Hello,
I'm still rather new to blast+ and I'm trying to get an implemented tool to work locally(that already works somewhere else).
The tool just completely skips blasting and doesn't even show me any error. It creates and fills all the required files perfectly, makes the database files and then tries to run the blastn module. But nothing happens. I just get a completely blank blast_output file. No errors in my error logs. So I tried to do some of the commands manually in the terminal.
Here is the makeblastdb command:
/home/student1/MGCV_liteTools/ncbi-blast-2.2.28+/bin/makeblastdb -in /var/www/localhost/blast_tmp/1386165610refseq_upload_file.fasta
-input_type fasta -max_file_sz 3500000000 -dbtype nucl -out /var/www/localhost/blast_tmp/1386165610_db
It seems to work fine, as I get the following result:
Building a new DB, current time: 12/04/2013 15:01:54
New DB name: /var/www/localhost/blast_tmp/1386165610_db
New DB title: /var/www/localhost/blast_tmp/1386165610refseq_upload_file.fasta
Sequence type: Nucleotide
Keep Linkouts: T
Keep MBits: T
Maximum file size: 3500000000B
Adding sequences from FASTA; added 7 sequences in 0.137179 seconds.
Then, I try to enter the blastn command:
/home/student1/MGCV_liteTools/ncbi-blast-2.2.28+/bin/blastn -db /var/www/localhost/blast_tmp/1386165610_db -query /var/www/localhost/blast_tmp/1386165610query_upload_file.fasta -evalue 0.001 -num_threads 4 -max_target_seqs 2000 -out /var/www/localhost/blast_ ...