query in human_genomic database

Question

[marghe08]

Hello to all. I present my problem. In my computer I have downloaded the "human_genomic database" from the ncbi site and then unzipped the various files. I have a fasta file "BRCA1.fa" that contains a nucleotide sequence. The command that I launched in unix terminal is:

blastn -query = BRCA1.fa -db = human_genomic -perc_identity =100 -word_size = 17 query_loc= 81022-81040

I want to see how many times the subsequence of BRCA1 files, specified by the indexes of "query loc", appears in the human genome with exact match. Few minutes after I run the command, the process is killed. I have two questions: 1) is my query right? 2)how can i see log files about this process?

Answer 1

[mastal511]

What version of standalone blast are you using? Are you getting any error messages at all when the process is running or when it dies? Have you checked whether your computer may be running out of memory before the process dies? What happens if you try just a simple version of your query:

blastn -query = BRCA1.fa -db = human_genomic

[marghe08]

The version is BLASTN 2.2.31+ I don't get any error message, the only message I get is "Killed". The human_genomic database is 11Gb. Do I require any particular RAM requirements? Do I require at least 11 GB of free RAM?

[mastal511]

Use 'top' to see how much memory is being used while it runs, before it gets killed.