Is there a way to peek at blast temporary file? I would like to know what sequence is analyzed in order to foresee how long the program will take to finish. top command shows that it uses around 4 gigs of memory, but I can't get hold of the file in the ram folders (/dev/shm). I could kill the job, but the temporary file would be erased. Anybody would know?
My blast inputs are rather basic :
blastn -query sequences.fasta -db nt.db -out output.xml -evalue 1e-4 -outfmt 5 -num_threads 14 -gapopen 5 -gapextend 2 -word_size 7
I have 2000 sequences inside the fasta file.
nt database file is enromous, so I'm expecting blastn to hang long...
EDITING: Although the file is working consuming more and more ram as the program is running, ls -l on my output folder gives:
-rw-rw-r-- 1 sara sara 0 Aug 16 15:57 output.xml
so I can't use grep or sed or wc -l... I have no idea where the information is put! That's why I was looking into the /dev/shm folder...
MORE EDITING: Although the file is empty (no octet in it, as shows the previous command), all the output information is store into the RAM (RAM's usage for the blastn is growing everyday) . When the job is finished, Blast transfers the content of the RAM onto the disk, i.e. the output.xml. At least, that's what I figure. My question is how to peek into the blast temporary output file that is on the RAM...