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

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Steven L. Miller

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Oct 14, 2021, 4:24:06 PM10/14/21

to maker...@yandell-lab.org

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@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:

#-------------------------------#

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@tlog2 testdata]$

Carson Holt

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Oct 19, 2021, 11:34:09 PM10/19/21

to Steven L. Miller, maker...@yandell-lab.org

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

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