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metaGmetapop / metapop

A pipeline for the macro- and micro-diversity analyses and visualization of metagenomic-derived populations
MIT License
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Error in micro diversity visualization #5

Open ZongzhiWu opened 3 years ago

ZongzhiWu commented 3 years ago

Error: The input file of fuction "fread" is codon_position_summary.tsv in Rscript, while there is no such file in metapop_microdiversity. Log: Error in fread("metapop_microdiversity/codon_position_summary.tsv", sep = "\t") : File 'metapop_microdiversity/codon_position_summary.tsv' does not exist or is non-readable. getwd()=='/lustre/home/liutang/41groundwater/05diversity/02metapop_test1' Calls: metapop_microdiv_viz -> fread Execution halted Rscript:

# SNP positions in codons code
  codon_pos_count <- fread("metapop_microdiversity/codon_position_summary.tsv", sep = "\t")

Microdiversity Output: -rw-rw-r-- 1 23K Dec 28 20:22 fixation_index.tsv -rw-rw-r-- 1 52K Dec 28 20:21 global_codon_position_summary.tsv -rw-rw-r-- 1 212K Dec 28 20:21 global_contig_microdiversity.tsv -rw-rw-r-- 1 2.2M Dec 28 20:21 global_gene_microdiversity.tsv -rw-rw-r-- 1 1.4M Dec 28 20:21 global_raw_microdiversity_data_snp_loci_only.tsv -rw-rw-r-- 1 52K Dec 28 20:22 local_codon_position_summary.tsv -rw-rw-r-- 1 211K Dec 28 20:22 local_contig_microdiversity.tsv -rw-rw-r-- 1 2.2M Dec 28 20:22 local_gene_microdiversity.tsv -rw-rw-r-- 1 1.2M Dec 28 20:22 local_raw_microdiversity_data_snp_loci_only.tsv

Thexiyang commented 3 years ago

Did you solve this issue? @ZongzhiWu

metaGmetapop commented 3 years ago

Sorry for the delay in response. We are working on updating the code with python in the front end. We are working on releasing the new version. These errors should be fixed in the newest version. More to come soon.