Hi Bastien Having used the suggestions you made below as to parameterizing ssaha2 to identify contaminating cloning adapters, I then launched mira (2.0.0) thusly: nohup mira --project=CRW_GEP_454_Body_10302009 --job=denovo,est,normal,454 COMMON_SETTINGS -GE:not=4 -FN:xtii='sample1_traceinfo_in.454.xml':svsi='sample1.fasta_vs_clonetech_adpaters.fasta.ssaha2' 454_SETTINGS -LR:mxti=yes -CL:msvs=yes >& log_assembly3.txt & $ tail log_assembly3.txt Merging data from XML trace info file sample1_traceinfo_in.454.xml ...Num reads: 1091861 Building hash table ... done. Localtime: Mon Jan 4 08:59:59 2010 Generated 1091861 unique template ids for 1091861 valid reads. Done merging XML data, matched 1091861 reads. Starting clips: done. Localtime: Mon Jan 4 09:00:07 2010 Merging vector screen data from SSAHA results file sample1.fasta_vs_clonetech_adpaters.fasta.ssaha2 ...Building hash table ... done. Here it has remained for several hours -bash-3.1$ top PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND 3660 rosema1 25 0 1958m 1.9g 1352 R 101 2.2 348:50.91 mira -bash-3.1$ strace -p 3660 -bash-3.1$ strace -p 3660 Process 3660 attached - interrupt to quit <after many minutes of no activity I quit> Process 3660 detached -bash-3.1$ Is something wrong here? I found a similar post in mira_talk but saw no followup to resolve it Thanks for your help. Mark -----Original Message----- From: Bastien Chevreux [mailto:bach@xxxxxxxxxxxx] Sent: Sunday, January 03, 2010 6:59 PM To: Rose Mark USRE Subject: Re: Ssaha-Mira question On Montag 04 Januar 2010 mark.rose@xxxxxxxxxxxx wrote: > I noticed your MIRA update that permits use of ssaha2 output to mask > sequence for a mira assembly. Thanks. Would you mind being a little more > explicit about any parameterization of ssaha2 required by MIRA (i.e. > output format, etc.)? Thanks Again Does this help? Note 1: the output format of SSAHA2 must the native output format (-output ssaha2). Other formats cannot be parsed by mira. Note 2: I currently use the following SSAHA2 options: -kmer 8 -skip 1 -seeds 1 -score 12 -cmatch 9 -ckmer 6 Note 3: the sequence vector clippings generated from SSAHA2 data do not replace sequence vector clippings loaded via the EXP, CAF or XML files, they rather extend them. From the main documentation file. There's also a very short example in mira_usage. Regards, Bastien -------------------------------------------------------------------------- This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited. -- You have received this mail because you are subscribed to the mira_talk mailing list. For information on how to subscribe or unsubscribe, please visit http://www.chevreux.org/mira_mailinglists.html