Problem with temporary files

[gdejana]

Problem temporary files

I am trying to use genotools pipeline to impute ancestry and perform qc on variants and subjects as it follows:

genotools --pfile /home/user/jojo/A --out /home/user/jojo/ --ref_panel /opt/tools/GenoTools/ref_panel/1kg_30x_hgdp_ashk_ref_panel --ancestry --ref_labels /opt/tools/GenoTools/ref_panel/1kg_30x_hgdp_ashk_ref_panel_labels.txt --subset_ancestry EUR --related True --prune_related False --prune_duplicated --all_sample True --all_variant Appartly genotools stops working as it searches for file "/home/utente/jojo/A_EUR". Should genotools search for it among temporary files? Am I missing something?

Thank you for your time!

[dvitale199]

/home/user/jojo/A is the path to the pfile prefix?

--out is pointing to a directory in your case. it has to point to an output file prefix

For example, if I have /my/path/to/my_pfile.{pgen,psam,pvar}, I would call it as genotools --pfile /my/path/to/my_pfile --out /my/path/to/my_pfile_out

[gdejana]

A was actually the name of the file, I tried to rerrun it but I end up having the same error:

Running: callrate with input /home/utente/jojo/baustelle/filtered_CIDR_HuntingtonsDS_Top_subject_level_c1_update_MERGED_FINAL_ancestry_EUR and output: /home/utente/jojo/baustelle/.19gqojjs_tmp/res_genotools_EUR_callrate Traceback (most recent call last): File "/home/utente/miniconda3/bin/genotools", line 8, in <module> sys.exit(handle_main()) ^^^^^^^^^^^^^ File "/home/utente/miniconda3/lib/python3.11/site-packages/genotools/__main__.py", line 164, in handle_main out_dict[label] = execute_pipeline(run_steps_list, ordered_steps, geno_path, out, samp_qc=samp_qc, var_qc=var_qc, assoc=assoc, args=args_dict, tmp_dir=tmp_dir) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/utente/miniconda3/lib/python3.11/site-packages/genotools/pipeline.py", line 157, in execute_pipeline out_dict[step] = steps_dict[step](args[step]) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/utente/miniconda3/lib/python3.11/site-packages/genotools/qc.py", line 64, in run_callrate_prune raise FileNotFoundError(f"{geno_path} does not exist.") FileNotFoundError: /home/utente/jojo/baustelle/filtered_CIDR_HuntingtonsDS_Top_subject_level_c1_update_MERGED_FINAL_ancestry_EUR does not exist.

Any ideas? I also attached the full log file:

res_genotools_all_logs.log

Thank you for your time!

[dvitale199]

could you attach the "cleaned_logs" file as well?

[gdejana]

Here it is!

Thank you again res_genotools_cleaned_logs.log