[maker-devel] Maker can not run repeatmasker

[Carson Holt]

The message is basically saying that RepeatMasker is not installed
correctly.  

Follow the instructions here --> http://www.repeatmasker.org/RMDownload.html

--Carson


From:  彭司华 <shpeng at shou.edu.cn>
Date:  Monday, June 2, 2014 at 8:30 PM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Maker can not run repeatmasker

Using the example data, I can not run maker successfully.

Please see the following:

[root at c0105 test3]# ls -l
total 72
-rw-r--r--. 1 root root 32712 May 29 02:46 dpp_contig.fasta
-rw-r--r--. 1 root root 19138 May 29 02:46 dpp_est.fasta
-rw-r--r--. 1 root root  3045 May 29 02:46 dpp_protein.fasta
-rw-r--r--. 1 root root  1413 May 29 02:46 maker_bopts.ctl
-rw-r--r--. 1 root root  1288 May 29 02:46 maker_exe.ctl
-rw-r--r--. 1 root root  4630 May 29 04:27 maker_opts.ctl
[root at c0105 test3]# maker
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:
/home/fastq/annotation/test3/dpp_contig.maker.output/dpp_contig_datastore

To access files for individual sequences use the datastore index:
/home/fastq/annotation/test3/dpp_contig.maker.output/dpp_contig_master_datas
tore_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_g7CIeW; /usr/local/RepeatMasker/RepeatMasker
/home/fastq/annotation/test3/dpp_contig.maker.output/dpp_contig_datastore/05
/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0/contig-dpp-500-500.0.al
l.rb -species all -dir
/home/fastq/annotation/test3/dpp_contig.maker.output/dpp_contig_datastore/05
/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0 -pa 1
#-------------------------------#
which: no cross_match in (/usr/local/bin)
CrossmatchSearchEngine::setPathToEngine( /usr/local/bin/cross_match ):
Program does not exist! at /usr/local/RepeatMasker/RepeatMasker line 519.
ERROR: RepeatMasker failed
--> rank=NA, hostname=c0105
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//theVo
id.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_g7CIeW; /usr/local/RepeatMasker/RepeatMasker
/home/fastq/annotation/test3/dpp_contig.maker.output/dpp_contig_datastore/05
/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0/contig-dpp-500-500.0.al
l.rb -species all -dir
/home/fastq/annotation/test3/dpp_contig.maker.output/dpp_contig_datastore/05
/1F/contig-dpp-500-500//theVoid.contig-dpp-500-500/0 -pa 1
#-------------------------------#
which: no cross_match in (/usr/local/bin)
CrossmatchSearchEngine::setPathToEngine( /usr/local/bin/cross_match ):
Program does not exist! at /usr/local/RepeatMasker/RepeatMasker line 519.
ERROR: RepeatMasker failed
--> rank=NA, hostname=c0105
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//theVo
id.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: 1401761680
End_time:   1401761688
Elapsed:    8

Thnaks.

Sihua
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