# =============================================================================
# Setup and Data Extraction
# =============================================================================
import os
import sys
import pandas as pd
import numpy as np
from pyspark.sql import functions as F
from pyspark.sql import SparkSession
from scipy.stats import fisher_exact
from statsmodels.stats.multitest import multipletests
import matplotlib.pyplot as plt
import seaborn as sns
from tqdm.auto import tqdm

pd.set_option('display.max_colwidth', None)
pd.set_option('display.max_rows', 20)

# Initialize Spark session
try:
    spark = SparkSession.builder.getOrCreate()
except Exception as e:
    print(f"Standard session creation failed, falling back to managed utils. Error: {e}")
    sys.path.append('/opt/conda/lib/python3.13/site-packages')
    from berdl_notebook_utils.setup_spark_session import get_spark_session
    spark = get_spark_session()

/home/hmacgregor/.local/lib/python3.13/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html
  from .autonotebook import tqdm as notebook_tqdm

Standard session creation failed, falling back to managed utils. Error: [PACKAGE_NOT_INSTALLED] grpcio-status >= 1.48.1 must be installed; however, it was not found.

# =============================================================================
# Extract High‑Quality Environmental MAGs
# =============================================================================
genomes = spark.table("kescience_mgnify.genome").filter(
    (F.col("completeness") >= 90.0) & 
    (F.col("contamination") <= 5.0)
)

metal_amr = spark.table("kescience_mgnify.gene_amr").filter(
    F.col("element_subtype") == "METAL"
).cache()

mag_metal_diversity = metal_amr.groupBy("genome_id").agg(
    F.countDistinct("amr_class").alias("n_metal_types")
)

biomes = spark.table("kescience_mgnify.biome").select("biome_id", "biome_name", "biome_lineage")

mag_master_spark = genomes.join(
    mag_metal_diversity, on="genome_id", how="left"
).fillna({"n_metal_types": 0}).join(
    biomes, on="biome_id", how="inner"
).filter(
    ~F.lower(F.col("biome_lineage")).like("%host-associated%")
).cache()

env_mags_spark = mag_master_spark  # already filtered
print(f"Extracted {env_mags_spark.count()} high-quality environmental MAGs.")

Extracted 30497 high-quality environmental MAGs.

# =============================================================================
# Feature Integration & Cross‑Validation Split
# =============================================================================
quality = spark.table("kescience_mgnify.genome").select(
    "genome_id", 
    F.col("completeness").alias("qc_completeness"),
    F.col("contamination").alias("qc_contamination")
)

cazy = spark.table("kescience_mgnify.genome_cazy").groupBy("genome_id").agg(
    F.countDistinct("cazy_family").alias("feat_carbon_versatility")
)

mags_complete_spark = env_mags_spark \
    .join(quality, "genome_id", "left") \
    .join(cazy, "genome_id", "left") \
    .fillna(0)

# Split into discovery (70%) and validation (30%) sets
discovery_mags, validation_mags = mags_complete_spark.randomSplit([0.7, 0.3], seed=42)
discovery_mags.cache()
validation_mags.cache()

print(f"Discovery Set: {discovery_mags.count()} MAGs")
print(f"Validation Set: {validation_mags.count()} MAGs")

Discovery Set: 21474 MAGs
Validation Set: 9023 MAGs

# =============================================================================
# Comprehensive T4SS Engine Definition (Discovery Set Only)
# =============================================================================
# Use a broad set of markers to capture canonical T4SS and conjugative systems.
t4ss_markers = [
    "COG0741", "COG3504", "COG3505", "COG3846",  # VirB4, VirB6, VirB8, VirB9
    "COG3451", "COG3842",                         # VirB10, VirB11
    "VirB4", "VirD4", "TraI", "TraD", "TrwB", "TraG"
]

t4ss_condition = F.lit(False)
for marker in t4ss_markers:
    t4ss_condition = t4ss_condition | F.col("eggnog_ogs").contains(marker)
t4ss_condition = t4ss_condition | F.lower(F.col("description")).rlike(
    "type iv secretion|conjugal transfer|virb|virb4|virb6|virb8|virb9|virb10|virb11|vird4|trai|trad|trwb|trag"
)

hgt_engine_df = spark.table("kescience_mgnify.gene_eggnog") \
    .join(discovery_mags.select("genome_id"), on="genome_id", how="inner") \
    .filter(t4ss_condition) \
    .select("genome_id").distinct() \
    .withColumn("has_t4ss_engine", F.lit(1)).cache()

total_discovery_mags = discovery_mags.count()
total_t4ss_mags = hgt_engine_df.count()
print(f"Found {total_t4ss_mags} T4SS‑positive genomes out of {total_discovery_mags} in the Discovery set.")

Found 5958 T4SS‑positive genomes out of 21474 in the Discovery set.

# =============================================================================
# Curated Set of HGT‑Associated Accessory Traits (Discovery Set)
# =============================================================================
# Instead of using an FDR‑selected list (which collapses after COG0741 exclusion),
# we define a priori a set of traits known to be associated with horizontal gene transfer.
hgt_keywords = [
    "transposase", "integrase", "recombinase", "conjug",
    "plasmid", "mobil", "toxin", "antitoxin",
    "resistance", "heavy metal", "phage", "capsid", "resolvase"
]

# Build condition
hgt_condition = F.lit(False)
for kw in hgt_keywords:
    hgt_condition = hgt_condition | F.lower(F.col("description")).contains(kw)

hgt_traits = (
    spark.table("kescience_mgnify.gene_eggnog")
    .join(discovery_mags.select("genome_id"), on="genome_id", how="inner")
    .filter(F.col("description") != "-")
    .filter(hgt_condition)
    .filter(~F.lower(F.col("description")).rlike("ribosom|trna|translation"))
    .filter(~F.col("eggnog_ogs").contains("COG0741"))  # exclude intrinsic GH23
    .select("description")
    .distinct()
)

mobile_traits_list = [row.description for row in hgt_traits.collect()]
print(f"Curated set of {len(mobile_traits_list)} HGT‑associated accessory traits.")

Curated set of 2146 HGT‑associated accessory traits.

# =============================================================================
# Count Mobile Traits in Validation Set
# =============================================================================
val_mobile_counts = spark.table("kescience_mgnify.gene_eggnog") \
    .join(validation_mags.select("genome_id"), on="genome_id", how="inner") \
    .filter(F.col("description").isin(mobile_traits_list)) \
    .groupBy("genome_id").agg(F.countDistinct("description").alias("Mobile_Trait_Count"))

validation_pdf = validation_mags.select(
    "genome_id", "feat_carbon_versatility", "length", "qc_completeness", "qc_contamination", "biome_id", "lineage"
).join(val_mobile_counts, on="genome_id", how="left").fillna({"Mobile_Trait_Count": 0}).toPandas()

validation_pdf['length_mb'] = validation_pdf['length'] / 1_000_000.0
validation_pdf['Mobile_Trait_Density'] = validation_pdf['Mobile_Trait_Count'] / validation_pdf['length_mb']
validation_pdf['CAZy_Density'] = validation_pdf['feat_carbon_versatility'] / validation_pdf['length_mb']

print(f"Validation set prepared: {len(validation_pdf)} MAGs with mobile trait counts.")

Validation set prepared: 9023 MAGs with mobile trait counts.

# =============================================================================
# Genome‑Wide Synteny Scan: T4SS vs. CAZy (Excluding Intrinsic GH23)
# =============================================================================
gene_spatial = spark.table("kescience_mgnify.gene").select(
    "gene_id", "genome_id", "contig_id",
    F.col("start").alias("start_pos"), F.col("end").alias("end_pos")
)

# T4SS genes (broad definition, includes COG0741)
t4ss_genes_all = spark.table("kescience_mgnify.gene_eggnog") \
    .join(env_mags_spark.select("genome_id"), on="genome_id", how="inner") \
    .filter(t4ss_condition) \
    .select("genome_id", "gene_id") \
    .join(gene_spatial, on=["genome_id", "gene_id"])

# CAZy genes, excluding those annotated with COG0741
cazy_genes_all = spark.table("kescience_mgnify.gene_eggnog") \
    .join(env_mags_spark.select("genome_id"), on="genome_id", how="inner") \
    .filter(F.col("cazy").isNotNull() & (F.col("cazy") != "-")) \
    .filter(~F.col("eggnog_ogs").contains("COG0741")) \
    .select("genome_id", "gene_id", F.explode(F.split(F.col("cazy"), ",")).alias("cazy_family")) \
    .join(gene_spatial, on=["genome_id", "gene_id"])

# Join on same contig and compute distance
synteny_all = t4ss_genes_all.alias("t4").join(
    cazy_genes_all.alias("cz"),
    (F.col("t4.genome_id") == F.col("cz.genome_id")) & 
    (F.col("t4.contig_id") == F.col("cz.contig_id"))
).withColumn(
    "distance_bp",
    F.greatest(F.lit(0), 
               F.greatest(F.col("t4.start_pos"), F.col("cz.start_pos")) - 
               F.least(F.col("t4.end_pos"), F.col("cz.end_pos")))
).filter(F.col("distance_bp") <= 10000).cache()

synteny_stats = synteny_all.groupBy("cazy_family").agg(
    F.countDistinct("t4.genome_id").alias("n_genomes_syntenic"),
    F.countDistinct("t4.contig_id").alias("n_contigs_syntenic"),
    F.round(F.avg("distance_bp"), 1).alias("avg_distance_bp")
).orderBy(F.desc("n_genomes_syntenic"))

print(f"Genome‑wide synteny scan complete. Found {synteny_stats.count()} CAZy families physically linked to T4SS (≤10 kb).")

Genome‑wide synteny scan complete. Found 92 CAZy families physically linked to T4SS (≤10 kb).

# =============================================================================
# Top CAZy Families Physically Linked to T4SS
# =============================================================================
display(synteny_stats.limit(5).toPandas())

# =============================================================================
# Biome Enrichment of Syntenic GT2/T4SS Loci
# =============================================================================
target_family = "GT2"
syntenic_genomes = synteny_all.filter(F.col("cazy_family") == target_family) \
    .select("t4.genome_id").distinct().withColumn("has_syntenic_locus", F.lit(1))

biome_data = env_mags_spark.select("genome_id", "biome_id", "biome_name") \
    .join(syntenic_genomes, on="genome_id", how="left").fillna({"has_syntenic_locus": 0})

biome_stats = biome_data.groupBy("biome_id", "biome_name").agg(
    F.count("genome_id").alias("total_MAGs"),
    F.sum("has_syntenic_locus").alias("syntenic_MAGs")
).withColumn("prevalence", F.col("syntenic_MAGs") / F.col("total_MAGs")).orderBy(F.desc("prevalence"))

biome_stats_pd = biome_stats.toPandas()

# Fisher exact test per biome
total_syntenic = biome_stats_pd["syntenic_MAGs"].sum()
total_mags = biome_stats_pd["total_MAGs"].sum()
results = []
for _, row in biome_stats_pd.iterrows():
    a = row["syntenic_MAGs"]
    b = row["total_MAGs"] - a
    c = total_syntenic - a
    d = total_mags - total_syntenic - b
    odds, p = fisher_exact([[a, b], [c, d]], alternative='greater') if a > 0 else (0.0, 1.0)
    results.append({"biome_name": row["biome_name"], "prevalence": row["prevalence"], "odds_ratio": odds, "p_value": p})

fisher_df = pd.DataFrame(results)
_, qvals, _, _ = multipletests(fisher_df["p_value"], method='fdr_bh')
fisher_df["q_value"] = qvals
fisher_df = fisher_df.sort_values("q_value")

display(fisher_df[fisher_df["q_value"] < 0.05])

# =============================================================================
# Export Gene IDs for Phylogenetic Validation (GT2)
# =============================================================================
os.makedirs("data/phylogeny", exist_ok=True)

# Syntenic GT2 genes
syntenic_gt2_genes = synteny_all.filter(F.col("cazy_family") == target_family) \
    .select("cz.genome_id", "cz.gene_id").distinct()
syntenic_ids_pd = syntenic_gt2_genes.toPandas()
with open(f"data/phylogeny/{target_family}_syntenic_gene_ids.txt", "w") as f:
    for _, row in syntenic_ids_pd.iterrows():
        f.write(f"{row['gene_id']}\n")

# Chromosomal GT2 genes (all GT2 genes not in syntenic set)
all_gt2_genes = spark.table("kescience_mgnify.gene_eggnog") \
    .join(env_mags_spark.select("genome_id"), on="genome_id", how="inner") \
    .filter(F.col("cazy").isNotNull() & (F.col("cazy") != "-")) \
    .withColumn("cazy_family", F.explode(F.split(F.col("cazy"), ","))) \
    .filter(F.col("cazy_family") == target_family) \
    .select("genome_id", "gene_id")

chromosomal_gt2_genes = all_gt2_genes.join(syntenic_gt2_genes, on=["genome_id", "gene_id"], how="left_anti")
chromosomal_path = f"data/phylogeny/{target_family}_chromosomal_gene_ids"
chromosomal_gt2_genes.select("gene_id").write.mode("overwrite").text(chromosomal_path)

print(f"Exported {len(syntenic_ids_pd)} syntenic GT2 gene IDs and {chromosomal_gt2_genes.count()} chromosomal GT2 gene IDs for phylogenetic analysis.")

Exported 851 syntenic GT2 gene IDs and 51579 chromosomal GT2 gene IDs for phylogenetic analysis.

# =============================================================================
# Export Gene IDs for Phylogenetic Validation (GT2) - Single File Version
# =============================================================================
import os
import pandas as pd

target_family = "GT2"
os.makedirs("data/phylogeny", exist_ok=True)

# Syntenic GT2 genes (small set, collect directly)
syntenic_gt2_genes = synteny_all.filter(F.col("cazy_family") == target_family) \
    .select("cz.gene_id").distinct()
syntenic_ids = [row.gene_id for row in syntenic_gt2_genes.collect()]
with open(f"data/phylogeny/{target_family}_syntenic_gene_ids.txt", "w") as f:
    for gid in syntenic_ids:
        f.write(f"{gid}\n")
print(f"Exported {len(syntenic_ids)} syntenic GT2 gene IDs.")

# All GT2 genes in environmental MAGs
all_gt2_genes = spark.table("kescience_mgnify.gene_eggnog") \
    .join(env_mags_spark.select("genome_id"), on="genome_id", how="inner") \
    .filter(F.col("cazy").isNotNull() & (F.col("cazy") != "-")) \
    .withColumn("cazy_family", F.explode(F.split(F.col("cazy"), ","))) \
    .filter(F.col("cazy_family") == target_family) \
    .select("gene_id").distinct()

# Chromosomal = all - syntenic
syntenic_set = set(syntenic_ids)
chromosomal_ids = [row.gene_id for row in all_gt2_genes.collect() if row.gene_id not in syntenic_set]

with open(f"data/phylogeny/{target_family}_chromosomal_gene_ids.txt", "w") as f:
    for gid in chromosomal_ids:
        f.write(f"{gid}\n")
print(f"Exported {len(chromosomal_ids)} chromosomal GT2 gene IDs.")

Exported 851 syntenic GT2 gene IDs.
Exported 33798 chromosomal GT2 gene IDs.

# =============================================================================
# Phylogenetic Validation: Fetch Sequences, Align, and Build Tree (FINAL)
# =============================================================================
import os
import subprocess
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio import Phylo
import matplotlib.pyplot as plt

target_family = "GT2"
syntenic_path = f"data/phylogeny/{target_family}_syntenic_gene_ids.txt"
chromosomal_path = f"data/phylogeny/{target_family}_chromosomal_gene_ids.txt"

# -----------------------------------------------------------------------------
# 1. Read gene IDs from the single text files
# -----------------------------------------------------------------------------
if not os.path.exists(syntenic_path):
    raise FileNotFoundError(f"{syntenic_path} not found. Run corrected Cell 10 first.")
if not os.path.exists(chromosomal_path):
    raise FileNotFoundError(f"{chromosomal_path} not found. Run corrected Cell 10 first.")

with open(syntenic_path, "r") as f:
    syntenic_ids = set(line.strip() for line in f if line.strip())
print(f"Read {len(syntenic_ids)} syntenic GT2 gene IDs.")

with open(chromosomal_path, "r") as f:
    chromosomal_ids = set(line.strip() for line in f if line.strip())
print(f"Read {len(chromosomal_ids)} chromosomal GT2 gene IDs.")

# (The rest of the cell continues as before, starting from sequence fetching)

Read 851 syntenic GT2 gene IDs.
Read 33798 chromosomal GT2 gene IDs.

# =============================================================================
# Cell 1 (Corrected): Environment Setup & Phylogenetic Sequence Extraction
# =============================================================================
import os
import sys
import urllib.request
import gzip
import pandas as pd
from pyspark.sql import functions as F
from pyspark.sql import SparkSession

# Ensure BioPython is installed for sequence parsing
try:
    from Bio import SeqIO
except ImportError:
    import subprocess
    subprocess.check_call([sys.executable, "-m", "pip", "install", "biopython"])
    from Bio import SeqIO

pd.set_option('display.max_colwidth', None)

# Initialize Spark with robust fallback handling
try:
    spark = SparkSession.builder.getOrCreate()
except Exception as e:
    print(f"Standard session creation failed, falling back to managed utils. Error: {e}")
    sys.path.append('/opt/conda/lib/python3.13/site-packages')
    from berdl_notebook_utils.setup_spark_session import get_spark_session
    spark = get_spark_session()

print("Identifying Syntenic vs Chromosomal GT2 genes...")

# 1. Quick re-derivation of Syntenic vs Chromosomal GT2 genes
target_cazy = "GT2"
window = 10000

# Get all environmental GT2 and T4SS genes
gene_coords = spark.table("kescience_mgnify.gene").select("genome_id", "gene_id", "contig_id", F.col("start").alias("start_pos"), F.col("end").alias("end_pos"))
eggnog = spark.table("kescience_mgnify.gene_eggnog")

t4ss_genes = eggnog.filter(F.col("eggnog_ogs").contains("COG0741") | F.lower(F.col("description")).rlike("type iv secretion|virb|t4ss|conjugal")) \
    .select("genome_id", "gene_id").join(gene_coords, on=["genome_id", "gene_id"])

cazy_genes = eggnog.filter(F.col("cazy").contains(target_cazy)) \
    .select("genome_id", "gene_id").join(gene_coords, on=["genome_id", "gene_id"])

# Find syntenic (within 10kb on same contig)
syntenic_pairs = t4ss_genes.alias("t4").join(cazy_genes.alias("cz"), (F.col("t4.genome_id") == F.col("cz.genome_id")) & (F.col("t4.contig_id") == F.col("cz.contig_id"))) \
    .withColumn("dist", F.greatest(F.lit(0), F.greatest(F.col("t4.start_pos"), F.col("cz.start_pos")) - F.least(F.col("t4.end_pos"), F.col("cz.end_pos")))) \
    .filter(F.col("dist") <= window)

syntenic_gt2_ids = set([row.gene_id for row in syntenic_pairs.select(F.col("cz.gene_id").alias("gene_id")).distinct().collect()])
chromosomal_gt2_ids = set([row.gene_id for row in cazy_genes.select("gene_id").collect()]) - syntenic_gt2_ids

# 2. Fetch FTP URLs for the genomes containing these genes
target_genome_ids = list(set([gid.split('_')[0] for gid in list(syntenic_gt2_ids) + list(chromosomal_gt2_ids)]))

ftp_df = spark.table("kescience_mgnify.genome").filter(F.col("genome_id").isin(target_genome_ids)) \
    .select("genome_id", "ftp_url").toPandas()

# 3. Download and Extract Sequences
os.makedirs("data/phylogeny/raw_faa", exist_ok=True)
extracted_records = []

print(f"Downloading protein FASTA files for {len(ftp_df)} genomes. This may take a moment...")

for _, row in ftp_df.iterrows():
    genome_id, base_ftp = row['genome_id'], row['ftp_url']
    if not base_ftp: continue
    
    # FIX: Only swap the file extension. The FAA files live in the same directory as the GFFs.
    faa_url = base_ftp.replace(".gff.gz", ".faa.gz")
    out_gz = f"data/phylogeny/raw_faa/{genome_id}.faa.gz"
    
    try:
        # Download the gzipped FASTA if we haven't already
        if not os.path.exists(out_gz):
            urllib.request.urlretrieve(faa_url, out_gz)
            
        # Open the gzip file directly and parse with Biopython
        with gzip.open(out_gz, "rt") as handle:
            for record in SeqIO.parse(handle, "fasta"):
                if record.id in syntenic_gt2_ids:
                    record.id, record.description = f"SYNTENIC_{record.id}", ""
                    extracted_records.append(record)
                elif record.id in chromosomal_gt2_ids:
                    record.id, record.description = f"CHROMOSOMAL_{record.id}", ""
                    extracted_records.append(record)
    except Exception as e:
        # Stop silently failing! Print the error so we know if a URL is broken.
        print(f"Failed to fetch or parse {genome_id} at {faa_url}: {e}")

output_fasta = "data/phylogeny/GT2_combined_sequences.fasta"
SeqIO.write(extracted_records, output_fasta, "fasta")
print(f"\nSuccess! Saved {len(extracted_records)} tagged sequences to {output_fasta}. Ready for MAFFT/FastTree.")

Standard session creation failed, falling back to managed utils. Error: [CONNECT_URL_NOT_SET] Cannot create a Spark Connect session because the Spark Connect remote URL has not been set. Please define the remote URL by setting either the 'spark.remote' option or the 'SPARK_REMOTE' environment variable.
Identifying Syntenic vs Chromosomal GT2 genes...
Downloading protein FASTA files for 31129 genomes. This may take a moment...
Failed to fetch or parse MGYG000000001 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000001/genomes1/MGYG000000001.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000002 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000002/genomes1/MGYG000000002.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000003 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000003/genomes1/MGYG000000003.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000004 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000004/genomes1/MGYG000000004.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000005 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000005/genomes1/MGYG000000005.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000006 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000006/genomes1/MGYG000000006.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000007 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000007/genomes1/MGYG000000007.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000008 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000008/genomes1/MGYG000000008.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000009 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000009/genomes1/MGYG000000009.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000010 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000010/genomes1/MGYG000000010.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000011 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000011/genomes1/MGYG000000011.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000012 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000012/genomes1/MGYG000000012.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000013 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000013/genomes1/MGYG000000013.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000014 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000014/genomes1/MGYG000000014.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000015 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000015/genomes1/MGYG000000015.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000016 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000016/genomes1/MGYG000000016.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000017 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000017/genomes1/MGYG000000017.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000018 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000018/genomes1/MGYG000000018.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000019 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000019/genomes1/MGYG000000019.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000020 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000020/genomes1/MGYG000000020.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000021 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000021/genomes1/MGYG000000021.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000022 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000022/genomes1/MGYG000000022.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000023 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000023/genomes1/MGYG000000023.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000024 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000024/genomes1/MGYG000000024.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000025 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000025/genomes1/MGYG000000025.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000026 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000026/genomes1/MGYG000000026.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000027 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000027/genomes1/MGYG000000027.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000028 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000028/genomes1/MGYG000000028.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000029 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000029/genomes1/MGYG000000029.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000030 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000030/genomes1/MGYG000000030.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000031 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000031/genomes1/MGYG000000031.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000032 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000032/genomes1/MGYG000000032.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000033 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000033/genomes1/MGYG000000033.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000034 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000034/genomes1/MGYG000000034.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000035 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000035/genomes1/MGYG000000035.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000036 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000036/genomes1/MGYG000000036.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000038 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000038/genomes1/MGYG000000038.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000039 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000039/genomes1/MGYG000000039.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000040 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000040/genomes1/MGYG000000040.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000041 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000041/genomes1/MGYG000000041.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000042 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000042/genomes1/MGYG000000042.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000043 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000043/genomes1/MGYG000000043.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000044 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000044/genomes1/MGYG000000044.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000045 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000045/genomes1/MGYG000000045.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000046 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000046/genomes1/MGYG000000046.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000047 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000047/genomes1/MGYG000000047.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000048 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000048/genomes1/MGYG000000048.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000049 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000049/genomes1/MGYG000000049.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000050 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000050/genomes1/MGYG000000050.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000051 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000051/genomes1/MGYG000000051.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000052 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000052/genomes1/MGYG000000052.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000053 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000053/genomes1/MGYG000000053.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000054 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000054/genomes1/MGYG000000054.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000055 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000055/genomes1/MGYG000000055.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000056 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000056/genomes1/MGYG000000056.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000057 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000057/genomes1/MGYG000000057.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000058 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000058/genomes1/MGYG000000058.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000059 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000059/genomes1/MGYG000000059.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000060 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000060/genomes1/MGYG000000060.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000061 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000061/genomes1/MGYG000000061.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000062 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000062/genomes1/MGYG000000062.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000063 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000063/genomes1/MGYG000000063.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000064 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000064/genomes1/MGYG000000064.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000065 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000065/genomes1/MGYG000000065.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000066 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000066/genomes1/MGYG000000066.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000067 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000067/genomes1/MGYG000000067.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000068 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000068/genomes1/MGYG000000068.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000069 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000069/genomes1/MGYG000000069.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000070 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000070/genomes1/MGYG000000070.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000071 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000071/genomes1/MGYG000000071.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000072 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000072/genomes1/MGYG000000072.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000073 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000073/genomes1/MGYG000000073.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000074 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000074/genomes1/MGYG000000074.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000076 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000076/genomes1/MGYG000000076.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000077 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000077/genomes1/MGYG000000077.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000078 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000078/genomes1/MGYG000000078.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000079 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000079/genomes1/MGYG000000079.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000080 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000080/genomes1/MGYG000000080.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000081 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000081/genomes1/MGYG000000081.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000082 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000082/genomes1/MGYG000000082.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000083 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000083/genomes1/MGYG000000083.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000084 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000084/genomes1/MGYG000000084.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000085 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000085/genomes1/MGYG000000085.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000086 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000086/genomes1/MGYG000000086.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000087 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000087/genomes1/MGYG000000087.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000088 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000088/genomes1/MGYG000000088.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000089 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000089/genomes1/MGYG000000089.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000090 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000090/genomes1/MGYG000000090.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000091 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000091/genomes1/MGYG000000091.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000092 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000092/genomes1/MGYG000000092.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000093 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000093/genomes1/MGYG000000093.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000094 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000094/genomes1/MGYG000000094.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000095 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000095/genomes1/MGYG000000095.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000096 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000096/genomes1/MGYG000000096.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000097 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000097/genomes1/MGYG000000097.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000098 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000098/genomes1/MGYG000000098.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000099 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000000/MGYG000000099/genomes1/MGYG000000099.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000100 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000100/genomes1/MGYG000000100.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000101 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000101/genomes1/MGYG000000101.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000104 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000104/genomes1/MGYG000000104.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000105 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000105/genomes1/MGYG000000105.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000109 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000109/genomes1/MGYG000000109.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000110 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000110/genomes1/MGYG000000110.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000112 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000112/genomes1/MGYG000000112.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000114 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000114/genomes1/MGYG000000114.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000115 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000115/genomes1/MGYG000000115.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000116 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000116/genomes1/MGYG000000116.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000117 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000117/genomes1/MGYG000000117.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000118 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000118/genomes1/MGYG000000118.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000119 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000119/genomes1/MGYG000000119.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000120 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000120/genomes1/MGYG000000120.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000121 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000121/genomes1/MGYG000000121.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000122 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000122/genomes1/MGYG000000122.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000123 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000123/genomes1/MGYG000000123.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000124 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000124/genomes1/MGYG000000124.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000125 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000125/genomes1/MGYG000000125.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000126 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000126/genomes1/MGYG000000126.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000127 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000127/genomes1/MGYG000000127.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000128 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000128/genomes1/MGYG000000128.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000129 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000129/genomes1/MGYG000000129.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000130 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000130/genomes1/MGYG000000130.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000132 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000132/genomes1/MGYG000000132.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000133 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000133/genomes1/MGYG000000133.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000134 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000134/genomes1/MGYG000000134.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000135 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000135/genomes1/MGYG000000135.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000136 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000136/genomes1/MGYG000000136.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000137 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000137/genomes1/MGYG000000137.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000138 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000138/genomes1/MGYG000000138.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000139 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000139/genomes1/MGYG000000139.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000140 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000140/genomes1/MGYG000000140.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000141 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000141/genomes1/MGYG000000141.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000142 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000142/genomes1/MGYG000000142.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000143 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000143/genomes1/MGYG000000143.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000144 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000144/genomes1/MGYG000000144.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000146 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000146/genomes1/MGYG000000146.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000148 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000148/genomes1/MGYG000000148.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000149 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000149/genomes1/MGYG000000149.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000150 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000150/genomes1/MGYG000000150.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000151 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000151/genomes1/MGYG000000151.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000153 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000153/genomes1/MGYG000000153.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000154 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000154/genomes1/MGYG000000154.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000155 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000155/genomes1/MGYG000000155.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000157 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000157/genomes1/MGYG000000157.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000158 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000158/genomes1/MGYG000000158.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000159 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000159/genomes1/MGYG000000159.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000160 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000160/genomes1/MGYG000000160.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000161 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000161/genomes1/MGYG000000161.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000162 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000162/genomes1/MGYG000000162.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000163 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000163/genomes1/MGYG000000163.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000164 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000164/genomes1/MGYG000000164.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000165 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000165/genomes1/MGYG000000165.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000166 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000166/genomes1/MGYG000000166.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000168 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000168/genomes1/MGYG000000168.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000174 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000174/genomes1/MGYG000000174.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000175 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000175/genomes1/MGYG000000175.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000176 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000176/genomes1/MGYG000000176.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000177 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000177/genomes1/MGYG000000177.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000178 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000178/genomes1/MGYG000000178.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000179 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000179/genomes1/MGYG000000179.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000180 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000180/genomes1/MGYG000000180.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000181 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000181/genomes1/MGYG000000181.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000182 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000182/genomes1/MGYG000000182.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000183 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000183/genomes1/MGYG000000183.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000186 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000186/genomes1/MGYG000000186.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000187 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000187/genomes1/MGYG000000187.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000188 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000188/genomes1/MGYG000000188.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000189 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000189/genomes1/MGYG000000189.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000190 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000190/genomes1/MGYG000000190.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000191 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000191/genomes1/MGYG000000191.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000193 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000193/genomes1/MGYG000000193.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000194 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000194/genomes1/MGYG000000194.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000195 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000195/genomes1/MGYG000000195.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000196 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000196/genomes1/MGYG000000196.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000197 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000197/genomes1/MGYG000000197.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000198 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000198/genomes1/MGYG000000198.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000199 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000001/MGYG000000199/genomes1/MGYG000000199.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000200 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000002/MGYG000000200/genomes1/MGYG000000200.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000202 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000002/MGYG000000202/genomes1/MGYG000000202.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000205 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000002/MGYG000000205/genomes1/MGYG000000205.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000206 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000002/MGYG000000206/genomes1/MGYG000000206.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000207 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000002/MGYG000000207/genomes1/MGYG000000207.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000208 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000002/MGYG000000208/genomes1/MGYG000000208.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000209 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000002/MGYG000000209/genomes1/MGYG000000209.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000210 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000002/MGYG000000210/genomes1/MGYG000000210.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000211 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000002/MGYG000000211/genomes1/MGYG000000211.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000212 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000002/MGYG000000212/genomes1/MGYG000000212.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000213 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000002/MGYG000000213/genomes1/MGYG000000213.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000214 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000002/MGYG000000214/genomes1/MGYG000000214.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000215 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000002/MGYG000000215/genomes1/MGYG000000215.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000216 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000002/MGYG000000216/genomes1/MGYG000000216.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000217 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000002/MGYG000000217/genomes1/MGYG000000217.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000218 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000002/MGYG000000218/genomes1/MGYG000000218.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000219 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000002/MGYG000000219/genomes1/MGYG000000219.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000220 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000002/MGYG000000220/genomes1/MGYG000000220.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000221 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000002/MGYG000000221/genomes1/MGYG000000221.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000222 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000002/MGYG000000222/genomes1/MGYG000000222.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000223 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000002/MGYG000000223/genomes1/MGYG000000223.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000224 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000002/MGYG000000224/genomes1/MGYG000000224.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000225 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000002/MGYG000000225/genomes1/MGYG000000225.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000226 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000002/MGYG000000226/genomes1/MGYG000000226.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000228 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000002/MGYG000000228/genomes1/MGYG000000228.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000229 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000002/MGYG000000229/genomes1/MGYG000000229.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000230 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000002/MGYG000000230/genomes1/MGYG000000230.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000231 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000002/MGYG000000231/genomes1/MGYG000000231.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000232 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000002/MGYG000000232/genomes1/MGYG000000232.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000233 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000002/MGYG000000233/genomes1/MGYG000000233.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000234 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000002/MGYG000000234/genomes1/MGYG000000234.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000235 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000002/MGYG000000235/genomes1/MGYG000000235.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000237 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000002/MGYG000000237/genomes1/MGYG000000237.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000239 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000002/MGYG000000239/genomes1/MGYG000000239.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000240 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000002/MGYG000000240/genomes1/MGYG000000240.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000241 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000002/MGYG000000241/genomes1/MGYG000000241.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000242 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000002/MGYG000000242/genomes1/MGYG000000242.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000243 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000002/MGYG000000243/genomes1/MGYG000000243.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000244 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000002/MGYG000000244/genomes1/MGYG000000244.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000245 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000002/MGYG000000245/genomes1/MGYG000000245.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000246 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000002/MGYG000000246/genomes1/MGYG000000246.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>
Failed to fetch or parse MGYG000000247 at ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0/all_genomes/MGYG0000002/MGYG000000247/genomes1/MGYG000000247.faa.gz: <urlopen error <urlopen error ftp error: error_perm('550 Failed to change directory.')>>

---------------------------------------------------------------------------
KeyboardInterrupt                         Traceback (most recent call last)
Cell In[33], line 89
     85                     extracted_records.append(record)
     86                 elif record.id in chromosomal_gt2_ids:
     87                     record.id, record.description = f"CHROMOSOMAL_{record.id}", ""
     88                     extracted_records.append(record)
---> 89     except Exception as e:
     90         # Stop silently failing! Print the error so we know if a URL is broken.
     91         print(f"Failed to fetch or parse {genome_id} at {faa_url}: {e}")
     92 

File ~/.local/envs/bio_env/lib/python3.13/urllib/request.py:214, in urlretrieve(url, filename, reporthook, data)
    197 """
    198 Retrieve a URL into a temporary location on disk.
    199 
   (...)    210 data file as well as the resulting HTTPMessage object.
    211 """
    212 url_type, path = _splittype(url)
--> 214 with contextlib.closing(urlopen(url, data)) as fp:
    215     headers = fp.info()
    217     # Just return the local path and the "headers" for file://
    218     # URLs. No sense in performing a copy unless requested.

File ~/.local/envs/bio_env/lib/python3.13/urllib/request.py:189, in urlopen(url, data, timeout, context)
    187 else:
    188     opener = _opener
--> 189 return opener.open(url, data, timeout)

File ~/.local/envs/bio_env/lib/python3.13/urllib/request.py:489, in OpenerDirector.open(self, fullurl, data, timeout)
    486     req = meth(req)
    488 sys.audit('urllib.Request', req.full_url, req.data, req.headers, req.get_method())
--> 489 response = self._open(req, data)
    491 # post-process response
    492 meth_name = protocol+"_response"

File ~/.local/envs/bio_env/lib/python3.13/urllib/request.py:506, in OpenerDirector._open(self, req, data)
    503     return result
    505 protocol = req.type
--> 506 result = self._call_chain(self.handle_open, protocol, protocol +
    507                           '_open', req)
    508 if result:
    509     return result

File ~/.local/envs/bio_env/lib/python3.13/urllib/request.py:466, in OpenerDirector._call_chain(self, chain, kind, meth_name, *args)
    464 for handler in handlers:
    465     func = getattr(handler, meth_name)
--> 466     result = func(*args)
    467     if result is not None:
    468         return result

File ~/.local/envs/bio_env/lib/python3.13/urllib/request.py:1542, in FTPHandler.ftp_open(self, req)
   1540 fw = None
   1541 try:
-> 1542     fw = self.connect_ftp(user, passwd, host, port, dirs, req.timeout)
   1543     type = file and 'I' or 'D'
   1544     for attr in attrs:

File ~/.local/envs/bio_env/lib/python3.13/urllib/request.py:1566, in FTPHandler.connect_ftp(self, user, passwd, host, port, dirs, timeout)
   1565 def connect_ftp(self, user, passwd, host, port, dirs, timeout):
-> 1566     return ftpwrapper(user, passwd, host, port, dirs, timeout,
   1567                       persistent=False)

File ~/.local/envs/bio_env/lib/python3.13/urllib/request.py:2420, in ftpwrapper.__init__(self, user, passwd, host, port, dirs, timeout, persistent)
   2418 self.keepalive = persistent
   2419 try:
-> 2420     self.init()
   2421 except:
   2422     self.close()

File ~/.local/envs/bio_env/lib/python3.13/urllib/request.py:2429, in ftpwrapper.init(self)
   2427 self.busy = 0
   2428 self.ftp = ftplib.FTP()
-> 2429 self.ftp.connect(self.host, self.port, self.timeout)
   2430 self.ftp.login(self.user, self.passwd)
   2431 _target = '/'.join(self.dirs)

File ~/.local/envs/bio_env/lib/python3.13/ftplib.py:158, in FTP.connect(self, host, port, timeout, source_address)
    156     self.source_address = source_address
    157 sys.audit("ftplib.connect", self, self.host, self.port)
--> 158 self.sock = socket.create_connection((self.host, self.port), self.timeout,
    159                                      source_address=self.source_address)
    160 self.af = self.sock.family
    161 self.file = self.sock.makefile('r', encoding=self.encoding)

File ~/.local/envs/bio_env/lib/python3.13/socket.py:849, in create_connection(address, timeout, source_address, all_errors)
    847 if source_address:
    848     sock.bind(source_address)
--> 849 sock.connect(sa)
    850 # Break explicitly a reference cycle
    851 exceptions.clear()

KeyboardInterrupt:

# =============================================================================
# Cell 2: Super-Accumulator Dynamics (IME vs ICE Hijacking)
# =============================================================================
print("Investigating 'Super-Accumulator' hijacking via ICEfinder...")

# 1. Identify Super-Accumulators (High CAZy density, no intrinsic T4SS)
# Using GT2 as a proxy for cargo density for brevity in a fresh notebook
accumulators_df = spark.table("kescience_mgnify.gene_eggnog") \
    .filter(F.col("cazy").contains("GT2")) \
    .groupBy("genome_id").agg(F.count("gene_id").alias("cargo_count")) \
    .orderBy(F.desc("cargo_count")).limit(100)

accumulator_ids = [row.genome_id for row in accumulators_df.collect()]

# 2. Query ICEfinder mobilome data
mobilome_data = spark.table("kescience_mgnify.gene_mobilome") \
    .filter(F.col("genome_id").isin(accumulator_ids)) \
    .filter(F.col("tool") == "ICEfinder") \
    .select("genome_id", "contig_id", "start_pos", "end_pos", "mobile_element_type")

# 3. Summarize IME vs ICE prevalence
mge_summary = mobilome_data.groupBy("mobile_element_type") \
    .agg(
        F.count("genome_id").alias("Total_Elements_Found"),
        F.countDistinct("genome_id").alias("Genomes_Containing_Element")
    ).orderBy(F.desc("Total_Elements_Found"))

print("\nPrevalence of IMEs vs ICEs in Top 100 Accumulators:")
display(mge_summary.toPandas())

# 4. Map CAZy genes structurally inside the IME boundaries
cazy_genes = spark.table("kescience_mgnify.gene_eggnog") \
    .filter(F.col("genome_id").isin(accumulator_ids) & F.col("cazy").isNotNull()) \
    .select("genome_id", "gene_id", F.explode(F.split(F.col("cazy"), ",")).alias("cazy_family"))

gene_coords = spark.table("kescience_mgnify.gene").select("genome_id", "gene_id", "contig_id", F.col("start").alias("g_start"), F.col("end").alias("g_end"))
cazy_coords = cazy_genes.join(gene_coords, on=["genome_id", "gene_id"])

ime_cargo = cazy_coords.join(
    mobilome_data.filter(F.col("mobile_element_type").like("%IME%")),
    on=["genome_id", "contig_id"]
).filter((F.col("g_start") >= F.col("start_pos")) & (F.col("g_end") <= F.col("end_pos")))

ime_cargo_summary = ime_cargo.groupBy("cazy_family").agg(
    F.countDistinct("genome_id").alias("Genomes_with_IME_Cargo"),
    F.count("gene_id").alias("Total_IME_Nested_Genes")
).orderBy(F.desc("Genomes_with_IME_Cargo"))

print("\nTop CAZy Families specifically hijacked within IMEs:")
display(ime_cargo_summary.limit(10).toPandas())

Investigating 'Super-Accumulator' hijacking via ICEfinder...

Prevalence of IMEs vs ICEs in Top 100 Accumulators:

Top CAZy Families specifically hijacked within IMEs:

# =============================================================================
# Cell 3 (Corrected): Functional Ecology (FitnessBrowser & BacDive Integration)
# =============================================================================
import pyspark.sql.functions as F

print("Linking Synteny to Experimental Phenotypes...")

# 1. Map GT2 genes to KEGG KOs to bridge to FitnessBrowser
# MGnify KEGG KOs usually have a 'ko:' prefix (e.g., ko:K01234). We strip it to match FitnessBrowser.
gt2_kegg = spark.table("kescience_mgnify.gene_eggnog") \
    .filter(F.col("cazy").contains("GT2") & F.col("kegg_ko").isNotNull() & (F.col("kegg_ko") != "-")) \
    .select(F.explode(F.split(F.col("kegg_ko"), ",")).alias("raw_ko")) \
    .withColumn("ko_id", F.regexp_replace(F.col("raw_ko"), "^ko:", "")) \
    .select("ko_id").distinct()

# Fetch FitnessBrowser orthologs linked to these KOs
fb_kegg = spark.table("kescience_fitnessbrowser.kgroupdesc") \
    .join(gt2_kegg, F.col("kgroup") == F.col("ko_id"), how="inner") \
    .select("kgroup", "desc").distinct().toPandas()

print("\n--- FITNESS BROWSER MAPPING ---")
print(f"Mapped {len(fb_kegg)} GT2 KEGG Orthologs to Fitness Browser descriptions.")
if not fb_kegg.empty:
    display(fb_kegg.head(5))

# 2. Map Host MAGs to BacDive to determine real-world diet & habitat
# Extract Genera of our syntenic genomes
syntenic_genera = spark.table("kescience_mgnify.genome") \
    .filter(F.col("genome_id").isin(target_genome_ids)) \
    .withColumn("mgnify_genus", F.regexp_extract(F.col("lineage"), r"g__([^;]+)", 1)) \
    .select("mgnify_genus").filter(F.col("mgnify_genus") != "").distinct()

# Cross-reference with BacDive Taxonomy using explicit aliasing to avoid case-insensitive collisions
bacdive_tax = spark.table("kescience_bacdive.taxonomy").select("bacdive_id", F.col("genus").alias("bacdive_genus"))
mapped_strains = bacdive_tax.join(
    syntenic_genera, 
    F.col("bacdive_genus") == F.col("mgnify_genus"), 
    how="inner"
).select("bacdive_id", "bacdive_genus").distinct()

# Pull real-world diets (Metabolite Utilization) for these matched Genera
bacdive_diet = spark.table("kescience_bacdive.metabolite_utilization") \
    .join(mapped_strains, on="bacdive_id", how="inner") \
    .filter(F.col("utilization") == "+") \
    .groupBy("bacdive_genus", "compound_name").agg(F.count("bacdive_id").alias("positive_strains")) \
    .orderBy(F.desc("positive_strains"))

print("\n--- BACDIVE ECOLOGY MAPPING ---")
print("Top consumed metabolites for Genera known to carry the GT2-T4SS cassette:")
display(bacdive_diet.limit(15).toPandas())

Linking Synteny to Experimental Phenotypes...

--- FITNESS BROWSER MAPPING ---
Mapped 126 GT2 KEGG Orthologs to Fitness Browser descriptions.

--- BACDIVE ECOLOGY MAPPING ---
Top consumed metabolites for Genera known to carry the GT2-T4SS cassette:

# =============================================================================
# Cell 3 (Final Fix): Functional Ecology (Combined Diet & Traits)
# =============================================================================
import pyspark.sql.functions as F

print("Linking Synteny to Experimental Phenotypes (Sugars + Respiration)...")

# 1. Map GT2 genes to KEGG KOs to bridge to FitnessBrowser
gt2_kegg = spark.table("kescience_mgnify.gene_eggnog") \
    .filter(F.col("cazy").contains("GT2") & F.col("kegg_ko").isNotNull() & (F.col("kegg_ko") != "-")) \
    .select(F.explode(F.split(F.col("kegg_ko"), ",")).alias("raw_ko")) \
    .withColumn("ko_id", F.regexp_replace(F.col("raw_ko"), "^ko:", "")) \
    .select("ko_id").distinct()

fb_kegg = spark.table("kescience_fitnessbrowser.kgroupdesc") \
    .join(gt2_kegg, F.col("kgroup") == F.col("ko_id"), how="inner") \
    .select("kgroup", "desc").distinct().toPandas()

print("\n--- FITNESS BROWSER MAPPING ---")
if not fb_kegg.empty:
    display(fb_kegg.head(5))

# 2. Map Host MAGs to BacDive Taxonomy
syntenic_genera = spark.table("kescience_mgnify.genome") \
    .filter(F.col("genome_id").isin(target_genome_ids)) \
    .withColumn("mgnify_genus", F.regexp_extract(F.col("lineage"), r"g__([^;]+)", 1)) \
    .select("mgnify_genus").filter(F.col("mgnify_genus") != "").distinct()

bacdive_tax = spark.table("kescience_bacdive.taxonomy").select("bacdive_id", F.col("genus").alias("bacdive_genus"))
mapped_strains = bacdive_tax.join(
    syntenic_genera, 
    F.col("bacdive_genus") == F.col("mgnify_genus"), 
    how="inner"
).select("bacdive_id", "bacdive_genus").distinct()

# 3. Pull ALL Metabolite & Phenotype Traits from the known table
# We pull everything into Pandas so we can filter easily without schema errors
full_bacdive_data = spark.table("kescience_bacdive.metabolite_utilization") \
    .join(mapped_strains, on="bacdive_id", how="inner") \
    .filter(F.col("utilization") == "+") \
    .groupBy("bacdive_genus", "compound_name").agg(F.count("bacdive_id").alias("positive_strains")) \
    .orderBy(F.desc("positive_strains")) \
    .toPandas()

# 4. Separate the results for your Results section
# Sugars/Carbs (Biofilm Raw Materials)
sugars = ['maltose', 'sucrose', 'lactose', 'glucose', 'D-glucose', 'fructose', 'trehalose', 'galactose', 'raffinose']
# Non-Carbs (Respiratory/Inorganic Machinery)
respiratory = ['nitrate', 'nitrite', 'citrate', 'malate', 'pyruvate', 'oxygen', 'sulfate']

bacdive_diet = full_bacdive_data[full_bacdive_data['compound_name'].str.lower().isin(sugars)]
bacdive_traits = full_bacdive_data[full_bacdive_data['compound_name'].str.lower().isin(respiratory)]

print("\n--- BACDIVE ECOLOGY MAPPING ---")
print("Top Carbohydrate Metabolites (The Biofilm Fuel):")
display(bacdive_diet.head(10))

print("\nTop Respiratory/Inorganic Markers (The Survival Engine):")
display(bacdive_traits.head(10))

Linking Synteny to Experimental Phenotypes (Sugars + Respiration)...

--- FITNESS BROWSER MAPPING ---

--- BACDIVE ECOLOGY MAPPING ---
Top Carbohydrate Metabolites (The Biofilm Fuel):

Top Respiratory/Inorganic Markers (The Survival Engine):

# =============================================================================
# Generate Figure: Cytoscape Export for Ecological Diet Network
# =============================================================================
import pandas as pd

# Assuming 'bacdive_diet' is your Pandas DataFrame from the previous BacDive cell
# If it's a Spark DataFrame, add .toPandas() first.
diet_df = bacdive_diet.toPandas() if hasattr(bacdive_diet, 'toPandas') else bacdive_diet

# Format for Cytoscape
edges = diet_df.rename(columns={
    "bacdive_genus": "Source", 
    "compound_name": "Target", 
    "positive_strains": "Weight"
})
edges['Interaction_Type'] = "Consumes"

# Filter to top interactions to keep the network clean
top_edges = edges[edges['Weight'] > 10]

# Save to your cytoscape folder
import os
os.makedirs("data/cytoscape", exist_ok=True)
top_edges.to_csv("data/cytoscape/ecological_diet_network_edges.csv", index=False)

print(f"Exported {len(top_edges)} interactions for Cytoscape.")
print("In Cytoscape: Import -> Map Source to 'Source', Target to 'Target', and set edge width by 'Weight'.")

Exported 2857 interactions for Cytoscape.
In Cytoscape: Import -> Map Source to 'Source', Target to 'Target', and set edge width by 'Weight'.

# =============================================================================
# Cell 4: Generate iTOL Taxonomy Color Strip (Self-Contained)
# =============================================================================
import pandas as pd
import seaborn as sns
from pyspark.sql import functions as F
from Bio import SeqIO
import os

print("Generating iTOL taxonomy annotation file...")

fasta_file = "data/phylogeny/GT2_combined_sequences.fasta"

if not os.path.exists(fasta_file):
    print(f"Error: {fasta_file} not found. Please ensure your extraction cell finished.")
else:
    syntenic_gt2_ids = []
    chromosomal_gt2_ids = []
    
    # 1. Read the FASTA file to get the exact genes we aligned
    for record in SeqIO.parse(fasta_file, "fasta"):
        if record.id.startswith("SYNTENIC_"):
            syntenic_gt2_ids.append(record.id.replace("SYNTENIC_", ""))
        elif record.id.startswith("CHROMOSOMAL_"):
            chromosomal_gt2_ids.append(record.id.replace("CHROMOSOMAL_", ""))
            
    all_gt2_genes = set(syntenic_gt2_ids + chromosomal_gt2_ids)
    
    # Extract genome IDs by grabbing the prefix before the underscore
    target_genome_ids = list(set([gene_id.split('_')[0] for gene_id in all_gt2_genes]))

    print(f"Loaded {len(all_gt2_genes)} genes across {len(target_genome_ids)} genomes from FASTA.")

    # 2. Fetch the Phylum for these genomes from the database
    genome_tax = spark.table("kescience_mgnify.genome") \
        .filter(F.col("genome_id").isin(target_genome_ids)) \
        .withColumn("Phylum", F.regexp_extract(F.col("lineage"), r"p__([^;]+)", 1)) \
        .select("genome_id", "Phylum").toPandas()

    # 3. Create a mapping of Gene ID -> Phylum
    itol_data = []
    tax_dict = dict(zip(genome_tax['genome_id'], genome_tax['Phylum']))

    for gene_id in all_gt2_genes:
        genome_id = gene_id.split('_')[0]
        phylum = tax_dict.get(genome_id, "Unknown")
        
        prefix = "SYNTENIC_" if gene_id in syntenic_gt2_ids else "CHROMOSOMAL_"
        leaf_name = f"{prefix}{gene_id}"
        itol_data.append({"leaf": leaf_name, "phylum": phylum})

    df_itol = pd.DataFrame(itol_data)

    # 4. Assign a unique HEX color to the top 10 Phyla
    top_phyla = df_itol['phylum'].value_counts().nlargest(10).index
    palette = sns.color_palette("Set3", len(top_phyla)).as_hex()
    color_map = dict(zip(top_phyla, palette))

    # Any rare phyla outside the top 10 will be colored light gray
    df_itol['color'] = df_itol['phylum'].map(lambda x: color_map.get(x, "#CCCCCC")) 

    # 5. Write the iTOL standard format file
    os.makedirs("data/phylogeny", exist_ok=True)
    output_file = "data/phylogeny/itol_phylum_ring.txt"
    
    with open(output_file, "w") as f:
        # iTOL formatting headers
        f.write("DATASET_COLORSTRIP\n")
        f.write("SEPARATOR COMMA\n")
        f.write("DATASET_LABEL,Phylum\n")
        f.write("COLOR,#000000\n")
        f.write("STRIP_WIDTH,25\n")
        f.write("SHOW_INTERNAL,0\n")
        f.write("DATA\n")
        
        # Write the actual mapped data
        for _, row in df_itol.iterrows():
            f.write(f"{row['leaf']},{row['color']},{row['phylum']}\n")

    print(f"Done! Download '{output_file}' to your computer and drag it directly onto your iTOL tree.")

Generating iTOL taxonomy annotation file...
Loaded 8245 genes across 1096 genomes from FASTA.
Done! Download 'data/phylogeny/itol_phylum_ring.txt' to your computer and drag it directly onto your iTOL tree.

# =============================================================================
# Cell: Visualize Annotated Tree in Python (Taxonomy & Hitchhikers)
# =============================================================================
import matplotlib.pyplot as plt
import matplotlib.patches as mpatches
import seaborn as sns
from Bio import Phylo
from pyspark.sql import functions as F
import os

tree_path = "data/phylogeny/GT2_gene_tree.nwk"

if not os.path.exists(tree_path):
    print(f"Error: {tree_path} not found. Please wait for FastTree to finish.")
else:
    print("Loading tree and fetching taxonomy data...")

    # 1. Load the Tree
    tree = Phylo.read(tree_path, "newick")

    # 2. Extract Genome IDs from the tree leaves
    leaf_names = [leaf.name for leaf in tree.get_terminals()]
    target_genome_ids = list(set([
        name.replace("SYNTENIC_", "").replace("CHROMOSOMAL_", "").split('_')[0] 
        for name in leaf_names if name
    ]))

    # 3. Fetch Taxonomy from Spark Database
    genome_tax = spark.table("kescience_mgnify.genome") \
        .filter(F.col("genome_id").isin(target_genome_ids)) \
        .withColumn("Phylum", F.regexp_extract(F.col("lineage"), r"p__([^;]+)", 1)) \
        .select("genome_id", "Phylum").toPandas()

    tax_dict = dict(zip(genome_tax['genome_id'], genome_tax['Phylum']))

    # 4. Generate a Color Palette for the Top 10 Phyla
    top_phyla = genome_tax['Phylum'].value_counts().nlargest(10).index.tolist()
    palette = sns.color_palette("tab10", len(top_phyla)).as_hex()
    color_map = dict(zip(top_phyla, palette))

    # 5. Apply Colors to the Tree Branches
    for clade in tree.find_clades():
        if clade.name:  # This is a terminal leaf (a gene)
            # Extract the raw genome ID
            genome_id = clade.name.replace("SYNTENIC_", "").replace("CHROMOSOMAL_", "").split('_')[0]
            phylum = tax_dict.get(genome_id, "Unknown")
            
            # Color the branch based on its Phylum (Default to light gray for rare phyla)
            clade.color = color_map.get(phylum, "#CCCCCC") 
        else:
            # Internal branches get a faint gray so the colorful tips pop out
            clade.color = "#E0E0E0"

    # 6. Define the "Hitchhiker" Labeling Function
    # We hide the messy gene IDs, but append a Star to the syntenic hitchhikers
    def highlight_hitchhikers(clade):
        if clade.name and "SYNTENIC" in clade.name:
            return " ★" 
        return ""

    # 7. Draw the Plot
    print("Rendering plot (this might take a few seconds for large trees)...")
    fig, ax = plt.subplots(figsize=(14, 25)) # Tall figure to accommodate thousands of leaves

    Phylo.draw(
        tree, 
        axes=ax, 
        do_show=False, 
        label_func=highlight_hitchhikers, 
        show_confidence=False,
        branch_labels=None
    )

    # 8. Create a Custom Legend
    legend_patches = [mpatches.Patch(color=color, label=phylum) for phylum, color in color_map.items()]
    legend_patches.append(mpatches.Patch(color="#CCCCCC", label="Other / Unknown"))
    ax.legend(handles=legend_patches, title="Host Phylum", loc="upper left", bbox_to_anchor=(1, 1), fontsize=12)

    plt.title("Phylogeny of GT2: Taxonomy vs. Hitchhiker Acquisition (★)", fontsize=18)
    plt.axis("off") # Turn off the numeric coordinate axes
    plt.tight_layout()
    plt.show()

Loading tree and fetching taxonomy data...
Rendering plot (this might take a few seconds for large trees)...

# =============================================================================
# Cell: Generate Figure 2 (Metabolic Diet Heatmap)
# =============================================================================
import pandas as pd
import seaborn as sns
import matplotlib.pyplot as plt

# Reconstructing your data so this cell is self-contained
data = {
    'bacdive_genus': [
        'Streptococcus', 'Streptococcus', 'Streptococcus', 'Streptococcus', 
        'Bacillus', 'Escherichia', 'Staphylococcus', 'Staphylococcus', 
        'Escherichia', 'Escherichia', 'Escherichia', 'Staphylococcus', 
        'Staphylococcus', 'Streptococcus', 'Staphylococcus'
    ],
    'compound_name': [
        'maltose', 'sucrose', 'lactose', 'trehalose', 
        'nitrate', 'D-glucose', 'D-glucose', 'D-fructose', 
        'D-mannitol', 'L-arabinose', 'L-rhamnose', 'nitrate', 
        'maltose', 'raffinose', 'sucrose'
    ],
    'positive_strains': [
        1509, 1505, 1381, 1200, 1028, 873, 836, 833, 
        809, 806, 805, 805, 791, 784, 782
    ]
}

df = pd.DataFrame(data)

# Pivot the data so Genera are rows and Compounds are columns
pivot_df = df.pivot(index='bacdive_genus', columns='compound_name', values='positive_strains').fillna(0)

# Sort by the most metabolically active genera
pivot_df = pivot_df.loc[pivot_df.sum(axis=1).sort_values(ascending=False).index]

# Set up the plot
plt.figure(figsize=(12, 6))

# Draw the heatmap
sns.heatmap(
    pivot_df, 
    annot=True,          # Show the raw numbers inside the boxes
    fmt=".0f",           # Format as whole numbers
    cmap="YlOrRd",       # Yellow to Orange to Red color scale
    linewidths=1, 
    linecolor='white',
    cbar_kws={'label': 'Number of Positive Strains'}
)

# Clean up labels
plt.title("Metabolic Profiles of Top T4SS-GT2 Host Genera", fontsize=16, pad=20)
plt.xlabel("Metabolized Compound", fontsize=14)
plt.ylabel("Host Genus", fontsize=14)
plt.xticks(rotation=45, ha='right', fontsize=12)
plt.yticks(rotation=0, fontsize=12, fontstyle='italic') # Genera should be italicized!

plt.tight_layout()

# Save the figure
output_heatmap = "data/Figure2_Metabolic_Heatmap.pdf"
plt.savefig(output_heatmap, format="pdf", dpi=300)
print(f"Success! Metabolic Heatmap securely saved to '{output_heatmap}'")

plt.show()

Success! Metabolic Heatmap securely saved to 'data/Figure2_Metabolic_Heatmap.pdf'

# =============================================================================
# Cell: Fixed Figure 2 (Integrated Metabolic Niche Heatmap)
# =============================================================================
import pandas as pd
import seaborn as sns
import matplotlib.pyplot as plt
import matplotlib.gridspec as gridspec

print("Generating corrected integrated metabolic niche visualization...")

# 1. DATA CONSOLIDATION
data = {
    'Genus': [
        'Streptococcus', 'Staphylococcus', 'Escherichia', 
        'Vibrio', 'Salmonella', 'Burkholderia', 'Bacillus', 'Streptomyces'
    ],
    'Maltose': [1509, 791, 0, 0, 0, 0, 0, 0],
    'Sucrose': [1505, 782, 0, 0, 0, 0, 0, 0],
    'D-Glucose': [0, 836, 873, 0, 0, 0, 0, 0],
    'Nitrate Reduction': [0, 805, 0, 294, 141, 147, 1028, 101], 
    'Citrate Utilization': [0, 0, 0, 110, 165, 0, 0, 184],
    'Malate Utilization': [0, 0, 0, 0, 0, 222, 0, 0]
}

df_plot = pd.DataFrame(data).set_index('Genus')
carb_traits = ['Maltose', 'Sucrose', 'D-Glucose']
respiratory_traits = ['Nitrate Reduction', 'Citrate Utilization', 'Malate Utilization']
df_plot = df_plot[carb_traits + respiratory_traits]

# 2. PLOT EXECUTION
fig = plt.figure(figsize=(16, 9))
gs = gridspec.GridSpec(1, 2, width_ratios=[1, 1], wspace=0.05)
ax1 = plt.subplot(gs[0])
ax2 = plt.subplot(gs[1])

# Plot 1: Carbohydrate Niche (Blues/Greens)
sns.heatmap(df_plot[carb_traits], ax=ax1, annot=True, fmt="g", cmap="YlGnBu", 
            cbar=False, linewidths=.5, annot_kws={"size": 11})
ax1.set_title("I. Carbohydrate Biofilm Materials", fontsize=15, pad=15, fontweight='bold')
ax1.set_ylabel("Genus (GT2-T4SS Carrier)", fontsize=14, fontweight='bold')

# Plot 2: Respiratory/Acid Niche (Reds/Oranges)
sns.heatmap(df_plot[respiratory_traits], ax=ax2, annot=True, fmt="g", cmap="YlOrRd", 
            cbar=False, linewidths=.5, annot_kws={"size": 11})
ax2.set_title("II. Respiratory/Organic Acid Machinery", fontsize=15, pad=15, fontweight='bold')
ax2.set_ylabel("")
ax2.tick_params(axis='y', left=False, labelleft=False)

# --- THE FIX: Italicize Genus Names ---
for ax in [ax1]:
    ax.set_yticklabels(ax.get_yticklabels(), fontstyle='italic', size=13)
    ax.set_xticklabels(ax.get_xticklabels(), size=12, rotation=45, ha='right')

for ax in [ax2]:
    ax.set_xticklabels(ax.get_xticklabels(), size=12, rotation=45, ha='right')

plt.suptitle("Figure 2: Ecological Niche Versatility of GT2-T4SS Carriers", fontsize=22, y=1.02)
plt.tight_layout()

# Save
output_heatmap = "data/Figure2_Metabolic_Niche_Final.pdf"
plt.savefig(output_heatmap, format="pdf", dpi=300, bbox_inches='tight')
print(f"Success! Final Figure 2 saved to '{output_heatmap}'")
plt.show()

Generating corrected integrated metabolic niche visualization...

/tmp/ipykernel_727/2999728849.py:58: UserWarning: This figure includes Axes that are not compatible with tight_layout, so results might be incorrect.
  plt.tight_layout()

Success! Final Figure 2 saved to 'data/Figure2_Metabolic_Niche_Final.pdf'

	cazy_family	n_genomes_syntenic	n_contigs_syntenic	avg_distance_bp
0	GT2	767	817	5041.8
1	GH3	653	677	4273.8
2	GH31	611	648	1922.4
3	GT51	611	627	4569.1
4	GH13	610	654	4680.1

	biome_name	prevalence	odds_ratio	p_value	q_value
2	Marine Sediment	0.084389	5.546383	1.259040e-99	7.554241e-99
0	Barley Rhizosphere	0.208955	10.410634	1.027656e-09	3.082968e-09
1	Maize Rhizosphere	0.093985	4.122675	1.972691e-08	3.945381e-08

	kgroup	desc
0	K12984	(heptosyl)LPS beta-1,4-glucosyltransferase
1	K00720	ceramide glucosyltransferase
2	K11936	biofilm PGA synthesis N-glycosyltransferase PgaC
3	K11740	bacteriophage N4 adsorption protein B
4	K00697	alpha,alpha-trehalose-phosphate synthase (UDP-forming)

	kgroup	desc
0	K00574	cyclopropane-fatty-acyl-phospholipid synthase
1	K01912	phenylacetate-CoA ligase
2	K12984	(heptosyl)LPS beta-1,4-glucosyltransferase
3	K00720	ceramide glucosyltransferase
4	K11936	biofilm PGA synthesis N-glycosyltransferase PgaC

	mobile_element_type	Total_Elements_Found	Genomes_Containing_Element
0	IME_without_identified_DR	12	12
1	ICE_without_identified_DR	6	5
2	AICE_without_identified_DR	2	2

	bacdive_genus	compound_name	positive_strains
0	Streptococcus	maltose	1509
1	Streptococcus	sucrose	1505
2	Streptococcus	lactose	1381
3	Streptococcus	trehalose	1200
4	Bacillus	nitrate	1028
5	Escherichia	D-glucose	873
6	Staphylococcus	D-glucose	836
7	Staphylococcus	D-fructose	833
8	Escherichia	D-mannitol	809
9	Escherichia	L-arabinose	806
10	Escherichia	L-rhamnose	805
11	Staphylococcus	nitrate	805
12	Staphylococcus	maltose	791
13	Streptococcus	raffinose	784
14	Staphylococcus	sucrose	782

	bacdive_genus	compound_name	positive_strains
28	Vibrio	nitrate	294
43	Burkholderia	malate	222
68	Streptomyces	citrate	184
74	Salmonella	citrate	165
89	Burkholderia	nitrate	147
94	Salmonella	nitrate	141
118	Vibrio	citrate	110
126	Streptomyces	nitrate	101
128	Serratia	citrate	100
133	Aeromonas	nitrate	98

01 T4Ss Identification And Enrichment