Problems with IDR using anaconda

[Pedro Barbosa]

Hello,

I've installed anaconda 2.5 to facilitate the installation of the dependencies required by idr. This version automatically updated my python version to 3.5, but using the command "python3 setup.py install' to install idr used somehow package information from python3.2.

Therefore, i decided to install idr 2.0.2  through anaconda and apparently it went ok (no more warnings on idr help message complaining about numpy and scipy versions):
 conda install --channel https://conda.anaconda.org/bioconda idr

When i run this first test, the parameters '--plot' seems to be badly parsed:

idr --samples ../chip1_L1_pooledMock1-noModelkeepDup30_peaks.narrowPeak ../chip1_L5_pooledMock1-noModelkeepDup30_peaks.narrowPeak --input-file-type narrowPeak --output-file teste-newIDR --log-output-file log-teste-newIDR --soft-idr-threshold 0.1 --plot test-plot
usage: idr [-h] --samples SAMPLES SAMPLES [--peak-list PEAK_LIST]
           [--input-file-type {narrowPeak,broadPeak,bed}] [--rank RANK]
           [--output-file OUTPUT_FILE] [--log-output-file LOG_OUTPUT_FILE]
           [--idr-threshold IDR_THRESHOLD]
           [--soft-idr-threshold SOFT_IDR_THRESHOLD] [--use-old-output-format]
           [--plot] [--use-nonoverlapping-peaks]
           [--peak-merge-method {sum,avg,min,max}] [--initial-mu INITIAL_MU]
           [--initial-sigma INITIAL_SIGMA] [--initial-rho INITIAL_RHO]
           [--initial-mix-param INITIAL_MIX_PARAM] [--fix-mu] [--fix-sigma]
           [--random-seed RANDOM_SEED] [--max-iter MAX_ITER]
           [--convergence-eps CONVERGENCE_EPS] [--only-merge-peaks]
           [--verbose] [--quiet] [--version]
idr: error: unrecognized arguments: test-plot
/usr/bin/anaconda3/bin/idr --samples ../chip1_L1_pooledMock1-noModelkeepDup30_peaks.narrowPeak ../chip1_L5_pooledMock1-noModelkeepDup30_peaks.narrowPeak --input-file-type narrowPeak --output-file teste-newIDR --log-output-file log-teste-newIDR --soft-idr-threshold 0.1 --plot test-plot

When i remove it, another error on the code is thrown:

idr --samples ../chip1_L1_pooledMock1-noModelkeepDup30_peaks.narrowPeak ../chip1_L5_pooledMock1-noModelkeepDup30_peaks.narrowPeak --input-file-type narrowPeak --output-file teste-newIDR --log-output-file log-teste-newIDR --soft-idr-threshold 0.1 --verbose
/usr/bin/anaconda3/bin/idr --samples ../chip1_L1_pooledMock1-noModelkeepDup30_peaks.narrowPeak ../chip1_L5_pooledMock1-noModelkeepDup30_peaks.narrowPeak --input-file-type narrowPeak --output-file teste-newIDR --log-output-file log-teste-newIDR --soft-idr-threshold 0.1 --verbose
Traceback (most recent call last):
  File "/usr/bin/anaconda3/bin/idr", line 4, in <module>
    __import__('pkg_resources').run_script('idr==2.0.2', 'idr')
  File "/usr/bin/anaconda3/lib/python3.5/site-packages/setuptools-20.3-py3.5.egg/pkg_resources/__init__.py", line 726, in run_script
  File "/usr/bin/anaconda3/lib/python3.5/site-packages/setuptools-20.3-py3.5.egg/pkg_resources/__init__.py", line 1484, in run_script
  File "/usr/bin/anaconda3/lib/python3.5/site-packages/idr-2.0.2-py3.5-linux-x86_64.egg/EGG-INFO/scripts/idr", line 10, in <module>
    idr.idr.main()
  File "/usr/bin/anaconda3/lib/python3.5/site-packages/idr-2.0.2-py3.5-linux-x86_64.egg/idr/idr.py", line 736, in main
    merged_peaks, signal_type = load_samples(args)
  File "/usr/bin/anaconda3/lib/python3.5/site-packages/idr-2.0.2-py3.5-linux-x86_64.egg/idr/idr.py", line 662, in load_samples
    oracle_pks, args.use_nonoverlapping_peaks)
  File "/usr/bin/anaconda3/lib/python3.5/site-packages/idr-2.0.2-py3.5-linux-x86_64.egg/idr/idr.py", line 250, in merge_peaks
    MergedPeak(*(key + pk)) for pk in merged_contig_peaks)
  File "/usr/bin/anaconda3/lib/python3.5/site-packages/idr-2.0.2-py3.5-linux-x86_64.egg/idr/idr.py", line 250, in <genexpr>
    MergedPeak(*(key + pk)) for pk in merged_contig_peaks)
TypeError: can only concatenate tuple (not "NoneType") to tuple

Any help on this would be much appreciated.
Cheers,
Pedro Barbosa

[Nathan Boley]

Hi Pedro,

When i run this first test, the parameters '--plot' seems to be badly parsed:

the --plot option doesn't take an argument - instead it save the plot to the specified output filename with a ".png" suffix attached. For example, if you run 

idr [OTHER OPTIONS] --output-file idr_res.txt --plot 

it will create the plot file: idr_res.txt.png

 

 

When i remove it, another error on the code is thrown:

idr --samples ../chip1_L1_pooledMock1-noModelkeepDup30_peaks.narrowPeak ../chip1_L5_pooledMock1-noModelkeepDup30_peaks.narrowPeak --input-file-type narrowPeak --output-file teste-newIDR --log-output-file log-teste-newIDR --soft-idr-threshold 0.1 --verbose

I'm not able to reproduce this. Could you please send me a self contained test case and I'll take a look?

Thanks, Nathan

 

[Pedro Barbosa]

Hi Nathan,

 

I'm not able to reproduce this. Could you please send me a self contained test case and I'll take a look?

Please find attached the first 2000 lines of each narrow peak file.

Thanks for you help,

Pedro

[Nathan Boley]

Hi Pedro,

I can't reproduce this with the files you sent using version 2.0.2 from:
https://github.com/nboley/idr/

and Anaconda python with version info:
Python 3.5.1 |Anaconda 4.0.0 (64-bit)| (default, Dec 7 2015, 11:16:01)

Can you please try downloading idr from the github link above to see
if that fixes your problem?

Best, Nathan

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[Pedro Barbosa]

Hi Nathan,

I finally could run IDR from the 2.0.2 version installed with anaconda 4.0.0 | python 3.5.1:

conda install --channel https://conda.anaconda.org/bioconda idr

I think the problem was related to some previously messy installation of IDR using python 3.2. If I called IDR,It would try to use some old dependencies linked to the older version of python (eg numpy 1.6). I removed from the server everything related to python 3.2 and installed again using the anaconda command. Now it's working.

Thank you for you help Nathan,

Pedro

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