Bipartition file missing from RAxML-HPC BlackBox analysis

[Dilara Jayasekera]

Hello!

I conducted a phylogenetic analysis of 360 ITS sequences using the RAxML-HPC BlackBox (8.2.12) tool on CIPRES. However, when I run the task, the bipartition file is not available under the output. I have attached screenshots of the parameters that I specified along with task message. 

Thank you

Best regards

Dilara

[Pfeiffer, Wayne]

Hi Dilara,

Your job did not run successfully because some of the taxon labels in your fasta file contain the character “)”. That is not allowed by RAxML.

* Please remove those labels and resubmit your job.

Best regards,

Wayne

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[Dilara Jayasekera]

Hi Wayne,

Thank you for the suggestion. I redid the phylogenetic analysis by removing '(', however, I'm still not getting the bipartition file. Perhaps, a change in the paraneters is required? I have attached a screenshot of the recent task message. 

Thank you
Best regards
Dilara

[Pfeiffer, Wayne]

Hi Dilara,

The first error message in the stdout.txt file is

ERROR: Taxon Name "GU300095.1_Xylaria_hypoxylon_isolate_95082001_18S_ribosomal_RNA_gene_partial_sequence_internal_transcribed_spacer_1_5.8S_ribosomal_RNA_gene_and_internal_transcribed_spacer_2_complete_sequence_and_28S)" is invalid at position 199, it contains illegal character )

Illegal characters in taxon-names are: tabulators, carriage returns, spaces, ":", ",", ")", "(", ";", "]", "[", "’" 

Note that the illegal character in your fasta file is a right parenthesis: “)”. That is the character that you need to remove.

Best regards,

Wayne