Re: maker-devel Digest, Vol 113, Issue 13

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Re: maker-devel Digest, Vol 113, Issue 13

Jia-Xing Yue-2
Dear maker developers,

I am trying to install maker-3.01.1-beta but encountered the warning message about uninitialized value (see the warning message below) although still finished the installation.

[jxyue@paralog src]$ ./Build install
Building MAKER
Use of uninitialized value $line in chomp at /home/jxyue/Projects/LRSDAY/build/maker/src/../../../build/cpanm/perlmods/lib/perl5/Module/Build/Base.pm line 3082.
Use of uninitialized value $line in substitution (s///) at /home/jxyue/Projects/LRSDAY/build/maker/src/../../../build/cpanm/perlmods/lib/perl5/Module/Build/Base.pm line 3083.
Installing MAKER...
Building MAKER
...

Also, when I ran this installation for the actual work, it  reported errors about cannot find my specified snaphmm model for the annotation, despite that I have specified "snaphmm=$LRSDAY_HOME/data/S288C.gene.hmm" in the "maker_opts.ctl" file and this configuration information has been successfully recognized by maker.

running  snap.
#--------- command -------------#
Widget::snap:
/home/jxyue/Projects/LRSDAY/build/SNAP/snap /home/jxyue/Projects/LRSDAY/data/S288C.gene.hmm /tmp/maker_m8TVEQ/chrI.abinit_masked.0 > /tmp/maker_m8TVEQ/chrI.abinit_masked.0.S288C%2Egene%2Ehmm.snap
#-------------------------------#

# (my comment: up to now everything looks fine)
....

running  snap.
#--------- command -------------#
Widget::snap:
/home/jxyue/Projects/LRSDAY/build/SNAP/snap -plus -xdef /tmp/maker_m8TVEQ/0/85_0.4044-4985.S288C.gene.hmm.auto_annotator.xdef.snap  S288C.gene.hmm /tmp
/maker_m8TVEQ/0/85_0.4044-4985.S288C.gene.hmm.auto_annotator.snap.fasta > /tmp/maker_m8TVEQ/0/85_0.4044-4985.S288C.gene.hmm.auto_annotator.snap
#-------------------------------#
ZOE ERROR (from /home/jxyue/Projects/LRSDAY/build/SNAP/snap): error opening file (/home/jxyue/Projects/LRSDAY/build/SNAP/Zoe/HMM/S288C.gene.hmm)
ZOE library version 2017-03-01
ERROR: Snap failed
--> rank=NA, hostname=paralog.itc.unipi.it
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:chrI

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:chrI

examining contents of the fasta file and run log

# (my comment: here the error occurred. As you can see, snap somehow forgot about the path to  my specified hmm file and instead looks for this file in its default installation location)

It is worth noting that the parallel installation and run with maker-3.00.0-beta finish smoothly without any problem. So I suspect both the installation warning and the executing error are caused by the changes during the version update from 3.00.0-beta to 3.01.1-beta.  Could you check about this issue? Thanks in advance!

Finally, is it possible to also provide access to older version of maker (e.g. 3.00.0-beta in this particular case) when the user finish the registration in the maker download page? This will help users to roll back to older version when needed.  Also this helps for the version control when other developers develop annotation pipelines that use maker as a dependency package. Thanks for the consideration!


Best,
Jia-Xing

--
Jia-Xing Yue

Population Genomics and Complex Traits Group
Tour Pasteur 8eme etage
Faculté de Médecine
Institute for Research on Cancer and Aging, Nice (IRCAN)
CNRS UMR 7284 - INSERM U 1081 - Université Côte d’Azur (UCA)
28 Avenue de Valombrose
06107 NICE Cedex 2
France

Personal website: http://www.iamphioxus.org/


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Re: maker-devel Digest, Vol 113, Issue 13

Carson Holt-2
Thanks. The map_fasta_ids script was empty in the bin directory for some reason, so the installer through an error because it could not find the #!/usr/bin/perl line. I have put it back in the bin directory where it was supposed to be and the issue goes away for the install.

For the second issue, I think I found it and have updated a new tar ball to the website.

Also here is a link to download the old 3.00-beta, although I would not recommend making it part of a pipeline because version 3 is still beta and still has bugs (you should use 2.31.9 instead for piplines).  —> http://topaz.genetics.utah.edu/maker_downloads/static/maker-3.00.0-beta.tgz

—Carson


 
On Oct 16, 2017, at 2:54 AM, Jia-Xing Yue <[hidden email]> wrote:

Dear maker developers,

I am trying to install maker-3.01.1-beta but encountered the warning message about uninitialized value (see the warning message below) although still finished the installation.

[jxyue@paralog src]$ ./Build install
Building MAKER
Use of uninitialized value $line in chomp at /home/jxyue/Projects/LRSDAY/build/maker/src/../../../build/cpanm/perlmods/lib/perl5/Module/Build/Base.pm line 3082.
Use of uninitialized value $line in substitution (s///) at /home/jxyue/Projects/LRSDAY/build/maker/src/../../../build/cpanm/perlmods/lib/perl5/Module/Build/Base.pm line 3083.
Installing MAKER...
Building MAKER
...

Also, when I ran this installation for the actual work, it  reported errors about cannot find my specified snaphmm model for the annotation, despite that I have specified "snaphmm=$LRSDAY_HOME/data/S288C.gene.hmm" in the "maker_opts.ctl" file and this configuration information has been successfully recognized by maker.

running  snap.
#--------- command -------------#
Widget::snap:
/home/jxyue/Projects/LRSDAY/build/SNAP/snap /home/jxyue/Projects/LRSDAY/data/S288C.gene.hmm /tmp/maker_m8TVEQ/chrI.abinit_masked.0 > /tmp/maker_m8TVEQ/chrI.abinit_masked.0.S288C%2Egene%2Ehmm.snap
#-------------------------------#

# (my comment: up to now everything looks fine)
....

running  snap.
#--------- command -------------#
Widget::snap:
/home/jxyue/Projects/LRSDAY/build/SNAP/snap -plus -xdef /tmp/maker_m8TVEQ/0/85_0.4044-4985.S288C.gene.hmm.auto_annotator.xdef.snap  S288C.gene.hmm /tmp
/maker_m8TVEQ/0/85_0.4044-4985.S288C.gene.hmm.auto_annotator.snap.fasta > /tmp/maker_m8TVEQ/0/85_0.4044-4985.S288C.gene.hmm.auto_annotator.snap
#-------------------------------#
ZOE ERROR (from /home/jxyue/Projects/LRSDAY/build/SNAP/snap): error opening file (/home/jxyue/Projects/LRSDAY/build/SNAP/Zoe/HMM/S288C.gene.hmm)
ZOE library version 2017-03-01
ERROR: Snap failed
--> rank=NA, hostname=paralog.itc.unipi.it
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:chrI

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:chrI

examining contents of the fasta file and run log

# (my comment: here the error occurred. As you can see, snap somehow forgot about the path to  my specified hmm file and instead looks for this file in its default installation location)

It is worth noting that the parallel installation and run with maker-3.00.0-beta finish smoothly without any problem. So I suspect both the installation warning and the executing error are caused by the changes during the version update from 3.00.0-beta to 3.01.1-beta.  Could you check about this issue? Thanks in advance!

Finally, is it possible to also provide access to older version of maker (e.g. 3.00.0-beta in this particular case) when the user finish the registration in the maker download page? This will help users to roll back to older version when needed.  Also this helps for the version control when other developers develop annotation pipelines that use maker as a dependency package. Thanks for the consideration!


Best,
Jia-Xing

--
Jia-Xing Yue

Population Genomics and Complex Traits Group
Tour Pasteur 8eme etage
Faculté de Médecine
Institute for Research on Cancer and Aging, Nice (IRCAN)
CNRS UMR 7284 - INSERM U 1081 - Université Côte d’Azur (UCA)
28 Avenue de Valombrose
06107 NICE Cedex 2
France

Personal website: http://www.iamphioxus.org/

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


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