MAJIQ v3.0.6.dev1 — psi quantification error: zarr.errors.FSPathExistNotDir & GroupNotFoundError

[CH Lin]

Environment:

• MAJIQ version: v3.0.6.dev1+g65397ab2

• Install source: official Academic Installer

• OS: macOS (Apple Silicon M1/M2, arm64)

• Python: 3.12

• Workflow: majiq build completed successfully, output directories exist as [sample_id].sorted.sj

• License: Academic license set correctly

• Build directory, TSV file, and BAMs match MAJIQ’s input requirements

---

Example command that triggers the error:

bash

majiq psi /Volumes/Expansion/ubuntu/WD40SRR/SMC/majiq/majiq_build \ /Volumes/Expansion/ubuntu/WD40SRR/SMC/majiq/experiments_test.tsv \ /Volumes/Expansion/ubuntu/WD40SRR/SMC/majiq/psi_out \ --nthreads 8

---

Main error output:

text

Traceback (most recent call last): File ".../xarray/backends/zarr.py", line 1307, in _get_open_params zarr_group = zarr.open_consolidated(store, **open_kwargs) File ".../zarr/convenience.py", line 1360, in open_consolidated meta_store = ConsolidatedStoreClass(store, metadata_key=metadata_key) File ".../zarr/storage.py", line 3046, in __init__ meta = json_loads(self.store[metadata_key]) File ".../zarr/storage.py", line 1120, in __getitem__ raise KeyError(key) KeyError: '.zmetadata' During handling of the above exception, another exception occurred: zarr.errors.GroupNotFoundError: group not found at path 'psi_coverage' During handling of the above exception, another exception occurred: FileNotFoundError: No such file or directory: '/Volumes/Expansion/ubuntu/WD40SRR/SMC/majiq/majiq_build'

---

Observed behavior:

• All sample .sorted.sj subdirectories exist and can be opened by xarray.open_zarr() manually (tested OK).

• majiq psi consistently fails with .zmetadata missing / psi_coverage group not found.

• Output directory and experiment sample sheet are correctly formatted.

---

Questions for the developers:

• Is this caused by missing or unconsolidated Zarr metadata after majiq build?

• Does the build step need additional parameters in v3 to produce the psi_coverage group?

• Is this a known issue with v3.0.6.dev1 on macOS arm64, and is there a recommended fix or stable build?

---

Thanks!

[San Jewell]

Hi Clin,

This is not an issue I've seen so far, but my guess is it involves the same zarr "file" (actually stored as directories) being specified to multiple commands and being opened as multiple filetypes, or perhaps a command is being repeated with a old or stale zarr file.

Are all of the output locations empty before beginning the run?

Are you able to specify the list of commands leading up to the error command (with sensitive information redacted) so that I can attempt to reproduce the issue?

Thanks,

-San