New MAKER

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New MAKER

Carson Hinton Holt
New MAKER A new version of MAKER is now available for download at http://www.yandell-lab.org/software/maker.html . When you go to the download page you will have the choice of downloading version 2.03 or the current 2.04-beta.  Download the 2.04-beta.

The MAKER update has better evidence processing and takes extra steps to find start and stop codons when programs like SNAP and Augustus call partial transcripts (the always_complete option in maker_opts.ctl).  I have also removed some redundancy from the control files, i.e. It is not longer required to both supply a value for snaphmm and then add snap to the predictor list, rather supplying the HMM is sufficient for MAKER to know you want to use SNAP as a predictor.  The same is true for Augustus, GeneMark, and FGENESH.

You can now provide comma separated lists to MAKER options that take a file, and you can provide an optional label for all results for that file by separating the file name from the label with a ‘:’ character.

Example:
    protein=/data/uniprot.fasta:uniprot,/data/Dmel.fasta:drosophila

Results will then have ‘blastx:uniprot’ and ‘blastx:drosophila’ in the GFF3 source tag.  This is a convenience feature for separating tags into separate tiers for GBrowse.

Also MAKER options are now separated from the values by an ‘=’ character, although MAKER still knows how to interpret the ‘:’ character from old maker_opts.ctl files.

Example:
est=/data/est.fasta     not      est:/data/est.fasta

To install the new version of MAKER, you must delete the old version, and then follow installation instructions that come with it.  Installation should be as easy as:
    cd maker/src/
    perl Build.PL
    ./Build install

Thanks,
Carson

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Re: New MAKER

Reith, Michael
Hi Carson,

Trying out the new MAKER (on Solaris), we've run into a couple of issues captured here:

#--------- command -------------#
Widget::genemark:
/software/packages/maker/bin/../lib/Widget/genemark/gmhmm_wrap -m t18.es.mod -g /software/wrappers/gmhmme3 -p /software/wrappers/probuild -o /data/reithme/t18r7c-anno/t18r7c_default.unpadded.maker.output/t18r7c_default.unpadded_datastore/CC/BD/c1007-c122_1//theVoid.c1007-c122_1/c1007-c122_1.all.t18%2Ees%2Emod.genemark /data/reithme/t18r7c-anno/t18r7c_default.unpadded.maker.output/t18r7c_default.unpadded_datastore/CC/BD/c1007-c122_1//theVoid.c1007-c122_1/query.fasta
#-------------------------------#
open3: exec of /software/packages/maker/bin/../lib/Widget/genemark/gmhmm_wrap -m t18.es.mod -g /software/wrappers/gmhmme3 -p /software/wrappers/probuild -o /data/reithme/t18r7c-anno/t18r7c_default.unpadded.maker.output/t18r7c_default.unpadded_datastore/CC/BD/c1007-c122_1//theVoid.c1007-c122_1/c1007-c122_1.all.t18%2Ees%2Emod.genemark /data/reithme/t18r7c-anno/t18r7c_default.unpadded.maker.output/t18r7c_default.unpadded_datastore/CC/BD/c1007-c122_1//theVoid.c1007-c122_1/query.fasta failed at /software/packages/maker/bin/../lib/Widget/genemark.pm line 44
ERROR: Genemark failed

FATAL ERROR
ERROR: Failed while preparing masked sequence and ab-inits!!

ERROR: Chunk failed at level 6
!!
FAILED CONTIG:c1007-c122_1

ps: unknown output format: -o command
usage: ps [ -aAdeflcjLPyZ ] [ -o format ] [ -t termlist ]
        [ -u userlist ] [ -U userlist ] [ -G grouplist ]
        [ -p proclist ] [ -g pgrplist ] [ -s sidlist ] [ -z zonelist ]
  'format' is one or more of:
        user ruser group rgroup uid ruid gid rgid pid ppid pgid sid taskid ctid
        pri opri pcpu pmem vsz rss osz nice class time etime stime zone zoneid
        f s c lwp nlwp psr tty addr wchan fname comm args projid project pset



The first is obviously at lib/Widget/genemark line 44 while the second (ps: unknown output format: -o command....) seems to arise from lib/Proc/Signal.pm.  Saw several of these warnings scroll by early in the MAKER run.  Both seem to deal with tracking processes - just wondering if there's something different in Solaris that causing this.

thanks for your help,
Mike
________________________________________
From: [hidden email] [[hidden email]] On Behalf Of Carson Holt [[hidden email]]
Sent: Sunday, October 24, 2010 8:27 AM
To: Kymberlie Hallsworth-Pepin; Xu Zhang; MAKER; [hidden email]; [hidden email]; Anastasia Gioti
Subject: [maker-devel] New MAKER

A new version of MAKER is now available for download at http://www.yandell-lab.org/software/maker.html . When you go to the download page you will have the choice of downloading version 2.03 or the current 2.04-beta.  Download the 2.04-beta.

The MAKER update has better evidence processing and takes extra steps to find start and stop codons when programs like SNAP and Augustus call partial transcripts (the always_complete option in maker_opts.ctl).  I have also removed some redundancy from the control files, i.e. It is not longer required to both supply a value for snaphmm and then add snap to the predictor list, rather supplying the HMM is sufficient for MAKER to know you want to use SNAP as a predictor.  The same is true for Augustus, GeneMark, and FGENESH.

You can now provide comma separated lists to MAKER options that take a file, and you can provide an optional label for all results for that file by separating the file name from the label with a ‘:’ character.

Example:
    protein=/data/uniprot.fasta:uniprot,/data/Dmel.fasta:drosophila

Results will then have ‘blastx:uniprot’ and ‘blastx:drosophila’ in the GFF3 source tag.  This is a convenience feature for separating tags into separate tiers for GBrowse.

Also MAKER options are now separated from the values by an ‘=’ character, although MAKER still knows how to interpret the ‘:’ character from old maker_opts.ctl files.

Example:
est=/data/est.fasta     not      est:/data/est.fasta

To install the new version of MAKER, you must delete the old version, and then follow installation instructions that come with it.  Installation should be as easy as:
    cd maker/src/
    perl Build.PL
    ./Build install

Thanks,
Carson

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Re: New MAKER

Carson Hinton Holt
Re: New MAKER Make sure you have the file .gm_key installed in your user’s $HOME directory, otherwise GeneMark always fails.  The error is the failure of IPC::Open3 which just means that GeneMark itself may be inducing a failure.  Also try running GeneMark all by itself on the genome file for the same user who is running MAKER.  There may be some more informative information provided that way.

Carson


On 10/25/10 5:11 PM, "Reith, Michael" <Michael.Reith@...> wrote:

Hi Carson,

Trying out the new MAKER (on Solaris), we've run into a couple of issues captured here:

#--------- command -------------#
Widget::genemark:
/software/packages/maker/bin/../lib/Widget/genemark/gmhmm_wrap -m t18.es.mod -g /software/wrappers/gmhmme3 -p /software/wrappers/probuild -o /data/reithme/t18r7c-anno/t18r7c_default.unpadded.maker.output/t18r7c_default.unpadded_datastore/CC/BD/c1007-c122_1//theVoid.c1007-c122_1/c1007-c122_1.all.t18%2Ees%2Emod.genemark /data/reithme/t18r7c-anno/t18r7c_default.unpadded.maker.output/t18r7c_default.unpadded_datastore/CC/BD/c1007-c122_1//theVoid.c1007-c122_1/query.fasta
#-------------------------------#
open3: exec of /software/packages/maker/bin/../lib/Widget/genemark/gmhmm_wrap -m t18.es.mod -g /software/wrappers/gmhmme3 -p /software/wrappers/probuild -o /data/reithme/t18r7c-anno/t18r7c_default.unpadded.maker.output/t18r7c_default.unpadded_datastore/CC/BD/c1007-c122_1//theVoid.c1007-c122_1/c1007-c122_1.all.t18%2Ees%2Emod.genemark /data/reithme/t18r7c-anno/t18r7c_default.unpadded.maker.output/t18r7c_default.unpadded_datastore/CC/BD/c1007-c122_1//theVoid.c1007-c122_1/query.fasta failed at /software/packages/maker/bin/../lib/Widget/genemark.pm line 44
ERROR: Genemark failed

FATAL ERROR
ERROR: Failed while preparing masked sequence and ab-inits!!

ERROR: Chunk failed at level 6
!!
FAILED CONTIG:c1007-c122_1

ps: unknown output format: -o command
usage: ps [ -aAdeflcjLPyZ ] [ -o format ] [ -t termlist ]
        [ -u userlist ] [ -U userlist ] [ -G grouplist ]
        [ -p proclist ] [ -g pgrplist ] [ -s sidlist ] [ -z zonelist ]
  'format' is one or more of:
        user ruser group rgroup uid ruid gid rgid pid ppid pgid sid taskid ctid
        pri opri pcpu pmem vsz rss osz nice class time etime stime zone zoneid
        f s c lwp nlwp psr tty addr wchan fname comm args projid project pset



The first is obviously at lib/Widget/genemark line 44 while the second (ps: unknown output format: -o command....) seems to arise from lib/Proc/Signal.pm.  Saw several of these warnings scroll by early in the MAKER run.  Both seem to deal with tracking processes - just wondering if there's something different in Solaris that causing this.

thanks for your help,
Mike
________________________________________
From: maker-devel-bounces@... [maker-devel-bounces@...] On Behalf Of Carson Holt [carson.holt@...]
Sent: Sunday, October 24, 2010 8:27 AM
To: Kymberlie Hallsworth-Pepin; Xu Zhang; MAKER; andregomes@...; raramayo@...; Anastasia Gioti
Subject: [maker-devel] New MAKER

A new version of MAKER is now available for download at http://www.yandell-lab.org/software/maker.html . When you go to the download page you will have the choice of downloading version 2.03 or the current 2.04-beta.  Download the 2.04-beta.

The MAKER update has better evidence processing and takes extra steps to find start and stop codons when programs like SNAP and Augustus call partial transcripts (the always_complete option in maker_opts.ctl).  I have also removed some redundancy from the control files, i.e. It is not longer required to both supply a value for snaphmm and then add snap to the predictor list, rather supplying the HMM is sufficient for MAKER to know you want to use SNAP as a predictor.  The same is true for Augustus, GeneMark, and FGENESH.

You can now provide comma separated lists to MAKER options that take a file, and you can provide an optional label for all results for that file by separating the file name from the label with a ‘:’ character.

Example:
    protein=/data/uniprot.fasta:uniprot,/data/Dmel.fasta:drosophila

Results will then have ‘blastx:uniprot’ and ‘blastx:drosophila’ in the GFF3 source tag.  This is a convenience feature for separating tags into separate tiers for GBrowse.

Also MAKER options are now separated from the values by an ‘=’ character, although MAKER still knows how to interpret the ‘:’ character from old maker_opts.ctl files.

Example:
est=/data/est.fasta     not      est:/data/est.fasta

To install the new version of MAKER, you must delete the old version, and then follow installation instructions that come with it.  Installation should be as easy as:
    cd maker/src/
    perl Build.PL
    ./Build install

Thanks,
Carson


_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org