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error in biomart connection #544

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AdotaLover opened this issue Feb 17, 2025 · 1 comment
Open

error in biomart connection #544

AdotaLover opened this issue Feb 17, 2025 · 1 comment

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@AdotaLover
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when im running the snakemare of scenic+,i met an error

(scenicplus) ~/Pipeline/scplus_pipeline/Snakemake# snakemake --cores 5
Assuming unrestricted shared filesystem usage for local execution.
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 5
Rules claiming more threads will be scaled down.
Job stats:
job count


AUCell_direct 1
AUCell_extended 1
all 1
download_genome_annotations 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 12

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

[Mon Feb 17 15:11:05 2025]
localrule download_genome_annotations:
output: /root/Pipeline/outs/genome_annotation.tsv, /root/Pipeline/outs/chromsizes.tsv
jobid: 8
reason: Missing output files: /root/Pipeline/outs/chromsizes.tsv, /root/Pipeline/outs/genome_annotation.tsv
resources: tmpdir=/tmp

Traceback (most recent call last):
File "/root/miniconda3/envs/scenicplus/bin/scenicplus", line 8, in
sys.exit(main())
^^^^^^
File "/root/miniconda3/envs/scenicplus/lib/python3.11/site-packages/scenicplus/cli/scenicplus.py", line 1143, in main
args.func(args)
File "/root/miniconda3/envs/scenicplus/lib/python3.11/site-packages/scenicplus/cli/scenicplus.py", line 169, in download_command
download_gene_annotation_chromsizes(
File "/root/miniconda3/envs/scenicplus/lib/python3.11/site-packages/scenicplus/cli/commands.py", line 600, in download_gene_annotation_chromsizes
result = download_gene_annotation_and_chromsizes(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/envs/scenicplus/lib/python3.11/site-packages/scenicplus/data_wrangling/gene_search_space.py", line 59, in download_gene_annotation_and_chromsizes
mart = server["ENSEMBL_MART_ENSEMBL"]
~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/envs/scenicplus/lib/python3.11/site-packages/pybiomart/server.py", line 55, in getitem
return self.marts[name]
^^^^^^^^^^
File "/root/miniconda3/envs/scenicplus/lib/python3.11/site-packages/pybiomart/server.py", line 61, in marts
self._marts = self._fetch_marts()
^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/envs/scenicplus/lib/python3.11/site-packages/pybiomart/server.py", line 81, in _fetch_marts
xml = xml_from_string(response.content)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/envs/scenicplus/lib/python3.11/xml/etree/ElementTree.py", line 1338, in XML
parser.feed(text)
xml.etree.ElementTree.ParseError: mismatched tag: line 62, column 2

it seems to be the problem from ensembl,and how to fix that,thanks!

@ghuls
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ghuls commented Feb 28, 2025

Remove the cached (incomplete / wrong) BioMart response:

rm .pybiomart.sqlite

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