request for output files

[nirmala...@gmail.com]

Hi,

I was able to install and run GRIT on the example files provided with some warnings. I got the output *.gft and *.bed files, but would like to see if the files were complete or incomplete due to the warnings I received.

Could someone who ran GRIT successfully on the example files upload their output files they got from the GRIT example provided?

Thank you very much.

Regards,
Nirmala

[Nathan Boley]

Hi Nirmala,

What warnings did you get?

Best, Nathan

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[nirmala...@gmail.com]

Thanks for your response Nathan.

Here are the messages:

[akulan@felix GRIT_tutorial]$ /data/akulan/local/bin/run_grit.py --control AdMatedF_Ecl_20days_Heads.control.txt --reference flybase-r5.45.chr4.gtf Process Process-2:

Traceback (most recent call last):

  File "/data/akulan/local/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap

    self.run()

  File "/data/akulan/local/lib/python2.7/multiprocessing/process.py", line 114, in run

    self._target(*self._args, **self._kwargs)

  File "/data/akulan/local/lib/python2.7/curses/wrapper.py", line 43, in wrapper

    return func(stdscr, *args, **kwds)

  File "build/bdist.linux-x86_64/egg/grit/lib/logging.py", line 13, in manage_curses_display

    curses.curs_set(0)

error: curs_set() returned ERR

/data/akulan/local/lib/python2.7/site-packages/GRIT-1.1.3-py2.7-linux-x86_64.egg/grit/f_matrix.py:747: FutureWarning: comparison to `None` will result in an elementwise object comparison in the future.

/data/akulan/local/lib/python2.7/site-packages/GRIT-1.1.3-py2.7-linux-x86_64.egg/grit/build_transcripts.py:768: FutureWarning: comparison to `None` will result in an elementwise object comparison in the future.

/data/akulan/local/lib/python2.7/site-packages/GRIT-1.1.3-py2.7-linux-x86_64.egg/grit/build_transcripts.py:322: FutureWarning: comparison to `None` will result in an elementwise object comparison in the future.

/data/akulan/local/lib/python2.7/site-packages/GRIT-1.1.3-py2.7-linux-x86_64.egg/grit/build_transcripts.py:332: FutureWarning: comparison to `None` will result in an elementwise object comparison in the future.

/data/akulan/local/lib/python2.7/site-packages/GRIT-1.1.3-py2.7-linux-x86_64.egg/grit/build_transcripts.py:322: FutureWarning: comparison to `None` will result in an elementwise object comparison in the future.

/data/akulan/local/lib/python2.7/site-packages/GRIT-1.1.3-py2.7-linux-x86_64.egg/grit/build_transcripts.py:332: FutureWarning: comparison to `None` will result in an elementwise object comparison in the future.

[Nathan Boley]

I was able to install and run GRIT on the example files provided with some warnings. I got the output *.gft and *.bed files, but would like to see if the files were complete or incomplete due to the warnings I received.

Could someone who ran GRIT successfully on the example files upload their output files they got from the GRIT example provided?

I posted output from the control file output  at:

http://grit-bio.org/GRIT_tutorial_controlfile_example_output.zip

 Best, Nathan

[Nathan Boley]

On Fri, Jan 16, 2015 at 10:25 AM, <nirmala...@gmail.com> wrote:

Thanks for your response Nathan.

Here are the messages:

[akulan@felix GRIT_tutorial]$ /data/akulan/local/bin/run_grit.py --control AdMatedF_Ecl_20days_Heads.control.txt --reference flybase-r5.45.chr4.gtf Process Process-2:

Traceback (most recent call last):

  File "/data/akulan/local/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap

    self.run()

  File "/data/akulan/local/lib/python2.7/multiprocessing/process.py", line 114, in run

    self._target(*self._args, **self._kwargs)

  File "/data/akulan/local/lib/python2.7/curses/wrapper.py", line 43, in wrapper

    return func(stdscr, *args, **kwds)

  File "build/bdist.linux-x86_64/egg/grit/lib/logging.py", line 13, in manage_curses_display

    curses.curs_set(0)

error: curs_set() returned ERR

this shouldn't affect the output, but, do you see an ncurses display? I've attached a screen shot of what this should look like. 

 

/data/akulan/local/lib/python2.7/site-packages/GRIT-1.1.3-py2.7-linux-x86_64.egg/grit/f_matrix.py:747: FutureWarning: comparison to `None` will result in an elementwise object comparison in the future.

[SNIP] 

/data/akulan/local/lib/python2.7/site-packages/GRIT-1.1.3-py2.7-linux-x86_64.egg/grit/build_transcripts.py:332: FutureWarning: comparison to `None` will result in an elementwise object comparison in the future.

These shouldn't affect the output - but thanks for letting me know.

Best, Nathan

[nirmala...@gmail.com]

Thank you for the output files. Is GRIT supposed to give the same answer for multiple runs on the same files?

Upon comparing the log, bed and gtf files there are seems to be several differences between my output files and the files you posted. Here's a summary of differences.

     1. My log file skipped 27 regions (listed below) versus your log file which shows only 2 regions as skipped.

     2. My bed file had 4104 features and yours had 4107 features. When I compared the start and end positions 2862 were common and the remaining were  different.
 
     3. *.rep1.gtf comaparison: My file has 341 features and yours had 950 features. Of which 309 were common.

     4. *.rep1.expression comparison: My file had 67 loci and yours had 187 loci and only 54 were present in both.

     5. *.rep2.gtf comparison: My file had 329 features and yours had 952 features. Of these 289 were the same.

     6. *.rep2.expression comparison: My file had 70 loci and yours had 189 loci and only 52 were common.


136743: Skipping chr4_m_23 (chr4:-:1275688-1276108): No observable bins
136717: Skipping chr4_m_22 (chr4:-:1050600-1051539): No observable bins
136726: Skipping chr4_m_20 (chr4:-:378999-379321): No observable bins
136717: Skipping chr4_m_16 (chr4:-:1143339-1143986): No observable bins
136761: Skipping chr4_m_12 (chr4:-:501387-504469): No observable bins
136743: Skipping chr4_m_4 (chr4:-:351804-370049): No observable bins
136751: Skipping chr4_m_2 (chr4:-:1057744-1074327): No observable bins
136771: Skipping chr4_p_27 (chr4:+:997418-997900): No observable bins
136726: Skipping chr4_p_25 (chr4:+:402927-403375): No observable bins
136743: Skipping chr4_p_22 (chr4:+:488097-488318): No observable bins
136751: Skipping chr4_p_19 (chr4:+:691741-692088): No observable bins
136761: Skipping chr4_p_20 (chr4:+:1052488-1055186): No observable bins
136782: Skipping chr4_p_16 (chr4:+:1144789-1145888): No observable bins
136751: Skipping chr4_p_10 (chr4:+:1219475-1226882): No observable bins
136873: Skipping chr4_p_11 (chr4:+:328719-331358):
137085: Skipping chr4_m_20 (chr4:-:378999-379321): No observable bins
137078: Skipping chr4_m_19 (chr4:-:64085-64404): No observable bins
137103: Skipping chr4_m_12 (chr4:-:501387-504469): No observable bins
137069: Skipping chr4_m_2 (chr4:-:1057744-1074327): No observable bins
137103: Skipping chr4_p_22 (chr4:+:488097-488318): No observable bins
137085: Skipping chr4_p_21 (chr4:+:466791-466936): No observable bins
137069: Skipping chr4_p_20 (chr4:+:1052488-1055186): No observable bins
137121: Skipping chr4_p_18 (chr4:+:700817-711278): No observable bins
137069: Skipping chr4_p_16 (chr4:+:1144789-1145888): No observable bins
137069: Skipping chr4_p_13 (chr4:+:1168076-1190969): No observable bins
137121: Skipping chr4_p_10 (chr4:+:1219475-1226882): No observable bins
137096: Skipping chr4_p_12 (chr4:+:1085530-1096834): No observable bins

Thank you
Nirmala

[Nathan Boley]

Thank you for the output files. Is GRIT supposed to give the same answer for multiple runs on the same files?

Upon comparing the log, bed and gtf files there are seems to be several differences between my output files and the files you posted. Here's a summary of differences.

     1. My log file skipped 27 regions (listed below) versus your log file which shows only 2 regions as skipped.

     2. My bed file had 4104 features and yours had 4107 features. When I compared the start and end positions 2862 were common and the remaining were  different.
 
     3. *.rep1.gtf comaparison: My file has 341 features and yours had 950 features. Of which 309 were common.

     4. *.rep1.expression comparison: My file had 67 loci and yours had 187 loci and only 54 were present in both.

     5. *.rep2.gtf comparison: My file had 329 features and yours had 952 features. Of these 289 were the same.

     6. *.rep2.expression comparison: My file had 70 loci and yours had 189 loci and only 52 were common.

No, that many differences is wrong.  

What type of system are you running this on?

Best, Nathan

[nirmala...@gmail.com]

Linux system.

[nirmala...@gmail.com]

Hi Nathan,

The possible cause for these differences could be the threading option (-t option). When I ran GRIT without this option the output files match exactly to yours.

Thanks for posting the output files.
Regards,
Nirmala

[Nathan Boley]

The possible cause for these differences could be the threading option (-t option). When I ran GRIT without this option the output files match exactly to yours.

That helps a lot - thanks. 

What version of scipy and numpy are you using?

Best, Nathan 

[nirmala...@gmail.com]

The versions I am using are listed below:

numpy-1.9.1
scipy-0.15.0b1

Regards,
Nirmala