I am trying to use the read extractor tool in a customized script for extracting a specific taxonomy rank.
I found that if it does have an space in its name this Taxonomy name is separated in “words”. For example, if I want to extract the reads classified as “Weivirus-like virus sp.”:
/home/human/megan/tools/read-extractor -v -i Pool1-bats_merged_ok_v2.rma -c Taxonomy -n Weivirus-like virus sp. -b -o ./families/Pool1-families/Pool1-contigs-Weivirus-like-sp.fasta
ReadExtractorTool - Extracts reads from a DAA or RMA file by classification
Input and Output
–classNames: Weivirus-like virus sp.
Version MEGAN Community Edition (version 6.25.3, built 15 Sep 2023)
Author(s) Daniel H. Huson
Copyright (C) 2023 Daniel H. Huson. This program comes with ABSOLUTELY NO WARRANTY.
Java version: 20.0.2; max memory: 7.8G
Loading ncbi.map: 2,396,736
Loading ncbi.tre: 2,396,740
Warning: unknown class: ‘Weivirus-like’
Warning: unknown class: ‘virus’
Warning: unknown class: ‘sp.’
Processing file: Pool1-bats_merged_ok_v2.rma
Extracting by Taxonomy
Writing to: ./families/Pool1-families/Pool1-contigs-Weivirus-like-sp.fasta
Reads extracted: 0
Total time: 4.1s
Peak memory: 0 of 7.8G
Same output if I try putting " " or ’ ’ in the Taxonomy name option (p.e.: /home/human/megan/tools/read-extractor -v -i Pool1-bats_merged_ok_v2.rma -c Taxonomy -n “Weivirus-like virus sp.” -b -o ./families/Pool1-families/Pool1-contigs-Weivirus-like-sp.fasta)
Is there a way to fix this? I need it to read the Taxonomy name without separating it with spaces
Thanks in advance!