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Memory for more than 50 sequences with length of 250K #118

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Yaoyx opened this issue Aug 4, 2024 · 0 comments
Open

Memory for more than 50 sequences with length of 250K #118

Yaoyx opened this issue Aug 4, 2024 · 0 comments

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@Yaoyx
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Yaoyx commented Aug 4, 2024

Hello,

Thank you for this fantastic tool! Recently, I encountered a memory issue when running TFmodisco. Here's my setting of TFmodisco, and I have 100GB memory.
I am just wondering if there is any suggestion for running TFmodisco on a larger sample size (> 50)? And, if there is anyway used to estimate memory need for a sample size?

tfmodisco_results = modisco.tfmodisco_workflow.workflow.TfModiscoWorkflow(
                    sliding_window_size=18,
                    flank_size=8,
                    max_seqlets_per_metacluster=40000,
                    seqlets_to_patterns_factory=
                        modisco.tfmodisco_workflow.seqlets_to_patterns.TfModiscoSeqletsToPatternsFactory(
                                trim_to_window_size=24,
                                initial_flank_to_add=8,
                                n_cores=40)
                )(
                 task_names=["task0"],
                 contrib_scores=contrib_scores,
                 hypothetical_contribs=hypothetical_contribs,
                 one_hot=one_hot)

Regards
Yao

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