ValueError: Experiments table does not have 'path' column

cheong cheong

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Jul 20, 2025, 3:49:46 AMJul 20

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Hi how are you?

just downloaded majiq today, but keep getting this error message when i rung majiq build

ValueError: Experiments table does not have 'path' column

could it be a problem in the my cofiguration file?

Thank you.

San Jewell

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Jul 22, 2025, 2:00:27 PMJul 22

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Hi Cheong,

Could you post the build command and the contents of the groups tsv file if you are using the argument --groups-tsv in the build command?

Thanks!

-San

cheong cheong

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Jul 22, 2025, 10:54:20 PMJul 22

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Hi Sa,

the build command i used:

majiq build /scratch/project/gencode.v43.primary_assembly.annotation.gff3

/scratch/project/config.tsv

/scratch/project/

--license /scratch/project/genetic_data_analysis/cheong/majiq/majiq_license_academic_official.lic

and i attached the config file

thank you.

config.tsv

San Jewell

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Jul 28, 2025, 11:44:39 AMJul 28

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Hi Cheong,

It sounds like you are using majiq v2 commands / config, but running majig v3 software. They are not reverse compatible. You may find instructions for downloading majiq v2 towards the bottom of the installation page you see after accepting the license agreement. If you would like to use majiq v3 instead, please check out the documentation to see how to properly run and format commands with the new version: https://biociphers.bitbucket.io/majiq-docs/v2-to-v3.html

Thanks!

-San

cheong cheong

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Jul 28, 2025, 10:21:55 PMJul 28

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Hi San,

Thanks for your reply.

Yes I found the new pipeline for majiq 3 and re-ran everything but still get stuck on the build command, basically the same error message

my command:

majiq-v3 build /scratch/project/genetic_data_analysis/cheong/majiq/sg.zarr /scratch/project/genetic_data_analysis/cheong/majiq/build/buildresult.zarr --groups-tsv /scratch/project/genetic_data_analysis/cheong/majiq/config.tsv --license /scratch/project/genetic_data_analysis/cheong/majiq/majiq_license_academic_official.lic

i attached the config file i used and the errror message is :

simplify_minreads_annotated = 0.0,

simplify_minreads_denovo = 0.0,

simplify_minreads_ir = 0.0,

nthreads = 1,

work_directory = None,

tmp_work_directory_parent = None,

overwrite = False,

logger = None,

logfile_only = False,

silent = False,

debug = False,

}

2025-07-27 11:18:03,309 (INFO) - ╔═══════════════════════════════════════════════════════════════╗

2025-07-27 11:18:03,309 (INFO) - ╠╡ ACADEMIC License applied ║

2025-07-27 11:18:03,309 (INFO) - ║ Name: Official Majiq Academic-only License ║

2025-07-27 11:18:03,309 (INFO) - ║ File: majiq_license_academic_official.lic ║

2025-07-27 11:18:03,309 (INFO) - ║ Expiration Date: Never ║

2025-07-27 11:18:03,309 (INFO) - ║ ║

2025-07-27 11:18:03,309 (INFO) - ╠╡ The academic license is for non-commercial purposes by ║

2025-07-27 11:18:03,309 (INFO) - ╠╡ individuals at an academic or not for profit institution. ║

2025-07-27 11:18:03,309 (INFO) - ╚═══════════════════════════════════════════════════════════════╝

2025-07-27 11:18:03,309 (INFO) - Using temporary work directory /scratch/temp/14999163/6a3d56a1c46295035feeb93d1d6089e29z__q4mg

2025-07-27 11:18:03,310 (INFO) - Loading experiment groups from /scratch/project_mnt/S0007/cheong/majiq/config.tsv

2025-07-27 11:18:03,312 (ERROR) - Exiting due to exception:

Traceback (most recent call last):

File "/scratch/project_mnt/S0007/cheong/maj/lib/python3.12/site-packages/rna_majiq/_run/_run.py", line 147, in run

self._run(args)

File "/scratch/project_mnt/S0007/cheong/maj/lib/python3.12/site-packages/rna_majiq/_run/build_update.py", line 128, in run

experiments = get_grouped_experiments(args.groups_tsv)

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

File "/scratch/project_mnt/S0007/cheong/maj/lib/python3.12/site-packages/rna_majiq/_run/build_update.py", line 91, in get_grouped_experiments

df = pd.read_csv(groups_tsv, sep="\t", usecols=["group", "sj"])

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

File "/scratch/project_mnt/S0007/cheong/maj/lib/python3.12/site-packages/pandas/io/parsers/readers.py", line 1026, in read_csv

return _read(filepath_or_buffer, kwds)

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

File "/scratch/project_mnt/S0007/cheong/maj/lib/python3.12/site-packages/pandas/io/parsers/readers.py", line 620, in _read

parser = TextFileReader(filepath_or_buffer, **kwds)

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

File "/scratch/project_mnt/S0007/cheong/maj/lib/python3.12/site-packages/pandas/io/parsers/readers.py", line 1620, in __init__

self._engine = self._make_engine(f, self.engine)

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

File "/scratch/project_mnt/S0007/cheong/maj/lib/python3.12/site-packages/pandas/io/parsers/readers.py", line 1898, in _make_engine

return mapping[engine](f, **self.options)

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

File "/scratch/project_mnt/S0007/cheong/maj/lib/python3.12/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 140, in __init__

self._validate_usecols_names(usecols, self.orig_names)

File "/scratch/project_mnt/S0007/cheong/maj/lib/python3.12/site-packages/pandas/io/parsers/base_parser.py", line 979, in _validate_usecols_names

raise ValueError(

ValueError: Usecols do not match columns, columns expected but not found: ['group', 'sj']

"errmaj" 82L, 5434C

config.tsv

San Jewell

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Jul 29, 2025, 1:35:21 PMJul 29

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Hi cheong,

It looks like you are using the v2 style config file (ini format). Even though your file it called "config.tsv" it looks like it's actually still in ini file. As the error message states, it's looking for columns "group" and "sj" in that input file. So you'd have something like this:

Let me know if it makes sense,

-San

cheong cheong

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Jul 31, 2025, 8:53:39 PMJul 31

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thank you San,

Currently at the moccasin step

command i used:

majiq-v3 moccasin-pipeline /scratch/project/genetic_data_analysis/cheong/majiq/moccasin/ \

/scratch/project/genetic_data_analysis/cheong/majiq/psi/control.psicov /scratch/project/genetic_data_analysis/cheong/majiq/psi/case.psicov \

--factors_tsv /scratch/project/genetic_data_analysis/cheong/majiq/model_matrix.tsv \

--confounding gender \

--overwrite \

--license /scratch/project/genetic_data_analysis/cheong/majiq/majiq_license_academic_official.lic

and the error message i got

majiq-v3 moccasin-pipeline: error: argument psicov: /scratch/project_mnt/S0007/cheong/ does not exist

/var/spool/slurmd/job15047194/slurm_script: line 23: /scratch/project/genetic_data_analysis/cheong/majiq/psi/control.psicov: Is a directory

cheong cheong

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Jul 31, 2025, 11:05:56 PMJul 31

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Hi San,

So i got passed that and have the moccasin result, but there is just one corrected.psicov

should i run the moccasin-pipeline sperately if i have two groups? meaning i run moccasin twice, each time with only one group?

thank you.

bsl...@seas.upenn.edu

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Aug 5, 2025, 12:48:27 PMAug 5

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Dear Cheong,

An execution of moccasin-pipeline outputs a single corrected.psicov which includes psi coverage for all the prefixes in factors.tsv. The .psicov files which you include in the execution command as inputs should collectively include the original psi coverage for all those prefixes.

You could execute moccasin-pipeline more than once if you want to model different collections of prefixes and confounders.