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rega-cev / virulign

VIRULIGN: fast codon-correct alignment and annotation of viral genomes
GNU General Public License v2.0
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Warning: NeedlemanWunsh: sequence contained gaps? Removed them. #6

Open thierryjanssens opened 6 years ago

thierryjanssens commented 6 years ago

Hello,

when performing a virulign analysis and exporting it as a global alignment the following error pops up (repeatedly for every element of the alignment). It confuses me somehow.

Warning: NeedlemanWunsh: sequence contained gaps? Removed them.

I assume that this is caused by the gaps introduced in the pairwise alignment. The error is not very informative because it is a statement followed by a question mark. It also suggests that action has been taken already by removal of the gaps. I assume this warning can just be ignored?

Kind regards,

Thierry

ktheyss commented 6 years ago

Hi Thierry, could you please provide a small example?

ktheyss commented 6 years ago

We can use the example given in the issue regarding the debug folder.

Command: virulign DENV1-NC001477.xml test.txt --nt-debug debugfolder/

Output: Warning: NeedlemanWunsh: sequence contained gaps? Removed them. Warning: NeedlemanWunsh: sequence contained gaps? Removed them. Warning: NeedlemanWunsh: sequence contained gaps? Removed them. Warning: NeedlemanWunsh: sequence contained gaps? Removed them. Warning: NeedlemanWunsh: sequence contained gaps? Removed them. Warning: NeedlemanWunsh: sequence contained gaps? Removed them. Warning: NeedlemanWunsh: sequence contained gaps? Removed them. Align target 0 (virus_A_sample_1_NODE_1-1) virus_A_sample_1_NODE_1-1: Alignment error. (scores nt: 33.9; codon: 0) Align target 1 (virus_A_sample_1_NODE_1-2) virus_A_sample_1_NODE_1-2: Alignment error. (scores nt: 33.9; codon: 0) .....

tseemann commented 5 years ago

Is it talking about the input sequences that were provided to the NW function?

tseemann commented 4 years ago 
Warning: NeedlemanWunsh: sequence contained gaps? Removed them.

I get this error too; when i give it 13 sequence .fasta input with NO GAPS, each 1035bp long.