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tijeco / FUSTr

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Error in running FUSTr: "NameError: name 'dynamic' is not defined" #8

Open pragyr opened 5 months ago

pragyr commented 5 months ago

Hi, We are trying to run FUSTr in a Linux Cluster. We installed all the required dependencies as you have mentioned in - "Installation without Docker". However, we are unable to run the analysis and this is the error that is showing up:

Traceback (most recent call last):
  File "/home/pragya/bin/miniconda3/envs/FUSTr_env/lib/python3.12/site-packages/snakemake/cli.py", line 1887, in args_to_api
    dag_api = workflow_api.dag(
              ^^^^^^^^^^^^^^^^^
  File "/home/pragya/bin/miniconda3/envs/FUSTr_env/lib/python3.12/site-packages/snakemake/api.py", line 326, in dag
    return DAGApi(
           ^^^^^^^
  File "<string>", line 6, in __init__
  File "/home/pragya/bin/miniconda3/envs/FUSTr_env/lib/python3.12/site-packages/snakemake/api.py", line 421, in __post_init__
    self.workflow_api._workflow.dag_settings = self.dag_settings
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/pragya/bin/miniconda3/envs/FUSTr_env/lib/python3.12/site-packages/snakemake/api.py", line 372, in _workflow
    workflow.include(
  File "/home/pragya/bin/miniconda3/envs/FUSTr_env/lib/python3.12/site-packages/snakemake/workflow.py", line 1369, in include
    exec(compile(code, snakefile.get_path_or_uri(), "exec"), self.globals)
  File "/home/pragya/bin/FUSTr/bin/FUSTrSnakefile", line 419, in <module>
    longIsoform_CDS_combined[GeneID] = seq
    ^^^^^^^
NameError: name 'dynamic' is not defined
Traceback (most recent call last):
  File "/home/pragya/bin/miniconda3/envs/FUSTr_env/lib/python3.12/site-packages/snakemake/cli.py", line 1887, in args_to_api
    dag_api = workflow_api.dag(
              ^^^^^^^^^^^^^^^^^
  File "/home/pragya/bin/miniconda3/envs/FUSTr_env/lib/python3.12/site-packages/snakemake/api.py", line 326, in dag
    return DAGApi(
           ^^^^^^^
  File "<string>", line 6, in __init__
  File "/home/pragya/bin/miniconda3/envs/FUSTr_env/lib/python3.12/site-packages/snakemake/api.py", line 421, in __post_init__
    self.workflow_api._workflow.dag_settings = self.dag_settings
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/pragya/bin/miniconda3/envs/FUSTr_env/lib/python3.12/site-packages/snakemake/api.py", line 372, in _workflow
    workflow.include(
  File "/home/pragya/bin/miniconda3/envs/FUSTr_env/lib/python3.12/site-packages/snakemake/workflow.py", line 1369, in include
    exec(compile(code, snakefile.get_path_or_uri(), "exec"), self.globals)
  File "/home/pragya/bin/FUSTr/bin/FUSTrSnakefile", line 419, in <module>
    longIsoform_CDS_combined[GeneID] = seq
    ^^^^^^^
NameError: name 'dynamic' is not defined
Picking up from where we left off!
1 snakemake --snakefile $(which FUSTrSnakefile) -d ./main_folder_annotated_trctms_CCMB --cores 32 --use-conda --configfile configure.json  --unlock
Traceback (most recent call last):
  File "/home/pragya/bin/FUSTr/bin/FUSTr", line 135, in <module>
    output = subprocess.check_output(['bash','-c', bashCommand])
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/pragya/bin/miniconda3/envs/FUSTr_env/lib/python3.12/subprocess.py", line 466, in check_output
    return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/pragya/bin/miniconda3/envs/FUSTr_env/lib/python3.12/subprocess.py", line 571, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['bash', '-c', 'snakemake --snakefile $(which FUSTrSnakefile) -d ./main_folder_annotated_trctms_CCMB --cores 32 --use-conda --configfile configure.json']' returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/pragya/bin/FUSTr/bin/FUSTr", line 141, in <module>
    output = subprocess.check_output(['bash','-c', bashCommand])
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/pragya/bin/miniconda3/envs/FUSTr_env/lib/python3.12/subprocess.py", line 466, in check_output
    return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/pragya/bin/miniconda3/envs/FUSTr_env/lib/python3.12/subprocess.py", line 571, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['bash', '-c', 'snakemake --snakefile $(which FUSTrSnakefile) -d ./main_folder_annotated_trctms_CCMB --cores 32 --use-conda --configfile configure.json  --unlock']' returned non-zero exit status 1.

Could you please us figure out the remedy? Thanks, pragyadeep