Failed to Resize Memory

[NicMAlexandre]

Hello,

I I am running the pre-ma.bf script like so: hyphy hyphy-analyses/codon-msa/pre-msa.bf --input combined_seq.fasta

I am running on a large memory node (1.5 Tb Memory) and get the following error:

**Analysis Description

Load nucleotide sequences (SOME of which must be in frame), perform frameshift correction as needed, and translate to amino-acids for subsequent alignment.

• Requirements: Sequences

• Citation: TBD

• Written by: Sergei L Kosakovsky Pond

• Contact Information: spond@temple.edu

• Analysis Version: 0.02

code: Universal Error: Failed to resize memory to '964000' bytes'

Function call stack 1 : [namespace = wVSxEEcW] DataSet ^dataset_name = ReadDataFile(PROMPT_FOR_FILE);

2 : filter.nuc_data=alignments.ReadNucleotideDataSet("filter.raw_data",None); -------**

Should I use fewer sequences? These are the entire genome CDS (all annotated gene CDS) for 10 species.

[spond]

Dear @nicolasalexandre21,

pre-msa.bf (and codon-msa in general) is designed to deal with gene-sized alignments. Specifically, it will break for long sequences, because one stage of the algorithm (error-correcting alignment) is memory hungry. These scripts are not meant to segment CDS into individual genes. For that you may try something like https://academic.oup.com/bioinformatics/article/35/5/871/5075035

Best, Sergei

[NicMAlexandre]

Oh I see thank you!