Errors when download species database

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hui...@ualberta.ca

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Feb 22, 2019, 1:29:58 AM2/22/19
to Alternative Splicing and Functional Prediction
Hello,

I successfully downloaded and installed the Altanalyzer Mac installer, when I tried to download Bos taurus database, an error named "Internet connection not established. Re-establish and try again" occurred. And I checked my internet and it's normal, could you help to overcome this problem? Thanks a lot!

Best regards,
Huizeng Sun, PhD
Postdoctoral
Department of Agricultural, Food & Nutritional Science
University of Alberta 

Nathan Salomonis

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Feb 22, 2019, 10:41:47 AM2/22/19
to Alternative Splicing and Functional Prediction
Greetings Huizeng,

Which operating system specific version are you using? If you try on another computer (or from home) does it work? If it does, you can copy over the AltDatabase folder to your primary machine.

Best,
Nathan


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Huizeng Sun

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Feb 23, 2019, 8:23:24 PM2/23/19
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Dear Nathan,

I appreciate your response. I use my Mac Pro laptop (macOS Mojave v10.14.3) to try again and now it works. However, when I perform "Process RNA-Seq reads" following all the default parameters, another error comes out, which may be detailed described in the attached report. The input files are 6 (two groups) bam files after tophat alignment. Could you have a look to see what't  the suddenly exit reason? Many thanks!

Kind regards,
Huizeng 

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Hui-Zeng Sun, PhD
AltAnalyze_report-20190222-122300.log

Nathan Salomonis

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Feb 25, 2019, 3:01:03 PM2/25/19
to Alternative Splicing and Functional Prediction, hui...@ualberta.ca
One more thing. Can you confirm what date you installed AltAnalyze on? If you still have the original file, you can also look on the date of that file. The reason I ask is that although the code has not changed in this version, we did have some issues on Mac with getting certain libraries to link. I thought we had fixed these issues, specifically with pysam and igraph after validating on Mac's without Python, but if this is truly not working on your machine with the latest version, this is a big problem.

One thing to check would be to download the current version and simply delete the old AltAnalyze executable and replace with the current one. If the problem persists, we need to re-build and test on new machine. The alternative is to install the python version through pip install, but please check the above first. I will have others test here.

Best,
Nathan

Huizeng Sun

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Mar 3, 2019, 10:38:05 AM3/3/19
to Nathan Salomonis, Alternative Splicing and Functional Prediction
Hi, Nathan,

I downloaded the latest version (AltAnalyze_v.2.1.2_OSX-64bit.dmg) from https://sourceforge.net/projects/altanalyze/files/ and deleted all the old versions. I successfully got the results with testing 6 samples (2 group). However, when I took another run using more samples (16*3 groups), it suddenly exit with the attached report. Then I used 6 testing samples to run, it died again. Unfortunately, re-install also doesn't work.

Huizeng
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