[maker-devel] failed to run MAKER tutorial test data

Carson Holt carsonhh at gmail.com
Tue Oct 19 21:33:05 MDT 2021 

RepeatMasker seems to be the issue. You may need to install it manually instead of letting MAKER install it for you.

*Delete the MAKER installed copy —> /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker
*Then download and install it yourself following the instructions here —> https://www.repeatmasker.org/RepeatMasker/
*Then change the location of RepeatMasker= in the maker_exe.ctl file to point to the new installation

At the very least you will be able to see any failure messages during the RepeatMasker install that will indicate what is happening on your local system.

—Carson


> On Oct 14, 2021, at 2:22 PM, Steven L. Miller <Fungi at uwyo.edu> wrote:
> 
> As a preliminary step to running my own WGS assembly data, I am trying to get MAKER 2.31.10 that has been installed on my HPC to run the test data genome (dpp_contig.fasta) from the MAKER 2018 tutorial.  It seems that a module Text/Soundex.pm used in the Repeat Masker is not installed on my system, which caused the failure (see below).  Can you confirm that is the problem and tell me where to find that module? 
> Thanks,
> Steve Miller
> University of Wyoming
> 
> [fungi at tlog2 testdata]$ maker
> 
> Possible precedence issue with control flow operator at /pfs/tc1/apps/el7-x86_64/u/opt/maker/bin/../perl/lib/Bio/DB/IndexedBase.pm line 845.
> 
> STATUS: Parsing control files...
> 
> STATUS: Processing and indexing input FASTA files...
> 
> STATUS: Setting up database for any GFF3 input...
> 
> A data structure will be created for you at:
> 
> /pfs/tc1/home/fungi/testdata/dpp_contig.maker.output/dpp_contig_datastore
> 
>  
> To access files for individual sequences use the datastore index:
> 
> /pfs/tc1/home/fungi/testdata/dpp_contig.maker.output/dpp_contig_master_datastore_index.log
> 
>  
> STATUS: Now running MAKER...
> 
> examining contents of the fasta file and run log
> 
>  
>  
>  
> --Next Contig--
> 
>  
> #---------------------------------------------------------------------
> 
> Now starting the contig!!
> 
> SeqID: contig-dpp-500-500
> 
> Length: 32156
> 
> #---------------------------------------------------------------------
> 
>  
>  
> setting up GFF3 output and fasta chunks
> 
> doing repeat masking
> 
> running  repeat masker.
> 
> #--------- command -------------#
> 
> Widget::RepeatMasker:
> 
> cd /tmp/maker_m8gIB4; /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/RepeatMasker /pfs/tc1/home/fungi/testdata/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0/contig-dpp-500-500.0.all.rb -species all -dir /pfs/tc1/home/fungi/testdata/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0 -pa 1
> 
> #-------------------------------#
> 
> Can't locate Text/Soundex.pm in @INC (you may need to install the Text::Soundex module) (@INC contains: /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker /apps/s/slurm/20.11/lib64/perl5 /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/perl5 /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/site_perl/5.26.2/x86_64-linux-thread-multi /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/site_perl/5.26.2 /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/5.26.2/x86_64-linux-thread-multi /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/5.26.2) at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/Taxonomy.pm line 83.
> 
> BEGIN failed--compilation aborted at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/Taxonomy.pm line 83.
> 
> Compilation failed in require at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/RepeatMasker line 313.
> 
> BEGIN failed--compilation aborted at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/RepeatMasker line 313.
> 
> ERROR: RepeatMasker failed
> 
> --> rank=NA, hostname=tlog2
> 
> ERROR: Failed while doing repeat masking
> 
> ERROR: Chunk failed at level:0, tier_type:1
> 
> FAILED CONTIG:contig-dpp-500-500
> 
>  
> ERROR: Chunk failed at level:2, tier_type:0
> 
> FAILED CONTIG:contig-dpp-500-500
> 
>  
> examining contents of the fasta file and run log
> 
>  
>  
>  
> --Next Contig--
> 
>  
> Processing run.log file...
> 
> MAKER WARNING: The file dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0/contig-dpp-500-500.0.all.rb.out
> 
> did not finish on the last run and must be erased
> 
> #---------------------------------------------------------------------
> 
> Now retrying the contig!!
> 
> SeqID: contig-dpp-500-500
> 
> Length: 32156
> 
> Tries: 2!!
> 
> #---------------------------------------------------------------------
> 
>  
>  
> setting up GFF3 output and fasta chunks
> 
> doing repeat masking
> 
> running  repeat masker.
> 
> #--------- command -------------#
> 
> Widget::RepeatMasker:
> 
> cd /tmp/maker_m8gIB4; /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/RepeatMasker /pfs/tc1/home/fungi/testdata/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0/contig-dpp-500-500.0.all.rb -species all -dir /pfs/tc1/home/fungi/testdata/dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0 -pa 1
> 
> #-------------------------------#
> 
> Can't locate Text/Soundex.pm in @INC (you may need to install the Text::Soundex module) (@INC contains: /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker /apps/s/slurm/20.11/lib64/perl5 /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/perl5 /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/site_perl/5.26.2/x86_64-linux-thread-multi /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/site_perl/5.26.2 /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/5.26.2/x86_64-linux-thread-multi /apps/u/gcc/7.3.0/perl/5.26.2-b5gdyho/lib/5.26.2) at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/Taxonomy.pm line 83.
> 
> BEGIN failed--compilation aborted at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/Taxonomy.pm line 83.
> 
> Compilation failed in require at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/RepeatMasker line 313.
> 
> BEGIN failed--compilation aborted at /pfs/tc1/apps/el7-x86_64/u/opt/maker/exe/RepeatMasker/RepeatMasker line 313.
> 
> ERROR: RepeatMasker failed
> 
> --> rank=NA, hostname=tlog2
> 
> ERROR: Failed while doing repeat masking
> 
> ERROR: Chunk failed at level:0, tier_type:1
> 
> FAILED CONTIG:contig-dpp-500-500
> 
>  
> ERROR: Chunk failed at level:2, tier_type:0
> 
> FAILED CONTIG:contig-dpp-500-500
> 
>  
> examining contents of the fasta file and run log
> 
>  
>  
>  
> --Next Contig--
> 
>  
> Processing run.log file...
> 
> MAKER WARNING: The file dpp_contig.maker.output/dpp_contig_datastore/05/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0/contig-dpp-500-500.0.all.rb.out
> 
> did not finish on the last run and must be erased
> 
>  
>  
> Maker is now finished!!!
> 
>  
>  
>  
> Start_time: 1634230718
> 
> End_time:   1634230724
> 
> Elapsed:    6
> 
> [fungi at tlog2 testdata]$
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

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