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