ERROR: Bad base (J) at site 444 of sequence 65
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Maryam
Mar 9, 2018, 4:00:18 PM3/9/18
to raxml
Hi,
I have an alignment consists of 6000 protein strains, and I run "./raxmlHPC-SSE3 -m PROTGAMMAAUTO -p 1 -T 12 -s alignment -n ProteinTree.tree" to infer the tree. However, I keep getting this error: ERROR: Bad base (J) at site 444 of sequence 65. Can you please let me know haw can I fix this problem?
I have an alignment consists of 6000 protein strains, and I run "./raxmlHPC-SSE3 -m PROTGAMMAAUTO -p 1 -T 12 -s alignment -n ProteinTree.tree" to infer the tree. However, I keep getting this error: ERROR: Bad base (J) at site 444 of sequence 65. Can you please let me know haw can I fix this problem?
Grimm
Mar 10, 2018, 7:46:23 AM3/10/18
to raxml
Hi Maryam,
there is no aminoacid labelled J. Your alignment may have a wrong number of specified sites. So part of an accession name is tried to be read in as part of the aligned proteine sequences.
For all PROT models, you need an alignmend with the valid aminoacid IUPAC codes: e.g. http://www.cbs.dtu.dk/courses/27619/codon.html
Cheers, Guido
there is no aminoacid labelled J. Your alignment may have a wrong number of specified sites. So part of an accession name is tried to be read in as part of the aligned proteine sequences.
For all PROT models, you need an alignmend with the valid aminoacid IUPAC codes: e.g. http://www.cbs.dtu.dk/courses/27619/codon.html
Cheers, Guido
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