Error in rpy2.rinterface.RRuntimeError about stream HOT 10 CLOSED

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Hi,

I am encountering similar problem. Is there any update on this?

In my case, I have 10 datasets that are formatted in same way. STREAM is able to run for all of them except one where I am running into following error "RRuntimeWarning: Error in NodePositionArrayAll[[i]] : subscript out of bounds".

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The docker runs well on the example dataset (Olsson_2016).
I downsample my data (=> 1000 cells) and it runs properly. With 3500 cells it does not work

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Thanks for reporting this. Can you please share the full dataset with 3500 with @huidongchen so we can investigate?

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Hi @ChaDuss @parveendabas, sorry about the errors. Can you also try to remove --EPG_shift and rerun it to see if this will help?

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Hi @ChaDuss @parveendabas, sorry about the errors. Can you also try to remove --EPG_shift and rerun it to see if this will help?

Hi
I got the same errors,

my cmd is(not docker):
stream -m exp.xls -l cell_label.tsv -c cell_label_color.tsv

but it would work without any error using the same file(small file):
cut -f 1-101 exp.xls >s_exp.xls
head -100 cell_label.tsv>s_cell_label.xls
stream -m s_exp.xls -l s_cell_label.xls -c cell_label_color.tsv

I do not know why.

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from stream.

I just wanted to add one comment. It seems to me that there is no branching event in your dataset so the default process 'optimize_branching' failed. What I would suggest is:

Check the output umap visualization plot to see if there is branching structure

if yes,
you can increase the number of initial clusters by adjusting the parameter --n_clusters(by default it's 10, you can increase it to 20)

if no,
simply adding the parameter --disable_EPG_optimize will help get rid of the errors.

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Hi Semir, Could you send us the full input? In this way we can try to reproduce your error and debug this. Best, Luca
…
On Fri, Jun 28, 2019 at 7:44 AM semir2 @.***> wrote: Hi @ChaDuss https://github.com/ChaDuss @parveendabas https://github.com/parveendabas, sorry about the errors. Can you also try to remove --EPG_shift and rerun it to see if this will help? Hi I got the same errors, [image: image] https://user-images.githubusercontent.com/46958122/60319669-c3805100-99a9-11e9-8034-7be584e039d7.png my cmd is(not docker): stream -m exp.xls -l cell_label.tsv -c cell_label_color.tsv but it would work without any error using the same file(small file): cut -f 1-101 exp.xls >s_exp.xls head -100 cell_label.tsv>s_cell_label.xls stream -m s_exp.xls -l s_cell_label.xls -c cell_label_color.tsv I do not know why. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#12?email_source=notifications&email_token=AAIH72X76OJZIPYYZVXVSM3P4WQKLA5CNFSM4HPOKQU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODYZD2KI#issuecomment-506608937>, or mute the thread https://github.com/notifications/unsubscribe-auth/AAIH72VQ6UFJCQ6XIZBN7QDP4WQKLANCNFSM4HPOKQUQ .

thanks for your reply！The problem was sovled with the solution of @huidongchen. It seems to be that there is no branching event in my dataset， so the default process 'optimize_branching' failed. Could you give us warnings with no branching event and set defaut parameter to be --disable_EPG_optimize?

@huidongchen Thanks for you solution, it worked well with your suggestion.

Thank you very much for your time and help!
Best

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I m glad it helped :) Thanks for your important feedback! We will add the warning info as you suggested.

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