[maker-devel] Help on error-Repeat masker

Mon Apr 1 15:47:38 MDT 2013

That's not too bad It's best to choose a few large contigs (1-2Mb total) to
run with at first and then use those results to help configure the rest of
the run.  For the final run you may want to consider splitting onto multiple
machines if your machine has limited cpu power.   It will take you ~150
hours on 1 cpu core depending on the size of alignment datasets - ESTs and
proteins.  More cpu cores will allow it to run faster (see graph below from
the MAKER2 paper).  I imagine that your machine probably has at least 4 cpu
cores.

Most bioinformatics labs have multi cpu Linux boxes (I.e. 24-32 cpu cores),
some have clusters available to them (100's to 1000's of cpu cores), and a
few just launch maker on multiple lab desktop machines all writing to the
same network mounted output directory.

Thanks,
Carson

Thanks,
Carson

From:  Hud Hud <hudarul at yahoo.com>
Reply-To:  Hud Hud <hudarul at yahoo.com>
Date:  Monday, 1 April, 2013 4:48 PM
To:  Carson Holt <carsonhh at gmail.com>
Subject:  Re: [maker-devel] Help on error-Repeat masker

Its  about 50mb

  From: Carson Holt <carsonhh at gmail.com>
 To: Hud Hud <hudarul at yahoo.com>
 Sent: Tuesday, April 2, 2013 4:44 AM
 Subject: Re: [maker-devel] Help on error-Repeat masker

How big is the genome?

--Carson

From:  Hud Hud <hudarul at yahoo.com>
Reply-To:  Hud Hud <hudarul at yahoo.com>
Date:  Monday, 1 April, 2013 4:37 PM
To:  Carson Holt <carsonhh at gmail.com>
Subject:  Re: [maker-devel] Help on error-Repeat masker

owh thanks so much,now i know whats going wrong, its the cygwin... i'll try
dual boot then as my genome over 10 mb..thanks for your time

  From: Carson Holt <carsonhh at gmail.com>
 To: Hud Hud <hudarul at yahoo.com>
Cc: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
 Sent: Tuesday, April 2, 2013 4:29 AM
 Subject: Re: [maker-devel] Help on error-Repeat masker

I found it odd because perl.exe is a windows extension not used in Linux,
but it confirmed my suspicions.  You can't use maker with cygwin.  There are
several things that will break because it's not really Linux.  You can use
Virtual Box instead to install a virtual Linux machine -->
https://www.virtualbox.org/.  Alternatively you can try and dual boot your
system with a Linux partition.

Virtual Box will allow you to run maker on small datasets, depending on the
size of the genome you want to run maker with it may be fine.  But I would
not recommend running anything over 10 megabases (it won't fail, it will
just take a very long time).

Thanks,
Carson

From:  Hud Hud <hudarul at yahoo.com>
Reply-To:  Hud Hud <hudarul at yahoo.com>
Date:  Monday, 1 April, 2013 4:21 PM
To:  Carson Holt <carsonhh at gmail.com>
Subject:  Re: [maker-devel] Help on error-Repeat masker

1. owh its odd?im using windows8 but for maker im using cygwin
2. when i type which perl i get this /usr/bin/perl
3. when i type ./Build repeatmasker i got this
cygwin warning: MS-DOS style path detected: \Users\Dora Preferred POSIX
equivalent is: /cygdrive/c/Users/Dora CYGWIN environment variable option
"nodosfilewarning" turns off this warning. Consult the user's guide for more
details about POSIX paths:
http://cygwin.com/cygwin-ug-net/using.html#using-pathnames WARNING:
RepeatMasker was already found on this system. Do you still want MAKER to
install RepeatMasker for you?
  is there any prob with this, or can i just proceed with the installation?

  From: Carson Holt <carsonhh at gmail.com>
 To: Hud Hud <hudarul at yahoo.com>
Cc: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
 Sent: Tuesday, April 2, 2013 3:59 AM
 Subject: Re: [maker-devel] Help on error-Repeat masker

What kind of system (OS) are you running on?  'perl.exe' seems odd.

It appears that the perl is different for maker and RepeatMasker.  What do
you get when you type 'which perl' on the command line?

I think you need to reinstall RepeatMasker at a minimum.  To do that -->
> cd  /home/maker-2.27-beta/maker/src
> ./Build repeatmasker

--Carson

From:  Hud Hud <hudarul at yahoo.com>
Reply-To:  Hud Hud <hudarul at yahoo.com>
Date:  Monday, 1 April, 2013 3:53 PM
To:  Carson Holt <carsonhh at gmail.com>
Subject:  Re: [maker-devel] Help on error-Repeat masker

Thanks for the reply
1. Yes i set up the maker myself as own user but i dont know how to check
for the mounting things
2. Im calling maker directly and  i've tried this cat
/home/maker-2.27-beta/maker/bin/maker | grep "#\!" and it gaves me this
#!/usr/bin/perl.exe

  From: Carson Holt <carsonhh at gmail.com>
 To: Hud Hud <hudarul at yahoo.com>; "maker-devel at yandell-lab.org"
<maker-devel at yandell-lab.org>
 Sent: Monday, April 1, 2013 10:50 PM
 Subject: Re: [maker-devel] Help on error-Repeat masker

This appears to be a permissions issue either for the  /u1/local/bin/
directory or RepeatMasker setup.  Did you set maker up yourself as your own
user or did someone else do it for you, perhaps as root? Is /u1/local/bin/
on an NFS mount.

If it's a mounting issue I found this via google the exact same issue-->
>> I needed to add the 'exec' option to the /etc/fstab file when mounting that
>> partition.
>> If it says 'defaults' on the line in /etc/fstab, then it also means you don't
>> have exec rights on it.

Are you using the same perl to run maker as you are using for RepeatMasker?
For example, are you calling perl directly and giving the path to maker or
are you calling maker directly and letting it use the version of perl it was
installed with.  Try this to see which perl maker was installed with -->
cat  /home/maker-2.27-beta/maker/bin/maker | grep "#\!"

You may have to have to reinstall RepeatMasker and possibly maker.

Thanks,
Carson

From:  Hud Hud <hudarul at yahoo.com>
Reply-To:  Hud Hud <hudarul at yahoo.com>
Date:  Sunday, 31 March, 2013 4:02 PM
To:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Help on error-Repeat masker

Hello, i have some problem when runnning maker, i've got this kind of error,
what could possibly go wrong here? Thnks so much

setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_WOVHsi;
/home/maker-2.27-beta/maker/exe/RepeatMasker/RepeatMasker
/home/maker-2.27-beta/maker/data/contig.maker.output/contig_datastore/61/0D/
contig172//theVoid 
.contig172/contig172.0.simple.rb -dir
/home/maker-2.27-beta/maker/data/contig.maker.output/contig_datastore/61/0D/
contig172//theVoid.contig172 -pa 1 - lib /tmp/maker_WOVHsi/b1piBcWHlH
#-------------------------------#
sh: /home/maker-2.27-beta/maker/exe/RepeatMasker/RepeatMasker:
/u1/local/bin/perl: bad interpreter: Permission denied
ERROR: RepeatMasker failed
--> rank=NA, hostname=Homis
ERROR: Failed while doing repeat masking
ERROR: Chunk failed at level:0, tier_type:1
FAILED CONTIG:contig172

ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:172

examining contents of the fasta file and run log

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