I have been trying out the Docker version you provided so that I may use this tool with custom eQTL statistics and GWAS data that is not available on the website.
I tried it out on a subset of my data (containing significant eQTLs and GWAS signals), just with coloc and fastenloc tools. I do get output from the tools themselves, but it seems I am unable to get the tool to generate any figures due to this error.
I was wondering if you had any suggestions on a workaround? Here is the error message:
2026-01-09 21:34:44,238::INFO::root::run_coloc.py::362::final_result_file: /root/locuscompare2-standalone/working_dir/processed/default/PD/Astrocytes_chr21_full_associations_with_se/EUR/eqtl/coloc/analyzed/coloc_output_20260109213444.tsv.gz
2026-01-09 21:34:44,239::INFO::root::run_coloc.py::363::working_dir: /root/locuscompare2-standalone/working_dir/processed/default/PD/Astrocytes_chr21_full_associations_with_se/EUR/eqtl/coloc
2026-01-09 21:34:44,493::INFO::root::run_coloc.py::213::Process completed, duration 0:00:04.771206, with params p1: 0.0001 p2:0.0001 p12:1e-05, check /root/locuscompare2-standalone/working_dir/processed/default/PD/Astrocytes_chr21_full_associations_with_se/EUR/eqtl/coloc/analyzed/coloc_output_20260109213444.tsv.gz for result!
2026-01-09 21:34:44,494::INFO::root::locuscompare2advanced.py::405::Tool coloc completed successfully!
Loading required package: RobustRankAggreg
2026-01-09 21:34:44,803::WARNING::root::intact.py::103::To run intact, you need both TWAS results and colocalization results, skipping
2026-01-09 21:34:44,806::INFO::root::locuscompare2advanced.py::433::coloctools complete at: 2026-01-09 21:34:44.806292,duration: 0:04:20.822996
2026-01-09 21:34:44,806::INFO::root::locuscompare2advanced.py::434::biological_context: Astrocytes_chr21_full_associations_with_se,trait: PD coloctools complete
report_data_processor.py
report_data_process
2026-01-09 21:34:44,815::INFO::root::report_data_processor.py::35::start report data process
report_data_processor.py
create_tissue_file
2026-01-09 21:34:44,816::INFO::root::report_data_processor.py::44::create_tissue_file
Traceback (most recent call last):
File "/root/locuscompare2-standalone/locuscompare2advanced.py", line 446, in <module>
run(parse_args.config_file, parse_args.log_file, True,
File "/root/locuscompare2-standalone/locuscompare2advanced.py", line 207, in run
redp.report_data_process(report_list)
File "/root/locuscompare2-standalone/figures/report_data_processor.py", line 37, in report_data_process
create_tissue_file(report_list)
File "/root/locuscompare2-standalone/figures/report_data_processor.py", line 58, in create_tissue_file
with open(os.path.join(output_base_dir, 'reports_path.json'), 'w', encoding='utf-8') as output_file:
File "/root/anaconda3/envs/locuscompare2/lib/python3.10/posixpath.py", line 76, in join
a = os.fspath(a)
TypeError: expected str, bytes or os.PathLike object, not NoneType
I've tried running with multiple configs for multiple eQTLs/tissues in one run but receive a similar error.
Dear locuscompare2 authors,
Thank you for providing this useful tool!
I have been trying out the Docker version you provided so that I may use this tool with custom eQTL statistics and GWAS data that is not available on the website.
I tried it out on a subset of my data (containing significant eQTLs and GWAS signals), just with coloc and fastenloc tools. I do get output from the tools themselves, but it seems I am unable to get the tool to generate any figures due to this error.
I was wondering if you had any suggestions on a workaround? Here is the error message:
I've tried running with multiple configs for multiple eQTLs/tissues in one run but receive a similar error.