Cannot Align My Consensus fasta

Question

[davidmaimoun]

Hello,

I need to execute variant calling and draw a phylogenetic tree on a bacterial strain

The steps after getting the vcf files (nextflow):

norm="./${sample}.norm"
filter="./${sample}.filter"

bcftools norm -f ${ref} \${vcf_output} -Ob -o \${norm}.bcf
bcftools filter -Oz -e "QUAL<40||DP<10||GT!='1/1'||TYPE='INDEL'" -o \${filter}.vcf.gz \${norm}.bcf 

bcftools index \${filter}.vcf.gz

bcftools consensus -f ${ref} \${filter}.vcf.gz > consensus.fasta

After that, I concatenate all the consensus fastas to one multifasta containing all my samples (35 samples)

My problem is when I try to execute multiple alignment via muscle, clustalo,mafft... all of these programs run hours (more than 5h) without creating output.

I tried also via Mega program and the program crash at some point. I suspect my multifasta too big for that (each sample have ~ 2 millions bp).

I would glad to get some help

Thank you