other posts on this but as far as I can tell neither apply..my apologies if I am incorrect.
I have used blast on mac before and am generally familiar with it but I need to run this on a windows machine and really struggling to get this to work. I installed: ncbi-blast-2.6.0+-win64.exe Which I am pretty sure is the only option for windows: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ I installed following this tutorial but got the ncbi.ini file elsewhere: https://www.blaststation.com/intl/members/en/howtoblastwin.html
I need the refseq_protein database, but because this does not have perl, I downloaded each preformatted refseq_protein file by hand and unpacked them by hand so they are all in one directory. One issue that did arise when I did this was that there are multiple "refseq_protein.pal" files, the manual does not say what to do in this case so I had it "auto rename". (What is the appropriate thing to do here?)
I can run "blastx -help" just fine. But when I run the blastx command as (in the directory with the refseq files: blastx -query file.fasta -db refseq_protein -max_target_seqs 1 -outfmt 5 -out file.xml
I get the following exception (apparently I cannot copy from the windows command so I have to type everything...hopefully no typos): Error: NCBI C++ Exception T0 "..........\src\corelib\ncbi.obj.cpp", line 977: Critical: ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL pointer. Stack trace: KERNEL32[C:\WINDOWS\System32\KERNEL32.DLL]:0 BasteThreadInitThunk offset=0x14 addr=0x00007FFA5A078364
Because the help command works, I am guessing that it is something with the database rather than the blastx command...? Any help is appreciated, thank you for your time