Open LliliansCalvo opened 5 months ago
I am pretty sure that "chrUn_DS483735v1.psl does not exist" indicates that no alignments were found for this reference scaffold. Given that drosophila and ants are separated by a huge evolutionary distance, this is not surprising (even Drosophila - Anopheles is already >1 subs per neutral site).
However, I don't understand why it crashes with this error message. @kirilenkobm Do you know what that means?
Thanks for the answer. I tried to install and run again just with the example and I get the same chain_run error:
./make_chains.py target query test_data/test_reference.fa test_data/test_query.fa --pd test_out -f --chaining_memory 16
### Nextflow process chain_run finished successfully
An error occurred while executing chain_run: Error! No non-empty files found at /work/FAC/FBM/make_lastz_chains/test_out/temp_chain_run/chain. The failed operation label is: chain_run
Traceback (most recent call last):
File "/work/FAC/FBM/make_lastz_chains/modules/step_manager.py", line 70, in execute_steps
step_result = step_to_function[step](params, project_paths, step_executables)
File "/work/FAC/FBM/make_lastz_chains/modules/pipeline_steps.py", line 64, in chain_run_step
do_chain_run(params, project_paths, executables)
File "/work/FAC/FBM/make_lastz_chains/steps_implementations/chain_run_step.py", line 109, in do_chain_run
has_non_empty_file(project_paths.chain_output_dir, "chain_run")
File "/work/FAC/FBM/make_lastz_chains/modules/common.py", line 51, in has_non_empty_file
raise PipelineFileNotFoundError(err_msg)
modules.error_classes.PipelineFileNotFoundError: Error! No non-empty files found at /work/FAC/FBM/make_lastz_chains/test_out/temp_chain_run/chain. The failed operation label is: chain_run
Hi,
I am trying it to run it and it fails at what looks like the last step after a long time running. I dont understand what this error means or how to fix it.
Hope someone can help