[mira_talk] miraconvert oddity (sam vs samnbb)

From: Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx>
To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
Date: Fri, 8 Nov 2013 12:22:33 +0000

Hi Bastien,

This is with MIRA 4.0 RC4 on Linux, using a de novo single
strain bacterial assembly, trying to produce a SAM file
(I intend to use the same script on mapping assemblies
where I want a SAM file without the long backbone reads).

This works:

$ miraconvert -f maf -t samnbb de_novo.maf x
...
$ ls x*
x.sam

This works (although the output filename is a little surprising):

$ rm x*
$ miraconvert -f maf -t samnbb de_novo.maf x.samnbb
...
$ ls x*
x.sam

Similarly this works:

$ rm x*
$ miraconvert -f maf de_novo.maf x.samnbb
$ ls x*
x.sam

This fails in what seems like a strange way - presumably
something about the outputs via the extension and the
command line clash (samnbb vs sam):

$ rm x*
$ miraconvert -f maf -t samnbb de_novo.maf x.sam
Loading from maf, saving to: sam samnbb
Collecting basic SAM info from MAF file
Sorting read info ... done
Collecting basic SAM info from MAF file
Duplicate: MIRA_c1
MAF file de_novo.maf at line 9:
CO    MIRA_c1

duplicate contig name?
Error in MAF format, aborting.

$ ls x*
x.sam

Regards,

Peter

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[mira_talk] miraconvert oddity (sam vs samnbb)

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