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Pipeline failed at last clean_chains step

Open Alchimic007 opened this issue 1 year ago • 7 comments

Hello, got an error at last Clean chains step: ### Clean Chains Step ###

Chains were filled: using /users/hpctestuser/mprylutskyi/makechains/make_lastz_chains/deschrambler_test_files/temp_chain_run/human.cow.filled.chain.gz as input Chain to be cleaned saved to: /users/hpctestuser/mprylutskyi/makechains/make_lastz_chains/deschrambler_test_files/temp_chain_run/human.cow.before_cleaning.chain.gz An error occurred while executing clean_chains: 'str' object has no attribute 'removesuffix'

I understand that script has some problems with .gz suffix in chain file, but I do not understand how to solve it. Here is server log Chains were filled: using /users/hpctestuser/mprylutskyi/makechains/make_lastz_chains/deschrambler_test_files/temp_chain_run/human.cow.filled.chain.gz as input Chain to be cleaned saved to: /users/hpctestuser/mprylutskyi/makechains/make_lastz_chains/deschrambler_test_files/temp_chain_run/human.cow.before_cleaning.chain.gz An error occurred while executing clean_chains: 'str' object has no attribute 'removesuffix' Traceback (most recent call last): File "/users/hpctestuser/mprylutskyi/makechains/make_lastz_chains/modules/step_manager.py", line 70, in execute_steps step_result = step_to_function[step](params, project_paths, step_executables) File "/users/hpctestuser/mprylutskyi/makechains/make_lastz_chains/modules/pipeline_steps.py", line 88, in clean_chains_step do_chains_clean(params, project_paths, executables) File "/users/hpctestuser/mprylutskyi/makechains/make_lastz_chains/steps_implementations/clean_chain_step.py", line 31, in do_chains_clean _output_chain = input_chain.removesuffix(".gz") AttributeError: 'str' object has no attribute 'removesuffix'

SGE job completed on Wed Nov 29 17:47:50 GMT 2023

I would be grateful for any help

Alchimic007 avatar Nov 30 '23 11:11 Alchimic007