[maker-devel] maker-devel Digest, Vol 113, Issue 13

[Jia-Xing Yue]

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 at paralog src]$ ./Build install
Building MAKER
Use of uninitialized value $line in chomp at /home/jxyue/Projects/LRSDAY/bu
ild/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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