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Old 01-29-2014, 09:37 AM   #1
ajthomas
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Location: Utah

Join Date: Mar 2010
Posts: 166
Default MIRA failure

I recently finished the first run on our new Ion Torrent Proton. The sample is genomic DNA from a non-model organism so I wanted to start with a de novo assembly using the Assembler plugin for Torrent Browser. This plugin is essentially an interface to MIRA.

It seems the process gets started, but when it gets to the point where it begins to load data it fails with the error message "Failure, wrapped MIRA process aborted."

I've never used MIRA before, so I don't know where to start. The log is fairly long, so I won't post it all here, but here's the last few lines of it:
Quote:
Deleting old directory rawlib.basecaller_assembly ... done.
Creating directory rawlib.basecaller_assembly ... done.
Creating directory rawlib.basecaller_assembly/rawlib.basecaller_d_results ... done.
Creating directory rawlib.basecaller_assembly/rawlib.basecaller_d_info ... done.
Creating directory rawlib.basecaller_assembly/rawlib.basecaller_d_chkpt ... done.
Creating directory rawlib.basecaller_assembly/rawlib.basecaller_d_tmp ... done.

Tmp directory is not on a NFS mount, good.

Localtime: Wed Jan 15 12:55:36 2014

Loading reads from /results/analysis/output/Home/Auto_user_PRO-3-System_Generic_Seq_Template_27_005/plugin_out/Assembler_out/Assembler/rawlib.basecaller_in.iontor.fastq type fastq
Localtime: Wed Jan 15 12:55:36 2014
Loading data from FASTQ file: /results/analysis/output/Home/Auto_user_PRO-3-System_Generic_Seq_Template_27_005/plugin_out/Assembler_out/Assembler/rawlib.basecaller_in.iontor.fastq
(sorry, no progress indicator for that, possible only with zlib >=1.34)


========================== Memory self assessment ==============================
Running in 64 bit mode.

Failure, wrapped MIRA process aborted.
Any ideas where to go from here?
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Old 01-29-2014, 09:56 AM   #2
sklages
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Location: Berlin, DE

Join Date: May 2008
Posts: 628
Default

You should probably ask the author of the plugin.
Why don't you use MIRA just as a standalone assembler? It's not really complicated.
Current version is somewhere around 4.0rc5 .. just give it a try :-)
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