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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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1. Suitable for the analysis of ssDNA viral population? 2. FileNotFoundError: 'MetaPop/09.Linked_SNPs/range_131_reads.txt' #24

Open ChenTianYi99 opened 1 year ago

ChenTianYi99 commented 1 year ago

Hi, Thanks for your pipeline for macro- and microdiversity analyses. It seems very helpful to my research. However, i have two major issues which need to be addressed.

  1. I noticed that this pipeline may usually work best for bacteria, archaea, and dsDNA phages. I was wondering if Metapop would be also applicable in analysis of ssDNA viral communities.

  2. I have tried to run an analysis on a few of my samples, but i encountered a problem when the software ran to the "09.Linked_SNPs" step: FileNotFoundError: [Errno 2] No such file or directory: 'MetaPop/09.Linked_SNPs/range_131_reads.txt'.

The code for the analysis is as follows (the format of used files correspond to that of the examples): metapop --input_samples /gpfs/share/home/2101212877/NSBD_virome/abundance/test_sorted_bam \ --reference /gpfs/share/home/2101212877/NSBD_virome/cdhit/combine/cdhit_fa/ \ --norm /gpfs/share/home/2101212877/NSBD_virome/abundance/sequence_stat_test.txt \ --threads 28

Looking forward to your reply. Thanks in advance.

Sincerely

arisandz commented 1 year ago

Hi! Im having the same error, could you be able to solve it? Thanks in advance

Ql-cy commented 1 year ago

Hi, have you solved this problem? My data is not ssDNA, but I also encountered this error: FileNotFoundError: [Errno 2] No such file or directory: 'MetaPop/09.Linked_SNPs/range_9_reads.txt'

Ql-cy commented 1 year ago

Hi, have you solved this problem? My data is not ssDNA, but I also encountered this error: FileNotFoundError: [Errno 2] No such file or directory: 'MetaPop/09.Linked_SNPs/range_9_reads.txt'

ChenTianYi99 commented 1 year ago

Sorry, i have not solved the problem. Maybe you could try instrain (https://github.com/MrOlm/inStrain) instead to calculate microdiversity.

Best Tianyi Chen