<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif;"><div>The message is basically saying that RepeatMasker is not installed correctly. </div><div><br></div><div>Follow the instructions here --> <a href="http://www.repeatmasker.org/RMDownload.html">http://www.repeatmasker.org/RMDownload.html</a></div><div><br></div><div>--Carson</div><div><br></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> 彭司华 <<a href="mailto:shpeng@shou.edu.cn">shpeng@shou.edu.cn</a>><br><span style="font-weight:bold">Date: </span> Monday, June 2, 2014 at 8:30 PM<br><span style="font-weight:bold">To: </span> <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] Maker can not run repeatmasker<br></div><div><br></div>Using the example data, I can not run maker successfully.<br><br>Please see the following:<br><br>[root@c0105 test3]# ls -l<br>total 72<br>-rw-r--r--. 1 root root 32712 May 29 02:46 dpp_contig.fasta<br>-rw-r--r--. 1 root root 19138 May 29 02:46 dpp_est.fasta<br>-rw-r--r--. 1 root root 3045 May 29 02:46 dpp_protein.fasta<br>-rw-r--r--. 1 root root 1413 May 29 02:46 maker_bopts.ctl<br>-rw-r--r--. 1 root root 1288 May 29 02:46 maker_exe.ctl<br>-rw-r--r--. 1 root root 4630 May 29 04:27 maker_opts.ctl<br>[root@c0105 test3]# maker<br>STATUS: Parsing control files...<br>STATUS: Processing and indexing input FASTA files...<br>STATUS: Setting up database for any GFF3 input...<br>A data structure will be created for you at:<br>/home/fastq/annotation/test3/dpp_contig.maker.output/dpp_contig_datastore<br><br>To access files for individual sequences use the datastore index:<br>/home/fastq/annotation/test3/dpp_contig.maker.output/dpp_contig_master_datastore_index.log<br><br>STATUS: Now running MAKER...<br>examining contents of the fasta file and run log<br><br><br><br>--Next Contig--<br><br>#---------------------------------------------------------------------<br>Now starting the contig!!<br>SeqID: contig-dpp-500-500<br>Length: 32156<br>#---------------------------------------------------------------------<br><br><br>setting up GFF3 output and fasta chunks<br>doing repeat masking<br>running repeat masker.<br>#--------- command -------------#<br>Widget::RepeatMasker:<br>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.all.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<br>#-------------------------------#<br>which: no cross_match in (/usr/local/bin)<br>CrossmatchSearchEngine::setPathToEngine( /usr/local/bin/cross_match ): Program does not exist! at /usr/local/RepeatMasker/RepeatMasker line 519.<br>ERROR: RepeatMasker failed<br>--> rank=NA, hostname=c0105<br>ERROR: Failed while doing repeat masking<br>ERROR: Chunk failed at level:0, tier_type:1<br>FAILED CONTIG:contig-dpp-500-500<br><br>ERROR: Chunk failed at level:2, tier_type:0<br>FAILED CONTIG:contig-dpp-500-500<br><br>examining contents of the fasta file and run log<br><br><br><br>--Next Contig--<br><br>Processing run.log file...<br>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<br>did not finish on the last run and must be erased<br>#---------------------------------------------------------------------<br>Now retrying the contig!!<br>SeqID: contig-dpp-500-500<br>Length: 32156<br>Tries: 2!!<br>#---------------------------------------------------------------------<br><br><br>setting up GFF3 output and fasta chunks<br>doing repeat masking<br>running repeat masker.<br>#--------- command -------------#<br>Widget::RepeatMasker:<br>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.all.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<br>#-------------------------------#<br>which: no cross_match in (/usr/local/bin)<br>CrossmatchSearchEngine::setPathToEngine( /usr/local/bin/cross_match ): Program does not exist! at /usr/local/RepeatMasker/RepeatMasker line 519.<br>ERROR: RepeatMasker failed<br>--> rank=NA, hostname=c0105<br>ERROR: Failed while doing repeat masking<br>ERROR: Chunk failed at level:0, tier_type:1<br>FAILED CONTIG:contig-dpp-500-500<br><br>ERROR: Chunk failed at level:2, tier_type:0<br>FAILED CONTIG:contig-dpp-500-500<br><br>examining contents of the fasta file and run log<br><br><br><br>--Next Contig--<br><br>Processing run.log file...<br>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<br>did not finish on the last run and must be erased<br><br><br>Maker is now finished!!!<br><br><br><br>Start_time: 1401761680<br>End_time: 1401761688<br>Elapsed: 8<br><br>Thnaks.<br><br>Sihua<br>_______________________________________________
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