Error in run of 732 genomes #180
Description
Hlw,
I am facing a few problems:
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I have 732 genomes and 10 of my own with a reference. All of these are assembled. When i am running parsnp, it’s showing failed. First it gives me a tree but no value. Other times failed except one time when it gave me a tree of only 20-25 genomes.
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Then i went through quast Qc, and saw rhat qc are not good enough in few genomes. Like few are not good at total legnth, few for contigs, few for N50, and few for N based pair.
So i have gone through few tactics. I have checked with only good QC of 20-30 genomes and it gives me tree.
Im second time, i have gone through only bad Qc genome of contigs, N50,L50 of 20-30 genomes, it also gives tree.
However, when i have run a few gemomes of bad N 100 base, it does not give me tree.
So i decided to exclude these. After excluding, i have run around 680 genomes from 732,,but it didnot give me tree. Direct terminated.
So how can i resolve these issue. What coulde be the error.
Let me know please