Majiq V3 deltapsi error

[GP]

Hi there,

I am trying to run Majiq on a dataset of 2 conditions, 3 technical replicates per condition.

Below are the steps taken so far.

1. Aligned the files with STAR with the following paramenters:

STAR --readFilesCommand zcat --twopassMode Basic --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --outSAMattributes Standard --sjdbGTFfile gencode.v46.annotation.gtf --sjdbOverhang 100

2. Run majiq build on the "Aligned.sortedByCoord.out.bam" files using the following command:

majiq build ./gencode.v48.annotation.gff3 ./samples.tsv ./majiq-out/ --license ./majiq_license_academic_official.lic 

3. Run majiq psi-coverage for all files, using the command below (example for one file):majiq psi-coverage ./majiq-out/splicegraph.zarr ./majiq-out/psi-cov-File_1/ ./majiq-out/File_1Aligned.sortedByCoord.out.sj

So far, so good! No errors whatsoever and I have the psi-coverage output for all the libraries (I have decided to skip the moccasin step since I don't have any information about confounding effects for this dataset.)

I now want to quantify LSV differences for the 2 conditions, but when I run the following command:

majiq deltapsi -psi1 ./psi-cov-file_1/ ./psi-cov-file_2/ ./psi-cov-file_3/ -psi2 ./psi-cov-file_4/ ./psi-cov-file_5/ ./psi-cov-file_6/  -n condition_A condition_B

I am getting the following error:

2025-07-25 14:37:16,021 (ERROR) - Exiting due to exception:

Traceback (most recent call last):

  File "/home/userX/anaconda3/envs/rna_seq/lib/python3.10/site-packages/rna_majiq/_run/_run.py", line 147, in run

    self._run(args)

  File "/home/userX/anaconda3/envs/rna_seq/lib/python3.10/site-packages/rna_majiq/_run/deltapsi.py", line 231, in run

    df = deltapsi_voila.to_dataframe(

  File "/home/userX/anaconda3/envs/rna_seq/lib/python3.10/site-packages/rna_majiq/voila/DeltaPsiDataset.py", line 365, in to_dataframe

    "raw_psi_mean": self.groups.raw_psi_mean,

  File "/home/userX/anaconda3/envs/rna_seq/lib/python3.10/site-packages/rna_majiq/core/MixinPsiInference.py", line 76, in raw_psi_mean

    return self.raw_posterior_mean

  File "/home/userX/anaconda3/envs/rna_seq/lib/python3.10/functools.py", line 981, in __get__

    val = self.func(instance)

  File "/home/userX/anaconda3/envs/rna_seq/lib/python3.10/site-packages/rna_majiq/core/MixinPsiInference.py", line 60, in raw_posterior_mean

    return self.raw_alpha / (self.raw_alpha_plus_beta)

  File "/home/userX/anaconda3/envs/rna_seq/lib/python3.10/site-packages/xarray/core/_typed_ops.py", line 258, in __truediv__

    return self._binary_op(other, operator.truediv)

  File "/home/userX/anaconda3/envs/rna_seq/lib/python3.10/site-packages/xarray/core/dataarray.py", line 4721, in _binary_op

    self, other = align(self, other, join=align_type, copy=False)

  File "/home/userX/anaconda3/envs/rna_seq/lib/python3.10/site-packages/xarray/core/alignment.py", line 882, in align

    aligner.align()

  File "/home/userX/anaconda3/envs/rna_seq/lib/python3.10/site-packages/xarray/core/alignment.py", line 573, in align

    self.assert_no_index_conflict()

  File "/home/userX/anaconda3/envs/rna_seq/lib/python3.10/site-packages/xarray/core/alignment.py", line 318, in assert_no_index_conflict

    raise ValueError(

ValueError: cannot re-index or align objects with conflicting indexes found for the following coordinates: 'grp' (2 conflicting indexes)

Conflicting indexes may occur when

- they relate to different sets of coordinate and/or dimension names

- they don't have the same type

- they may be used to reindex data along common dimensions

I'd appreciate any suggestion about what is causing this and how to fix it!

Thank you very much in advance,

GP

[San Jewell]

Hi GP,

I ran through this list using some of my example data and ran commands similarly, and I've not yet been able to reproduce. From the error it looks like it's possible the group definitions per psicov file are somehow in conflict but it's  not easy to figure out the cause based on this information. I do thank you for being comprehensive about the walkthrough of commands used, though!

Do you think you could also post or private message me the format of the "samples.tsv", as there are groups defined there also and perhaps there was a confusion in their definition.

Thanks,

-San