From: ajay <aj...@nr...> - 2011-09-12 09:20:36
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Respected sir, i have successfully installed the bambus package on my work station. but i am getting en error as i run the goBambus i am getting the error during Grommit running i am not able to understand why this error is coming also this error is coming when i run the BAMBUS on the test data provided along with the BAMBUS. kindly help me out so that i can use this promising tool and finish my contig scaffolding. i am very much thankful to you if can you answer my few queries regarding BAMBUS 1) Sir i have got few contigs after the deno-assembly, i have fosmid paired end data and i want to use this data for making scaffold using BAMBUS so kindly tell A) how i cam prepared the .fasta file and mate file should i need to put contigs sequence and the fosmid paired end sequence in one single fasta file liketest.fasta B)i have prepared the .mate file for my fosmid paired end library (30 kb -43 Kb) long for your kind perusal i am attaching the .mate file sir kindly help me and send me the solution of the said problem i shall be very thankful to you BELOW IS THE ERROR LOG ON RUNNING BAMBUS Thanking and Regards Ajay Kumar ******************************************************************************************************************************************************************************** 20110912|124552| 25320| START: goBambus -c mcc.fasta -m mcc.mates -o test-bambus 20110912|124552| 25320| Username: ajay 20110912|124552| 25320| Hostname: AJAY-WORKSTATION 20110912|124552| 25320| Step 100: running detective 20110912|124552| 25320| running /usr/local/packages/bambus/bin/detective -C mcc.fasta -o test-bambus.detective.xml -m mcc.mates -appendlog 1 -logfile goBambus.log -debug 1 20110912|124552| 25321| START: detective -C mcc.fasta -o test-bambus.detective.xml -m mcc.mates -appendlog 1 -logfile goBambus.log -debug 1 20110912|124552| 25321| Username: ajay 20110912|124552| 25321| Hostname: AJAY-WORKSTATION 20110912|124553| 25321| FINISH: detective, elapsed 000-00:00:01 20110912|124553| 25320| Step 200: making xmls 20110912|124553| 25320| running /usr/local/packages/bambus/bin/catXML -o test-bambus.evidence.xml test-bambus.detective.xml 20110912|124553| 25320| Step 300: preparing contig links 20110912|124553| 25320| running /usr/local/packages/bambus/bin/xml2grommit -i test-bambus.evidence.xml -o test-bambus.inp -l test-bambus.lib -oc test-bambus.grommit.conf -appendlog 1 -logfile goBambus.log -debug 1 20110912|124553| 25325| START: xml2grommit -i test-bambus.evidence.xml -o test-bambus.inp -l test-bambus.lib -oc test-bambus.grommit.conf -appendlog 1 -logfile goBambus.log -debug 1 20110912|124553| 25325| Username: ajay 20110912|124553| 25325| Hostname: AJAY-WORKSTATION 20110912|124553| 25325| FINISH: xml2grommit, elapsed 000-00:00:00 20110912|124553| 25320| Step 400: Running scaffolder 20110912|124553| 25320| running /usr/local/packages/bambus/bin/grommit -i test-bambus.inp -o test-bambus.out.xml -C test-bambus.grommit.conf --append --logfile goBambus.log --debug 1 20110912|124553| 25320| Grommit(/usr/local/packages/bambus/bin/grommit -i test-bambus.inp -o test-bambus.out.xml -C test-bambus.grommit.conf --append --logfile goBambus.log --debug 1) script failed ******************************************************************************************************************************************************************************** ------- End of Forwarded Message ------- -- Open WebMail Project (http://openwebmail.org) |