[mira_talk] Unpaired reads and segment_placement = ? or unknown
- From: Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Tue, 11 Feb 2014 11:18:52 +0000
Hi Bastien,
I'm working on a MIRA 4 wrapper for Galaxy, and just hit something which
I think is a regression in segment_placement (or segmentplacement)
for unpaired reads.
Here's a simple manifest for an unpaired FASTQ file, available here:
https://github.com/peterjc/pico_galaxy/blob/master/test-data/ecoli.fastq
For unpaired read groups, I had used something like this:
project = MIRA
job = denovo,genome,accurate
parameters = -NW:cmrnl=no -DI:trt=/tmp
readgroup
technology = solexa
#Same result with a question mark instead:
#segment_placement = ?
segment_placement = unknown
data = ecoli.fastq
That worked with MIRA 4.0 RC4, but fails with MIRA 4.0 RC5 and
MIRA 4.0 (final),
$ ~/downloads/mira_4.0_linux-gnu_x86_64_static/bin/mira x.manifest
...
WARNING: in the above readgroup, no read is paired although the
manifest says there should be pairs. This is fishy!
...
Fatal error (may be due to problems of the input data or parameters):
********************************************************************************
* MIRA found readgroups where pairs are expected but no read has a partner. *
* See log above and then check your input please (either manifest file or data *
* files loaded or segment_naming scheme). *
********************************************************************************
If I comment out the segment_placement line it works - but I wanted
to tell MIRA to treat this as unpaired data. I'm guessing this is a
regression - otherwise the manual is confusing me:
<quote>
segment_placement = placementcode [infoonly|exclusion_criterion].
Allowed placement codes are:
? or unknown which are place-holders for "well, in the end: don't
care." Segments of a template can be reads in any direction and in any
relationship to each other.
This is typically used for unpaired libraries (sometimes called
shotgun libraries), but may be also useful for, e.g., primer walking
with Sanger.
</quote>
Thanks,
Peter
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