Error while creating an MSA for custom database creation

[hites77]

I ran the following code: First I ran the command to to build ffindex for my sequences kept in fasta file named as pgpb and then i ran command to generate MSA for each sequences:

mpirun -np 24 hhblits_mpi -i pgpb -d /scratch/users/nus/eriht/databases/uniclust30_2018_08 /uniclust30_2018_08 -oa3m pgpb_a3m_wo_ss -n 2 -cpu 24 -v 0

Got the following error

• 17:46:54.836 ERROR: Error in /home/users/nus/eriht/scratch/hh-suite/src/hhalignment.cpp:1267: Compress:

• 17:46:55.425 ERROR: no match states found in 1!

• 17:46:55.434 ERROR: Better use '-M first' option or reduce gap percentage threshold for match states

Even put the -M 50 paramater but the error remain the same. Does for a sequence in my fasta file no match was found in uniprot database ?

[martin-steinegger]

It looks like one or your input MSAs has no column with more than 50% gaps. Is this possible? Does it also crash with -M first?

[hites77]

MSA are to be build using this command. The same error occur even if I put -M first and even whne change the threshold to -M 10.