New to DuctApe

[Nasser-4960]

I am new to DuctApe and try to organize my data in CSV file as input. I have only six tables as PM1-6 however after the run I got curves for all 13 PM reading, How this happen?

[mgalardini]

Hi,

I'm sorry, can you provide more details about the problem you are encountering? Do I understand it correctly that your csv file contains data for 6 plates but you see results for 13? That should not happen so I might be confused as to what you are seeing.

Best, Marco

On Thu, May 7, 2020 at 1:12 PM Nasser-4960 notifications@github.com wrote:

I am new to DuctApe and try to organize my data in CSV file as input. I have only six tables as PM1-6 however after the run I got curves for all 13 PM reading, How this happen?

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-- Marco Galardini

[Nasser-4960]

Hi Marco,

I downloaded some examples to run DuctApe. Then, I made a CSV file with 6 tables representing 6 PM plates then I ran DuctApe to perform Phenome analysis. I noticed that I have figures for the 20 plates. Some if the plates did not have 96 wells, but the curves PNG had 96 curves!

I attached the input data file and example of the curves I got.

Thanks a lot for your help,

Nasser

On Thu, May 7, 2020 at 5:18 PM Marco Galardini notifications@github.com wrote:

Hi,

I'm sorry, can you provide more details about the problem you are encountering? Do I understand it correctly that your csv file contains data for 6 plates but you see results for 13? That should not happen so I might be confused as to what you are seeing.

Best, Marco

On Thu, May 7, 2020 at 1:12 PM Nasser-4960 notifications@github.com wrote:

I am new to DuctApe and try to organize my data in CSV file as input. I have only six tables as PM1-6 however after the run I got curves for all 13 PM reading, How this happen?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/combogenomics/DuctApe/issues/3, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AAISWX3GVZ3IOUYN5GYH7RTRQLTXZANCNFSM4M3QEVVA

.

-- Marco Galardini

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[mgalardini]

Sorry, you seem to have forgotten to attach your input files; can you please try again?

[Nasser-4960]

Hi Marco,

It showed on my sent email. I attached it to this email again.

Regards, Nasser

On Fri, May 8, 2020 at 2:04 PM Marco Galardini notifications@github.com wrote:

Sorry, you seem to have forgotten to attach your input files; can you please try again?

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[mgalardini]

Maybe you can email me directly? mgala AT bu DOT edu

[mgalardini]

Thanks for sending the files, I can see what you mean; I think you are plotting data that you already had in there (in the ductape.db file I mean), since when I try to load your file I get this error:

$ dphenome add ZM4.csv Pa39-7
14:25:39 - YAML/OPM parsing failed!
14:25:39 - Well G7 is not known!
Traceback (most recent call last):
  File "/usr/local/bin/dphenome", line 654, in <module>
    ret = options.func(options, wdir, project)
  File "/usr/local/bin/dphenome", line 44, in dadd
    return dPhenomeAdd(project, options.orgID, options.file)
  File "/home/user/.local/lib/python2.7/site-packages/ductape/actions.py", line 198, in dPhenomeAdd
    biolog.addWells(wells, clustered=False)
  File "/home/user/.local/lib/python2.7/site-packages/ductape/storage/SQLite/database.py", line 3706, in addWells
    raise Exception('This well (%s) is not known!'%w.well_id)
Exception: This well (G7) is not known!

It seems to me that you might have manually edited this file? The time is not in floating point format (e.g. 0:29:22 instead of ~0.5) and the well names have one digit only instead of two (e.g. G7 instead of G07). Could you try to delete the ductape.db file and start from scratch?

[Nasser-4960]

Hi Marco, Thanks a lot, Yes, I edit it manually. the reason for that is I am using Bioteck reader and not Omnilog instrument itself. I will re-edit and run it again, I will send you then.

I appreciate it, Nasser

On Fri, May 8, 2020 at 2:29 PM Marco Galardini notifications@github.com wrote:

Thanks for sending the files, I can see what you mean; I think you are plotting data that you already had in there (in the ductape.db file I mean), since when I try to load your file I get this error:

$ dphenome add ZM4.csv Pa39-7 14:25:39 - YAML/OPM parsing failed! 14:25:39 - Well G7 is not known! Traceback (most recent call last): File "/usr/local/bin/dphenome", line 654, in ret = options.func(options, wdir, project) File "/usr/local/bin/dphenome", line 44, in dadd return dPhenomeAdd(project, options.orgID, options.file) File "/home/user/.local/lib/python2.7/site-packages/ductape/actions.py", line 198, in dPhenomeAdd biolog.addWells(wells, clustered=False) File "/home/user/.local/lib/python2.7/site-packages/ductape/storage/SQLite/database.py", line 3706, in addWells raise Exception('This well (%s) is not known!'%w.well_id) Exception: This well (G7) is not known!

It seems to me that you might have manually edited this file? The time is not in floating point format (e.g. 0:29:22 instead of ~0.5) and the well names have one digit only instead of two (e.g. G7 instead of G07). Could you try to delete the ductape.db file and start from scratch?

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[mgalardini]

Great, I'll close the issue for now as it is unclear if anything is actually wrong with the software itself

[Nasser-4960]

Hi Marco,

I have the same error (see below) even after modifying the Time format and well numbers as you mentioned before.

It seems that software does not read my CSV file. Any suggestions? I edit the file manually as I mentioned before and then export it from Numbers (Mac) or Excel (Mac) as CSV but have the same problem.

Could you help me with this?

Regards, Nasser

MacBook-Pro-193:Zmobilis macintoshhd$ dphenome add-dir phenome

19:39:53 - Looking for files with extension csv

19:39:54 - YAML/OPM parsing failed!

19:39:54 - Found the following organism IDs: Pa39-7

19:39:54 - Organism Pa39-7 is not present yet! Skipping...

19:39:54 - Added 1 phenomic data files from phenome

(ductape) MacBook-Pro-193:Zmobilis macintoshhd$ dphenome start

19:40:06 - No phenotypic data available!

(ductape) MacBook-Pro-193:Zmobilis macintoshhd$ dphenome start -e -g

19:40:15 - No phenotypic data available!

On Fri, May 8, 2020 at 3:37 PM Marco Galardini notifications@github.com wrote:

Closed #3 https://github.com/combogenomics/DuctApe/issues/3.

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[mgalardini]

You first need to add your organism ID using the dape add Pa39-7 command. Please have a look at the tutorial if anything is unclear ( http://combogenomics.github.io/DuctApe/tutorial.html)

On Sat, May 9, 2020 at 7:52 PM Nasser-4960 notifications@github.com wrote:

Hi Marco,

I have the same error (see below) even after modifying the Time format and well numbers as you mentioned before.

It seems that software does not read my CSV file. Any suggestions? I edit the file manually as I mentioned before and then export it from Numbers (Mac) or Excel (Mac) as CSV but have the same problem.

Could you help me with this?

Regards, Nasser

MacBook-Pro-193:Zmobilis macintoshhd$ dphenome add-dir phenome

19:39:53 - Looking for files with extension csv

19:39:54 - YAML/OPM parsing failed!

19:39:54 - Found the following organism IDs: Pa39-7

19:39:54 - Organism Pa39-7 is not present yet! Skipping...

19:39:54 - Added 1 phenomic data files from phenome

(ductape) MacBook-Pro-193:Zmobilis macintoshhd$ dphenome start

19:40:06 - No phenotypic data available!

(ductape) MacBook-Pro-193:Zmobilis macintoshhd$ dphenome start -e -g

19:40:15 - No phenotypic data available!

On Fri, May 8, 2020 at 3:37 PM Marco Galardini notifications@github.com wrote:

Closed #3 https://github.com/combogenomics/DuctApe/issues/3.

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.

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-- Marco Galardini