Question: Blastp giving empty output file
0
gravatar for pes
2.6 years ago by
pes0
pes0 wrote:

I am very new to blasting. I am using the terminal to do a blastp, it starts running but has taken up to 2 days and the output file is also empty. I have read somewhere that we can't see anything from the output file until blast has stopped and that's why I have used commands like watch and list to see if anything gets added to this file but those are also blank!

I would appreciate any help!

my script: pwd/ncbi-blast-2.6.0+/bin/blastp -query XXX -db XXX -outfmt 6 -out XXX.txt

output terminal blast blastp • 1.3k views
ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by pes0

Thanks for answering! the size of the query I am using is 53680861, nothing is beind added to output file even when I run ls -l there is a zero. I will try running with more threads

ADD REPLYlink written 2.6 years ago by pes0

PLEASE click ADD COMMENT below answers to respond.

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by shenwei3564.9k

Thanks for answering! the size of the query I am using is 53680861, nothing is being added to output file even when I run ls -l there is a zero. I will try running with more threads when I look at top I am seeing it running!

ADD REPLYlink written 2.6 years ago by pes0

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

Do not use SUBMIT ANSWER to add new information for original question.

ADD REPLYlink written 2.6 years ago by genomax75k
2
gravatar for shenwei356
2.6 years ago by
shenwei3564.9k
China
shenwei3564.9k wrote:

These are lots of factors affecting the computation time:

  • BLAST database size. e.g., NCBI NR is very very big.
  • Query sequences size.
  • Parameters.
    • -num_threads. You did not set -num_threads, which defines number of CPUs to use. I think this the main cause for your case.
  • Computer hardware, including CPU, RAM, HDD and so on.

And I suggest your save result in -outfmt 11 and then convert it the other formats, in case you want more information than these in -outfmt 6.

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by shenwei3564.9k

Thank you for your help!

ADD REPLYlink written 2.6 years ago by pes0
2
gravatar for Jake Warner
2.6 years ago by
Jake Warner780
Jake Warner780 wrote:

What is that number? Surely you're not blasting 53 million sequences? If so, and you are blasting against nr, with the one thread above I would guess it will take a few years to run.

Could you provide the results to:

grep -c '^>' query.fasta

To answer your question, if I remember correctly BLAST+ buffers the results stream so at some point ~100 results should appear in out.txt. In addition to the -num_threads parameter you can also set the word size higher eg: -word_size 5

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by Jake Warner780

Thank you for your help!

ADD REPLYlink written 2.6 years ago by pes0
1
gravatar for 328558608
2.6 years ago by
32855860860
32855860860 wrote:

first´╝îcheck your query file type is protein sequence and your db index is protein type; In ordinary, you could see the result adding to the out file when blast+ is running. Make sure your command is correct and the command is in system background during 2 days.

ADD COMMENTlink written 2.6 years ago by 32855860860

Thank you for your help!

ADD REPLYlink written 2.6 years ago by pes0
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