PSI-BLAST out put is empty
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3.2 years ago

Hi guys, I'm new in bio and I'm trying to make pssm matrix with psi-blast. This is the code I use:

blastdb$../ncbi-blast-2.9.0+/bin/psiblast -query /home/sepehr/blastdb/Butyrylation/Butyrylation/P02294.seq -db nr -out$P02294.out -num_iterations 3 -out_ascii_pssm $Pxxx.pssm -inclusion_ethresh 0.001 -num_threads 4;  I get this warning: Warning: [psiblast] Query_1 P02294: Composition-based score adjustment conditioned on sequence properties and unconditional composition-based score adjustment is not supported with PSSMs, resetting to default value of standard composition-based statistics I have changed the mode for all blast apps like psi-blast, blastp ... every thing in bin folder to 777 but app's result just create .out file that is empty and no .pssm matrix can any one tell me how to fix it? I really appreciate any help... BLAST output psiblast • 1.3k views ADD COMMENT 1 Entering edit mode Don't know what shell you are using, but putting $ before any word refers to environmental variables. Try the same command without dollar signs and see if that works.

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hi, thank you for your help I'm using Ubuntu 18 terminal I tried without $and it doesn't make any output. do you have any other suggestion or thought? ADD REPLY 0 Entering edit mode hi, thnk you for your help, I tried it and now it doesn't even create .out file any suggestion? ADD REPLY 0 Entering edit mode hi, thnk you for your help, I tried it and now it doesn't even create .out file any suggestion? You are not giving us much to work with. What is the exact command you are using now? How long does a command run? Does it print anything on the screen? What happens if you simply type ../ncbi-blast-2.9.0+/bin/psiblast -h? It is unlikely that a command will produce no file or screen output, especially if it goes for a while. ADD REPLY 0 Entering edit mode Hi thank for your help, My problem is fixed now the previous problem was due to some other problem The correct way to write command in linux terminal is what @biofalconch said.${xxxx}.out thank you every one for help :)

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I think shell its confusing the environmental variable, so instead of searching for $Pxxx it is looking for a variable called$Pxxx.pssm for example. To fix this, maybe try using brackets like this \${Pxxx}.pssm. Good Luck!