Work with 1000 genomes

[OrsonMM]

Dear team parsnp

I have a directory with 1320 assemblies genomes. I run the command

parsnp -g ../../DB_all/genome_reference_VP/CP007004.gbk,../../DB_all/genome_reference_VP/CP007005.gbk -d ../../Data/all_v_p_for_parsnp/ -p 6

It works well but only aligment 73 genomes.

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For detailed documentation please see --> http://harvest.readthedocs.org/en/latest

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SETTINGS: |-refgenome: ../../DB_all/genome_reference_VP/CP007004.gbk.fna |-aligner: libMUSCLE |-seqdir: ../../Data/all_v_p_for_parsnp/ |-outdir: /home/ubuntu/Results/all_1327_parsnp/P_2018_06_11_185050006955 |-OS: Linux |-threads: 6

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-->Reading Genome (asm, fasta) files from ../../Data/all_v_p_for_parsnp/.. |->[OK] -->Reading Genbank file(s) for reference (.gbk) ../../DB_all/genome_reference_VP/CP007004.gbk,../../DB_all/genome_reference_VP/CP007005.gbk.. |->[OK] -->Calculating MUMi.. |->[OK] -->Running Parsnp multi-MUM search and libMUSCLE aligner..

|->[OK] -->Running PhiPack on LCBs to detect recombination.. |->[SKIP] -->Reconstructing core genome phylogeny.. |->[OK] -->Creating Gingr input file.. |->[OK] -->Calculating wall clock time.. |->Aligned 73 genomes in 1.00 hours

<<Parsnp finished! All output available in /home/ubuntu/Results/all_1327_parsnp/P_2018_06_11_185050006955>>

Validating output directory contents... 1)parsnp.tree: newick format tree [OK] 2)parsnp.ggr: harvest input file for gingr (GUI) [OK] 3)parsnp.xmfa: XMFA formatted multi-alignment [OK]

[slvrshot]

You you need to pass -C to run all the genomes