Hello every one i'm trying to open a .mat model with cobraPy it was running for a week in Jupyter but I received an error after one week.can you please explain to me how can I fix this error ?
Thank You very much I
Please explain:
what I'm trying to open .mat model with cobraPy,
how you went about it (referring to the code sample), and
why the current behaviour is a problem and what output
you expected instead.
UserWarning: malformed gene_reaction_rule '[]' for <Reaction Blautia_hydrogenotrophica_DSM_10507_IEX_val_L[u]tr at 0x7f3dfae24860>
warn("malformed gene_reaction_rule '%s' for %s" % (new_rule, repr(self)))
/opt/python-3.6.9/lib/python3.6/site-packages/cobra/core/reaction.py:438: UserWarning: malformed gene_reaction_rule '[]' for <Reaction Blautia_hydrogenotrophica_DSM_10507_IEX_zn2[u]tr at 0x7f3dfae248d0>
warn("malformed gene_reaction_rule '%s' for %s" % (new_rule, repr(self)))
/opt/python-3.6.9/lib/python3.6/site-packages/cobra/core/reaction.py:438: UserWarning: malformed gene_reaction_rule '[]' for <Reaction Blautia_hydrogenotrophica_DSM_10507_IEX_no3[u]tr at 0x7f3dfae24940>
warn("malformed gene_reaction_rule '%s' for %s" % (new_rule, repr(self)))
IOPub data rate exceeded.
The notebook server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
--NotebookApp.iopub_data_rate_limit.
Current values:
NotebookApp.iopub_data_rate_limit=1000000.0 (bytes/sec)
NotebookApp.rate_limit_window=3.0 (secs)
Problem description
Hello every one i'm trying to open a .mat model with cobraPy it was running for a week in Jupyter but I received an error after one week.can you please explain to me how can I fix this error ? Thank You very much I
Please explain:
Code Sample
Create a minimal, complete, verifiable example.
UserWarning: malformed gene_reaction_rule '[]' for <Reaction Blautia_hydrogenotrophica_DSM_10507_IEX_val_L[u]tr at 0x7f3dfae24860> warn("malformed gene_reaction_rule '%s' for %s" % (new_rule, repr(self))) /opt/python-3.6.9/lib/python3.6/site-packages/cobra/core/reaction.py:438: UserWarning: malformed gene_reaction_rule '[]' for <Reaction Blautia_hydrogenotrophica_DSM_10507_IEX_zn2[u]tr at 0x7f3dfae248d0> warn("malformed gene_reaction_rule '%s' for %s" % (new_rule, repr(self))) /opt/python-3.6.9/lib/python3.6/site-packages/cobra/core/reaction.py:438: UserWarning: malformed gene_reaction_rule '[]' for <Reaction Blautia_hydrogenotrophica_DSM_10507_IEX_no3[u]tr at 0x7f3dfae24940> warn("malformed gene_reaction_rule '%s' for %s" % (new_rule, repr(self))) IOPub data rate exceeded. The notebook server will temporarily stop sending output to the client in order to avoid crashing it. To change this limit, set the config variable
--NotebookApp.iopub_data_rate_limit
.Current values: NotebookApp.iopub_data_rate_limit=1000000.0 (bytes/sec) NotebookApp.rate_limit_window=3.0 (secs)
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