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pylelab / rMSA

RNA Multiple Sequence Alignment
https://figshare.com/articles/dataset/Benchmark_dataset_for_rMSA/20288745
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cannot find any MSA for certain fasta, and find some errors #2

Open llk15 opened 7 months ago

llk15 commented 7 months ago

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 commented 6 days ago

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.