Re: [wgs-assembler-users] Error: .mcidx is not a merylStream index file!

[Walenz, B. <bw...@jc...>]

Hi, Arjun-

Thanks for attaching the spec file.  overlapper=mer is the problem.  It, and the trimming we do on Illumina reads, are incompatible.  Use overlapper=ovl instead.  There isn't much gain from overlapper=mer anymore (it was designed for early 454 reads with lots of homopolymer errors) and it doesn't scale much past a microbe.

We (still) haven't written a pipeline for this, but our current strategy for correcting and trimming Illumina reads is at:

http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=Preprocessing

If you don't have outtie matepair libraries it amounts to a run of meryl, and a run of merTrim.

b


________________________________________
From: Arjun Prasad [ap...@ma...]
Sent: Friday, November 30, 2012 5:12 PM
To: wgs...@li...
Subject: [wgs-assembler-users] Error: .mcidx is not a merylStream index file!

Hi,

I've been trying to assemble some 2x250bp Illumina reads and I'm getting
the following error in 0-mertrim/*.err:

% cat miseq5.0001.err
opening gkStore '/cluster/ifs/projects/pcoat/celass/miseq5/miseq5.gkpStore'
loading mer database.
merylStreamReader()-- ERROR: /cluster/ifs/projects/pcoat/celass/miseq5/0-mercounts/miseq5-C-ms22-cm0.mcidx is not a merylStream index file!
merylStreamReader()-- ERROR: /cluster/ifs/projects/pcoat/celass/miseq5/0-mercounts/miseq5-C-ms22-cm0.mcdat is not a merylStream data file!

% ls -l /cluster/ifs/projects/pcoat/celass/miseq5/0-mercounts/miseq5-C-ms22-cm?.mcdat
-rw-r--r-- 1 aprasad zoo        32 Nov 30 14:50 /cluster/ifs/projects/pcoat/celass/miseq5/0-mercounts/miseq5-C-ms22-cm0.mcdat
-rw-r--r-- 1 aprasad zoo 486424472 Nov 30 14:50 /cluster/ifs/projects/pcoat/celass/miseq5/0-mercounts/miseq5-C-ms22-cm1.mcdat

I've been able to run CA on several other datasets including 454 and older
illumina sequence, so I'm guessing there's a path or format issue.

Any ideas as to what might be wrong?

Thanks,
Arjun

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