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

[Steven L. Miller]

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]$
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