Error in rule get_search_space: jobid: 11 second

[vcleon88]

I created my own chromsize.tsv:
it looks like
Chromosome Start End
0 chr1 0 248956422
1 chr2 0 242193529
2 chr3 0 198295559
3 chr4 0 190214555
4 chr5 0 181538259
Index(['Chromosome', 'Start', 'End'], dtype='object')

and the genomo_annotataion.tsv with filtered chromosome be like:
Chromosome Start End Strand Gene Transcription_Start_Site
0 chrM 3307 4262 + MT-ND1 3307
1 chrM 4470 5511 + MT-ND2 4470
2 chrM 5904 7445 + MT-CO1 5904
3 chrM 7586 8269 + MT-CO2 7586
4 chrM 8366 8572 + MT-ATP8 8366

Transcript_type
0 protein_coding
1 protein_coding
2 protein_coding
3 protein_coding
4 protein_coding
Index(['Chromosome', 'Start', 'End', 'Strand', 'Gene',
'Transcription_Start_Site', 'Transcript_type'],
dtype='object')

however when i run the Snakemake
the error comes again

:~/scplus_pipeline/Snakemake$ Assuming unrestricted shared filesystem usage for local execution.
Building DAG of jobs...
Using shell: /bin/bash
Provided cores: 40
Rules claiming more threads will be scaled down.
Job stats:
job count

---

AUCell_direct 1
AUCell_extended 1
all 1
eGRN_direct 1
eGRN_extended 1
get_search_space 1
motif_enrichment_dem 1
prepare_menr 1
region_to_gene 1
scplus_mudata 1
tf_to_gene 1
total 11

Select jobs to execute...
Execute 1 jobs...

[Thu Oct 24 15:57:03 2024]
localrule get_search_space:
input: /home/gu/scecis/plusout/ACC_GEX.h5mu, /home/gu/scecis/plusout/genome_annotation.tsv, /home/gu/scecis/plusout/chromsizes.tsv
output: /home/gu/scecis/plusout/search_space.tsv
jobid: 11
reason: Missing output files: /home/gu/scecis/plusout/search_space.tsv
resources: tmpdir=/tmp

2024-10-24 15:57:08,201 SCENIC+ INFO Reading data
(scenicplus) gu@s166:~/scplus_pipeline/Snakemake$ /home/gu/miniconda3/envs/scenicplus/lib/python3.11/site-packages/anndata/_core/anndata.py:522: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
warnings.warn(
/home/gu/miniconda3/envs/scenicplus/lib/python3.11/site-packages/anndata/_core/anndata.py:522: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
warnings.warn(
Traceback (most recent call last):
File "/home/gu/miniconda3/envs/scenicplus/bin/scenicplus", line 8, in
sys.exit(main())
^^^^^^
File "/home/gu/miniconda3/envs/scenicplus/lib/python3.11/site-packages/scenicplus/cli/scenicplus.py", line 1137, in main
args.func(args)
File "/home/gu/miniconda3/envs/scenicplus/lib/python3.11/site-packages/scenicplus/cli/scenicplus.py", line 208, in search_space
get_search_space_command(
File "/home/gu/miniconda3/envs/scenicplus/lib/python3.11/site-packages/scenicplus/cli/commands.py", line 661, in get_search_space_command
search_space = get_search_space(
^^^^^^^^^^^^^^^^^
File "/home/gu/miniconda3/envs/scenicplus/lib/python3.11/site-packages/scenicplus/data_wrangling/gene_search_space.py", line 294, in get_search_space
pr_regions = pr.PyRanges(region_names_to_coordinates(scplus_region))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/gu/miniconda3/envs/scenicplus/lib/python3.11/site-packages/scenicplus/utils.py", line 223, in region_names_to_coordinates
regiondf.columns = ['Chromosome', 'Start', 'End']
^^^^^^^^^^^^^^^^
File "/home/gu/miniconda3/envs/scenicplus/lib/python3.11/site-packages/pandas/core/generic.py", line 5920, in setattr
return object.setattr(self, name, value)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "pandas/_libs/properties.pyx", line 69, in pandas._libs.properties.AxisProperty.set
File "/home/gu/miniconda3/envs/scenicplus/lib/python3.11/site-packages/pandas/core/generic.py", line 822, in _set_axis
self._mgr.set_axis(axis, labels)
File "/home/gu/miniconda3/envs/scenicplus/lib/python3.11/site-packages/pandas/core/internals/managers.py", line 228, in set_axis
self._validate_set_axis(axis, new_labels)
File "/home/gu/miniconda3/envs/scenicplus/lib/python3.11/site-packages/pandas/core/internals/base.py", line 70, in _validate_set_axis
raise ValueError(
ValueError: Length mismatch: Expected axis has 0 elements, new values have 3 elements
[Thu Oct 24 15:57:18 2024]
Error in rule get_search_space:
jobid: 11
input: /home/gu/scecis/plusout/ACC_GEX.h5mu, /home/gu/scecis/plusout/genome_annotation.tsv, /home/gu/scecis/plusout/chromsizes.tsv
output: /home/gu/scecis/plusout/search_space.tsv
shell:

    scenicplus prepare_data search_spance             --multiome_mudata_fname /home/gu/scecis/plusout/ACC_GEX.h5mu             --gene_annotation_fname /home/gu/scecis/plusout/genome_annotation.tsv             --chromsizes_fname /home/gu/scecis/plusout/chromsizes.tsv             --out_fname /home/gu/scecis/plusout/search_space.tsv             --upstream 1000 150000             --downstream 1000 150000             --extend_tss 10 10

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2024-10-24T155703.261548.snakemake.log
WorkflowError:
At least one job did not complete successfully.

is there anyone have idea of this issue ？

Thanks in advance.

[kennethho04]

Hi @vcleon88

I got the same issue and was able to resolve it. Your problem is similar to what was mentioned in issue #426

The problem is likely due to the format of your mudata var.names.
You can check the format by running the following:

import mudata

mdata = mudata.read(<PATH_TO_ ACC_GEX.h5mu>)
mdata["scATAC"].var_names

The format should be "chr:start-end". In my case it was formatted as "chr-start-end" so I reformatted mdata["scATAC"].var_names to "chr:start-end" and saved it as a new mudata to replace the old one in my out folder. Hope that helps.

[vcleon88]

Hi @vcleon88

I got the same issue and was able to resolve it. Your problem is similar to what was mentioned in issue #426

The problem is likely due to the format of your mudata var.names. You can check the format by running the following:

import mudata

mdata = mudata.read(<PATH_TO_ ACC_GEX.h5mu>)
mdata["scATAC"].var_names

The format should be "chr:start-end". In my case it was formatted as "chr-start-end" so I reformatted mdata["scATAC"].var_names to "chr:start-end" and saved it as a new mudata to replace the old one in my out folder. Hope that helps.

Hi @kennethho04

Thank you so much!!!! I solved this problem!!!

[Melody-cell]

Hi, @vcleon88 , @kennethho04 , @SeppeDeWinter , i got the same error,
but my mudata is all good, i don't know why.
Did anyone know how to solve it?

[SeppeDeWinter]

Hi @Melody-cell

Could you post the entire error log please (just copy paste the output).

All the best,

Seppe