Hi, I'm trying to run tblastn, but whatever I try, I always get back the following error:
BLAST Database error: No alias or index file found for nucleotide database [Ptr_protDB] in search path [/home/cadav/Thesis/VanDePeerPSgenes/Shiu_Pipeline/BLAST_output::]
I've looked around the internet for help and found multiple similar answers such as:
- BLAST Database error: No alias or index file found for nucleotide database
- Why I Am Getting This Error " No Alias Or Index File Found For ..... Database"
But unfortunately, I haven't been able to solve my problem. Though it really shouldn't be that hard... The commands I used were:
makeblastdb -in Ptrichocarpa_210_v3.0.protein.fa -input_type fasta -dbtype 'prot' -title Ptr_protDB -parse_seqids -out Ptr_protDB Building a new DB, current time: 05/17/2018 13:42:43 New DB name: /home/cadav/Thesis/VanDePeerPSgenes/Shiu_Pipeline/BLAST_output/Ptr_protDB New DB title: Ptr_protDB Sequence type: Protein Keep MBits: T Maximum file size: 1000000000B Adding sequences from FASTA; added 73013 sequences in 2.85026 seconds.
tblastn -db Ptr_protDB -query AnchorPoint/AnchorPoint_masked01.fa -out AP01.blasted -evalue 0.0001 -outfmt 7 -matrix BLOSUM50 -lcase_masking
I've tried using the whole path to the database name, but that unfortunately didn't work. I can't see what I'm doing wrong. Also, why does it does it say: nuclueotide database [Ptr_protDB], even though it's a protein database? I specified it and even created the the 6 files (phr, pin, pog, psd, psi and psq instead of nhr, nin,...)