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roseorenbuch / arcasHLA-quant

GNU General Public License v3.0
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Issues with arcasHLA customize & quant #1

Closed srdea93 closed 3 years ago

srdea93 commented 3 years ago

Hi all,

I've been trying to run some of my samples through the arcasHLA toolkit and I've been encountering some errors when attempting to run my samples using both the customize and quant steps. For both, I've received the following traceback:

Traceback (most recent call last):
  File "/rnd/users/sdea/XXX/software/arcasHLA/scripts/customize.py", line 299, in <module>
    build_custom_reference(subject, genotype, args.grouping, args.transcriptome, temp)
  File "/rnd/users/sdea/XXX/software/arcasHLA/scripts/customize.py", line 77, in build_custom_reference
    dummy_HLA_dict = SeqIO.to_dict(SeqIO.parse(dummy_HLA_fa, 'fasta')) 
  File "/home/sdea/anaconda3/envs/arcashla_env/lib/python3.6/site-packages/Bio/SeqIO/__init__.py", line 627, in parse
    i = iterator_generator(handle)
  File "/home/sdea/anaconda3/envs/arcashla_env/lib/python3.6/site-packages/Bio/SeqIO/FastaIO.py", line 181, in __init__
    super().__init__(source, alphabet=alphabet, mode="t", fmt="Fasta")
  File "/home/sdea/anaconda3/envs/arcashla_env/lib/python3.6/site-packages/Bio/SeqIO/Interfaces.py", line 42, in __init__
    self.stream = open(source, "r" + mode)
FileNotFoundError: [Errno 2] No such file or directory: '/rnd/users/sdea/XXX/software/arcasHLA/scripts/../dat/ref/GRCh38.chr6.HLA.fasta'

Following the path to where this file is supposed to be in the arcasHLA directory shows that there is no such file present. Am I missing a step prior to generate this file?

Additionally, the "wget https://www.dropbox.com/s/pcmwc4o1dxw7owk/arcasHLA-quant_reference.zip" returns an error stating that the dropbox location has since been deleted.

Thank you for your time!

IoanFilip2 commented 3 years ago

Thank you for your interest in our tool. Please note that we have updated the /dat/ref/ folder in github to include the missing fasta files. Please use the customization step with the --chr6 flag only. With these files added, you should not need the arcasHLA-quant_reference.zip file any longer. Let us know if you encounter other issues. The github README will be updated for arcas-quant once we vet the repo through the peer review process.