Hello Dear Aaron Darling and Mauve fans, thank you for providing Mauve. A very useful package! I've been using the mauveAligner program a few times in the last couple of years. It has been working fine so far, but I'm running into problems now with the 2.3.1 version on Linux. I got a "std::bad_alloc" exception when trying to align 67 bacterial genome sequences of 5 Mbp each. The error occurs at the 1st alignment step after reading the sequences and creating the sorted mer lists. The command line and the end of the output are shown below. It is likely to be a problem with memory allocation related to a C++ "new" statement. I would think it's a problem with a program statement, because I'm running mauveAligner on a supercomputer with 16GB RAM CPUs and the crash occurs when 4GB are used, so it's probably not a problem of available RAM on the computer. Maybe the allocation statement makes the program ask for more memory than it should use. In fact, the program works fine when I align only 20 of the genomes.
Would you be able to help me with this problem? Thanks in advance, Have a nice weekend, Sincerely, Nicolas Tourasse. University of Oslo, Norway. ----------------------------------------------------------------------- mauveAligner --output=Mauve_67genomes.mauve --coverage-output=Mauve_67genomes.coverage --alignment-output-dir=Mauve_67genomes_align --alignment-output-format=clustal --output-alignment=Mauve_67genomes.alignment --seed-size=15 --weight=50 --island-size=50 --island-output=Mauve_67genomes.islands --backbone-size=0 --max-backbone-gap=50 --backbone-output=Mauve_67genomes.backbone Mauve_67genomes.fasta Output: .... Creating sorted mer list Create time was: 4 seconds. Creating sorted mer list Create time was: 4 seconds. Creating sorted mer list Create time was: 3 seconds. Creating sorted mer list Create time was: 4 seconds. 0%..1%..2%..3%..4%..5%..6%..7%..8%..9%..10%.. 11%..12%..13%..14%..15%..16%..17%..18%..19%..20%.. 21%..22%..23%..24%..25%..26%..27%..28%..29%..30%.. 31%..32%..33%..34%..35%..36%..37%..38%..39%..40%.. 41%..42%..43%..44%..45%..46%..47%..48%..49%..50%.. 51%..52%..53%..54%..55%..56%..57%..58%..59%..60%.. 61%..62%..63%..64%..65%..66%..67%..68%..69%..70%.. 71%..72%..73%..74%..75%..76%..77%..78%..79%..80%.. 81%..82%..83%..84%..85%..86%..87%..88%..89%..90%.. 91%..92%..93%..94%..95%..96%..97%..98%..99%..Unhandled exception: std::bad_alloc -- Tourasse Nicolas, PhD University of Oslo, Laboratory for Microbial Dynamics (LaMDa), School of Pharmacy, Department of Pharmaceutical Biosciences, P.O. Box 1068 Blindern, 0316 Oslo, Norway. Tel: (+47) 22 84 49 41 FAX: (+47) 22 84 49 44 e-mail: nico...@biotek.uio.no website: http://lamda.uio.no/lamda.html ------------------------------------------------------------------------------ The Planet: dedicated and managed hosting, cloud storage, colocation Stay online with enterprise data centers and the best network in the business Choose flexible plans and management services without long-term contracts Personal 24x7 support from experience hosting pros just a phone call away. http://p.sf.net/sfu/theplanet-com _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
