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View Code? Open in Web Editor NEWWES HLA Typing based on multiple alternative tools
License: MIT License
WES HLA Typing based on multiple alternative tools
License: MIT License
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!
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
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?
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