ncbi-blast-2.9.0+ Generate PSSm profile using PSI blast for multiple fasta sequences

Question

[Rana]

Hi I want to generate PSSm profile for multiple Fasta sequences. However, I encountered several problems. At First I run the PSI Blast and it seems it was working fine but in the end there was no output stored in the generated output file.

/ncbi-blast-2.9.0+/bin$ psiblast -db /data/BlastDB/uniref50.fasta -query Test_1999.fasta -evalue 0.001 -out Test.txt -out_ascii_pssm seq.1.pssm -num_threads 8 –num_iterations 2

So I thought to try again but now I am getting error stating that " BLAST failed to write output" if anyone can help me to solve these issues. I will be very grateful to him/her.

Thanks in advance.

[lieven.sterck]

do you still have storage (quota?) available where you want to write out the file ?

and do you have permissions to write the output file? it seems like you want to write the output file in the dir where blast is installed, perhaps you don't have permissions to write files in that location?

Answer 1

[GenoMax]

As @lieven indicated /add_a_valid directory location to command line below to save the results.

/ncbi-blast-2.9.0+/bin$ psiblast -db /data/BlastDB/uniref50.fasta -query Test_1999.fasta -evalue 0.001 -out /add_valid_path/Test.txt -out_ascii_pssm /add_valid_path/seq.1.pssm -num_threads 8 –num_iterations 2

[Rana]

Thankyou so much for your response your suggestion helped and now I am able to generate and store output. Thank you