RAxML can't parse alignments for which there are sequences made entirely of undetermined characters

[RyanCook94]

Hi, thanks for the amazing tool by the way! I'm having an issue where RAxML can't parse alignments for which there are sequences made entirely of undetermined characters:

[e] error while refining gene tree
{'program_name': '/opt/miniconda3/envs/phylophlan/bin/raxmlHPC', 'params': '-p 1989', 'database': '-t', 'input': '-s', 'output_path': '-w', 'output': '-n', 'version': '-v', 'model': '-m', 'command_line': '#program_name# #model# #params# #database# #output_path# #input# #output#'}
PROTCATRTREV
/home/ubuntu/Evelien-Adriaenssens/James_Doc/james_phylophlan_bif/take_two/james_phylophlan_bif_phylophlan/tmp/trim_not_variant/p0094.aln
/home/ubuntu/Evelien-Adriaenssens/James_Doc/james_phylophlan_bif/take_two/james_phylophlan_bif_phylophlan/tmp/gene_tree1_polytomies/p0094.tre
/home/ubuntu/Evelien-Adriaenssens/James_Doc/james_phylophlan_bif/take_two/james_phylophlan_bif_phylophlan/tmp/gene_tree2
p0094.tre

[e] Command '['/opt/miniconda3/envs/phylophlan/bin/raxmlHPC', '-m', 'PROTCATRTREV', '-p', '1989', '-t', '/home/ubuntu/Evelien-Adriaenssens/James_Doc/james_phylophlan_bif/take_two/james_phylophlan_bif_phylophlan/tmp/gene_tree1_polytomies/p0094.tre', '-w', '/home/ubuntu/Evelien-Adriaenssens/James_Doc/james_phylophlan_bif/take_two/james_phylophlan_bif_phylophlan/tmp/gene_tree2', '-s', '/home/ubuntu/Evelien-Adriaenssens/James_Doc/james_phylophlan_bif/take_two/james_phylophlan_bif_phylophlan/tmp/trim_not_variant/p0094.aln', '-n', 'p0094.tre']' returned non-zero exit status 255.

If I run the individual command, I get:

ubuntu@viral-metagenomics:~/Evelien-Adriaenssens/James_Doc/james_phylophlan_bif$ /opt/miniconda3/envs/phylophlan/bin/raxmlHPC -m PROTCATRTREV -p 1989 -t /home/ubuntu/Evelien-Adriaenssens/James_Doc/james_phylophlan_bif/take_two/james_phylophlan_bif_phylophlan/tmp/gene_tree1_polytomies/p0094.tre -w /home/ubuntu/Evelien-Adriaenssens/James_Doc/james_phylophlan_bif/take_two/james_phylophlan_bif_phylophlan/tmp/gene_tree2 -s /home/ubuntu/Evelien-Adriaenssens/James_Doc/james_phylophlan_bif/take_two/james_phylophlan_bif_phylophlan/tmp/trim_not_variant/p0094.aln -n p0094.tre
Warning, you specified a working directory via "-w"
Keep in mind that RAxML only accepts absolute path names, not relative ones!

RAxML can't, parse the alignment file as phylip file
it will now try to parse it as FASTA file

ERROR: Sequence PROKKA_Bifidobacterium_bifidum_GCA_022731955.1_ASM2273195v1_genomic consists entirely of undetermined values which will be treated as missing data
ERROR: Sequence PROKKA_Bifidobacterium_bifidum_GCA_022728715.1_ASM2272871v1_genomic consists entirely of undetermined values which will be treated as missing data
ERROR: Found 2 sequences that consist entirely of undetermined values, exiting...

This is similar to an issue Mick Watson reported previously (https://forum.biobakery.org/t/raxmlhpc-failed-e-refine-gene-tree-crashed/1606/5). I've followed the same steps suggested (cloned the git repository and call the script that's in the repo), but haven't resolved the issue. Any advice?

Many thanks and best wishes,
Ryan

[schmittel]

I'm having the same issue. I've run phylophlan with various combinations of both --fragmentary_threshold and --remove_fragmentary_entries but I'm still getting the same error. This error has been reported previously but none of the solutions seem to help in my case.