lkuchenb/multihla

WES HLA Typing based on multiple alternative tools

multihla's Issues

Error No rule to produce ....

It was not possible for me to run the code on the HPC at my institution. I replicated all steps in the README page, even naming the .tsv file the same as in the example. Unfortunately, an error occurred:

I ran the following command in the hla_typing directory with "(snakemake)" at the start of the command line.
snakemake --use-conda --use-singularity --cores 1 typing/dataset_1.all.multihla

~/miniconda3/envs/snakemake/lib/python3.11/site-packages/google/protobuf/internal/api_implementation.py:110: UserWarning: Selected implementation cpp is not available.
warnings.warn(
Building DAG of jobs...
MissingRuleException:
No rule to produce typing/dataset_1.all.multihla (if you use input functions make sure that they don't raise unexpected exceptions).

Next to this, I got an error using exactly the same code as in the README page because the number of cores needed to be noted.
Can you help me?

Kind regards,
Adam

HLA typing on Nanopore and PacBio reads

Hello @lkuchenb ,

I wanted to ask if this tool can handle fastq reads from Nanopore or PacBio. With a different aligner I can run xHLA and HLA-LA. My question is mostly about Optitype. Will it be able to handle long reads?

AttributeError: module 'pulp' has no attribute 'list_solvers'. Did you mean: 'listSolvers'?

Hi, I wanted to make sure I'm going about this correctly? I have placed the .fastq.gz files in the fastq folder, the dataset.tsv file that defines the set of samples, nothing in the ref folder since I wanted to go with the default human genome references (?), and ran the workflow. However, running snakemake --use-conda --use-singularity typing/dataset.all.multihla resulted in the following error:
Traceback (most recent call last):
File "/Users/mewu/opt/anaconda3/envs/snakemake/lib/python3.12/site-packages/snakemake/cli.py", line 2037, in main
parser, args = parse_args(argv)
^^^^^^^^^^^^^^^^
File "/Users/mewu/opt/anaconda3/envs/snakemake/lib/python3.12/site-packages/snakemake/cli.py", line 1629, in parse_args
parser = get_argument_parser()
^^^^^^^^^^^^^^^^^^^^^
File "/Users/mewu/opt/anaconda3/envs/snakemake/lib/python3.12/site-packages/snakemake/cli.py", line 770, in get_argument_parser
lp_solvers = pulp.list_solvers(onlyAvailable=True)
^^^^^^^^^^^^^^^^^
AttributeError: module 'pulp' has no attribute 'list_solvers'. Did you mean: 'listSolvers'?

Please advise. Thank you!