HATCHet fails with new version of bcftools 1.21

[simozacca]

The new version of bcftools 1.21 requires to specify that the AD field is in INFO in the query command used by HATCHet in

https://github.com/raphael-group/hatchet/blob/783058042cc3ef78b3f46ff7478edb5b6dfd9f44/src/hatchet/utils/count_alleles.py#L236C22-L236C53

Specifically, the following command of bcftools called by HATCHet fails and hang with the new version of bcftools 1.21:

bcftools mpileup ${BAM} -Ou -f ${REF} --skip-indels -a INFO/AD -q 13 -Q 13 -d 30 | bcftools query -f '%CHROM\\t%POS\\t%REF,%ALT\\t%AD\\n' -i 'SUM(AD)<=1000 & SUM(AD)>=1' > output

failing with the message:

[mpileup] 1 samples in 1 input files
Error: ambiguous filtering expression, both INFO/AD and FORMAT/AD are defined in the VCF header.

The temporary solution is to install HATCHet with a previous version of samtools/bcftools, like 1.19, after correct setting up of bioconda channells:

conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict

conda create -n hatchet hatchet "bcftools==1.19" "samtools==1.19"

In the meanwhile, @mmyers1 can we please fix this by making the bcftools command compatible, or changing bioconda recipe of HATCHet to only use a compatible version of bcftools/samtools please?

[tahashmi]

Hi, any update on this bug? For some reason, this forced command: conda create -n hatchet hatchet "bcftools==1.19" "samtools==1.19" doesn't work at my side, with some conflicts issues.
`

[RunpengLuo]

Hi, any update on this bug? For some reason, this forced command: conda create -n hatchet hatchet "bcftools==1.19" "samtools==1.19" doesn't work at my side, with some conflicts issues. `

Hi tahashmi, I've pushed the fix so it should work with default conda recipe for HATCHetv2.1.0. Please try to reinstall it (without the specific version for bcftools and samtools) and let me know if it fixes your problem. Thank you.

[tahashmi]

Hi @RunpengLuo , Thanks for this. Unfortunately due to removing and installing bcftools manually on HPC, I am having some issue with my account, hopefully it will be resolved today and then will try again.

[tahashmi]

Hi, @RunpengLuo

I have installed fresh hatchet conda env.

Issue still exists:

(hatchet) -bash-4.4$ python -m hatchet
HATCHet v2.1.0
Usage: hatchet <command> <arguments ..>

The following commands are supported:
 count-reads
 count-reads-fw
 genotype-snps
 count-alleles
 combine-counts
 combine-counts-fw
 cluster-bins
 plot-bins
 compute-cn
 plot-cn
 run
 check
 download-panel
 phase-snps
 cluster-bins-gmm
 plot-cn-1d2d
 plot-bins-1d2d
(hatchet) -bash-4.4$ vi run_1937.sh 
(hatchet) -bash-4.4$ vi hatchet_1937.ini
(hatchet) -bash-4.4$ vi hatchet_2009.ini 
(hatchet) -bash-4.4$ vi run_1937.out 
(hatchet) -bash-4.4$ vi 1937/normal_chr10_bcftools.log

[mpileup] 1 samples in 1 input files
Error: ambiguous filtering expression, both INFO/AD and FORMAT/AD are defined in the VCF header.
[mpileup] maximum number of reads per input file set to -d 1000

[RunpengLuo]

hatchet_v2.1.0_conda.yaml.zip

Hi @tahashmi, sorry for the inconvenience, I think the BioConda hasn't sync the latest commit on the main branch, and I will work on this ASAP and let you know when it is done. At the mean time, do you mind to install HATCHet directly from source, the detailed steps are shown as follows. Thank you.

0. remove previous HATCHet installed via Conda.
1. create&activate the conda environment with the attached YAML file (skip if all dependencies already installed)
   • conda env create -f hatchet_v2.1.0.conda.yaml
   • conda activate hatchet-v2.1.0
2. Download&install hatchet directly from GitHub
   • git clone https://github.com/raphael-group/hatchet.git
   • cd hatchet
   • export HATCHET_BUILD_NOEXT=1; #also works if unset.
   • module load gurobi/9.1.2; #unnecessary if using cbc solver
   • export HATCHET_COMPUTE_CN_SOLVER=gurobi; #change to cbc if cbc solver is used instead
   • pip install . #before this step, try to clean up cache as well, most likely in $HOME/.cache/pip
   • hatchet check #check all dependencies.

[tahashmi]

Thanks for the prompt reply. I can wait once you fix this issue. My hatchet workflow is already setup with default installation method, and it already took some time to setup gurobi.

[RunpengLuo]

Thanks for the prompt reply. I can wait once you fix this issue. My hatchet workflow is already setup with default installation method, and it already took some time to setup gurobi.

We have upload the Bioconda version to v2.1.1, feel free to try and let me know how it goes. Thank you.