Versioning of Duct Ape's dependencies

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Nicolas Bargues

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May 22, 2019, 4:31:38 AM5/22/19
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Hi,

I start to use Duct Ape a few days ago. It seems to works but I have some warning ( matplotlib, scipy ... ) regarding versioning of the dependencies. I suppose that new version of dependencies have caused those warning. 

Can you please specify the version of all the dependencies you use with your latest version of duct ape ( 0.17.12 ) ?

Cheers,

Nicolas Bargues

Marco Galardini

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May 22, 2019, 1:17:25 PM5/22/19
to Nicolas Bargues, DuctApe
Hi,

thanks for picking ductape! Are they just warning or are you also getting errors?

Best,
Marco

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Nicolas Bargues

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May 23, 2019, 2:21:07 AM5/23/19
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Hi, i'm linking my log file for you to see. There are several warning during: creating plates plots, overall plots, generate a genomic metabolic map.

Regards,

Nicolas Bargues


Le mercredi 22 mai 2019 19:17:25 UTC+2, Marco Galardini a écrit :
Hi,

thanks for picking ductape! Are they just warning or are you also getting errors?

Best,
Marco

On Wed, May 22, 2019 at 4:31 AM Nicolas Bargues <nicolas...@gmail.com> wrote:
Hi,

I start to use Duct Ape a few days ago. It seems to works but I have some warning ( matplotlib, scipy ... ) regarding versioning of the dependencies. I suppose that new version of dependencies have caused those warning. 

Can you please specify the version of all the dependencies you use with your latest version of duct ape ( 0.17.12 ) ?

Cheers,

Nicolas Bargues

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Marco Galardini
ductape_nb.log

Marco Galardini

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May 23, 2019, 11:03:25 AM5/23/19
to Nicolas Bargues, DuctApe
Hi,

these are all the warning I've found in your log file; they all seem fine to me, so I wouldn't worry about them.

Marco

$ grep WARNING ductape_nb.log
2019-05-22 13:06:24 - ductape.kegg - [WARNING] - Using RCLASS attribute of KEGG reactions, as the RPAIR database has now been discontinued
2019-05-22 13:22:04 - ductape.kegg - [WARNING] - Using RCLASS attribute of KEGG reactions, as the RPAIR database has now been discontinued
2019-05-22 13:28:27 - ductape.kegg - [WARNING] - Using RCLASS attribute of KEGG reactions, as the RPAIR database has now been discontinued
2019-05-22 13:29:42 - ductape.kegg - [WARNING] - Using RCLASS attribute of KEGG reactions, as the RPAIR database has now been discontinued
2019-05-22 13:30:15 - ductape.biolog - [WARNING] - YAML/OPM parsing failed!
2019-05-22 13:30:32 - ductape - [WARNING] - Activity index has not been calculated yet!
2019-05-22 13:30:32 - ductape - [WARNING] - Skipping Kegg mapping
2019-05-22 13:30:47 - ductape.kegg - [WARNING] - Using RCLASS attribute of KEGG reactions, as the RPAIR database has now been discontinued
2019-05-22 13:30:50 - ductape.kegg - [WARNING] - Using RCLASS attribute of KEGG reactions, as the RPAIR database has now been discontinued
2019-05-22 14:01:34 - ductape - [WARNING] - No compounds available for category nitrogen (ecoli25922)
2019-05-22 14:01:34 - ductape - [WARNING] - No compounds available for category phosphate & sulphur (ecoli25922)
2019-05-22 14:01:34 - ductape - [WARNING] - No compounds available for category nutrient stimulation (ecoli25922)
2019-05-22 14:01:34 - ductape - [WARNING] - No compounds available for category nitrogen peptides (ecoli25922)
2019-05-22 14:01:34 - ductape - [WARNING] - No compounds available for category osmolytes & ph (ecoli25922)
2019-05-22 14:01:39 - ductape - [WARNING] - No compounds available for category chemicals (ecoli25922)

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Nicolas Bargues

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May 27, 2019, 2:39:18 AM5/27/19
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Hi,
Thanks for the response. Ok for the warning. Last check, I have those package errors, what do you think about it ? ( I mark in red what's bothering me )

13:30:14 - Saved 2033 EC numbers links for ecoli25922 (ecnumbers_ecoli25922.tsv)
/site/ly/home/nbargues/Documents/DuctApe/ductape/phenome/biolog.py:1753: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
  data = yaml.load(open(self.file))
13:30:15 - YAML/OPM parsing failed!

13:30:27 - 1 - Calculating parameters
                                                                                               Calculating parameters                                                                                        0% [=--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------]
                                                                                                Item 1 on 192 total                                                                                                /site/ly/home/nbargues/.conda/envs/nbg_test/lib/python2.7/site-packages/numpy/core/_methods.py:140: RuntimeWarning: Degrees of freedom <= 0 for slice


13:30:55 - 6 - Creating plates plots
                                                                                               Creating plates plots                                                                                               
  0% [---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------]
                                                                                                 Item 0 on 96 total                                                                                                Exception in thread Thread-1:
Traceback (most recent call last):
  File "/site/ly/home/nbargues/.conda/envs/nbg_test/lib/python2.7/threading.py", line 801, in __bootstrap_inner
    self.run()
  File "/site/ly/home/nbargues/Documents/DuctApe/ductape/phenome/biolog.py", line 2237, in run
    for i in self.results[plate_id].plotAll():
  File "/site/ly/home/nbargues/Documents/DuctApe/ductape/phenome/biolog.py", line 582, in plotAll
    self._plot(well_id, strain_signals, ax)
  File "/site/ly/home/nbargues/Documents/DuctApe/ductape/phenome/biolog.py", line 481, in _plot
    maxsig = smooth(maxsig, window_len=self.window)
  File "/site/ly/home/nbargues/Documents/DuctApe/ductape/common/utils.py", line 82, in smooth
    raise ValueError("Input vector needs to be bigger than window size.")
ValueError: Input vector needs to be bigger than window size.

13:31:24 - Going to generate a genomic metabolic map
/site/ly/home/nbargues/.conda/envs/nbg_test/lib/python2.7/site-packages/matplotlib/cbook/deprecation.py:106: MatplotlibDeprecationWarning: The axisbg attribute was deprecated in version 2.0. Use facecolor instead.
  warnings.warn(message, mplDeprecation, stacklevel=1)

Marco Galardini

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May 27, 2019, 10:47:40 AM5/27/19
to Nicolas Bargues, DuctApe
Hi,

sorry, I should have digged more carefully through your log file. The yaml and matplotlib messages are simply warnings, and I will commit changes to silence them ASAP (they could become proper errors in the future). The other message is an actual error, and I think it might be due to your phenotypic data not having enough data points? Would you mind sending your biolog files over for me to have a look at?

Many thanks,
Marco

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Nicolas Bargues

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May 28, 2019, 10:43:51 AM5/28/19
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Hi,

thank you for your response. In comparaison with your datatest, my data (ecoli_nt.csv) seems to not have the full infos of the biolog's plates. I will try to talk to my biomol engineer about that.

One other question different that before, I just try to run the pangenomic part of the test in duct ape but i have an error that stop the run (ductape.log); do you have a clue why a protein is not found in the database ? 

Cheers
ecoli_nt.csv
ductape.log

Marco Galardini

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May 28, 2019, 4:37:45 PM5/28/19
to Nicolas Bargues, DuctApe
Hi Nicolas,

the problem with your biolog file is that there is only one time point (0 hours); ductape expects you to have a full experiment (at least 11 time points if I remember correctly, but a "real" phenotype microarray will have hundreds of them). Regarding the other error, could you try to install the latest version of ductape and try again? I uploaded the latest version yesterday.

marco

p.s. if you are exclusively interested in reading phenotype microarray data there is also a specialized module inside biopython: https://biopython.readthedocs.io/en/latest/Tutorial/chapter_phenotype.html

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Nicolas Bargues

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May 29, 2019, 9:41:13 AM5/29/19
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Hi Marco, 

We fix the problem with our biolog data, now we have the full infos in the csv file. I have a question regarding our experimenting plan; We want to compare the phenomic profil with the same organism but at different concentration of antibiotics (we have a biolog file for each concentration and one that resume all the data). To do so you recommand which experimental setup of Duct Ape, Mutant or Pangenome ?

Ps: the problem with the test data in the pangenome section persist even with the last version of duct ape. Do you have an idea why ?

Thanks for your disponibility,

Nicolas

Marco Galardini

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May 29, 2019, 9:51:07 AM5/29/19
to Nicolas Bargues, DuctApe
Hi,

sorry you are still encountering problems; I think someone else encountered a similar problem before and it was due to blast acting up. The easiest way to fix it might be to just change the fasta headers. Would you mind sending me your input protein fasta files please? You can send them to me privately if you like.

Best,
Marco

p.s. since you seems interested manly in a phenotypic comparison I would suggest to just use the phenomics module, or the biopython library I linked yesterday. What would you need the genomic bit for?

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