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Part 3 — Graph Initialization & Management

Last updated: 2026-01-08

This notebook shows how to build and cache an IDTrack graph snapshot for:

  • homo_sapiens (human)

  • mus_musculus (mouse)

  • sus_scrofa (pig)

A graph build is the most expensive step. The good news:

  • you usually do it once per organism + snapshot boundary + external YAML configuration

  • the snapshot can be multi-assembly (human has overlapping GRCh38/GRCh37; mouse/pig are clean-handoff by release but legacy builds are supported)

  • then you reuse the cached graph for fast conversions

Learning objectives

  • Build (or load) a graph snapshot for each organism.

  • Verify that the snapshot exists on disk.

  • Learn practical graph-management habits (reload vs rebuild, cache hygiene).

Prerequisite: run 02_prepare_new_external_yaml.ipynb first (especially important for mouse and pig).

3.0 — What you should expect (time / disk)

Graph building can take:

  • minutes to hours (depends on organism, enabled externals, and cache status)

  • multiple GB of disk for cached tables + the graph pickle

Plan for this like you would plan for downloading a reference genome + annotation.

1

# Load notebook utilities (collapsible output magic for tutorials)
%load_ext _notebook_utils

2

# 1) Setup
from __future__ import annotations

import os
from pathlib import Path

import idtrack

LOCAL_REPOSITORY = Path(os.environ.get('IDTRACK_LOCAL_REPO', './idtrack_cache')).resolve()
LOCAL_REPOSITORY.mkdir(parents=True, exist_ok=True)

api = idtrack.API(local_repository=str(LOCAL_REPOSITORY))
api.configure_logger()

print('Local repository:', LOCAL_REPOSITORY)

Local repository: /Users/kemalinecik/git_nosync/master_idtrack/idtrack/docs/_notebooks/idtrack_cache

3.0.1 — Sanity check: do your external YAML files exist?

Human has a packaged default, but for mouse and pig you should have local *_externals_modified.yml files.

3

# External YAML presence (created in Part 2)
human_yaml = LOCAL_REPOSITORY / 'homo_sapiens_externals_modified.yml'
mouse_yaml = LOCAL_REPOSITORY / 'mus_musculus_externals_modified.yml'
pig_yaml = LOCAL_REPOSITORY / 'sus_scrofa_externals_modified.yml'

HAS_HUMAN_YAML = human_yaml.exists()
HAS_MOUSE_YAML = mouse_yaml.exists()
HAS_PIG_YAML = pig_yaml.exists()

print(("OK" if HAS_HUMAN_YAML else "NOTE: missing (human can fall back to packaged default)").ljust(55), human_yaml.name)
print(("OK" if HAS_MOUSE_YAML else "MISSING (create in Part 2 for mouse)").ljust(55), mouse_yaml.name)
print(("OK" if HAS_PIG_YAML else "MISSING (create in Part 2 for pig)").ljust(55), pig_yaml.name)

OK                                                      homo_sapiens_externals_modified.yml
OK                                                      mus_musculus_externals_modified.yml
OK                                                      sus_scrofa_externals_modified.yml

If a file is missing:

  • go back to 02_prepare_new_external_yaml.ipynb

  • generate the template and create the _modified.yml file

3.1–3.3 — Build graph snapshots (one per organism)

The canonical pattern is:

  1. resolve organism name

  2. pick snapshot release

  3. (optional) choose a primary genome assembly for output (defaults to the newest/highest-priority assembly for that organism)

  4. api.build_graph(...)

  5. inspect + reuse

We do this for each organism below. If you only need one organism, run only that section.

3.1 — Human graph initialization (multi-assembly)

By default, the human snapshot is built with GRCh38 as the primary assembly (assembly code 38), while also including GRCh37 (37) and older archives when they exist within the snapshot window.

This is what enables atlas-building workflows where different datasets were annotated with different genome builds, but you want one unified identifier space.

4

organism, latest_release = api.resolve_organism('human')
SNAPSHOT_RELEASE = latest_release  # pin to a specific release if needed
organism, SNAPSHOT_RELEASE

2026-01-11 21:05:28 INFO:verify_organism: Ensembl Rest API query to get the organism names and associated releases.

4

('homo_sapiens', 115)

5

%%collapse Click to show build logs
# Included for tutorial purposes only.

# Build (or load) the graph snapshot
# - calculate_caches=True speeds up later queries (slower build, faster use).
api.build_graph(organism_name=organism, snapshot_release=SNAPSHOT_RELEASE, calculate_caches=False)
Click to show build logs 
2026-01-11 21:05:39 INFO:database_manager: Using assembly-specific release range for homo_sapiens assembly 38: releases 76-115 (from config [76, None])
2026-01-11 21:05:46 INFO:graph_maker: The graph is being constructed: /Users/kemalinecik/git_nosync/master_idtrack/idtrack/docs/_notebooks/idtrack_cache/graph_homo_sapiens_min48_max115_narrow.pickle
2026-01-11 21:05:46 INFO:graph_maker: Graph is being created: gene
2026-01-11 21:05:48 INFO:database_manager: Using assembly-specific release range for homo_sapiens assembly 37: releases 55-115 (from config [55, None])
2026-01-11 21:06:04 INFO:database_manager: Using assembly-specific release range for homo_sapiens assembly 36: releases 48-54 (from config [48, 54])
2026-01-11 21:06:09 WARNING:graph_maker: Edge weights ignored due to duplicate entries: 2.
2026-01-11 21:06:09 INFO:graph_maker: Edges between across different IDs and self loops are being added.
2026-01-11 21:06:11 INFO:graph_maker: Edges between the same IDs are being added.
2026-01-11 21:06:36 WARNING:graph_maker: Retired ID come alive again: 8.
2026-01-11 21:06:36 INFO:graph_maker: Edges showing the retirement of IDs are being added.
2026-01-11 21:06:43 INFO:graph_maker: Problematic nodes in Ensembl ID history are being removed.
2026-01-11 21:06:51 WARNING:graph_maker: Nodes are deleted due to Ensembl ID history mistake: 3.
2026-01-11 21:06:51 INFO:graph_maker: Self-loops for latest release entries are being added.
2026-01-11 21:06:53 INFO:graph_maker: Node attributes are being added.
2026-01-11 21:06:54 INFO:graph_maker: Graph is being created: transcript
2026-01-11 21:06:56 INFO:graph_maker: Edges between across different IDs and self loops are being added.
2026-01-11 21:07:02 INFO:graph_maker: Edges between the same IDs are being added.
2026-01-11 21:08:43 WARNING:graph_maker: Retired ID come alive again: 5.
2026-01-11 21:08:43 INFO:graph_maker: Edges showing the retirement of IDs are being added.
2026-01-11 21:09:16 INFO:graph_maker: Problematic nodes in Ensembl ID history are being removed.
2026-01-11 21:09:47 INFO:graph_maker: Self-loops for latest release entries are being added.
2026-01-11 21:09:59 INFO:graph_maker: Node attributes are being added.
2026-01-11 21:10:10 INFO:graph_maker: Graph is being created: translation
2026-01-11 21:10:10 WARNING:graph_maker: Edge weights ignored due to duplicate entries: 4.
2026-01-11 21:10:10 INFO:graph_maker: Edges between across different IDs and self loops are being added.
2026-01-11 21:10:11 INFO:graph_maker: Edges between the same IDs are being added.
2026-01-11 21:10:50 WARNING:graph_maker: Retired ID come alive again: 166.
2026-01-11 21:10:50 INFO:graph_maker: Edges showing the retirement of IDs are being added.
2026-01-11 21:11:07 INFO:graph_maker: Problematic nodes in Ensembl ID history are being removed.
2026-01-11 21:11:22 WARNING:graph_maker: Nodes are deleted due to Ensembl ID history mistake: 1.
2026-01-11 21:11:22 INFO:graph_maker: Self-loops for latest release entries are being added.
2026-01-11 21:11:27 INFO:graph_maker: Node attributes are being added.
2026-01-11 21:11:31 WARNING:graph_maker: Intersecting Ensembl nodes: Nodes in 'transcript' will be replaced by 'translation': 'ENST00000515292.1'.
2026-01-11 21:11:39 INFO:graph_maker: Establishing connection between different forms.
2026-01-11 21:18:08 INFO:graph_maker: Edges between external IDs to Ensembl IDs is being added for 'gene'.
2026-01-11 21:32:15 INFO:graph_maker: Edges between external IDs to Ensembl IDs is being added for 'transcript'.
2026-01-11 21:45:25 INFO:graph_maker: Edges between external IDs to Ensembl IDs is being added for 'translation'.
2026-01-11 21:57:42 INFO:graph_maker: Versionless Ensembl IDs are being connected.
2026-01-11 21:57:44 INFO:graph_maker: Edges between versionless ID to version ID has been added for 'gene', assembly 36.
2026-01-11 21:57:55 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens77_processed_versioninfo_gene`
2026-01-11 21:57:55 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens77_processed_ids_gene`
2026-01-11 21:57:58 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens78_processed_versioninfo_gene`
2026-01-11 21:57:58 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens78_processed_ids_gene`
2026-01-11 21:58:01 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens79_processed_versioninfo_gene`
2026-01-11 21:58:01 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens79_processed_ids_gene`
2026-01-11 21:58:04 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens80_processed_versioninfo_gene`
2026-01-11 21:58:04 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens80_processed_ids_gene`
2026-01-11 21:58:07 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens81_processed_versioninfo_gene`
2026-01-11 21:58:07 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens81_processed_ids_gene`
2026-01-11 21:58:10 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens82_processed_versioninfo_gene`
2026-01-11 21:58:10 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens82_processed_ids_gene`
2026-01-11 21:58:13 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens83_processed_versioninfo_gene`
2026-01-11 21:58:13 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens83_processed_ids_gene`
2026-01-11 21:58:16 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens84_processed_versioninfo_gene`
2026-01-11 21:58:16 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens84_processed_ids_gene`
2026-01-11 21:58:19 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens85_processed_versioninfo_gene`
2026-01-11 21:58:19 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens85_processed_ids_gene`
2026-01-11 21:58:22 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens86_processed_versioninfo_gene`
2026-01-11 21:58:22 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens86_processed_ids_gene`
2026-01-11 21:58:25 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens87_processed_versioninfo_gene`
2026-01-11 21:58:25 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens87_processed_ids_gene`
2026-01-11 21:58:28 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens88_processed_versioninfo_gene`
2026-01-11 21:58:28 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens88_processed_ids_gene`
2026-01-11 21:58:31 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens89_processed_versioninfo_gene`
2026-01-11 21:58:31 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens89_processed_ids_gene`
2026-01-11 21:58:34 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens90_processed_versioninfo_gene`
2026-01-11 21:58:34 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens90_processed_ids_gene`
2026-01-11 21:58:37 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens91_processed_versioninfo_gene`
2026-01-11 21:58:37 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens91_processed_ids_gene`
2026-01-11 21:58:40 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens92_processed_versioninfo_gene`
2026-01-11 21:58:40 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens92_processed_ids_gene`
2026-01-11 21:58:43 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens93_processed_versioninfo_gene`
2026-01-11 21:58:43 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens93_processed_ids_gene`
2026-01-11 21:58:46 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens94_processed_versioninfo_gene`
2026-01-11 21:58:46 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens94_processed_ids_gene`
2026-01-11 21:58:49 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens95_processed_versioninfo_gene`
2026-01-11 21:58:49 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens95_processed_ids_gene`
2026-01-11 21:58:52 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens96_processed_versioninfo_gene`
2026-01-11 21:58:52 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens96_processed_ids_gene`
2026-01-11 21:58:55 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens97_processed_versioninfo_gene`
2026-01-11 21:58:55 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens97_processed_ids_gene`
2026-01-11 21:58:58 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens98_processed_versioninfo_gene`
2026-01-11 21:58:58 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens98_processed_ids_gene`
2026-01-11 21:59:01 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens99_processed_versioninfo_gene`
2026-01-11 21:59:01 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens99_processed_ids_gene`
2026-01-11 21:59:04 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens100_processed_versioninfo_gene`
2026-01-11 21:59:04 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens100_processed_ids_gene`
2026-01-11 21:59:07 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens101_processed_versioninfo_gene`
2026-01-11 21:59:07 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens101_processed_ids_gene`
2026-01-11 21:59:10 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens102_processed_versioninfo_gene`
2026-01-11 21:59:10 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens102_processed_ids_gene`
2026-01-11 21:59:13 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens103_processed_versioninfo_gene`
2026-01-11 21:59:13 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens103_processed_ids_gene`
2026-01-11 21:59:16 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens104_processed_versioninfo_gene`
2026-01-11 21:59:16 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens104_processed_ids_gene`
2026-01-11 21:59:19 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens105_processed_versioninfo_gene`
2026-01-11 21:59:19 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens105_processed_ids_gene`
2026-01-11 21:59:22 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens106_processed_versioninfo_gene`
2026-01-11 21:59:22 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens106_processed_ids_gene`
2026-01-11 21:59:25 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens107_processed_versioninfo_gene`
2026-01-11 21:59:25 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens107_processed_ids_gene`
2026-01-11 21:59:28 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens108_processed_versioninfo_gene`
2026-01-11 21:59:28 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens108_processed_ids_gene`
2026-01-11 21:59:31 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens109_processed_versioninfo_gene`
2026-01-11 21:59:31 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens109_processed_ids_gene`
2026-01-11 21:59:34 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens110_processed_versioninfo_gene`
2026-01-11 21:59:34 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens110_processed_ids_gene`
2026-01-11 21:59:37 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens111_processed_versioninfo_gene`
2026-01-11 21:59:37 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens111_processed_ids_gene`
2026-01-11 21:59:40 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens112_processed_versioninfo_gene`
2026-01-11 21:59:40 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens112_processed_ids_gene`
2026-01-11 21:59:43 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens113_processed_versioninfo_gene`
2026-01-11 21:59:43 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens113_processed_ids_gene`
2026-01-11 21:59:46 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens114_processed_versioninfo_gene`
2026-01-11 21:59:46 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens114_processed_ids_gene`
2026-01-11 21:59:49 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens115_processed_versioninfo_gene`
2026-01-11 21:59:49 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-37.h5` with key `ens115_processed_ids_gene`
2026-01-11 21:59:51 INFO:graph_maker: Edges between versionless ID to version ID has been added for 'gene', assembly 37.
2026-01-11 21:59:51 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens76_processed_ids_gene`
2026-01-11 21:59:52 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens77_processed_ids_gene`
2026-01-11 21:59:53 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens78_processed_ids_gene`
2026-01-11 21:59:54 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens79_processed_ids_gene`
2026-01-11 21:59:56 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens80_processed_ids_gene`
2026-01-11 21:59:57 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens81_processed_ids_gene`
2026-01-11 21:59:58 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens82_processed_ids_gene`
2026-01-11 21:59:59 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens83_processed_ids_gene`
2026-01-11 22:00:01 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens84_processed_ids_gene`
2026-01-11 22:00:02 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens85_processed_ids_gene`
2026-01-11 22:00:03 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens86_processed_ids_gene`
2026-01-11 22:00:04 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens87_processed_ids_gene`
2026-01-11 22:00:05 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens88_processed_ids_gene`
2026-01-11 22:00:07 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens89_processed_ids_gene`
2026-01-11 22:00:08 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens90_processed_ids_gene`
2026-01-11 22:00:09 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens91_processed_ids_gene`
2026-01-11 22:00:10 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens92_processed_ids_gene`
2026-01-11 22:00:12 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens93_processed_ids_gene`
2026-01-11 22:00:13 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens94_processed_ids_gene`
2026-01-11 22:00:14 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens95_processed_ids_gene`
2026-01-11 22:00:15 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens96_processed_ids_gene`
2026-01-11 22:00:17 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens97_processed_ids_gene`
2026-01-11 22:00:18 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens98_processed_ids_gene`
2026-01-11 22:00:19 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens99_processed_ids_gene`
2026-01-11 22:00:21 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens100_processed_ids_gene`
2026-01-11 22:00:22 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens101_processed_ids_gene`
2026-01-11 22:00:23 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens102_processed_ids_gene`
2026-01-11 22:00:24 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens103_processed_ids_gene`
2026-01-11 22:00:26 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens104_processed_ids_gene`
2026-01-11 22:00:27 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens105_processed_ids_gene`
2026-01-11 22:00:28 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens106_processed_ids_gene`
2026-01-11 22:00:29 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens107_processed_ids_gene`
2026-01-11 22:00:31 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens108_processed_ids_gene`
2026-01-11 22:00:32 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens109_processed_ids_gene`
2026-01-11 22:00:33 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens110_processed_ids_gene`
2026-01-11 22:00:35 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens111_processed_ids_gene`
2026-01-11 22:00:36 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens112_processed_ids_gene`
2026-01-11 22:00:38 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens113_processed_ids_gene`
2026-01-11 22:00:39 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens114_processed_ids_gene`
2026-01-11 22:00:41 INFO:database_manager: Exporting to the following file `homo_sapiens_assembly-38.h5` with key `ens115_processed_ids_gene`
2026-01-11 22:00:42 INFO:graph_maker: Edges between versionless ID to version ID has been added for 'gene', assembly 38.
2026-01-11 22:00:42 INFO:graph_maker: Synonymous external nodes are being merged into one.
2026-01-11 22:00:47 INFO:graph_maker: Number of removed nodes in the process of merging synonymous nodes: 13316
2026-01-11 22:02:30 INFO:graph_maker: The graph is being exported as '/Users/kemalinecik/git_nosync/master_idtrack/idtrack/docs/_notebooks/idtrack_cache/graph_homo_sapiens_min48_max115_narrow.pickle'.
2026-01-11 22:04:59 INFO:the_graph: Cached properties being calculated: available_genome_assemblies
2026-01-11 22:04:59 INFO:the_graph: Cached properties being calculated: combined_edges
2026-01-11 22:07:33 INFO:the_graph: Cached properties being calculated: combined_edges_genes
2026-01-11 22:08:28 INFO:the_graph: Cached properties being calculated: combined_edges_assembly_specific_genes
6

# Quick inspection
g = api.track.graph
print('Organism:', g.graph.get('organism'))
print('Snapshot release:', g.graph.get('ensembl_release'))
print('Main assembly:', g.graph.get('genome_assembly'))
print('Assemblies in this graph:', sorted(api.list_genome_assemblies()))
print('Nodes:', g.number_of_nodes())
print('Edges:', g.number_of_edges())

aed = sorted(getattr(g, 'available_external_databases', []))
print('External DBs enabled (count):', len(aed))
print('External DBs (first 20):', aed[:20])

Organism: homo_sapiens
Snapshot release: 115
Main assembly: 38
Assemblies in this graph: [36, 37, 38]
Nodes: 3682041

2026-01-11 22:08:48 INFO:the_graph: Cached properties being calculated: available_external_databases

Edges: 8615426
External DBs enabled (count): 27
External DBs (first 20): ['CCDS', 'Clone_based_ensembl_gene', 'Clone_based_vega_gene', 'EntrezGene', 'HGNC Symbol', 'Havana gene', 'Havana transcript', 'Havana translation', 'NCBI gene', 'NCBI gene (formerly Entrezgene)', 'RFAM', 'RefSeq_mRNA', 'RefSeq_mRNA_predicted', 'RefSeq_ncRNA', 'RefSeq_ncRNA_predicted', 'RefSeq_peptide', 'RefSeq_peptide_predicted', 'UniProtKB Gene Name', 'Uniprot/SPTREMBL', 'Uniprot/SWISSPROT']

7

# Where is the graph file stored?
sorted(LOCAL_REPOSITORY.glob('graph_homo_sapiens*.pickle'))[-5:]

7

[PosixPath('/Users/kemalinecik/git_nosync/master_idtrack/idtrack/docs/_notebooks/idtrack_cache/graph_homo_sapiens_min48_max115_narrow.pickle')]

3.2 — Mouse graph initialization (clean handoff)

Mouse is a clean-handoff species (one maintained assembly per release: GRCm37 → GRCm38 → GRCm39). Older assemblies mainly matter for legacy datasets and archive releases; you typically do not have overlapping assemblies within the same release.

4

organism, latest_release = api.resolve_organism('mus musculus')
SNAPSHOT_RELEASE = latest_release
organism, SNAPSHOT_RELEASE

2026-01-11 22:44:22 INFO:verify_organism: Ensembl Rest API query to get the organism names and associated releases.

4

('mus_musculus', 115)

5

%%collapse Click to show build logs
# Included for tutorial purposes only.

# Build (or load) the mouse graph snapshot
if HAS_MOUSE_YAML:
    api.build_graph(organism_name=organism, snapshot_release=SNAPSHOT_RELEASE, calculate_caches=False)
else:
    print('Skipping mouse build: mus_musculus_externals_modified.yml is missing (run Part 2 first).')
Click to show build logs 
2026-01-11 22:44:34 INFO:database_manager: Using assembly-specific release range for mus_musculus assembly 39: releases 103-115 (from config [103, None])
2026-01-11 22:44:36 INFO:graph_maker: The graph is being constructed: /Users/kemalinecik/git_nosync/master_idtrack/idtrack/docs/_notebooks/idtrack_cache/graph_mus_musculus_min48_max115_narrow.pickle
2026-01-11 22:44:36 INFO:graph_maker: Graph is being created: gene
2026-01-11 22:44:38 INFO:database_manager: Using assembly-specific release range for mus_musculus assembly 38: releases 68-102 (from config [68, 102])
2026-01-11 22:44:46 INFO:database_manager: Using assembly-specific release range for mus_musculus assembly 37: releases 48-67 (from config [48, 67])
2026-01-11 22:44:58 INFO:graph_maker: Edges between across different IDs and self loops are being added.
2026-01-11 22:45:01 INFO:graph_maker: Edges between the same IDs are being added.
2026-01-11 22:45:21 WARNING:graph_maker: Retired ID come alive again: 2.
2026-01-11 22:45:21 INFO:graph_maker: Edges showing the retirement of IDs are being added.
2026-01-11 22:45:27 INFO:graph_maker: Problematic nodes in Ensembl ID history are being removed.
2026-01-11 22:45:33 INFO:graph_maker: Self-loops for latest release entries are being added.
2026-01-11 22:45:35 INFO:graph_maker: Node attributes are being added.
2026-01-11 22:45:36 INFO:graph_maker: Graph is being created: transcript
2026-01-11 22:45:37 INFO:graph_maker: Edges between across different IDs and self loops are being added.
2026-01-11 22:45:41 INFO:graph_maker: Edges between the same IDs are being added.
2026-01-11 22:46:38 WARNING:graph_maker: Retired ID come alive again: 3.
2026-01-11 22:46:38 INFO:graph_maker: Edges showing the retirement of IDs are being added.
2026-01-11 22:46:56 INFO:graph_maker: Problematic nodes in Ensembl ID history are being removed.
2026-01-11 22:47:13 INFO:graph_maker: Self-loops for latest release entries are being added.
2026-01-11 22:47:19 INFO:graph_maker: Node attributes are being added.
2026-01-11 22:47:25 INFO:graph_maker: Graph is being created: translation
2026-01-11 22:47:25 INFO:graph_maker: Edges between across different IDs and self loops are being added.
2026-01-11 22:47:26 INFO:graph_maker: Edges between the same IDs are being added.
2026-01-11 22:47:46 WARNING:graph_maker: Retired ID come alive again: 2.
2026-01-11 22:47:46 INFO:graph_maker: Edges showing the retirement of IDs are being added.
2026-01-11 22:47:56 INFO:graph_maker: Problematic nodes in Ensembl ID history are being removed.
2026-01-11 22:48:05 INFO:graph_maker: Self-loops for latest release entries are being added.
2026-01-11 22:48:06 INFO:graph_maker: Node attributes are being added.
2026-01-11 22:48:12 INFO:graph_maker: Establishing connection between different forms.
2026-01-11 22:48:48 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens62_processed_idsraw_transcript_gene`
2026-01-11 22:48:50 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens62_processed_idsraw_translation_gene`
2026-01-11 22:48:51 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens62_common_relationcurrent`
2026-01-11 22:48:55 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens63_processed_idsraw_transcript_gene`
2026-01-11 22:48:57 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens63_processed_idsraw_translation_gene`
2026-01-11 22:48:59 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens63_common_relationcurrent`
2026-01-11 22:49:12 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens64_processed_idsraw_transcript_gene`
2026-01-11 22:49:14 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens64_processed_idsraw_translation_gene`
2026-01-11 22:49:15 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens64_common_relationcurrent`
2026-01-11 22:49:19 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens65_processed_idsraw_transcript_gene`
2026-01-11 22:49:20 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens65_processed_idsraw_translation_gene`
2026-01-11 22:49:21 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens65_common_relationcurrent`
2026-01-11 22:49:25 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens66_processed_idsraw_transcript_gene`
2026-01-11 22:49:26 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens66_processed_idsraw_translation_gene`
2026-01-11 22:49:27 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens66_common_relationcurrent`
2026-01-11 22:49:31 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens67_processed_idsraw_transcript_gene`
2026-01-11 22:49:32 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens67_processed_idsraw_translation_gene`
2026-01-11 22:49:33 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens67_common_relationcurrent`
2026-01-11 22:49:37 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens68_processed_idsraw_transcript_gene`
2026-01-11 22:49:39 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens68_processed_idsraw_translation_gene`
2026-01-11 22:49:40 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens68_common_relationcurrent`
2026-01-11 22:49:45 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens69_processed_idsraw_transcript_gene`
2026-01-11 22:49:46 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens69_processed_idsraw_translation_gene`
2026-01-11 22:49:47 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens69_common_relationcurrent`
2026-01-11 22:49:51 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens70_processed_idsraw_transcript_gene`
2026-01-11 22:49:52 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens70_processed_idsraw_translation_gene`
2026-01-11 22:49:53 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens70_common_relationcurrent`
2026-01-11 22:49:56 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens71_processed_idsraw_transcript_gene`
2026-01-11 22:49:57 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens71_processed_idsraw_translation_gene`
2026-01-11 22:49:59 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens71_common_relationcurrent`
2026-01-11 22:50:02 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens72_processed_idsraw_transcript_gene`
2026-01-11 22:50:03 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens72_processed_idsraw_translation_gene`
2026-01-11 22:50:05 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens72_common_relationcurrent`
2026-01-11 22:50:08 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens73_processed_idsraw_transcript_gene`
2026-01-11 22:50:09 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens73_processed_idsraw_translation_gene`
2026-01-11 22:50:10 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens73_common_relationcurrent`
2026-01-11 22:50:14 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens74_processed_idsraw_transcript_gene`
2026-01-11 22:50:15 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens74_processed_idsraw_translation_gene`
2026-01-11 22:50:16 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens74_common_relationcurrent`
2026-01-11 22:50:20 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens75_processed_idsraw_transcript_gene`
2026-01-11 22:50:21 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens75_processed_idsraw_translation_gene`
2026-01-11 22:50:22 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens75_common_relationcurrent`
2026-01-11 22:50:26 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens76_processed_idsraw_transcript_gene`
2026-01-11 22:50:27 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens76_processed_idsraw_translation_gene`
2026-01-11 22:50:28 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens76_common_relationcurrent`
2026-01-11 22:50:32 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens77_processed_idsraw_transcript_gene`
2026-01-11 22:50:33 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens77_processed_idsraw_translation_gene`
2026-01-11 22:50:34 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens77_common_relationcurrent`
2026-01-11 22:50:38 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens78_processed_idsraw_transcript_gene`
2026-01-11 22:50:39 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens78_processed_idsraw_translation_gene`
2026-01-11 22:50:40 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens78_common_relationcurrent`
2026-01-11 22:50:46 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens79_processed_idsraw_transcript_gene`
2026-01-11 22:50:47 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens79_processed_idsraw_translation_gene`
2026-01-11 22:50:48 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens79_common_relationcurrent`
2026-01-11 22:50:52 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens80_processed_idsraw_transcript_gene`
2026-01-11 22:50:54 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens80_processed_idsraw_translation_gene`
2026-01-11 22:50:55 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens80_common_relationcurrent`
2026-01-11 22:50:59 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens81_processed_idsraw_transcript_gene`
2026-01-11 22:51:01 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens81_processed_idsraw_translation_gene`
2026-01-11 22:51:02 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens81_common_relationcurrent`
2026-01-11 22:51:08 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens82_processed_idsraw_transcript_gene`
2026-01-11 22:51:10 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens82_processed_idsraw_translation_gene`
2026-01-11 22:51:11 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens82_common_relationcurrent`
2026-01-11 22:51:16 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens83_processed_idsraw_transcript_gene`
2026-01-11 22:51:17 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens83_processed_idsraw_translation_gene`
2026-01-11 22:51:19 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens83_common_relationcurrent`
2026-01-11 22:51:23 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens84_processed_idsraw_transcript_gene`
2026-01-11 22:51:25 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens84_processed_idsraw_translation_gene`
2026-01-11 22:51:26 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens84_common_relationcurrent`
2026-01-11 22:51:31 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens85_processed_idsraw_transcript_gene`
2026-01-11 22:51:32 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens85_processed_idsraw_translation_gene`
2026-01-11 22:51:34 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens85_common_relationcurrent`
2026-01-11 22:51:38 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens86_processed_idsraw_transcript_gene`
2026-01-11 22:51:40 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens86_processed_idsraw_translation_gene`
2026-01-11 22:51:41 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens86_common_relationcurrent`
2026-01-11 22:51:46 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens87_processed_idsraw_transcript_gene`
2026-01-11 22:51:47 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens87_processed_idsraw_translation_gene`
2026-01-11 22:51:49 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens87_common_relationcurrent`
2026-01-11 22:51:54 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens88_processed_idsraw_transcript_gene`
2026-01-11 22:51:56 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens88_processed_idsraw_translation_gene`
2026-01-11 22:51:57 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens88_common_relationcurrent`
2026-01-11 22:52:02 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens89_processed_idsraw_transcript_gene`
2026-01-11 22:52:04 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens89_processed_idsraw_translation_gene`
2026-01-11 22:52:05 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens89_common_relationcurrent`
2026-01-11 22:52:10 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens90_processed_idsraw_transcript_gene`
2026-01-11 22:52:12 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens90_processed_idsraw_translation_gene`
2026-01-11 22:52:14 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens90_common_relationcurrent`
2026-01-11 22:52:19 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens91_processed_idsraw_transcript_gene`
2026-01-11 22:52:21 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens91_processed_idsraw_translation_gene`
2026-01-11 22:52:23 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens91_common_relationcurrent`
2026-01-11 22:52:28 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens92_processed_idsraw_transcript_gene`
2026-01-11 22:52:30 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens92_processed_idsraw_translation_gene`
2026-01-11 22:52:32 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens92_common_relationcurrent`
2026-01-11 22:52:37 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens93_processed_idsraw_transcript_gene`
2026-01-11 22:52:39 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens93_processed_idsraw_translation_gene`
2026-01-11 22:52:41 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens93_common_relationcurrent`
2026-01-11 22:52:46 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens94_processed_idsraw_transcript_gene`
2026-01-11 22:52:48 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens94_processed_idsraw_translation_gene`
2026-01-11 22:52:50 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens94_common_relationcurrent`
2026-01-11 22:52:55 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens95_processed_idsraw_transcript_gene`
2026-01-11 22:52:57 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens95_processed_idsraw_translation_gene`
2026-01-11 22:52:59 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens95_common_relationcurrent`
2026-01-11 22:53:05 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens96_processed_idsraw_transcript_gene`
2026-01-11 22:53:07 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens96_processed_idsraw_translation_gene`
2026-01-11 22:53:08 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens96_common_relationcurrent`
2026-01-11 22:53:14 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens97_processed_idsraw_transcript_gene`
2026-01-11 22:53:16 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens97_processed_idsraw_translation_gene`
2026-01-11 22:53:18 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens97_common_relationcurrent`
2026-01-11 22:53:26 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens98_processed_idsraw_transcript_gene`
2026-01-11 22:53:28 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens98_processed_idsraw_translation_gene`
2026-01-11 22:53:29 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens98_common_relationcurrent`
2026-01-11 22:53:35 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens99_processed_idsraw_transcript_gene`
2026-01-11 22:53:37 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens99_processed_idsraw_translation_gene`
2026-01-11 22:53:39 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens99_common_relationcurrent`
2026-01-11 22:53:45 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens100_processed_idsraw_transcript_gene`
2026-01-11 22:53:47 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens100_processed_idsraw_translation_gene`
2026-01-11 22:53:48 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens100_common_relationcurrent`
2026-01-11 22:53:54 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens101_processed_idsraw_transcript_gene`
2026-01-11 22:53:56 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens101_processed_idsraw_translation_gene`
2026-01-11 22:53:58 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens101_common_relationcurrent`
2026-01-11 22:54:04 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens102_processed_idsraw_transcript_gene`
2026-01-11 22:54:06 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens102_processed_idsraw_translation_gene`
2026-01-11 22:54:07 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens102_common_relationcurrent`
2026-01-11 22:54:13 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens103_processed_idsraw_transcript_gene`
2026-01-11 22:54:16 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens103_processed_idsraw_translation_gene`
2026-01-11 22:54:18 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens103_common_relationcurrent`
2026-01-11 22:54:23 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens104_processed_idsraw_transcript_gene`
2026-01-11 22:54:26 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens104_processed_idsraw_translation_gene`
2026-01-11 22:54:28 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens104_common_relationcurrent`
2026-01-11 22:54:33 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens105_processed_idsraw_transcript_gene`
2026-01-11 22:54:36 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens105_processed_idsraw_translation_gene`
2026-01-11 22:54:38 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens105_common_relationcurrent`
2026-01-11 22:54:44 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens106_processed_idsraw_transcript_gene`
2026-01-11 22:54:46 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens106_processed_idsraw_translation_gene`
2026-01-11 22:54:48 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens106_common_relationcurrent`
2026-01-11 22:54:54 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens107_processed_idsraw_transcript_gene`
2026-01-11 22:54:56 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens107_processed_idsraw_translation_gene`
2026-01-11 22:54:58 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens107_common_relationcurrent`
2026-01-11 22:55:05 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens108_processed_idsraw_transcript_gene`
2026-01-11 22:55:07 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens108_processed_idsraw_translation_gene`
2026-01-11 22:55:09 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens108_common_relationcurrent`
2026-01-11 22:55:15 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens109_processed_idsraw_transcript_gene`
2026-01-11 22:55:18 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens109_processed_idsraw_translation_gene`
2026-01-11 22:55:20 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens109_common_relationcurrent`
2026-01-11 22:55:26 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens110_processed_idsraw_transcript_gene`
2026-01-11 22:55:29 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens110_processed_idsraw_translation_gene`
2026-01-11 22:55:31 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens110_common_relationcurrent`
2026-01-11 22:55:37 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens111_processed_idsraw_transcript_gene`
2026-01-11 22:55:39 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens111_processed_idsraw_translation_gene`
2026-01-11 22:55:41 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens111_common_relationcurrent`
2026-01-11 22:55:47 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens112_processed_idsraw_transcript_gene`
2026-01-11 22:55:50 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens112_processed_idsraw_translation_gene`
2026-01-11 22:55:52 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens112_common_relationcurrent`
2026-01-11 22:55:58 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens113_processed_idsraw_transcript_gene`
2026-01-11 22:56:02 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens113_processed_idsraw_translation_gene`
2026-01-11 22:56:05 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens113_common_relationcurrent`
2026-01-11 22:56:18 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens114_processed_idsraw_transcript_gene`
2026-01-11 22:56:22 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens114_processed_idsraw_translation_gene`
2026-01-11 22:56:25 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens114_common_relationcurrent`
2026-01-11 22:56:36 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens115_processed_idsraw_transcript_gene`
2026-01-11 22:56:39 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens115_processed_idsraw_translation_gene`
2026-01-11 22:56:42 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens115_common_relationcurrent`
2026-01-11 22:56:52 INFO:graph_maker: Edges between external IDs to Ensembl IDs is being added for 'gene'.
2026-01-11 22:56:56 INFO:database_manager: Using legacy column names (target_identity, query_identity) for identity_xref table in Ensembl release 52.
2026-01-11 22:56:58 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens52_processed_external_relevant_gene`
2026-01-11 22:57:06 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens53_processed_external_relevant_gene`
2026-01-11 22:57:15 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens54_processed_external_relevant_gene`
2026-01-11 22:57:23 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens55_processed_external_relevant_gene`
2026-01-11 22:57:27 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens56_processed_external_relevant_gene`
2026-01-11 22:57:33 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens57_processed_external_relevant_gene`
2026-01-11 22:57:39 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens58_processed_external_relevant_gene`
2026-01-11 22:57:45 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens59_processed_external_relevant_gene`
2026-01-11 22:57:52 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens60_processed_external_relevant_gene`
2026-01-11 22:57:58 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens61_processed_external_relevant_gene`
2026-01-11 22:58:05 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens62_processed_external_relevant_gene`
2026-01-11 22:58:13 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens63_processed_external_relevant_gene`
2026-01-11 22:58:27 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens64_processed_external_relevant_gene`
2026-01-11 22:58:41 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens65_processed_external_relevant_gene`
2026-01-11 22:59:00 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens66_processed_external_relevant_gene`
2026-01-11 22:59:14 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens67_processed_external_relevant_gene`
2026-01-11 22:59:27 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens68_processed_external_relevant_gene`
2026-01-11 22:59:41 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens69_processed_external_relevant_gene`
2026-01-11 22:59:55 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens70_processed_external_relevant_gene`
2026-01-11 23:00:09 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens71_processed_external_relevant_gene`
2026-01-11 23:00:23 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens72_processed_external_relevant_gene`
2026-01-11 23:00:37 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens73_processed_external_relevant_gene`
2026-01-11 23:00:52 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens74_processed_external_relevant_gene`
2026-01-11 23:01:07 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens75_processed_external_relevant_gene`
2026-01-11 23:01:23 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens76_processed_external_relevant_gene`
2026-01-11 23:01:42 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens77_processed_external_relevant_gene`
2026-01-11 23:02:02 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens78_processed_external_relevant_gene`
2026-01-11 23:02:22 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens79_processed_external_relevant_gene`
2026-01-11 23:02:42 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens80_processed_external_relevant_gene`
2026-01-11 23:03:11 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens81_processed_external_relevant_gene`
2026-01-11 23:03:32 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens82_processed_external_relevant_gene`
2026-01-11 23:03:54 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens83_processed_external_relevant_gene`
2026-01-11 23:04:15 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens84_processed_external_relevant_gene`
2026-01-11 23:04:36 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens85_processed_external_relevant_gene`
2026-01-11 23:04:55 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens86_processed_external_relevant_gene`
2026-01-11 23:05:18 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens87_processed_external_relevant_gene`
2026-01-11 23:05:41 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens88_processed_external_relevant_gene`
2026-01-11 23:05:59 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens89_processed_external_relevant_gene`
2026-01-11 23:06:12 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens90_processed_external_relevant_gene`
2026-01-11 23:06:26 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens91_processed_external_relevant_gene`
2026-01-11 23:06:46 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens92_processed_external_relevant_gene`
2026-01-11 23:06:58 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens93_processed_external_relevant_gene`
2026-01-11 23:07:11 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens94_processed_external_relevant_gene`
2026-01-11 23:07:23 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens95_processed_external_relevant_gene`
2026-01-11 23:07:36 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens96_processed_external_relevant_gene`
2026-01-11 23:07:49 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens97_processed_external_relevant_gene`
2026-01-11 23:08:02 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens98_processed_external_relevant_gene`
2026-01-11 23:08:15 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens99_processed_external_relevant_gene`
2026-01-11 23:08:31 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens100_processed_external_relevant_gene`
2026-01-11 23:08:56 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens101_processed_external_relevant_gene`
2026-01-11 23:09:21 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens102_processed_external_relevant_gene`
2026-01-11 23:09:42 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens103_processed_external_relevant_gene`
2026-01-11 23:10:08 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens104_processed_external_relevant_gene`
2026-01-11 23:10:22 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens105_processed_external_relevant_gene`
2026-01-11 23:10:35 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens106_processed_external_relevant_gene`
2026-01-11 23:10:49 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens107_processed_external_relevant_gene`
2026-01-11 23:11:02 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens108_processed_external_relevant_gene`
2026-01-11 23:11:16 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens109_processed_external_relevant_gene`
2026-01-11 23:11:30 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens110_processed_external_relevant_gene`
2026-01-11 23:11:44 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens111_processed_external_relevant_gene`
2026-01-11 23:11:58 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens112_processed_external_relevant_gene`
2026-01-11 23:12:12 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens113_processed_external_relevant_gene`
2026-01-11 23:12:26 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens114_processed_external_relevant_gene`
2026-01-11 23:12:40 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens115_processed_external_relevant_gene`
2026-01-11 23:12:48 INFO:graph_maker: Edges between external IDs to Ensembl IDs is being added for 'transcript'.
2026-01-11 23:12:52 INFO:database_manager: Using legacy column names (target_identity, query_identity) for identity_xref table in Ensembl release 50.
2026-01-11 23:12:57 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens50_processed_external_relevant_transcript`
2026-01-11 23:13:00 INFO:database_manager: Using legacy column names (target_identity, query_identity) for identity_xref table in Ensembl release 51.
2026-01-11 23:13:06 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens51_processed_external_relevant_transcript`
2026-01-11 23:13:09 INFO:database_manager: Using legacy column names (target_identity, query_identity) for identity_xref table in Ensembl release 52.
2026-01-11 23:13:15 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens52_processed_external_relevant_transcript`
2026-01-11 23:13:32 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens53_processed_external_relevant_transcript`
2026-01-11 23:13:51 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens54_processed_external_relevant_transcript`
2026-01-11 23:14:09 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens55_processed_external_relevant_transcript`
2026-01-11 23:14:15 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens56_processed_external_relevant_transcript`
2026-01-11 23:14:23 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens57_processed_external_relevant_transcript`
2026-01-11 23:14:33 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens58_processed_external_relevant_transcript`
2026-01-11 23:14:44 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens59_processed_external_relevant_transcript`
2026-01-11 23:14:55 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens60_processed_external_relevant_transcript`
2026-01-11 23:15:06 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens61_processed_external_relevant_transcript`
2026-01-11 23:15:17 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens62_processed_external_relevant_transcript`
2026-01-11 23:15:28 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens63_processed_external_relevant_transcript`
2026-01-11 23:15:40 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens64_processed_external_relevant_transcript`
2026-01-11 23:15:55 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens65_processed_external_relevant_transcript`
2026-01-11 23:16:09 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens66_processed_external_relevant_transcript`
2026-01-11 23:16:23 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens67_processed_external_relevant_transcript`
2026-01-11 23:16:36 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens68_processed_external_relevant_transcript`
2026-01-11 23:16:50 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens69_processed_external_relevant_transcript`
2026-01-11 23:17:04 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens70_processed_external_relevant_transcript`
2026-01-11 23:17:17 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens71_processed_external_relevant_transcript`
2026-01-11 23:17:31 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens72_processed_external_relevant_transcript`
2026-01-11 23:17:46 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens73_processed_external_relevant_transcript`
2026-01-11 23:18:00 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens74_processed_external_relevant_transcript`
2026-01-11 23:18:15 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens75_processed_external_relevant_transcript`
2026-01-11 23:18:31 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens76_processed_external_relevant_transcript`
2026-01-11 23:18:49 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens77_processed_external_relevant_transcript`
2026-01-11 23:19:07 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens78_processed_external_relevant_transcript`
2026-01-11 23:19:25 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens79_processed_external_relevant_transcript`
2026-01-11 23:19:43 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens80_processed_external_relevant_transcript`
2026-01-11 23:20:17 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens81_processed_external_relevant_transcript`
2026-01-11 23:20:36 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens82_processed_external_relevant_transcript`
2026-01-11 23:20:54 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens83_processed_external_relevant_transcript`
2026-01-11 23:21:14 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens84_processed_external_relevant_transcript`
2026-01-11 23:21:33 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens85_processed_external_relevant_transcript`
2026-01-11 23:21:53 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens86_processed_external_relevant_transcript`
2026-01-11 23:22:13 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens87_processed_external_relevant_transcript`
2026-01-11 23:22:32 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens88_processed_external_relevant_transcript`
2026-01-11 23:22:52 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens89_processed_external_relevant_transcript`
2026-01-11 23:23:08 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens90_processed_external_relevant_transcript`
2026-01-11 23:23:29 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens91_processed_external_relevant_transcript`
2026-01-11 23:23:51 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens92_processed_external_relevant_transcript`
2026-01-11 23:24:08 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens93_processed_external_relevant_transcript`
2026-01-11 23:24:25 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens94_processed_external_relevant_transcript`
2026-01-11 23:24:42 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens95_processed_external_relevant_transcript`
2026-01-11 23:24:59 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens96_processed_external_relevant_transcript`
2026-01-11 23:25:17 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens97_processed_external_relevant_transcript`
2026-01-11 23:25:37 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens98_processed_external_relevant_transcript`
2026-01-11 23:25:56 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens99_processed_external_relevant_transcript`
2026-01-11 23:26:20 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens100_processed_external_relevant_transcript`
2026-01-11 23:26:50 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens101_processed_external_relevant_transcript`
2026-01-11 23:27:19 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens102_processed_external_relevant_transcript`
2026-01-11 23:27:37 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens103_processed_external_relevant_transcript`
2026-01-11 23:27:56 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens104_processed_external_relevant_transcript`
2026-01-11 23:28:15 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens105_processed_external_relevant_transcript`
2026-01-11 23:28:34 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens106_processed_external_relevant_transcript`
2026-01-11 23:28:53 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens107_processed_external_relevant_transcript`
2026-01-11 23:29:15 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens108_processed_external_relevant_transcript`
2026-01-11 23:29:35 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens109_processed_external_relevant_transcript`
2026-01-11 23:29:55 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens110_processed_external_relevant_transcript`
2026-01-11 23:30:16 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens111_processed_external_relevant_transcript`
2026-01-11 23:30:36 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens112_processed_external_relevant_transcript`
2026-01-11 23:30:56 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens113_processed_external_relevant_transcript`
2026-01-11 23:31:16 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens114_processed_external_relevant_transcript`
2026-01-11 23:31:39 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens115_processed_external_relevant_transcript`
2026-01-11 23:31:47 INFO:graph_maker: Edges between external IDs to Ensembl IDs is being added for 'translation'.
2026-01-11 23:31:50 INFO:database_manager: Using legacy column names (target_identity, query_identity) for identity_xref table in Ensembl release 48.
2026-01-11 23:31:58 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens48_processed_external_relevant_translation`
2026-01-11 23:32:09 INFO:database_manager: Using legacy column names (target_identity, query_identity) for identity_xref table in Ensembl release 49.
2026-01-11 23:32:17 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens49_processed_external_relevant_translation`
2026-01-11 23:32:25 INFO:database_manager: Using legacy column names (target_identity, query_identity) for identity_xref table in Ensembl release 50.
2026-01-11 23:32:32 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens50_processed_external_relevant_translation`
2026-01-11 23:32:40 INFO:database_manager: Using legacy column names (target_identity, query_identity) for identity_xref table in Ensembl release 51.
2026-01-11 23:32:47 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens51_processed_external_relevant_translation`
2026-01-11 23:32:54 INFO:database_manager: Using legacy column names (target_identity, query_identity) for identity_xref table in Ensembl release 52.
2026-01-11 23:33:01 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens52_processed_external_relevant_translation`
2026-01-11 23:33:17 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens53_processed_external_relevant_translation`
2026-01-11 23:33:33 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens54_processed_external_relevant_translation`
2026-01-11 23:33:50 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens55_processed_external_relevant_translation`
2026-01-11 23:34:04 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens56_processed_external_relevant_translation`
2026-01-11 23:34:21 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens57_processed_external_relevant_translation`
2026-01-11 23:35:06 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens58_processed_external_relevant_translation`
2026-01-11 23:35:25 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens59_processed_external_relevant_translation`
2026-01-11 23:35:46 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens60_processed_external_relevant_translation`
2026-01-11 23:36:05 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens61_processed_external_relevant_translation`
2026-01-11 23:36:23 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens62_processed_external_relevant_translation`
2026-01-11 23:36:40 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens63_processed_external_relevant_translation`
2026-01-11 23:36:57 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens64_processed_external_relevant_translation`
2026-01-11 23:37:16 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens65_processed_external_relevant_translation`
2026-01-11 23:37:35 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens66_processed_external_relevant_translation`
2026-01-11 23:37:56 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens67_processed_external_relevant_translation`
2026-01-11 23:38:15 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens68_processed_external_relevant_translation`
2026-01-11 23:38:34 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens69_processed_external_relevant_translation`
2026-01-11 23:38:53 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens70_processed_external_relevant_translation`
2026-01-11 23:39:11 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens71_processed_external_relevant_translation`
2026-01-11 23:39:28 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens72_processed_external_relevant_translation`
2026-01-11 23:39:46 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens73_processed_external_relevant_translation`
2026-01-11 23:40:04 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens74_processed_external_relevant_translation`
2026-01-11 23:40:23 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens75_processed_external_relevant_translation`
2026-01-11 23:40:44 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens76_processed_external_relevant_translation`
2026-01-11 23:41:10 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens77_processed_external_relevant_translation`
2026-01-11 23:41:34 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens78_processed_external_relevant_translation`
2026-01-11 23:41:58 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens79_processed_external_relevant_translation`
2026-01-11 23:42:22 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens80_processed_external_relevant_translation`
2026-01-11 23:42:46 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens81_processed_external_relevant_translation`
2026-01-11 23:43:11 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens82_processed_external_relevant_translation`
2026-01-11 23:43:37 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens83_processed_external_relevant_translation`
2026-01-11 23:43:57 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens84_processed_external_relevant_translation`
2026-01-11 23:44:19 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens85_processed_external_relevant_translation`
2026-01-11 23:44:42 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens86_processed_external_relevant_translation`
2026-01-11 23:45:06 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens87_processed_external_relevant_translation`
2026-01-11 23:45:32 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens88_processed_external_relevant_translation`
2026-01-11 23:45:50 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens89_processed_external_relevant_translation`
2026-01-11 23:46:05 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens90_processed_external_relevant_translation`
2026-01-11 23:46:23 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens91_processed_external_relevant_translation`
2026-01-11 23:46:42 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens92_processed_external_relevant_translation`
2026-01-11 23:46:58 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens93_processed_external_relevant_translation`
2026-01-11 23:47:13 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens94_processed_external_relevant_translation`
2026-01-11 23:47:28 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens95_processed_external_relevant_translation`
2026-01-11 23:47:43 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens96_processed_external_relevant_translation`
2026-01-11 23:47:58 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens97_processed_external_relevant_translation`
2026-01-11 23:48:16 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens98_processed_external_relevant_translation`
2026-01-11 23:48:32 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens99_processed_external_relevant_translation`
2026-01-11 23:48:52 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens100_processed_external_relevant_translation`
2026-01-11 23:49:16 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens101_processed_external_relevant_translation`
2026-01-11 23:49:38 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens102_processed_external_relevant_translation`
2026-01-11 23:49:56 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens103_processed_external_relevant_translation`
2026-01-11 23:50:17 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens104_processed_external_relevant_translation`
2026-01-11 23:50:32 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens105_processed_external_relevant_translation`
2026-01-11 23:50:45 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens106_processed_external_relevant_translation`
2026-01-11 23:51:00 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens107_processed_external_relevant_translation`
2026-01-11 23:51:14 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens108_processed_external_relevant_translation`
2026-01-11 23:51:29 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens109_processed_external_relevant_translation`
2026-01-11 23:51:45 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens110_processed_external_relevant_translation`
2026-01-11 23:52:01 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens111_processed_external_relevant_translation`
2026-01-11 23:52:16 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens112_processed_external_relevant_translation`
2026-01-11 23:52:31 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens113_processed_external_relevant_translation`
2026-01-11 23:52:47 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens114_processed_external_relevant_translation`
2026-01-11 23:53:03 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens115_processed_external_relevant_translation`
2026-01-11 23:53:10 INFO:graph_maker: Versionless Ensembl IDs are being connected.
2026-01-11 23:53:10 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens48_processed_ids_gene`
2026-01-11 23:53:11 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens49_processed_ids_gene`
2026-01-11 23:53:11 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens50_processed_ids_gene`
2026-01-11 23:53:12 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens51_processed_ids_gene`
2026-01-11 23:53:12 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens52_processed_ids_gene`
2026-01-11 23:53:13 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens53_processed_ids_gene`
2026-01-11 23:53:14 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens54_processed_ids_gene`
2026-01-11 23:53:14 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens55_processed_ids_gene`
2026-01-11 23:53:15 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens56_processed_ids_gene`
2026-01-11 23:53:15 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens57_processed_ids_gene`
2026-01-11 23:53:16 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens58_processed_ids_gene`
2026-01-11 23:53:16 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens59_processed_ids_gene`
2026-01-11 23:53:17 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens60_processed_ids_gene`
2026-01-11 23:53:18 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens61_processed_ids_gene`
2026-01-11 23:53:18 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens62_processed_ids_gene`
2026-01-11 23:53:19 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens63_processed_ids_gene`
2026-01-11 23:53:20 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens64_processed_ids_gene`
2026-01-11 23:53:20 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens65_processed_ids_gene`
2026-01-11 23:53:21 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens66_processed_ids_gene`
2026-01-11 23:53:21 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-37.h5` with key `ens67_processed_ids_gene`
2026-01-11 23:53:22 INFO:graph_maker: Edges between versionless ID to version ID has been added for 'gene', assembly 37.
2026-01-11 23:53:22 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens68_processed_ids_gene`
2026-01-11 23:53:23 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens69_processed_ids_gene`
2026-01-11 23:53:23 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens70_processed_ids_gene`
2026-01-11 23:53:24 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens71_processed_ids_gene`
2026-01-11 23:53:25 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens72_processed_ids_gene`
2026-01-11 23:53:25 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens73_processed_ids_gene`
2026-01-11 23:53:26 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens74_processed_ids_gene`
2026-01-11 23:53:26 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens75_processed_ids_gene`
2026-01-11 23:53:27 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens76_processed_ids_gene`
2026-01-11 23:53:28 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens77_processed_ids_gene`
2026-01-11 23:53:29 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens78_processed_ids_gene`
2026-01-11 23:53:29 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens79_processed_ids_gene`
2026-01-11 23:53:30 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens80_processed_ids_gene`
2026-01-11 23:53:31 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens81_processed_ids_gene`
2026-01-11 23:53:32 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens82_processed_ids_gene`
2026-01-11 23:53:33 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens83_processed_ids_gene`
2026-01-11 23:53:34 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens84_processed_ids_gene`
2026-01-11 23:53:35 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens85_processed_ids_gene`
2026-01-11 23:53:35 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens86_processed_ids_gene`
2026-01-11 23:53:36 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens87_processed_ids_gene`
2026-01-11 23:53:37 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens88_processed_ids_gene`
2026-01-11 23:53:38 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens89_processed_ids_gene`
2026-01-11 23:53:39 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens90_processed_ids_gene`
2026-01-11 23:53:40 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens91_processed_ids_gene`
2026-01-11 23:53:41 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens92_processed_ids_gene`
2026-01-11 23:53:42 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens93_processed_ids_gene`
2026-01-11 23:53:43 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens94_processed_ids_gene`
2026-01-11 23:53:44 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens95_processed_ids_gene`
2026-01-11 23:53:45 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens96_processed_ids_gene`
2026-01-11 23:53:46 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens97_processed_ids_gene`
2026-01-11 23:53:47 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens98_processed_ids_gene`
2026-01-11 23:53:48 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens99_processed_ids_gene`
2026-01-11 23:53:49 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens100_processed_ids_gene`
2026-01-11 23:53:50 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens101_processed_ids_gene`
2026-01-11 23:53:51 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-38.h5` with key `ens102_processed_ids_gene`
2026-01-11 23:53:52 INFO:graph_maker: Edges between versionless ID to version ID has been added for 'gene', assembly 38.
2026-01-11 23:53:52 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens103_processed_ids_gene`
2026-01-11 23:53:54 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens104_processed_ids_gene`
2026-01-11 23:53:55 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens105_processed_ids_gene`
2026-01-11 23:53:56 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens106_processed_ids_gene`
2026-01-11 23:53:57 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens107_processed_ids_gene`
2026-01-11 23:53:58 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens108_processed_ids_gene`
2026-01-11 23:53:59 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens109_processed_ids_gene`
2026-01-11 23:54:00 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens110_processed_ids_gene`
2026-01-11 23:54:02 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens111_processed_ids_gene`
2026-01-11 23:54:03 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens112_processed_ids_gene`
2026-01-11 23:54:04 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens113_processed_ids_gene`
2026-01-11 23:54:06 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens114_processed_ids_gene`
2026-01-11 23:54:07 INFO:database_manager: Exporting to the following file `mus_musculus_assembly-39.h5` with key `ens115_processed_ids_gene`
2026-01-11 23:54:09 INFO:graph_maker: Edges between versionless ID to version ID has been added for 'gene', assembly 39.
2026-01-11 23:54:09 INFO:graph_maker: Synonymous external nodes are being merged into one.
2026-01-11 23:54:52 INFO:graph_maker: Number of removed nodes in the process of merging synonymous nodes: 38082
2026-01-11 23:55:12 INFO:graph_maker: The graph is being exported as '/Users/kemalinecik/git_nosync/master_idtrack/idtrack/docs/_notebooks/idtrack_cache/graph_mus_musculus_min48_max115_narrow.pickle'.
2026-01-11 23:56:06 INFO:the_graph: Cached properties being calculated: available_genome_assemblies
2026-01-11 23:56:06 INFO:the_graph: Cached properties being calculated: combined_edges
2026-01-11 23:57:03 INFO:the_graph: Cached properties being calculated: combined_edges_genes
2026-01-11 23:58:12 INFO:the_graph: Cached properties being calculated: combined_edges_assembly_specific_genes
6

if HAS_MOUSE_YAML:
    g = api.track.graph
    print('Organism:', g.graph.get('organism'))
    print('Snapshot release:', g.graph.get('ensembl_release'))
    print('Main assembly:', g.graph.get('genome_assembly'))
    print('Assemblies in this graph:', sorted(api.list_genome_assemblies()))
    print('Nodes:', g.number_of_nodes())
    print('Edges:', g.number_of_edges())

    aed = sorted(getattr(g, 'available_external_databases', []))
    print('External DBs enabled (count):', len(aed))
    print('External DBs (first 20):', aed[:20])
else:
    print('Mouse graph not built (missing YAML).')

Organism: mus_musculus
Snapshot release: 115
Main assembly: 39
Assemblies in this graph: [37, 38, 39]
Nodes: 2476278

2026-01-11 23:58:19 INFO:the_graph: Cached properties being calculated: available_external_databases

Edges: 5367328
External DBs enabled (count): 28
External DBs (first 20): ['CCDS', 'Clone_based_ensembl_gene', 'Clone_based_vega_gene', 'EntrezGene', 'Havana gene', 'Havana transcript', 'Havana translation', 'MGI Symbol', 'NCBI gene', 'NCBI gene (formerly Entrezgene)', 'RFAM', 'RefSeq_mRNA', 'RefSeq_mRNA_predicted', 'RefSeq_ncRNA', 'RefSeq_ncRNA_predicted', 'RefSeq_peptide', 'RefSeq_peptide_predicted', 'UniProtKB Gene Name', 'Uniprot/SPTREMBL', 'Uniprot/SWISSPROT']

7

sorted(LOCAL_REPOSITORY.glob('graph_mus_musculus*.pickle'))[-5:]

7

[PosixPath('/Users/kemalinecik/git_nosync/master_idtrack/idtrack/docs/_notebooks/idtrack_cache/graph_mus_musculus_min48_max115_narrow.pickle')]

3.3 — Pig graph initialization (clean handoff)

Pig is a clean-handoff species (one maintained assembly per release: Sscrofa9.2 → Sscrofa10.2 → Sscrofa11.1). Older assemblies mainly matter for legacy datasets and archive releases; you typically do not have overlapping assemblies within the same release.

8

organism, latest_release = api.resolve_organism('sus scrofa')
SNAPSHOT_RELEASE = latest_release
organism, SNAPSHOT_RELEASE

2026-01-11 23:58:21 INFO:verify_organism: Ensembl Rest API query to get the organism names and associated releases.

8

('sus_scrofa', 115)

9

%%collapse Click to show build logs
# Included for tutorial purposes only.

# Build (or load) the pig graph snapshot
if HAS_PIG_YAML:
    api.build_graph(organism_name=organism, snapshot_release=SNAPSHOT_RELEASE, calculate_caches=False)
else:
    print('Skipping pig build: sus_scrofa_externals_modified.yml is missing (run Part 2 first).')
Click to show build logs 
2026-01-11 23:58:41 INFO:database_manager: Using assembly-specific release range for sus_scrofa assembly 111: releases 90-115 (from config [90, None])
2026-01-11 23:58:46 INFO:graph_maker: The graph is being constructed: /Users/kemalinecik/git_nosync/master_idtrack/idtrack/docs/_notebooks/idtrack_cache/graph_sus_scrofa_min48_max115_narrow.pickle
2026-01-11 23:58:46 INFO:graph_maker: Graph is being created: gene
2026-01-11 23:58:47 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens115_processed_versioninfo_gene`
2026-01-11 23:58:49 INFO:database_manager: Using assembly-specific release range for sus_scrofa assembly 102: releases 67-89 (from config [67, 89])
2026-01-11 23:58:54 INFO:database_manager: Using assembly-specific release range for sus_scrofa assembly 9: releases 56-66 (from config [56, 66])
2026-01-11 23:59:07 INFO:database_manager: Raw table for `stable_id_event` on ensembl release `115` was downloaded.
2026-01-11 23:59:07 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens115_mysql_stable_id_event`
2026-01-11 23:59:20 INFO:database_manager: Raw table for `mapping_session` on ensembl release `115` was downloaded.
2026-01-11 23:59:20 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens115_mysql_mapping_session`
2026-01-11 23:59:21 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens115_processed_idhistory_narrow_gene`
2026-01-11 23:59:24 INFO:graph_maker: Edges between across different IDs and self loops are being added.
2026-01-11 23:59:25 INFO:graph_maker: Edges between the same IDs are being added.
2026-01-11 23:59:31 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens89_processed_versioninfo_gene`
2026-01-11 23:59:34 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens66_processed_versioninfo_gene`
2026-01-11 23:59:35 INFO:graph_maker: Edges showing the retirement of IDs are being added.
2026-01-11 23:59:39 INFO:graph_maker: Problematic nodes in Ensembl ID history are being removed.
2026-01-11 23:59:43 INFO:graph_maker: Self-loops for latest release entries are being added.
2026-01-11 23:59:44 INFO:graph_maker: Node attributes are being added.
2026-01-11 23:59:45 INFO:graph_maker: Graph is being created: transcript
2026-01-11 23:59:46 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens115_processed_versioninfo_transcript`
2026-01-11 23:59:48 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens115_processed_idhistory_narrow_transcript`
2026-01-11 23:59:52 INFO:graph_maker: Edges between across different IDs and self loops are being added.
2026-01-11 23:59:53 INFO:graph_maker: Edges between the same IDs are being added.
2026-01-12 00:00:04 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens89_processed_versioninfo_transcript`
2026-01-12 00:00:08 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens66_processed_versioninfo_transcript`
2026-01-12 00:00:10 INFO:graph_maker: Edges showing the retirement of IDs are being added.
2026-01-12 00:00:16 INFO:graph_maker: Problematic nodes in Ensembl ID history are being removed.
2026-01-12 00:00:22 INFO:graph_maker: Self-loops for latest release entries are being added.
2026-01-12 00:00:23 INFO:graph_maker: Node attributes are being added.
2026-01-12 00:00:25 INFO:graph_maker: Graph is being created: translation
2026-01-12 00:00:26 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens115_processed_versioninfo_translation`
2026-01-12 00:00:28 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens115_processed_idhistory_narrow_translation`
2026-01-12 00:00:32 INFO:graph_maker: Edges between across different IDs and self loops are being added.
2026-01-12 00:00:34 INFO:graph_maker: Edges between the same IDs are being added.
2026-01-12 00:00:42 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens89_processed_versioninfo_translation`
2026-01-12 00:00:45 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens66_processed_versioninfo_translation`
2026-01-12 00:00:47 INFO:graph_maker: Edges showing the retirement of IDs are being added.
2026-01-12 00:00:52 INFO:graph_maker: Problematic nodes in Ensembl ID history are being removed.
2026-01-12 00:00:57 INFO:graph_maker: Self-loops for latest release entries are being added.
2026-01-12 00:00:58 INFO:graph_maker: Node attributes are being added.
2026-01-12 00:01:01 INFO:graph_maker: Establishing connection between different forms.
2026-01-12 00:01:02 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens56_processed_idsraw_transcript_gene`
2026-01-12 00:01:03 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens56_processed_idsraw_translation_gene`
2026-01-12 00:01:03 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens56_common_relationcurrent`
2026-01-12 00:01:05 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens57_processed_idsraw_transcript_gene`
2026-01-12 00:01:06 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens57_processed_idsraw_translation_gene`
2026-01-12 00:01:06 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens57_common_relationcurrent`
2026-01-12 00:01:08 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens58_processed_idsraw_transcript_gene`
2026-01-12 00:01:09 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens58_processed_idsraw_translation_gene`
2026-01-12 00:01:09 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens58_common_relationcurrent`
2026-01-12 00:01:11 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens59_processed_idsraw_transcript_gene`
2026-01-12 00:01:12 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens59_processed_idsraw_translation_gene`
2026-01-12 00:01:12 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens59_common_relationcurrent`
2026-01-12 00:01:14 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens60_processed_idsraw_transcript_gene`
2026-01-12 00:01:15 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens60_processed_idsraw_translation_gene`
2026-01-12 00:01:15 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens60_common_relationcurrent`
2026-01-12 00:01:17 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens61_processed_idsraw_transcript_gene`
2026-01-12 00:01:18 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens61_processed_idsraw_translation_gene`
2026-01-12 00:01:18 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens61_common_relationcurrent`
2026-01-12 00:01:20 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens62_processed_idsraw_transcript_gene`
2026-01-12 00:01:21 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens62_processed_idsraw_translation_gene`
2026-01-12 00:01:21 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens62_common_relationcurrent`
2026-01-12 00:01:23 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens63_processed_idsraw_transcript_gene`
2026-01-12 00:01:24 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens63_processed_idsraw_translation_gene`
2026-01-12 00:01:24 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens63_common_relationcurrent`
2026-01-12 00:01:26 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens64_processed_idsraw_transcript_gene`
2026-01-12 00:01:38 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens64_processed_idsraw_translation_gene`
2026-01-12 00:01:39 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens64_common_relationcurrent`
2026-01-12 00:01:40 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens65_processed_idsraw_transcript_gene`
2026-01-12 00:01:40 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens65_processed_idsraw_translation_gene`
2026-01-12 00:01:40 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens65_common_relationcurrent`
2026-01-12 00:01:41 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens66_processed_idsraw_transcript_gene`
2026-01-12 00:01:42 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens66_processed_idsraw_translation_gene`
2026-01-12 00:01:42 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens66_common_relationcurrent`
2026-01-12 00:01:43 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens67_processed_idsraw_transcript_gene`
2026-01-12 00:01:44 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens67_processed_idsraw_translation_gene`
2026-01-12 00:01:44 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens67_common_relationcurrent`
2026-01-12 00:01:46 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens68_processed_idsraw_transcript_gene`
2026-01-12 00:01:46 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens68_processed_idsraw_translation_gene`
2026-01-12 00:01:47 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens68_common_relationcurrent`
2026-01-12 00:01:48 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens69_processed_idsraw_transcript_gene`
2026-01-12 00:01:49 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens69_processed_idsraw_translation_gene`
2026-01-12 00:01:49 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens69_common_relationcurrent`
2026-01-12 00:01:51 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens70_processed_idsraw_transcript_gene`
2026-01-12 00:01:51 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens70_processed_idsraw_translation_gene`
2026-01-12 00:01:52 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens70_common_relationcurrent`
2026-01-12 00:01:53 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens71_processed_idsraw_transcript_gene`
2026-01-12 00:01:54 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens71_processed_idsraw_translation_gene`
2026-01-12 00:01:55 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens71_common_relationcurrent`
2026-01-12 00:01:56 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens72_processed_idsraw_transcript_gene`
2026-01-12 00:01:57 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens72_processed_idsraw_translation_gene`
2026-01-12 00:01:58 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens72_common_relationcurrent`
2026-01-12 00:01:59 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens73_processed_idsraw_transcript_gene`
2026-01-12 00:02:00 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens73_processed_idsraw_translation_gene`
2026-01-12 00:02:00 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens73_common_relationcurrent`
2026-01-12 00:02:02 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens74_processed_idsraw_transcript_gene`
2026-01-12 00:02:02 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens74_processed_idsraw_translation_gene`
2026-01-12 00:02:03 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens74_common_relationcurrent`
2026-01-12 00:02:05 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens75_processed_idsraw_transcript_gene`
2026-01-12 00:02:05 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens75_processed_idsraw_translation_gene`
2026-01-12 00:02:06 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens75_common_relationcurrent`
2026-01-12 00:02:07 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens76_processed_idsraw_transcript_gene`
2026-01-12 00:02:08 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens76_processed_idsraw_translation_gene`
2026-01-12 00:02:09 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens76_common_relationcurrent`
2026-01-12 00:02:10 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens77_processed_idsraw_transcript_gene`
2026-01-12 00:02:11 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens77_processed_idsraw_translation_gene`
2026-01-12 00:02:11 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens77_common_relationcurrent`
2026-01-12 00:02:13 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens78_processed_idsraw_transcript_gene`
2026-01-12 00:02:13 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens78_processed_idsraw_translation_gene`
2026-01-12 00:02:14 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens78_common_relationcurrent`
2026-01-12 00:02:15 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens79_processed_idsraw_transcript_gene`
2026-01-12 00:02:16 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens79_processed_idsraw_translation_gene`
2026-01-12 00:02:17 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens79_common_relationcurrent`
2026-01-12 00:02:18 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens80_processed_idsraw_transcript_gene`
2026-01-12 00:02:19 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens80_processed_idsraw_translation_gene`
2026-01-12 00:02:20 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens80_common_relationcurrent`
2026-01-12 00:02:21 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens81_processed_idsraw_transcript_gene`
2026-01-12 00:02:22 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens81_processed_idsraw_translation_gene`
2026-01-12 00:02:22 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens81_common_relationcurrent`
2026-01-12 00:02:24 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens82_processed_idsraw_transcript_gene`
2026-01-12 00:02:24 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens82_processed_idsraw_translation_gene`
2026-01-12 00:02:25 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens82_common_relationcurrent`
2026-01-12 00:02:26 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens83_processed_idsraw_transcript_gene`
2026-01-12 00:02:27 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens83_processed_idsraw_translation_gene`
2026-01-12 00:02:28 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens83_common_relationcurrent`
2026-01-12 00:02:29 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens84_processed_idsraw_transcript_gene`
2026-01-12 00:02:30 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens84_processed_idsraw_translation_gene`
2026-01-12 00:02:30 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens84_common_relationcurrent`
2026-01-12 00:02:32 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens85_processed_idsraw_transcript_gene`
2026-01-12 00:02:32 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens85_processed_idsraw_translation_gene`
2026-01-12 00:02:33 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens85_common_relationcurrent`
2026-01-12 00:02:34 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens86_processed_idsraw_transcript_gene`
2026-01-12 00:02:35 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens86_processed_idsraw_translation_gene`
2026-01-12 00:02:36 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens86_common_relationcurrent`
2026-01-12 00:02:37 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens87_processed_idsraw_transcript_gene`
2026-01-12 00:02:38 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens87_processed_idsraw_translation_gene`
2026-01-12 00:02:39 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens87_common_relationcurrent`
2026-01-12 00:02:40 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens88_processed_idsraw_transcript_gene`
2026-01-12 00:02:41 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens88_processed_idsraw_translation_gene`
2026-01-12 00:02:41 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens88_common_relationcurrent`
2026-01-12 00:02:43 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens89_processed_idsraw_transcript_gene`
2026-01-12 00:02:43 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens89_processed_idsraw_translation_gene`
2026-01-12 00:02:44 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens89_common_relationcurrent`
2026-01-12 00:02:45 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens90_processed_idsraw_transcript_gene`
2026-01-12 00:02:46 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens90_processed_idsraw_translation_gene`
2026-01-12 00:02:47 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens90_common_relationcurrent`
2026-01-12 00:02:49 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens91_processed_idsraw_transcript_gene`
2026-01-12 00:02:50 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens91_processed_idsraw_translation_gene`
2026-01-12 00:02:51 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens91_common_relationcurrent`
2026-01-12 00:02:53 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens92_processed_idsraw_transcript_gene`
2026-01-12 00:02:54 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens92_processed_idsraw_translation_gene`
2026-01-12 00:02:55 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens92_common_relationcurrent`
2026-01-12 00:02:57 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens93_processed_idsraw_transcript_gene`
2026-01-12 00:02:58 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens93_processed_idsraw_translation_gene`
2026-01-12 00:02:59 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens93_common_relationcurrent`
2026-01-12 00:03:01 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens94_processed_idsraw_transcript_gene`
2026-01-12 00:03:02 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens94_processed_idsraw_translation_gene`
2026-01-12 00:03:03 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens94_common_relationcurrent`
2026-01-12 00:03:05 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens95_processed_idsraw_transcript_gene`
2026-01-12 00:03:06 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens95_processed_idsraw_translation_gene`
2026-01-12 00:03:07 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens95_common_relationcurrent`
2026-01-12 00:03:09 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens96_processed_idsraw_transcript_gene`
2026-01-12 00:03:10 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens96_processed_idsraw_translation_gene`
2026-01-12 00:03:11 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens96_common_relationcurrent`
2026-01-12 00:03:13 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens97_processed_idsraw_transcript_gene`
2026-01-12 00:03:14 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens97_processed_idsraw_translation_gene`
2026-01-12 00:03:15 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens97_common_relationcurrent`
2026-01-12 00:03:17 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens98_processed_idsraw_transcript_gene`
2026-01-12 00:03:18 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens98_processed_idsraw_translation_gene`
2026-01-12 00:03:19 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens98_common_relationcurrent`
2026-01-12 00:03:22 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens99_processed_idsraw_transcript_gene`
2026-01-12 00:03:23 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens99_processed_idsraw_translation_gene`
2026-01-12 00:03:24 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens99_common_relationcurrent`
2026-01-12 00:03:27 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens100_processed_idsraw_transcript_gene`
2026-01-12 00:03:28 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens100_processed_idsraw_translation_gene`
2026-01-12 00:03:30 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens100_common_relationcurrent`
2026-01-12 00:03:32 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens101_processed_idsraw_transcript_gene`
2026-01-12 00:03:34 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens101_processed_idsraw_translation_gene`
2026-01-12 00:03:35 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens101_common_relationcurrent`
2026-01-12 00:03:37 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens102_processed_idsraw_transcript_gene`
2026-01-12 00:03:38 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens102_processed_idsraw_translation_gene`
2026-01-12 00:03:39 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens102_common_relationcurrent`
2026-01-12 00:03:42 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens103_processed_idsraw_transcript_gene`
2026-01-12 00:03:43 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens103_processed_idsraw_translation_gene`
2026-01-12 00:03:44 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens103_common_relationcurrent`
2026-01-12 00:03:47 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens104_processed_idsraw_transcript_gene`
2026-01-12 00:03:48 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens104_processed_idsraw_translation_gene`
2026-01-12 00:03:49 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens104_common_relationcurrent`
2026-01-12 00:03:52 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens105_processed_idsraw_transcript_gene`
2026-01-12 00:03:53 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens105_processed_idsraw_translation_gene`
2026-01-12 00:03:54 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens105_common_relationcurrent`
2026-01-12 00:03:57 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens106_processed_idsraw_transcript_gene`
2026-01-12 00:03:58 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens106_processed_idsraw_translation_gene`
2026-01-12 00:03:59 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens106_common_relationcurrent`
2026-01-12 00:04:02 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens107_processed_idsraw_transcript_gene`
2026-01-12 00:04:03 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens107_processed_idsraw_translation_gene`
2026-01-12 00:04:04 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens107_common_relationcurrent`
2026-01-12 00:04:07 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens108_processed_idsraw_transcript_gene`
2026-01-12 00:04:08 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens108_processed_idsraw_translation_gene`
2026-01-12 00:04:09 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens108_common_relationcurrent`
2026-01-12 00:04:12 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens109_processed_idsraw_transcript_gene`
2026-01-12 00:04:13 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens109_processed_idsraw_translation_gene`
2026-01-12 00:04:14 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens109_common_relationcurrent`
2026-01-12 00:04:17 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens110_processed_idsraw_transcript_gene`
2026-01-12 00:04:18 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens110_processed_idsraw_translation_gene`
2026-01-12 00:04:20 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens110_common_relationcurrent`
2026-01-12 00:04:22 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens111_processed_idsraw_transcript_gene`
2026-01-12 00:04:23 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens111_processed_idsraw_translation_gene`
2026-01-12 00:04:25 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens111_common_relationcurrent`
2026-01-12 00:04:27 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens112_processed_idsraw_transcript_gene`
2026-01-12 00:04:29 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens112_processed_idsraw_translation_gene`
2026-01-12 00:04:30 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens112_common_relationcurrent`
2026-01-12 00:04:32 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens113_processed_idsraw_transcript_gene`
2026-01-12 00:04:34 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens113_processed_idsraw_translation_gene`
2026-01-12 00:04:35 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens113_common_relationcurrent`
2026-01-12 00:04:38 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens114_processed_idsraw_transcript_gene`
2026-01-12 00:04:39 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens114_processed_idsraw_translation_gene`
2026-01-12 00:04:40 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens114_common_relationcurrent`
2026-01-12 00:04:43 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens115_processed_idsraw_transcript_gene`
2026-01-12 00:04:44 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens115_processed_idsraw_translation_gene`
2026-01-12 00:04:45 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens115_common_relationcurrent`
2026-01-12 00:04:48 INFO:graph_maker: Edges between external IDs to Ensembl IDs is being added for 'gene'.
2026-01-12 00:04:49 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens61_processed_external_relevant_gene`
2026-01-12 00:04:51 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens62_processed_external_relevant_gene`
2026-01-12 00:04:52 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens63_processed_external_relevant_gene`
2026-01-12 00:04:55 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens64_processed_external_relevant_gene`
2026-01-12 00:04:58 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens65_processed_external_relevant_gene`
2026-01-12 00:05:02 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens66_processed_external_relevant_gene`
2026-01-12 00:05:07 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens67_processed_external_relevant_gene`
2026-01-12 00:05:11 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens68_processed_external_relevant_gene`
2026-01-12 00:05:16 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens69_processed_external_relevant_gene`
2026-01-12 00:05:23 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens70_processed_external_relevant_gene`
2026-01-12 00:05:28 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens71_processed_external_relevant_gene`
2026-01-12 00:05:32 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens72_processed_external_relevant_gene`
2026-01-12 00:05:37 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens73_processed_external_relevant_gene`
2026-01-12 00:05:43 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens74_processed_external_relevant_gene`
2026-01-12 00:05:48 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens75_processed_external_relevant_gene`
2026-01-12 00:05:53 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens76_processed_external_relevant_gene`
2026-01-12 00:05:58 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens77_processed_external_relevant_gene`
2026-01-12 00:06:04 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens78_processed_external_relevant_gene`
2026-01-12 00:06:09 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens79_processed_external_relevant_gene`
2026-01-12 00:06:14 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens80_processed_external_relevant_gene`
2026-01-12 00:06:19 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens81_processed_external_relevant_gene`
2026-01-12 00:06:25 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens82_processed_external_relevant_gene`
2026-01-12 00:06:30 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens83_processed_external_relevant_gene`
2026-01-12 00:06:36 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens84_processed_external_relevant_gene`
2026-01-12 00:06:41 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens85_processed_external_relevant_gene`
2026-01-12 00:06:46 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens86_processed_external_relevant_gene`
2026-01-12 00:06:52 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens87_processed_external_relevant_gene`
2026-01-12 00:06:57 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens88_processed_external_relevant_gene`
2026-01-12 00:07:02 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens89_processed_external_relevant_gene`
2026-01-12 00:07:08 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens90_processed_external_relevant_gene`
2026-01-12 00:07:11 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens90_processed_external_relevant_gene`
2026-01-12 00:07:19 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens91_processed_external_relevant_gene`
2026-01-12 00:07:22 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens91_processed_external_relevant_gene`
2026-01-12 00:07:29 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens92_processed_external_relevant_gene`
2026-01-12 00:07:33 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens92_processed_external_relevant_gene`
2026-01-12 00:07:41 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens93_processed_external_relevant_gene`
2026-01-12 00:07:44 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens93_processed_external_relevant_gene`
2026-01-12 00:07:52 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens94_processed_external_relevant_gene`
2026-01-12 00:07:57 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens94_processed_external_relevant_gene`
2026-01-12 00:08:06 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens95_processed_external_relevant_gene`
2026-01-12 00:08:10 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens95_processed_external_relevant_gene`
2026-01-12 00:08:19 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens96_processed_external_relevant_gene`
2026-01-12 00:08:22 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens96_processed_external_relevant_gene`
2026-01-12 00:08:30 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens97_processed_external_relevant_gene`
2026-01-12 00:08:34 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens97_processed_external_relevant_gene`
2026-01-12 00:08:44 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens98_processed_external_relevant_gene`
2026-01-12 00:08:47 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens98_processed_external_relevant_gene`
2026-01-12 00:08:57 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens99_processed_external_relevant_gene`
2026-01-12 00:09:01 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens99_processed_external_relevant_gene`
2026-01-12 00:09:09 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens100_processed_external_relevant_gene`
2026-01-12 00:09:16 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens101_processed_external_relevant_gene`
2026-01-12 00:09:23 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens102_processed_external_relevant_gene`
2026-01-12 00:09:29 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens103_processed_external_relevant_gene`
2026-01-12 00:09:36 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens104_processed_external_relevant_gene`
2026-01-12 00:09:43 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens105_processed_external_relevant_gene`
2026-01-12 00:09:49 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens106_processed_external_relevant_gene`
2026-01-12 00:09:56 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens107_processed_external_relevant_gene`
2026-01-12 00:10:02 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens108_processed_external_relevant_gene`
2026-01-12 00:10:08 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens109_processed_external_relevant_gene`
2026-01-12 00:10:15 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens110_processed_external_relevant_gene`
2026-01-12 00:10:23 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens111_processed_external_relevant_gene`
2026-01-12 00:10:30 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens112_processed_external_relevant_gene`
2026-01-12 00:10:38 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens113_processed_external_relevant_gene`
2026-01-12 00:10:45 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens114_processed_external_relevant_gene`
2026-01-12 00:10:52 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens115_processed_external_relevant_gene`
2026-01-12 00:10:55 INFO:graph_maker: Edges between external IDs to Ensembl IDs is being added for 'transcript'.
2026-01-12 00:10:57 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens64_processed_external_relevant_transcript`
2026-01-12 00:10:58 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens65_processed_external_relevant_transcript`
2026-01-12 00:11:00 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens66_processed_external_relevant_transcript`
2026-01-12 00:11:02 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens67_processed_external_relevant_transcript`
2026-01-12 00:11:03 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens68_processed_external_relevant_transcript`
2026-01-12 00:11:06 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens69_processed_external_relevant_transcript`
2026-01-12 00:11:08 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens70_processed_external_relevant_transcript`
2026-01-12 00:11:11 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens71_processed_external_relevant_transcript`
2026-01-12 00:11:13 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens72_processed_external_relevant_transcript`
2026-01-12 00:11:16 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens73_processed_external_relevant_transcript`
2026-01-12 00:11:18 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens74_processed_external_relevant_transcript`
2026-01-12 00:11:21 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens75_processed_external_relevant_transcript`
2026-01-12 00:11:23 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens76_processed_external_relevant_transcript`
2026-01-12 00:11:26 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens77_processed_external_relevant_transcript`
2026-01-12 00:11:28 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens78_processed_external_relevant_transcript`
2026-01-12 00:11:32 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens79_processed_external_relevant_transcript`
2026-01-12 00:11:35 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens80_processed_external_relevant_transcript`
2026-01-12 00:11:37 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens81_processed_external_relevant_transcript`
2026-01-12 00:11:40 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens82_processed_external_relevant_transcript`
2026-01-12 00:11:45 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens83_processed_external_relevant_transcript`
2026-01-12 00:11:48 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens84_processed_external_relevant_transcript`
2026-01-12 00:11:51 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens85_processed_external_relevant_transcript`
2026-01-12 00:11:54 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens86_processed_external_relevant_transcript`
2026-01-12 00:11:57 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens87_processed_external_relevant_transcript`
2026-01-12 00:12:00 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens88_processed_external_relevant_transcript`
2026-01-12 00:12:57 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens89_processed_external_relevant_transcript`
2026-01-12 00:13:01 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens90_processed_external_relevant_transcript`
2026-01-12 00:13:03 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens90_processed_external_relevant_transcript`
2026-01-12 00:13:07 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens91_processed_external_relevant_transcript`
2026-01-12 00:13:09 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens91_processed_external_relevant_transcript`
2026-01-12 00:13:14 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens92_processed_external_relevant_transcript`
2026-01-12 00:13:17 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens92_processed_external_relevant_transcript`
2026-01-12 00:13:22 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens93_processed_external_relevant_transcript`
2026-01-12 00:13:25 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens93_processed_external_relevant_transcript`
2026-01-12 00:13:31 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens94_processed_external_relevant_transcript`
2026-01-12 00:13:34 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens94_processed_external_relevant_transcript`
2026-01-12 00:13:40 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens95_processed_external_relevant_transcript`
2026-01-12 00:13:42 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens95_processed_external_relevant_transcript`
2026-01-12 00:13:49 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens96_processed_external_relevant_transcript`
2026-01-12 00:13:52 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens96_processed_external_relevant_transcript`
2026-01-12 00:13:58 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens97_processed_external_relevant_transcript`
2026-01-12 00:14:01 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens97_processed_external_relevant_transcript`
2026-01-12 00:14:08 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens98_processed_external_relevant_transcript`
2026-01-12 00:14:11 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens98_processed_external_relevant_transcript`
2026-01-12 00:14:18 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens99_processed_external_relevant_transcript`
2026-01-12 00:14:21 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens99_processed_external_relevant_transcript`
2026-01-12 00:14:28 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens100_processed_external_relevant_transcript`
2026-01-12 00:14:35 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens101_processed_external_relevant_transcript`
2026-01-12 00:14:42 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens102_processed_external_relevant_transcript`
2026-01-12 00:14:48 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens103_processed_external_relevant_transcript`
2026-01-12 00:14:54 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens104_processed_external_relevant_transcript`
2026-01-12 00:15:01 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens105_processed_external_relevant_transcript`
2026-01-12 00:15:09 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens106_processed_external_relevant_transcript`
2026-01-12 00:15:15 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens107_processed_external_relevant_transcript`
2026-01-12 00:15:22 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens108_processed_external_relevant_transcript`
2026-01-12 00:15:30 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens109_processed_external_relevant_transcript`
2026-01-12 00:15:38 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens110_processed_external_relevant_transcript`
2026-01-12 00:15:46 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens111_processed_external_relevant_transcript`
2026-01-12 00:15:53 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens112_processed_external_relevant_transcript`
2026-01-12 00:16:02 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens113_processed_external_relevant_transcript`
2026-01-12 00:16:10 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens114_processed_external_relevant_transcript`
2026-01-12 00:16:19 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens115_processed_external_relevant_transcript`
2026-01-12 00:16:21 INFO:graph_maker: Edges between external IDs to Ensembl IDs is being added for 'translation'.
2026-01-12 00:16:22 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens56_processed_external_relevant_translation`
2026-01-12 00:16:24 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens57_processed_external_relevant_translation`
2026-01-12 00:16:25 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens58_processed_external_relevant_translation`
2026-01-12 00:16:27 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens59_processed_external_relevant_translation`
2026-01-12 00:16:28 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens60_processed_external_relevant_translation`
2026-01-12 00:16:30 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens61_processed_external_relevant_translation`
2026-01-12 00:16:31 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens62_processed_external_relevant_translation`
2026-01-12 00:16:33 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens63_processed_external_relevant_translation`
2026-01-12 00:16:36 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens64_processed_external_relevant_translation`
2026-01-12 00:16:40 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens65_processed_external_relevant_translation`
2026-01-12 00:16:44 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens66_processed_external_relevant_translation`
2026-01-12 00:16:49 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens67_processed_external_relevant_translation`
2026-01-12 00:16:53 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens68_processed_external_relevant_translation`
2026-01-12 00:16:58 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens69_processed_external_relevant_translation`
2026-01-12 00:17:04 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens70_processed_external_relevant_translation`
2026-01-12 00:17:09 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens71_processed_external_relevant_translation`
2026-01-12 00:17:15 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens72_processed_external_relevant_translation`
2026-01-12 00:17:21 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens73_processed_external_relevant_translation`
2026-01-12 00:17:26 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens74_processed_external_relevant_translation`
2026-01-12 00:17:32 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens75_processed_external_relevant_translation`
2026-01-12 00:17:38 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens76_processed_external_relevant_translation`
2026-01-12 00:17:44 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens77_processed_external_relevant_translation`
2026-01-12 00:17:50 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens78_processed_external_relevant_translation`
2026-01-12 00:17:56 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens79_processed_external_relevant_translation`
2026-01-12 00:18:02 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens80_processed_external_relevant_translation`
2026-01-12 00:18:08 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens81_processed_external_relevant_translation`
2026-01-12 00:18:14 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens82_processed_external_relevant_translation`
2026-01-12 00:18:21 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens83_processed_external_relevant_translation`
2026-01-12 00:18:26 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens84_processed_external_relevant_translation`
2026-01-12 00:18:31 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens85_processed_external_relevant_translation`
2026-01-12 00:18:37 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens86_processed_external_relevant_translation`
2026-01-12 00:18:42 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens87_processed_external_relevant_translation`
2026-01-12 00:18:47 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens88_processed_external_relevant_translation`
2026-01-12 00:18:52 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens89_processed_external_relevant_translation`
2026-01-12 00:18:56 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens90_processed_external_relevant_translation`
2026-01-12 00:19:01 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens90_processed_external_relevant_translation`
2026-01-12 00:19:08 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens91_processed_external_relevant_translation`
2026-01-12 00:19:13 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens91_processed_external_relevant_translation`
2026-01-12 00:19:20 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens92_processed_external_relevant_translation`
2026-01-12 00:19:26 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens92_processed_external_relevant_translation`
2026-01-12 00:19:33 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens93_processed_external_relevant_translation`
2026-01-12 00:19:39 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens93_processed_external_relevant_translation`
2026-01-12 00:19:46 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens94_processed_external_relevant_translation`
2026-01-12 00:19:51 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens94_processed_external_relevant_translation`
2026-01-12 00:20:01 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens95_processed_external_relevant_translation`
2026-01-12 00:20:06 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens95_processed_external_relevant_translation`
2026-01-12 00:20:14 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens96_processed_external_relevant_translation`
2026-01-12 00:20:19 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens96_processed_external_relevant_translation`
2026-01-12 00:20:26 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens97_processed_external_relevant_translation`
2026-01-12 00:20:31 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens97_processed_external_relevant_translation`
2026-01-12 00:20:40 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens98_processed_external_relevant_translation`
2026-01-12 00:20:45 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens98_processed_external_relevant_translation`
2026-01-12 00:20:54 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens99_processed_external_relevant_translation`
2026-01-12 00:20:59 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens99_processed_external_relevant_translation`
2026-01-12 00:21:07 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens100_processed_external_relevant_translation`
2026-01-12 00:21:16 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens101_processed_external_relevant_translation`
2026-01-12 00:21:25 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens102_processed_external_relevant_translation`
2026-01-12 00:21:33 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens103_processed_external_relevant_translation`
2026-01-12 00:21:46 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens104_processed_external_relevant_translation`
2026-01-12 00:21:54 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens105_processed_external_relevant_translation`
2026-01-12 00:22:03 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens106_processed_external_relevant_translation`
2026-01-12 00:22:10 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens107_processed_external_relevant_translation`
2026-01-12 00:22:19 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens108_processed_external_relevant_translation`
2026-01-12 00:22:28 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens109_processed_external_relevant_translation`
2026-01-12 00:22:36 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens110_processed_external_relevant_translation`
2026-01-12 00:22:45 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens111_processed_external_relevant_translation`
2026-01-12 00:22:54 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens112_processed_external_relevant_translation`
2026-01-12 00:23:02 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens113_processed_external_relevant_translation`
2026-01-12 00:23:11 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens114_processed_external_relevant_translation`
2026-01-12 00:23:20 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens115_processed_external_relevant_translation`
2026-01-12 00:23:25 INFO:graph_maker: Versionless Ensembl IDs are being connected.
2026-01-12 00:23:25 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens56_processed_ids_gene`
2026-01-12 00:23:25 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens57_processed_ids_gene`
2026-01-12 00:23:26 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens58_processed_ids_gene`
2026-01-12 00:23:26 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens59_processed_ids_gene`
2026-01-12 00:23:26 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens60_processed_ids_gene`
2026-01-12 00:23:27 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens61_processed_ids_gene`
2026-01-12 00:23:27 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens62_processed_ids_gene`
2026-01-12 00:23:27 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens63_processed_ids_gene`
2026-01-12 00:23:27 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens64_processed_ids_gene`
2026-01-12 00:23:28 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens65_processed_ids_gene`
2026-01-12 00:23:28 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-9.h5` with key `ens66_processed_ids_gene`
2026-01-12 00:23:28 INFO:graph_maker: Edges between versionless ID to version ID has been added for 'gene', assembly 9.
2026-01-12 00:23:28 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens67_processed_ids_gene`
2026-01-12 00:23:29 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens68_processed_ids_gene`
2026-01-12 00:23:29 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens69_processed_ids_gene`
2026-01-12 00:23:30 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens70_processed_ids_gene`
2026-01-12 00:23:30 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens71_processed_ids_gene`
2026-01-12 00:23:30 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens72_processed_ids_gene`
2026-01-12 00:23:31 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens73_processed_ids_gene`
2026-01-12 00:23:31 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens74_processed_ids_gene`
2026-01-12 00:23:32 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens75_processed_ids_gene`
2026-01-12 00:23:32 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens76_processed_ids_gene`
2026-01-12 00:23:32 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens77_processed_ids_gene`
2026-01-12 00:23:33 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens78_processed_ids_gene`
2026-01-12 00:23:33 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens79_processed_ids_gene`
2026-01-12 00:23:34 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens80_processed_ids_gene`
2026-01-12 00:23:34 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens81_processed_ids_gene`
2026-01-12 00:23:34 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens82_processed_ids_gene`
2026-01-12 00:23:35 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens83_processed_ids_gene`
2026-01-12 00:23:35 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens84_processed_ids_gene`
2026-01-12 00:23:36 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens85_processed_ids_gene`
2026-01-12 00:23:36 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens86_processed_ids_gene`
2026-01-12 00:23:37 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens87_processed_ids_gene`
2026-01-12 00:23:37 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens88_processed_ids_gene`
2026-01-12 00:23:37 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens89_processed_ids_gene`
2026-01-12 00:23:38 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens90_processed_versioninfo_gene`
2026-01-12 00:23:38 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens90_processed_ids_gene`
2026-01-12 00:23:39 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens91_processed_versioninfo_gene`
2026-01-12 00:23:39 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens91_processed_ids_gene`
2026-01-12 00:23:40 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens92_processed_versioninfo_gene`
2026-01-12 00:23:40 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens92_processed_ids_gene`
2026-01-12 00:23:41 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens93_processed_versioninfo_gene`
2026-01-12 00:23:41 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens93_processed_ids_gene`
2026-01-12 00:23:42 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens94_processed_versioninfo_gene`
2026-01-12 00:23:42 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens94_processed_ids_gene`
2026-01-12 00:23:43 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens95_processed_versioninfo_gene`
2026-01-12 00:23:43 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens95_processed_ids_gene`
2026-01-12 00:23:43 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens96_processed_versioninfo_gene`
2026-01-12 00:23:43 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens96_processed_ids_gene`
2026-01-12 00:23:44 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens97_processed_versioninfo_gene`
2026-01-12 00:23:44 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens97_processed_ids_gene`
2026-01-12 00:23:45 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens98_processed_versioninfo_gene`
2026-01-12 00:23:45 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens98_processed_ids_gene`
2026-01-12 00:23:46 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens99_processed_versioninfo_gene`
2026-01-12 00:23:46 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-102.h5` with key `ens99_processed_ids_gene`
2026-01-12 00:23:46 INFO:graph_maker: Edges between versionless ID to version ID has been added for 'gene', assembly 102.
2026-01-12 00:23:46 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens90_processed_ids_gene`
2026-01-12 00:23:47 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens91_processed_ids_gene`
2026-01-12 00:23:47 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens92_processed_ids_gene`
2026-01-12 00:23:48 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens93_processed_ids_gene`
2026-01-12 00:23:48 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens94_processed_ids_gene`
2026-01-12 00:23:49 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens95_processed_ids_gene`
2026-01-12 00:23:49 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens96_processed_ids_gene`
2026-01-12 00:23:49 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens97_processed_ids_gene`
2026-01-12 00:23:50 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens98_processed_ids_gene`
2026-01-12 00:23:51 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens99_processed_ids_gene`
2026-01-12 00:23:51 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens100_processed_ids_gene`
2026-01-12 00:23:52 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens101_processed_ids_gene`
2026-01-12 00:23:52 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens102_processed_ids_gene`
2026-01-12 00:23:53 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens103_processed_ids_gene`
2026-01-12 00:23:53 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens104_processed_ids_gene`
2026-01-12 00:23:54 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens105_processed_ids_gene`
2026-01-12 00:23:54 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens106_processed_ids_gene`
2026-01-12 00:23:55 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens107_processed_ids_gene`
2026-01-12 00:23:56 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens108_processed_ids_gene`
2026-01-12 00:23:56 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens109_processed_ids_gene`
2026-01-12 00:23:57 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens110_processed_ids_gene`
2026-01-12 00:23:57 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens111_processed_ids_gene`
2026-01-12 00:23:58 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens112_processed_ids_gene`
2026-01-12 00:23:58 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens113_processed_ids_gene`
2026-01-12 00:23:59 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens114_processed_ids_gene`
2026-01-12 00:23:59 INFO:database_manager: Exporting to the following file `sus_scrofa_assembly-111.h5` with key `ens115_processed_ids_gene`
2026-01-12 00:24:00 INFO:graph_maker: Edges between versionless ID to version ID has been added for 'gene', assembly 111.
2026-01-12 00:24:00 INFO:graph_maker: Synonymous external nodes are being merged into one.
2026-01-12 00:24:00 INFO:graph_maker: Number of removed nodes in the process of merging synonymous nodes: 1290
2026-01-12 00:24:07 INFO:graph_maker: The graph is being exported as '/Users/kemalinecik/git_nosync/master_idtrack/idtrack/docs/_notebooks/idtrack_cache/graph_sus_scrofa_min48_max115_narrow.pickle'.
2026-01-12 00:24:17 INFO:the_graph: Cached properties being calculated: available_genome_assemblies
2026-01-12 00:24:17 INFO:the_graph: Cached properties being calculated: combined_edges
2026-01-12 00:24:24 INFO:the_graph: Cached properties being calculated: combined_edges_genes
2026-01-12 00:24:30 INFO:the_graph: Cached properties being calculated: combined_edges_assembly_specific_genes
10

if HAS_PIG_YAML:
    g = api.track.graph
    print('Organism:', g.graph.get('organism'))
    print('Snapshot release:', g.graph.get('ensembl_release'))
    print('Main assembly:', g.graph.get('genome_assembly'))
    print('Assemblies in this graph:', sorted(api.list_genome_assemblies()))
    print('Nodes:', g.number_of_nodes())
    print('Edges:', g.number_of_edges())

    aed = sorted(getattr(g, 'available_external_databases', []))
    print('External DBs enabled (count):', len(aed))
    print('External DBs (first 20):', aed[:20])
else:
    print('Pig graph not built (missing YAML).')

Organism: sus_scrofa
Snapshot release: 115
Main assembly: 111
Assemblies in this graph: [9, 102, 111]
Nodes: 1073214

2026-01-12 00:24:32 INFO:the_graph: Cached properties being calculated: available_external_databases

Edges: 1757774
External DBs enabled (count): 24
External DBs (first 20): ['Clone_based_ensembl_gene', 'Clone_based_vega_gene', 'EntrezGene', 'HGNC Symbol', 'Havana gene', 'Havana transcript', 'NCBI gene', 'NCBI gene (formerly Entrezgene)', 'RFAM', 'RefSeq_mRNA', 'RefSeq_mRNA_predicted', 'RefSeq_ncRNA', 'RefSeq_ncRNA_predicted', 'RefSeq_peptide', 'RefSeq_peptide_predicted', 'UniProtKB Gene Name', 'Uniprot/SPTREMBL', 'Uniprot/SWISSPROT', 'VGNC Symbol', 'synonym_id::EntrezGene']

11

sorted(LOCAL_REPOSITORY.glob('graph_sus_scrofa*.pickle'))[-5:]

11

[PosixPath('/Users/kemalinecik/git_nosync/master_idtrack/idtrack/docs/_notebooks/idtrack_cache/graph_sus_scrofa_min48_max115_narrow.pickle')]

3.4 — Graph management (all species)

Reloading vs rebuilding

  • api.build_graph(...) is safe to call repeatedly.

    • If the snapshot already exists on disk, IDTrack will load it.

    • If it does not exist yet, IDTrack will build it (slow, first-time only).

Cache hygiene

Your local repository can accumulate:

  • downloaded tables

  • graph snapshot pickle files

  • intermediate files used during builds

Tip: Treat your local repository as project infrastructure. Keep it stable so you get the benefits of caching.

Switching organisms / assemblies

A graph snapshot is specific to:

  • organism

  • snapshot boundary (max release)

  • external YAML contents

  • the chosen primary assembly (the default output coordinate system)

Even though the snapshot can include multiple assemblies, changing the primary assembly changes the snapshot and requires a rebuild.

Tip: The cached graph filename does not include the assembly. If you want to keep two different primary assemblies side-by-side, use separate local repositories (or copy the graph pickle file).

Performance tips

  • Use calculate_caches=True during builds when you plan to do many conversions afterward.

  • Keep your external YAML allowlist small to reduce ambiguity and search space.

Warning: Do not delete caches unless you understand the consequence (you may force a full rebuild).

12

# Helper: list what IDTrack has cached in your local repository.
# Safe: this does NOT delete anything.

from pathlib import Path

cache = LOCAL_REPOSITORY

print('Local repository:', cache)

patterns = [
    'graph_*.pickle',
    '*_externals_modified.yml',
    '*_externals_template.yml',
]

for pat in patterns:
    hits = sorted(cache.glob(pat))
    print()
    print(f'{pat} ({len(hits)}):')
    for p in hits[:10]:
        print('  ', p.name)
    if len(hits) > 10:
        print('  ...')

Local repository: /Users/kemalinecik/git_nosync/master_idtrack/idtrack/docs/_notebooks/idtrack_cache

graph_*.pickle (3):
   graph_homo_sapiens_min48_max115_narrow.pickle
   graph_mus_musculus_min48_max115_narrow.pickle
   graph_sus_scrofa_min48_max115_narrow.pickle

*_externals_modified.yml (3):
   homo_sapiens_externals_modified.yml
   mus_musculus_externals_modified.yml
   sus_scrofa_externals_modified.yml

*_externals_template.yml (3):
   homo_sapiens_externals_template.yml
   mus_musculus_externals_template.yml
   sus_scrofa_externals_template.yml