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dieterich-lab / DCC

DCC uses output from the STAR read mapper to systematically detect back-splice junctions in next-generation sequencing data. DCC applies a series of filters and integrates data across replicate sets to arrive at a precise list of circRNA candidates.
https://dieterichlab.org/software/
GNU General Public License v3.0
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Index error when running DCC #7

Closed ShobanaSekar closed 8 years ago

ShobanaSekar commented 8 years ago

Hi,

I am getting this below error when running DCC. Could you help resolve this issue?

Traceback (most recent call last): File "/home/ssekar/tools/circRNA/DCC-0.3.2/DCC/main.py", line 507, in main() File "/home/ssekar/tools/circRNA/DCC-0.3.2/DCC/main.py", line 292, in main filt.intersectLeftandRightRegions(nonrep_left,nonrep_right,indx0,count0) File "/home/ssekar/tools/circRNA/DCC-0.3.2/DCC/circFilter.py", line 119, in intersectLeftandRightRegions nonrep = np.concatenate((indx0[position],count0[position]),axis=1) IndexError: axis 1 out of bounds [0, 1)

Thanks in advance, Shobana

tjakobi commented 8 years ago

Hi Shobana,

would it be possible to get a minimal sample data collection in order to reproduce this error? Without the corresponding input data (and complete command line) it is hard to track down what the error caused.

Cheers, Tobias

ShobanaSekar commented 8 years ago

Hi,

Apologies for my late reply. Sure I can share the dataset. I have attached my out/error log here DCC_Errorlog.txt

I am getting this error: IndexError: list index out of range

Would this log file suffice or would you like the input fastqs as well? If so I can share it in dropbox to your email id.

Thanks, Shobana

hydraphenix commented 8 years ago

I met the error too. And I un-installed the numpy package and re-install numpy1.9.2, then no bugs. Maybe you can try it.

tjakobi commented 8 years ago

Hi @hydraphenix,

thank you for your input, it is generally a good idea to keep packages updated, I did not notice any errors with newer numpy versions.

@ShobanaS88: The error containted in the error messages should have been fixed recently. Please clone the current master branch and update your installation: "python setup.py install --force".

Cheers, Tobias

hydraphenix commented 8 years ago

@tjakobi Thank you for your reply and your advice. Maybe I will do more test to check the real reason of the error report later. It may be caused by other reasons. I can run DCC now and thank you for your deverloping work.

ShobanaSekar commented 8 years ago

Thank you @hydraphenix and @tjakobi for the suggestions. I was able to run DCC with the latest commit as you mentioned. Thank you once again!

Shobana

tjakobi commented 8 years ago

Thanks for your feedback @ShobanaS88! I'll close the issue since the problem could be solved. In case of further problems, don't hesitate to open a new issue.

Cheers, Tobias