Trouble for running AltAnalyze

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Mar 8, 2019, 7:57:37 AM3/8/19
to Alternative Splicing and Functional Prediction
Hello, and thank you for your tremendous work !

I want to use your program to analyze the Alternative splicing events in RNA-seq data, between to conditions (Homo vs Hetero)
I have the FASTQ files, and the BAM/BAI
I understood that the FASTQ were better, so I wanted to run a complete analysis, but I got the following error (see attached). I have some results at the end, but I cannot be confident knowing the number of errors that seems to happend.
I'm kind of new to programming, so there may be something I did completely wrong !
I have AltAnalyze on a virtual environnement of Anaconda, with python 2.7; I tried to have all the dependencies needed, but some for instance cairo I can't find...

I hope you may help me. Thanks a lot...
Capture d’écran 2019-03-08 à 11.37.03.png

Nathan Salomonis

Mar 8, 2019, 4:35:53 PM3/8/19
to Alternative Splicing and Functional Prediction,
Hi David,

AltAnalyze has a number of Python dependencies which are not installed by default in anaconda. The warnings you are getting relate to missing python packages. It is for this reason we provide two alternative ways to run AltAnalyze on a Mac:

1) The pre-compiled version as Mac and Windows binaries:

2) PyPI installer: pip install altanalyze (Python 2.7 only)

The latter will not properly bring down iGraph which is a pain to get installed correctly, hence, I would try 1. If you want to keep with the anaconda solution, then try the following:

pip install umap-learn, nimfa, numba, community, annoy, networkx, R 3+, fastcluster, pillow, pysam, requests, pandas, patsy, lxml, python-igraph, cairo

For iGraph, try installing with:


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David Benacom

Mar 22, 2019, 6:14:07 AM3/22/19
Hi Nathan, thank you for your fast answer ! 
However, I still get some trouble when I try this pre-compiled version...
I can't even download the genomes this time...

Last login: Fri Mar 22 10:45:21 on ttys000
(base) C07NP206G1J2:~ david.benacom$ /Applications/AltAnalyze/ ; exit;

AltAnalyze depedency not met for: wx
...The AltAnalyze Results Viewer requires wx

WARNING!!!! Some dependencies are not currently met.
This may impact AltAnalyze's performance

Traceback (most recent call last):
  File "/Applications/AltAnalyze/", line 112, in <module>
  File "/Applications/AltAnalyze/", line 82, in _run
    exec(compile(source, path, 'exec'), globals(), globals())
  File "/Applications/AltAnalyze/", line 8560, in <module>
    if use_Tkinter == 'yes': AltAnalyzeSetup(skip_intro)
  File "/Applications/AltAnalyze/", line 5144, in AltAnalyzeSetup
    expr_var, alt_var, additional_var, goelite_var, exp_file_location_db = UI.getUserParameters(skip_intro,Multi=mlp)
  File "UI.pyc", line 4993, in getUserParameters
  File "UI.pyc", line 4685, in addOnlineSpeciesDatabases
UnboundLocalError: local variable 'sc' referenced before assignment
2019-03-22 11:11:34.539 AltAnalyze[42113:2012030] AltAnalyze Error
Saving session...
...copying shared history...
...saving history...truncating history files...
Deleting expired sessions...77 completed.

[Opération terminée]

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