Problems with dphenome (YAML/OPM parsing failed!) and Failure to calculate activity index

[frmuc...@gmail.com]

Hi

Thank you for the wonderful program.

I am having problems running dphenome start it gives the error Illegal instruction (core dumped)

Also when i add the phenome data i get the message (YAML/OPM parsing failed!)

Below is the extract from the Ductape i was trying to run.


How can i resolve this

Kind regards

Francis

 

ubuntu@ubuntu-VirtualBox:~/Ductape/ductape$ dphenome add ./phenome/N843.csv N843

12:13:01 - YAML/OPM parsing failed!

12:13:02 - Added phenome N843, having 4 biolog plates (384 wells)

ubuntu@ubuntu-VirtualBox:~/Ductape/ductape$ dphenome plot

^[[A12:13:11 - The activity index must be calculated first (run dphenome start)

ubuntu@ubuntu-VirtualBox:~/Ductape/ductape$ dphenome add ./phenome/LMN586.csv LMN586

12:13:23 - YAML/OPM parsing failed!

12:13:24 - Added phenome LMN586, having 4 biolog plates (384 wells)

ubuntu@ubuntu-VirtualBox:~/Ductape/ductape$ dphenome zero

12:13:40 - Normal zero subtraction

12:13:40 - Zero subtraction done on 4 plates

ubuntu@ubuntu-VirtualBox:~/Ductape/ductape$ dphenome trim

12:13:48 - Trimming 4 phenomic plates

12:13:48 - Trimmed 4 plates at 23.750000

12:13:48 - Updating the plates

12:13:49 - The parameters and the activity must be recalculated

ubuntu@ubuntu-VirtualBox:~/Ductape/ductape$ dphenome start -n 3 -f

12:14:08 - 1 - Calculating parameters

                                                           Calculating parameters                                                          

  0% [----------------------------------------------------------------------------------------------------------------------------------]

                                                            Item 1 on 768 total                                                             /usr/local/lib/python2.7/dist-packages/scipy/optimize/minpack.py:779: OptimizeWarning: Covariance of the parameters could not be estimated

100% [==================================================================================================================================]

                                                           Item 768 on 768 total                                                            12:14:51 - 2 - Clustering

Illegal instruction (core dumped)

ubuntu@ubuntu-VirtualBox:~/Ductape/ductape$ dphenome plot

12:15:06 - The activity index must be calculated first (run dphenome start)

 

[Marco Galardini]

Hi,

sorry to hear you encountered some problems.

The first warning message ("YAML/OPM parsing failed!") is expected to happen, as you provided phenotype microarray data in csv format. DuctApe tries first assumes the phenotypic data is in YAML/JSON format and tries to parse them as such before using the CSV parser. No need to worry then.

Regarding the second error, I believe it might be due to you having an old version of either scipy or scikit-learn. Could you try updating them and retry?

Best,

M

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