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AmpliconSuite / AmpliconSuite-pipeline

A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior to running AmpliconArchitect. Previously called PrepareAA.
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reference genome path #21

Closed gneedle1 closed 1 year ago

gneedle1 commented 2 years ago

Hi! When I run prepareAA it can't find mt reference genome (GRCh38.tar). The first error I got was: Traceback (most recent call last): File "PrepareAA.py", line 505, in ref = gdir + refFnames[args.ref] TypeError: can only concatenate str (not "NoneType") to str

So I changed the refFnames array, but now I get: Traceback (most recent call last): File "PrepareAA.py", line 14, in import check_reference File "/home/gabe/PrepareAA/check_reference.py", line 12 def get_ref_fname(aa_dr_path, rname): with open(aa_dr_path + "/" + rname + "/file_list.txt") as infile:

Traceback (most recent call last): File "PrepareAA.py", line 480, in refFnames[rname] = check_reference.get_ref_fname(AA_REPO, rname) File "/home/gabe/PrepareAA/check_reference.py", line 13, in get_ref_fname with open(aa_dr_path + "/" + rname + "/file_list.txt") as infile: FileNotFoundError: [Errno 2] No such file or directory: '/home/gabe/AmpliconArchitect/data_repo//GRCh38/file_list.txt'

It seems like I should name my file differently but I am not sure. Thoughts? Thank you!

jluebeck commented 2 years ago

Hi, can you confirm that you have downloaded the data repo? If you list do ls $AA_DATA_REPO/GRCh38, do you see anything present? You can obtain it from https://datasets.genepattern.org/?prefix=data/module_support_files/AmpliconArchitect/

There are versions containing both the bwa indexed (GRCh38_indexed.tar.gz) and smaller unindexed (GRCh38.tar.gz) forms.

Please let me know if you have any questions or issues persist.

Thanks, Jens