cannot find any MSA for certain fasta, and find some errors

[llk15]

here is the outputs when executing rMSA.pl

creating /tmp/root/rMSA_23925_928759702
>/home/rMSA/fasta/3/3.fasta	length=15
AAAATCAAAAAGAAG
using 4 cpu
cp /home/rMSA/fasta/3/3.dbn /tmp/root/rMSA_23925_928759702/RNAfold.dbn
==== rfam pre-screening ====
wc: /tmp/root/rMSA_23925_928759702/rfam*.db: No such file or directory
wc: /tmp/root/rMSA_23925_928759702/db0: No such file or directory
0 total
==== blastn-short pre-screening ====
/home/rMSA/bin/blastn -num_threads 4 -query /tmp/root/rMSA_23925_928759702/seq.fasta -strand plus -db /home/rMSA/database/rnacentral.fasta -out /tmp/root/rMSA_23925_928759702/blastn0.tab -task blastn-short -max_target_seqs 50000 -outfmt '6 saccver sstart send evalue bitscore nident staxids'
cut -f1 /tmp/root/rMSA_23925_928759702/blastn0.tab|sort|uniq > /tmp/root/rMSA_23925_928759702/blastn0.list
split -l 5000 /tmp/root/rMSA_23925_928759702/blastn0.list /tmp/root/rMSA_23925_928759702/blastn0.list.split.
cat /tmp/root/rMSA_23925_928759702/blastn0.trim.split.* | /home/rMSA/bin/fasta2pfam - | sort -u -k2 | /home/rMSA/bin/pfam2fasta - > /tmp/root/rMSA_23925_928759702/blastn0.db
cat: /tmp/root/rMSA_23925_928759702/blastn0.trim.split.*: No such file or directory
rm  /tmp/root/rMSA_23925_928759702/blastn0.trim.split.*
rm: cannot remove ‘/tmp/root/rMSA_23925_928759702/blastn0.trim.split.*’: No such file or directory
/home/rMSA/bin/blastn -num_threads 4 -query /tmp/root/rMSA_23925_928759702/seq.fasta -strand both -db /home/rMSA/database/nt -out /tmp/root/rMSA_23925_928759702/blastn1.tab -task blastn-short -max_target_seqs 50000 -outfmt '6 saccver sstart send evalue bitscore nident staxids'

[kad-ecoli]

The sequence you provide is very short, making blastn unable to find any hit.
You sequence does not contain any base pair either, making infernal unable to perform covariance model based sequence search. Therefore, your search just cannot generate any alignment.

[LittletreeZou]

What is the minimum sequence length rMSA supports? @kad-ecoli