Conda installation -- issue with header definitions when running truvari

[tdelhomme]

Version :

truvari conda last version: v0.1.2018.08.10

Describe the bug :

I tested truvari on same vcf for base and comparison, I get this error from the log file:

2022-07-26 16:10:52,652 [INFO] Running /home/tdelhomme/.conda/envs/truvari/bin/truvari -b PAM56393_1_0_sort.vcf.gz -c PAM56393_1_0_sort.vcf.gz -f /g/strcombio/fsupek_cancer3/own_genomes_tumors/from_CNAG/Osteosarcoma_project/ONT/Tumor/hg38.fa -o test_output_dir
2022-07-26 16:10:52,652 [INFO] Params:
{
    "pctovl": 0.0, 
    "sizemax": 50000, 
    "includebed": null, 
    "sizefilt": 30, 
    "cSample": null, 
    "reference": "/g/strcombio/fsupek_cancer3/own_genomes_tumors/from_CNAG/Osteosarcoma_project/ONT/Tumor/hg38.fa", 
    "no_ref": false, 
    "multimatch": false, 
    "comp": "PAM56393_1_0_sort.vcf.gz", 
    "typeignore": false, 
    "refdist": 500, 
    "pctsize": 0.7, 
    "passonly": false, 
    "base": "PAM56393_1_0_sort.vcf.gz", 
    "pctsim": 0.7, 
    "gtcomp": false, 
    "giabreport": false, 
    "debug": false, 
    "output": "test_output_dir", 
    "bSample": null, 
    "sizemin": 50
}
2022-07-26 16:10:52,709 [INFO] Creating call interval tree for overlap search
2022-07-26 16:10:53,189 [ERROR] Unable to parse comparison vcf file. Please check header definitions
2022-07-26 16:10:53,190 [ERROR] Specific error: "IntervalTree: Null Interval objects not allowed in IntervalTree: Interval(264856, 264856, 264856)"

To Reproduce :

truvari -b PAM56393_1_0_sort.vcf.gz -c PAM56393_1_0_sort.vcf.gz -f hg38.fa -o test_output_dir

Expected behavior :
Output folder as described in the documentation

Example Data :

Additional context :
Maybe the conda is not updated because the bench command (and probably the others) is not available

[ACEnglish]

This is a very old version which I didn't even release onto conda. I'm unfamiliar with conda and had help getting the newer versions auto-deployed onto bioconda, so I'm not sure what's happening here.

But digging in a little bit, I can see that v3.4 is out there:
https://anaconda.org/bioconda/truvari

And it looks like the v0.1.* (which, again, I didn't make) is somehow considered the latest version? https://anaconda.org/bioconda/truvari/labels

Did you install off the main label instead of this old/unsupported one? e.g. conda install -c bioconda truvari and not conda install -c bioconda/label/cf201901 truvari?

[tdelhomme]

I used conda install -c bioconda truvari, would you suggest to install it not using conda?

[tdelhomme]

Installing into a conda environment using the latest version works correctly on the same files, I think the conda version is obselete. Could you mention it in the documentation for other users? thanks!
Here are the commands that can be used to create the environment:

# create and go inside the environment
conda create --name truvari python=3.9
conda activate truvari

# install last stable truvari and run a test
python3 -m pip install truvari
truvari -b PAM56393_1_0_sort.vcf.gz -c PAM56393_1_0_sort.vcf.gz -f hg38.fa -o test_output_dir

# go outside the environment 
conda deactivate truvary

[ACEnglish]

Thanks for following up on this. I've referenced your comment in updated documentation on the wiki. When I get time, I'll try to figure out how to sort out the old release on conda.