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sjteresi / TE_Density

Python script calculating transposable element density for all genes in a genome. Publication: https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-022-00264-4
GNU General Public License v3.0
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Stack limit reached ? #142

Closed asdfjohnny1 closed 1 year ago

asdfjohnny1 commented 1 year ago

Good morning,

I am new to using Python and i keep getting this error when trying to use the "make system_test"

Traceback (most recent call last): File "/Users/immlerlab/Documents/TE/TE_Density/process_genome.py", line 293, in preprocessor.process() File "/Users/immlerlab/Documents/TE/TE_Density/transposon/preprocess.py", line 108, in process transposon_frame = self._revise_transposons(transposon_frame) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/immlerlab/Documents/TE/TE_Density/transposon/preprocess.py", line 189, in _revise_transposons te_data_unwrapped = revise_annotation( ^^^^^^^^^^^^^^^^^^ File "/Users/immlerlab/Documents/TE/TE_Density/transposon/verify_cache.py", line 168, in revise_annotation revised_te_data = ReviseAnno( ^^^^^^^^^^^ File "/Users/immlerlab/Documents/TE/TE_Density/transposon/revise_annotation.py", line 65, in init resource.setrlimit(resource.RLIMIT_STACK, (1000, -1)) ValueError: not allowed to raise maximum limit make: *** [system_test] Error 1

I've tried manually setting the stack but that ddoesnt seem to help.

any ideas ?

Johnny

teresi commented 1 year ago

I understand from a cursory investigation that resource module is not available on Windows.

Are you using Windows? (or maybe even WSL?)

Does the test succeed if you comment that line out?