Status code: 502 Reason: Bad Gateway

[lakishadavid]

I'm using lineage==4.3.1. I use it in my code block as I typically do, but I'm now getting a Bac Gateway error message.

This is my code block:

from lineage import Lineage

# https://snps.readthedocs.io/en/stable/
# https://lineage.readthedocs.io/en/stable/

# initialize Lineage object
l = Lineage(
    output_dir = output_dir,
    resources_dir = f"{references_directory}",
    parallelize = True,
    processes = 8
)

# initialize dictionary variables
individuals_dict = {}
sex_determination = {}
# initialize count variable
count = 0

directory_path = os.path.join(data_directory, "opensnp_data")
file_pattern = os.path.join(directory_path, "*.ancestry.txt")
opensnp_files = glob.glob(file_pattern)
len_opensnp_files = len(opensnp_files)

# Path for the sex determination TSV file
sex_determination_file = os.path.join(results_directory, "opensnp_sex_determination.tsv")

# Create a lineage individual object for each Ancestry file
# Loop through file names and create individuals_dict
for file_path in opensnp_files:
    count = count + 1
    filename = os.path.basename(file_path)
    username = filename.split("_")[0]

    print(f"Processing file {count} in {len_opensnp_files}: {username}")
    
    # print(username)
    # assign_par_snps (bool) – assign PAR SNPs to the X and Y chromosomes
    # with = True, error message: Chromosome PAR not remapped; removing chromosome from SNPs for consistency
    # deduplicate_MT_chrom (bool) – deduplicate alleles on MT; see SNPs.heterozygous_MT
    # deduplicate_XY_chrom (bool or str) – deduplicate alleles in the non-PAR regions of X and Y for males
    # Why message: Chromosome PAR not remapped; removing chromosome from SNPs for consistency
    individuals_dict[username] = l.create_individual(username, 
                                                     file=file_path,
                                                     assign_par_snps=True,
                                                     deduplicate_MT_chrom=True,
                                                     deduplicate_XY_chrom=True)
    
    if individuals_dict[username].build != 38:
        individuals_dict[username].remap(38)
        
    individuals_dict[username].sort()
    individuals_dict[username].to_tsv(os.path.join(output_dir, f"{username}.tsv"))

    # Determine sex
    # heterozygous_x_snps_threshold (float) – percentage heterozygous X SNPs; above this threshold, Female is determined
    # y_snps_not_null_threshold (float) – percentage Y SNPs that are not null; above this threshold, Male is determined
    # chrom ({“X”, “Y”}) – use X or Y chromosome SNPs to determine sex
    # Returns ‘Male’ or ‘Female’ if detected, else empty str
    sex_determination[username] = individuals_dict[username].determine_sex(
        heterozygous_x_snps_threshold=0.03, 
        y_snps_not_null_threshold=0.3, 
        chrom='X'
        )
    # print(sex_determination[username])

# Save sex determinations to TSV
with open(sex_determination_file, 'w', newline='') as file:
    writer = csv.writer(file, delimiter='\t')
    writer.writerow(['Username', 'Sex'])
    for username, sex in sex_determination.items():
        writer.writerow([username, sex])

print("All files processed.")

And this is the error message

Processing file 1 in 3: user6579
Request failed for /variation/v0/refsnp/34943879: Status code: 502 Reason: Bad Gateway
---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Cell In[10], [line 43](vscode-notebook-cell:?execution_count=10&line=43)
     [35](vscode-notebook-cell:?execution_count=10&line=35) print(f"Processing file {count} in {len_opensnp_files}: {username}")
     [37](vscode-notebook-cell:?execution_count=10&line=37) # print(username)
     [38](vscode-notebook-cell:?execution_count=10&line=38) # assign_par_snps (bool) – assign PAR SNPs to the X and Y chromosomes
     [39](vscode-notebook-cell:?execution_count=10&line=39) # with = True, error message: Chromosome PAR not remapped; removing chromosome from SNPs for consistency
     [40](vscode-notebook-cell:?execution_count=10&line=40) # deduplicate_MT_chrom (bool) – deduplicate alleles on MT; see SNPs.heterozygous_MT
     [41](vscode-notebook-cell:?execution_count=10&line=41) # deduplicate_XY_chrom (bool or str) – deduplicate alleles in the non-PAR regions of X and Y for males
     [42](vscode-notebook-cell:?execution_count=10&line=42) # Why message: Chromosome PAR not remapped; removing chromosome from SNPs for consistency
---> [43](vscode-notebook-cell:?execution_count=10&line=43) individuals_dict[username] = l.create_individual(username, 
     [44](vscode-notebook-cell:?execution_count=10&line=44)                                                  file=file_path,
     [45](vscode-notebook-cell:?execution_count=10&line=45)                                                  assign_par_snps=True,
     [46](vscode-notebook-cell:?execution_count=10&line=46)                                                  deduplicate_MT_chrom=True,
     [47](vscode-notebook-cell:?execution_count=10&line=47)                                                  deduplicate_XY_chrom=True)
     [49](vscode-notebook-cell:?execution_count=10&line=49) if individuals_dict[username].build != 38:
     [50](vscode-notebook-cell:?execution_count=10&line=50)     individuals_dict[username].remap(38)

File [~/.venv/lib/python3.10/site-packages/lineage/__init__.py:104](https://vscode-remote+wsl-002bubuntu-002d22-002e04.vscode-resource.vscode-cdn.net/home/lakishadavid/anthropology_genetic_genealogy/~/.venv/lib/python3.10/site-packages/lineage/__init__.py:104), in Lineage.create_individual(self, name, raw_data, **kwargs)
    [101](https://vscode-remote+wsl-002bubuntu-002d22-002e04.vscode-resource.vscode-cdn.net/home/lakishadavid/anthropology_genetic_genealogy/~/.venv/lib/python3.10/site-packages/lineage/__init__.py:101) if "resources_dir" not in kwargs:
    [102](https://vscode-remote+wsl-002bubuntu-002d22-002e04.vscode-resource.vscode-cdn.net/home/lakishadavid/anthropology_genetic_genealogy/~/.venv/lib/python3.10/site-packages/lineage/__init__.py:102)     kwargs["resources_dir"] = self._resources_dir
--> [104](https://vscode-remote+wsl-002bubuntu-002d22-002e04.vscode-resource.vscode-cdn.net/home/lakishadavid/anthropology_genetic_genealogy/~/.venv/lib/python3.10/site-packages/lineage/__init__.py:104) return Individual(name, raw_data, **kwargs)

File [~/.venv/lib/python3.10/site-packages/lineage/individual.py:61](https://vscode-remote+wsl-002bubuntu-002d22-002e04.vscode-resource.vscode-cdn.net/home/lakishadavid/anthropology_genetic_genealogy/~/.venv/lib/python3.10/site-packages/lineage/individual.py:61), in Individual.__init__(self, name, raw_data, **kwargs)
     [58](https://vscode-remote+wsl-002bubuntu-002d22-002e04.vscode-resource.vscode-cdn.net/home/lakishadavid/anthropology_genetic_genealogy/~/.venv/lib/python3.10/site-packages/lineage/individual.py:58) init_args = self._get_defined_kwargs(SNPs, kwargs)
...
    [905](https://vscode-remote+wsl-002bubuntu-002d22-002e04.vscode-resource.vscode-cdn.net/home/lakishadavid/anthropology_genetic_genealogy/~/.venv/lib/python3.10/site-packages/snps/snps.py:905)     # we'll pick the first one to decide which chromosome this PAR will be assigned to
    [906](https://vscode-remote+wsl-002bubuntu-002d22-002e04.vscode-resource.vscode-cdn.net/home/lakishadavid/anthropology_genetic_genealogy/~/.venv/lib/python3.10/site-packages/snps/snps.py:906)     merged_id = "rs" + response["merged_snapshot_data"]["merged_into"][0]
    [907](https://vscode-remote+wsl-002bubuntu-002d22-002e04.vscode-resource.vscode-cdn.net/home/lakishadavid/anthropology_genetic_genealogy/~/.venv/lib/python3.10/site-packages/snps/snps.py:907)     logger.info(f"SNP id {rsid} has been merged into id {merged_id}")

TypeError: argument of type 'NoneType' is not iterable