Re: error in run AltAnalyze in commandline manner

[Nathan Salomonis]

Greetings,

All looks good except that the full filepath needs to be listed currently (no ~). I also recommend moving to the last version of AltAnalyze v. 2.0.7. To support the associate, QC, pathway visualization and lineage analyses see:

http://code.google.com/p/altanalyze/wiki/StandAloneDependencies

http://www.altanalyze.org/help.htm#commandline

Best,

Nathan

On Aug 28, 2012, at 6:04 PM, shengzhen <shen...@live.cn> wrote:

Hi,there,

I run AltAnalyze with Tophat bed input on our romote server in a commandline manner, and I get this error. As you seen, I have designated the --output option. Why i still get this error?

By the way, I run AltAnalyze on Ubuntu with 3.8G memory. yet it run out of the memory and stopped.

waiting online.

Thank you.

 

[shengzhen@anode1 AltAnalyze_v.2.0.6-Py]$ python AltAnalyze.py --species Hs --platform RNASeq --bedDir "~/tophat20120827_Ensemble/altanalyze" --groupdir "~/tophat20120827_Ensemble/altanalyze/ExpressionInput/groups.B_Ens.txt" --compdir "~/tophat20120827_Ensemble/altanalyze/ExpressionInput/comps.B_Ens.txt" --expname "B_Ens" --runGOElite yes --output "~/tophat20120827_Ensemble/altanalyze"

AltAnalyze 2.0.6 beta - Running commandline options

 

Arguments input: ['AltAnalyze.py', '--species', 'Hs', '--platform', 'RNASeq', '--bedDir', '~/tophat20120827_Ensemble/altanalyze', '--groupdir', '~/tophat20120827_Ensemble/altanalyze/ExpressionInput/groups.B_Ens.txt', '--compdir', '~/tophat20120827_Ensemble/altanalyze/ExpressionInput/comps.B_Ens.txt', '--expname', 'B_Ens', '--runGOElite', 'yes', '--output', '~/tophat20120827_Ensemble/altanalyze']

 

Please designate an output directory before proceeding (e.g., --output "C:\RNASeq)
[shengzhen@anode1 AltAnalyze_v.2.0.6-Py]$

 

2012-08-29

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shengzhen