Error when running python commandline.

[smk5g5]

I am getting this error when I try to run it directly through python script any particular reason for this?

Traceback (most recent call last): File "/opt/ibm/lsfsuite/lsf/10.1/linux2.6-glibc2.3-x86_64/etc/docker1_monitor.py", line 385, in <module> main(sys.argv[1:]) File "/opt/ibm/lsfsuite/lsf/10.1/linux2.6-glibc2.3-x86_64/etc/docker1_monitor.py", line 378, in main if driverMonitor.start_monitor() < 0 : File "/opt/ibm/lsfsuite/lsf/10.1/linux2.6-glibc2.3-x86_64/etc/docker1_monitor.py", line 175, in start_monitor if self.__collect_rusage() < 0 : File "/opt/ibm/lsfsuite/lsf/10.1/linux2.6-glibc2.3-x86_64/etc/docker1_monitor.py", line 225, in __collect_rusage self.dbHandler.update_db(resources) File "/opt/ibm/lsfsuite/lsf/10.1/linux2.6-glibc2.3-x86_64/etc/docker1_monitor.py", line 131, in update_db conn.rollback() sqlite3.OperationalError: cannot rollback - no transaction is active

Also for some reason qc plots are not saved even if I specify 'save_fig=True'. (This does not even work inside Jupiter notebook either)

st.plot_qc(adata,jitter=0.3,save_fig=True,fig_name='qc.pdf') st.plot_qc(adata,jitter=0.3,log_scale=[0,1,4,5],hist_plot=[0,1,4,5],save_fig=True,fig_name='qc2.pdf')

[huidongchen]

Re the first issue, it seems something related to your platform. Given this information, i can't say much.

For the second problem, it's indeed a bug. I will fix it in the new version. Thanks for the feedback.

[smk5g5]

Thanks Huidong,

Another bug I found is that if cell labels have spaces in them e.g. 'CD34+ LMPP' , 'CD34+ Lymphoid UNK', 'CD34+ MDP-1' etc the marker found step throws and error probably because of spaces in cell names. Just wanted to point that out!

[huidongchen]

That's good to know. I will look into it as well! Thanks!

[smk5g5]

Cool software btw!