pinellolab · lucapinello · Apr 21, 2026
diff --git a/audits/2026-04-21_v21_fresh_install/logs/00_pre_nuke.txt b/audits/2026-04-21_v21_fresh_install/logs/00_pre_nuke.txt
@@ -0,0 +1,23 @@
+=== Pre-nuke state (Tue Apr 21 17:15:48 EDT 2026) ===
+1.5G	/Users/lp698/.chorus/backgrounds/
+3.0G	genomes/
+
+/Users/lp698/.chorus/backgrounds/:
+total 3189032
+drwxr-xr-x@ 9 lp698  staff        288 Apr 21 09:22 .
+drwxr-xr-x@ 3 lp698  staff         96 Apr 21 09:22 ..
+drwxr-xr-x@ 3 lp698  staff         96 Apr 20 16:43 .cache
+-rw-r--r--@ 1 lp698  staff  275523684 Apr 20 16:55 alphagenome_pertrack.npz
+-rw-r--r--@ 1 lp698  staff  803275951 Apr 20 17:53 borzoi_pertrack.npz
+-rw-r--r--@ 1 lp698  staff    2541952 Apr 20 16:55 chrombpnet_pertrack.npz
+-rw-r--r--@ 1 lp698  staff  548316718 Apr 20 16:55 enformer_pertrack.npz
+-rw-r--r--@ 1 lp698  staff     212800 Apr 21 09:22 legnet_pertrack.npz
+-rw-r--r--@ 1 lp698  staff    2903709 Apr 21 09:22 sei_pertrack.npz
+
+genomes/:
+total 6393568
+drwxr-xr-x@  5 lp698  staff         160 Apr 15 00:31 .
+drwxr-xr-x@ 29 lp698  staff         928 Apr 21 15:09 ..
+-rw-r--r--@  1 lp698  staff         170 Apr 14 23:18 .gitkeep
+-rw-r--r--@  1 lp698  staff  3273481150 Apr 15 00:15 hg38.fa
+-rw-r--r--@  1 lp698  staff       19381 Apr 15 00:31 hg38.fa.fai
diff --git a/audits/2026-04-21_v21_fresh_install/logs/01_post_nuke.txt b/audits/2026-04-21_v21_fresh_install/logs/01_post_nuke.txt
@@ -0,0 +1,3 @@
+=== Post-nuke state ===
+  0B	/Users/lp698/.chorus/
+4.0K	genomes/
diff --git a/audits/2026-04-21_v21_fresh_install/logs/02_cli.txt b/audits/2026-04-21_v21_fresh_install/logs/02_cli.txt
@@ -0,0 +1,18 @@
+=== §1 CLI availability ===
+/Users/lp698/.local/share/mamba/envs/chorus/bin/chorus
+usage: chorus [-h] {setup,list,validate,remove,health,genome} ...
+
+Chorus: Modular framework for genomic foundation models
+
+positional arguments:
+  {setup,list,validate,remove,health,genome}
+                        Available commands
+    setup               Set up oracle environments
+    list                List available environments
+    validate            Validate environments
+    remove              Remove an environment
+    health              Check environment health
+    genome              Manage reference genomes
+
+options:
+  -h, --help            show this help message and exit
diff --git a/audits/2026-04-21_v21_fresh_install/logs/03_genome_download.txt b/audits/2026-04-21_v21_fresh_install/logs/03_genome_download.txt
@@ -0,0 +1,16 @@
+2026-04-21 17:16:14,341 - chorus.cli.main - INFO - Downloading hg38...
+2026-04-21 17:16:14,341 - chorus.utils.genome - INFO - Downloading hg38 from https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz...
+2026-04-21 17:16:14,341 - chorus.utils.genome - INFO - This may take several minutes depending on your connection speed...
+2026-04-21 17:17:16,249 - chorus.utils.http - INFO -   hg38 genome: 0.10/0.98 GB (10.7%)
+2026-04-21 17:18:15,709 - chorus.utils.http - INFO -   hg38 genome: 0.21/0.98 GB (21.3%)
+2026-04-21 17:19:14,882 - chorus.utils.http - INFO -   hg38 genome: 0.31/0.98 GB (32.0%)
+2026-04-21 17:20:14,148 - chorus.utils.http - INFO -   hg38 genome: 0.42/0.98 GB (42.6%)
+2026-04-21 17:21:13,352 - chorus.utils.http - INFO -   hg38 genome: 0.52/0.98 GB (53.3%)
+2026-04-21 17:22:12,542 - chorus.utils.http - INFO -   hg38 genome: 0.63/0.98 GB (64.0%)
+2026-04-21 17:23:11,837 - chorus.utils.http - INFO -   hg38 genome: 0.73/0.98 GB (74.6%)
+2026-04-21 17:24:11,208 - chorus.utils.http - INFO -   hg38 genome: 0.84/0.98 GB (85.3%)
+2026-04-21 17:25:10,463 - chorus.utils.http - INFO -   hg38 genome: 0.94/0.98 GB (95.9%)
+2026-04-21 17:25:33,062 - chorus.utils.genome - INFO - Decompressing hg38...
+2026-04-21 17:25:40,589 - chorus.utils.genome - INFO - Creating FASTA index for hg38...
+2026-04-21 17:25:46,933 - chorus.utils.genome - INFO - Successfully downloaded hg38 to /Users/lp698/chorus_test/chorus/genomes/hg38.fa
+2026-04-21 17:25:46,933 - chorus.cli.main - INFO - Successfully downloaded hg38
diff --git a/audits/2026-04-21_v21_fresh_install/logs/04_cdf_fresh_download.txt b/audits/2026-04-21_v21_fresh_install/logs/04_cdf_fresh_download.txt
@@ -0,0 +1,10 @@
+§4 CDFs — FRESH DOWNLOAD from HuggingFace (empty cache)
+oracle       |   secs | n_tracks | CDFs                  | mono | p50<=p95<=p99 | signed%
+--------------------------------------------------------------------------------------------------
+enformer     |  14.2s |     5313 | effect, summary, perbin | OK   | OK            |      0%
+borzoi       |  16.7s |     7611 | effect, summary, perbin | OK   | OK            |     20%
+chrombpnet   |   0.5s |       24 | effect, summary, perbin | OK   | OK            |      0%
+sei          |   0.5s |       40 | effect, summary       | OK   | OK            |    100%
+legnet       |   0.5s |        3 | effect, summary       | OK   | OK            |    100%
+alphagenome  |  11.4s |     5168 | effect, summary, perbin | OK   | OK            |     13%
+Total elapsed: 43.8s
diff --git a/audits/2026-04-21_v21_fresh_install/logs/05_device_probe.txt b/audits/2026-04-21_v21_fresh_install/logs/05_device_probe.txt
@@ -0,0 +1,24 @@
+=== §3 device probe ===
+2026-04-21 17:16:40,980 - chorus.core.platform - INFO - Detected platform: Darwin arm64 (key=macos_arm64, cuda=False)
+base: macos_arm64 has_cuda= False
+
+== chorus-enformer ==
+tf devs: ['/physical_device:CPU:0', '/physical_device:GPU:0']
+
+== chorus-borzoi ==
+torch cuda: False mps: True
+
+== chorus-chrombpnet ==
+tf devs: ['/physical_device:CPU:0', '/physical_device:GPU:0']
+
+== chorus-sei ==
+torch cuda: False mps: True
+
+== chorus-legnet ==
+torch cuda: False mps: True
+
+== chorus-alphagenome ==
+tf devs: ['/physical_device:CPU:0']
+jax devs: ['METAL:0']
+
+
diff --git a/audits/2026-04-21_v21_fresh_install/logs/06_api_sanity.txt b/audits/2026-04-21_v21_fresh_install/logs/06_api_sanity.txt
@@ -0,0 +1,14 @@
+oracle       | seq_length vs spec
+---------------------------------------------
+enformer     |  393216 (393216) ✓
+borzoi       |  524288 (524288) ✓
+chrombpnet   |    2114 (2114) ✓
+sei          |    4096 (4096) ✓
+legnet       |     200 (200) ✓
+alphagenome  | 1048576 (1048576) ✓
+
+-- invalid name --
+ValueError: Unknown oracle: bogus. Available: ['enformer', 'borzoi', 'chrombpnet', 'sei', 'legnet', 'alphagenome']
+
+-- §14.4 chrZZ validation --
+OSError: file `/tmp/nonexistent.fa` not found
diff --git a/audits/2026-04-21_v21_fresh_install/logs/07_consistency.txt b/audits/2026-04-21_v21_fresh_install/logs/07_consistency.txt
@@ -0,0 +1,9 @@
+=== §10 canonical-number drift in live code ===
+
+=== §10 old examples/applications/ path in live docs ===
+
+=== §15 runtime CDN fetches in shipped HTML ===
+(if empty: reports are offline-safe)
+
+=== §16 leaked HF tokens / AWS keys ===
+(if empty: no secrets committed)
diff --git a/audits/2026-04-21_v21_fresh_install/logs/08_selenium.txt b/audits/2026-04-21_v21_fresh_install/logs/08_selenium.txt
@@ -0,0 +1,21 @@
+Rendering 18 HTML reports with full JS (IGV loads)
+  ✓ batch_sort1_locus_scoring (0 JS errs)
+  ✓ rs12740374_SORT1_locus_causal_report (0 JS errs)
+  ✓ chr1_109274968_G_T_SORT1_alphagenome_amniotic_epithelial_cell_report (0 JS errs)
+  ✓ chr1_109274968_G_T_SORT1_alphagenome_fibroblast_of_mammary_gland_report (0 JS errs)
+  ✓ chr1_109274968_G_T_SORT1_alphagenome_fibroblast_of_pulmonary_artery_report (0 JS errs)
+  ✓ integration_CMV_PPP1R12C_report (0 JS errs)
+  ✓ region_swap_SORT1_K562_report (0 JS errs)
+  ✓ rs12740374_SORT1_alphagenome_report (0 JS errs)
+  ✓ rs12740374_SORT1_chrombpnet_report (0 JS errs)
+  ✓ rs12740374_SORT1_legnet_report (0 JS errs)
+  ✓ rs12740374_SORT1_multioracle_report (0 JS errs)
+  ✓ rs12740374_SORT1_CEBP_validation_report (0 JS errs)
+  ✓ chr5_1295046_T_G_TERT_alphagenome_report (0 JS errs)
+  ✓ rs1427407_BCL11A_alphagenome_report (0 JS errs)
+  ✓ rs1421085_FTO_alphagenome_report (0 JS errs)
+  ✓ rs12740374_SORT1_chrombpnet_report (0 JS errs)
+  ✓ rs12740374_SORT1_enformer_report (0 JS errs)
+  ✓ rs12740374_SORT1_alphagenome_report (0 JS errs)
+
+Total JS errors across 18 reports: 0