Argument "query". Incompatible with argument: `in_pssm' blast+

Question

[rachid.fermi]

hello, i have a command in old blast **

blastall -i $refseq -d $seqFilename -p psitblastn -R $chkpFile -F F -M BLOSUM62 -t -1 -e $max_Evalue -v 10000 -b 10000 > $outputFile

** and i want to translate it to new blast+, i did as fellow i'm not really sure if i'm it right

tblastn -query $refseq -db $seqFilename -in_pssm $chkpFile  -seg no -matrix BLOSUM62 -max_intron_length 1 -evalue $max_Evalue -num_descriptions 10000 -num_alignments 10000 -out $outputFile

i have changed max-intron value from the old blast which is -1 to 1 in blast+ and i got the following error which is normal because in tblastn -help says

-query <File_In>    Input file name    Default = `-'
    * Incompatible with:  in_pssm

how can i translate the command above

Answer 1

[Mensur Dlakic]

You simply issue your command without -query $refseq because the -in_pssm file already contains the sequence.

However, there is a good chance this still won't work. Old blast commands save their checkpoints as binary files, while more recent versions save them as ascii (text) files. You may have to run this search from the scratch, meaning without -in_pssm $chkpFile.