classifiedRefiner and extract errors！ #168
Description
Hello author, I am very interested in Metabuli. I have successfully run Metabuli on the ref-virus database and got the results. I want to run classifiedRefiner and extract and encounter the following error.
And my Metabuli is built on github source code
git clone --recurse-submodules https://github.com/steineggerlab/Metabuli.git
cmake -DCMAKE_BUILD_TYPE=Release .. -DCMAKE_INSTALL_PREFIX=/home/zhangwenda/biosoft/virus/Metabuli/
make -j 16 ;
make install
Hope for your help, @thanks！
metabuli classifiedRefiner SRR25775928.unmapped_classifications.tsv ~/database/taxonomy/ --threads 60 --remove-unclassified 1
classifiedRefiner SRR25775928.unmapped_classifications.tsv /home/zhangwenda/database/taxonomy/ --threads 60 --remove-unclassified 1
Metabuli Version (commit): b9ab2a3
Remove unclassified reads true
Exclude taxId as well as its children
Select taxId as well as its children
Select columns with number, (7:full lineage, generated if absent)
Make report of refined classification file false
Adjust classification to the specified rank
0: without higher rank, 1: with higher rank, 2: separate file for higher rank classification 0
Threads 60
Min. sequence similarity score 0
Loading nodes file ... Done, got 2711630 nodes
Loading merged file ... Done, added 94921 merged nodes.
Loading names file ... Done
Init computeSparseTable ...Done
Write refined classification results to:
SRR25775928.unmapped_classifications_refined.tsv
Segmentation fault (core dumped)
metabuli extract --taxonomy-path ~/database/taxonomy/ --outdir ./ ../../5.unmapping/SRR25775928.unmapped.R1.fq.gz ../../5.unmapping/SRR25775928.unmapped.R2.fq.gz SRR25775928.unmapped_classifications.tsv ~/database/virus-db/metabuli_db/refvirus/ --tax-id -1
usage: metabuli extract <i:query file(s)> <i:read-by-read result> <i:database directory> [options]
By Jaebeom Kim jbeom0731@gmail.com
options: misc:
--taxonomy-path STR Directory where the taxonomy dump files are stored [/home/zhangwenda/database/taxonomy/]
--seq-mode INT Single-end: 1, Paired-end: 2, Long read: 3 [2]
--tax-id INT Tax. ID of clade. -1 for unclassified reads [0]
--extract-format INT 0: original format, 1: FASTA, 2: FASTQ [0]
--outdir STR Output directory [./]
references:
Error in argument --tax-id