I think you should copy & paste the error message you got.

It will help others to understand what is wrong.

C:\NCBI\blast-2.2.26+\bin>psiblast -query C:\NCBI\blast-2.2.26+\db\test.txt -db

C:\NCBI\blast-2.2.26+\db\nac -out C:\NCBI\blast-2.2.26+\db\output.txt -num_itera

tions 2 -out_pssm C:\NCBI\blast-2.2.26+\db\testnacpssm

Warning: lcl|Query_1 tr|D0AB71|D0AB71_ORYSI NAC domain-containing protein OS=Ory

za sativa subsp. indica GN=nac PE=2 SV=1: Warning: Composition-based score adjus

tment conditioned on sequence properties and unconditional composition-based sco

re adjustment is not supported with PSSMs, resetting to default value of standar

d composition-based statistics

Warning: lcl|Query_2 tr|F7J4C2|F7J4C2_ORYSI Similar to NAC-domain containing pro

tein 18 (Fragment) OS=Oryza sativa subsp. indica GN=Os01g0888300 PE=4 SV=1: Warn

ing: Composition-based score adjustment conditioned on sequence properties and u

nconditional composition-based score adjustment is not supported with PSSMs, res

etting to default value of standard composition-based statistics

Warning: lcl|Query_3 tr|A6N0N2|A6N0N2_ORYSI Nac domain-containing protein OS=Ory

za sativa subsp. indica PE=4 SV=1: Warning: Composition-based score adjustment c

onditioned on sequence properties and unconditional composition-based score adju

stment is not supported with PSSMs, resetting to default value of standard compo

sition-based statistics

Warning: lcl|Query_4 tr|D0V3Z4|D0V3Z4_ORYSI Stress-induced transcription factor

NAC1 OS=Oryza sativa subsp. indica GN=Snac1 PE=2 SV=1: Warning: Composition-base

d score adjustment conditioned on sequence properties and unconditional composit

ion-based score adjustment is not supported with PSSMs, resetting to default val

ue of standard composition-based statistics

Above the error message which was generated

C:\NCBI\blast-2.2.26+\bin>psiblast -query C:\NCBI\blast-2.2.26+\db\test.txt -db

C:\NCBI\blast-2.2.26+\db\nac -out C:\NCBI\blast-2.2.26+\db\output.txt -num_itera

tions 2 -out_pssm C:\NCBI\blast-2.2.26+\db\testnacpssm

Warning: lcl|Query_1 tr|D0AB71|D0AB71_ORYSI NAC domain-containing protein OS=Oryza sativa subsp. indica GN=nac PE=2 SV=1: Warning: 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

Warning: lcl|Query_2 tr|F7J4C2|F7J4C2_ORYSI Similar to NAC-domain containing protein 18 (Fragment) OS=Oryza sativa subsp. indica GN=Os01g0888300 PE=4 SV=1: Warning: 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 statisticsWarning: lcl|Query_3 tr|A6N0N2|A6N0N2_ORYSI Nac domain-containing protein OS=Oryza sativa subsp. indica PE=4 SV=1: Warning: 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

Warning: lcl|Query_4 tr|D0V3Z4|D0V3Z4_ORYSI Stress-induced transcription factor

NAC1 OS=Oryza sativa subsp. indica GN=Snac1 PE=2 SV=1: Warning: 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

Sorry previous one I forgot to format

It is not an "error" message. It is a "warning" message which usually you can ignore.

The message means that the option you set (or default) about composition based statistics in psiblast is not supported with PSSM.

If you add option

-comp_based_stats 1

or

-comp_based_stats 0

, the waring message will not appear.

By the way, I think the result you wanted to get is the file generated when you add option

-out_ascii_pssm

Please check.

Thankyou Mr.Toshiyuki Oda . I never thought of trying -out_ascii_pssm and moreover could not understand that warning message. Now I am getting the PSSM file.

To generate a PSSM file I think 3 iteration will be file no. Becoz with iteration 3 and 4 I am getting same scores almost.