Description
Hi,
I'm trying to run dadaist2 on macOS 14.5, but unfortunately I am unable to replicate the tutorial.
I installed dadaist2 using:
mamba create -n dadaist -c conda-forge -c bioconda dadaist2
When I run dadaist2 -i data/16S/ -o example-output -d refs/SILVA_SSU_r138_2019.RData -t 2 -m metadata.tsv --verbose, I receive this output:
`[2024-07-02 16:54:14] Ready to log in /Users/jzrapp/example-output/dadaist.log
[2024-07-02 16:54:14] dadaist2 1.3.0
[2024-07-02 16:54:14] DECIPHER Taxonomy database found: refs/SILVA_SSU_r138_2019.RData
Use of uninitialized value in concatenation (.) or string at /Users/jzrapp/miniconda/envs/dadaist2/bin/dadaist2 line 535.
[2024-07-02 16:54:14] Parameter: taxonomy-type:
[2024-07-02 16:54:14] Parameter: taxonomy-db: skip
- Input directory: data/16S/
- Output directory: example-output/
- Metadata: metadata.tsv
- Reference database: skip
- Threads: 2
- Temporary directory: /var/folders/_m/_2ckc70s5q776c448cvkx2n40000gn/T/dadaist2_mswkKi
- QC strategy: skip
[2024-07-02 16:54:14] QC: Checking quality profile with SeqFu
[2024-07-02 16:54:15] SeqFu quality truncation at (trunc-len-1 and trunc-len-2): 277 - 224
[2024-07-02 16:54:15] Checking dependencies
FATAL ERROR:
Dependency 'DECIPHER' returned non zero exit value.
Shell: echo "library(DECIPHER)" | R --no-save > /dev/null
Dadaist2 execution finished (4.00s)`
I thought there was an issue with DECIPHER, so I also tried running it with a different database dadaist2 -i data/16S/ -o example-output -d refs/silva_nr_v138_train_set.fa.gz -t 2 -m metadata.tsv --verbose
`
[2024-07-02 16:54:28] Ready to log in /Users/jzrapp/example-output/dadaist.log
[2024-07-02 16:54:28] dadaist2 1.3.0
[2024-07-02 16:54:28] Taxonomy database found: refs/silva_nr_v138_train_set.fa.gz
[2024-07-02 16:54:28] Parameter: taxonomy-type: dada2
[2024-07-02 16:54:28] Parameter: taxonomy-db: refs/silva_nr_v138_train_set.fa.gz
- Input directory: data/16S/
- Output directory: example-output/
- Metadata: metadata.tsv
- Reference database: refs/silva_nr_v138_train_set.fa.gz
- Threads: 2
- Temporary directory: /var/folders/_m/_2ckc70s5q776c448cvkx2n40000gn/T/dadaist2_2EmI4D
- QC strategy: skip
[2024-07-02 16:54:28] QC: Checking quality profile with SeqFu
[2024-07-02 16:54:28] SeqFu quality truncation at (trunc-len-1 and trunc-len-2): 277 - 224
[2024-07-02 16:54:28] Checking dependencies - RScript: R scripting front-end version 4.0.5 (2021-03-31)
- Taxonomy: dadaist2-assigntax 1.1.3
- assign-taxonomy: dadaist2-assigntax 1.1.3
- clustalo: 1.2.4
FATAL ERROR:
Dependency 'dada2 (lib)' returned non zero exit value.
Shell: echo "library(dada2)" | R --no-save > /dev/null
Dadaist2 execution finished (2.00s)
`
I am not sure what the problem is. I thought maybe some dependencies were not installed correctly, so I also tried to install dadaist2 via mamba env create --file dadaist2-1.2.5-Darwin.yaml -n dadaist2 but it failed and gave a very long list of reasons, which mostly said conflicts with any installable versions previously reported.
Do you have any idea what the issue might be, @telatin?
Thanks a lot!