and running it with clustalo -i error.fasta, one gets the following error message:
HHalignWrapper:hhalign_wrapper.c:1419: problem in alignment (profile sizes: 1 + 2) (p3 + p1), forcing Viterbi
hh-error-code=4 (mac-ram=8000)
hhalign:hhalign.cpp:961: Problem Reading/Preparing profiles (len(q)=75/len(t)=0)
HHalignWrapper:hhalign_wrapper.c:1447: problem in alignment, Viterbi did not work
hh-error-code=4 (mac-ram=64000)
hhalign:hhalign.cpp:961: Problem Reading/Preparing profiles (len(q)=75/len(t)=0)
FATAL: could not perform alignment -- bailing out
I would expect the error message to be something like:
Cannot align sequence with only unknown amino acids
FATAL: could not perform alignment -- bailing out
Sure, this is a low priority issue (I can check so myself as well), but it would have save me quite some debugging. The sequences are from SARS-CoV-2, the E (from Envelope) protein: apparently one sequence went sideways :-).
I hope you will take my suggestion into account.
Thanks for again for writing and/or maintaining Clustal and cheers, Richel Bilderbeek
22 September 2020 08:28 9 KB From: Richel Bilderbeek To: clustalw@ucd.ie
Dear Clusal developers,
I contact you to help give ClustalOmega even more helpful error messages.
First, thanks for writing and/or maintaining Clustal!
Second, here is my suggestion to help ClustalOmega give a better error message:
For a FASTA file this (also attached):
and running it with
clustalo -i error.fasta, one gets the following error message:I would expect the error message to be something like:
Sure, this is a low priority issue (I can check so myself as well), but it would have save me quite some debugging. The sequences are from SARS-CoV-2, the E (from Envelope) protein: apparently one sequence went sideways :-).
I hope you will take my suggestion into account.
Thanks for again for writing and/or maintaining Clustal and cheers, Richel Bilderbeek
Attachments