Hi This is Bartek Tomiczek form University Collage London. I am trying to make a genome alignment with: -rwxr-xr-x 1 bartek bartek 3858328 Nov 11 2009 progressiveMauve -rwxr-xr-x 1 bartek bartek 2901448 Nov 11 2009 mauveAligner form the command line version for linux. Since the visual interface is working fine for me the command line is constantly exiting with the error:
attempt 1: -rw-r--r-- 1 bartek bartek 372948 Nov 11 2009 mauve_user_guide.pdf -rwxr-xr-x 1 bartek bartek 3858328 Nov 11 2009 progressiveMauve -rwxr-xr-x 1 bartek bartek 2901448 Nov 11 2009 mauveAligner -rwxr-xr-x 1 bartek bartek 855 Nov 11 2009 Mauve -rw-r--r-- 1 bartek bartek 3563 Nov 11 2009 README -rw-r--r-- 1 bartek bartek 18332 Nov 11 2009 COPYING -rw-r--r-- 1 bartek bartek 422194 Nov 12 2009 Mauve.jar -rw-r--r-- 1 bartek bartek 31510 Nov 12 2009 ChangeLog.html drwxrwxr-x 2 bartek bartek 1024 Nov 29 13:22 linux-x64 drwxrwxr-x 2 bartek bartek 1024 Nov 29 13:22 ext -rw-r--r-- 1 bartek bartek 19760 Nov 29 14:19 Sp.may2011.extras_mito.fasta -rw-r--r-- 1 bartek bartek 84856 Nov 29 14:20 Sp.may2011.extras_mito.fasta.sslist -rw-r--r-- 1 bartek bartek 12531568 Nov 29 14:21 jb50contigs.fa -rw-r--r-- 1 bartek bartek 52296828 Nov 29 14:21 jb50contigs.fa.sslist [bartek@jb-analysis1 mauve_2.3.1]$ mauveAligner -- output=jb50vsSpmito.mauve --output-alignment=jb50vsSpmito.alignment jb50contigs.fa Sp.may2011.extras_mito.fasta -bash: mauveAligner: command not found [bartek@jb-analysis1 mauve_2.3.1]$ ./mauveAligner -- output=jb50vsSpmito.mauve --output-alignment=jb50vsSpmito.alignment jb50contigs.fa Sp.may2011.extras_mito.fasta Sequence loaded successfully. jb50contigs.fa 12304601 base pairs. Using weight 17 mers for initial seeds Creating sorted mer list Create time was: 8 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%..Starting with 0 MUMs Eliminating overlaps yields 0 MUMs *** ERROR *** Clust::SetLeafCount(0) attempt 2: [bartek@jb-analysis1 mauve_2.3.1]$ ./mauveAligner -- output=jb50vsSpmito.mauve --output-alignment=jb50vsSpmito.alignment jb50contigs.fa jb50contigs.fa.sslist Sp.may2011.extras_mito.fasta Sp.may2011.extras_mito.fasta.sslist Sequence loaded successfully. jb50contigs.fa 12304601 base pairs. Sequence loaded successfully. Sp.may2011.extras_mito.fasta 6835866 base pairs. Using weight 17 mers for initial seeds Sorted mer list loaded successfully Sorted mer list loaded successfully Segmentation fault attempt 3: [bartek@jb-analysis1 mauve_2.3.1]$ ./progressiveMauve -- output=jb50vsSpmito.mauve jb50contigs.fa Sp.may2011.extras_mito.fasta Storing raw sequence at /tmp/rawseq21551.000 Sequence loaded successfully. jb50contigs.fa 12304601 base pairs. Storing raw sequence at /tmp/rawseq21551.001 Sequence loaded successfully. Sp.may2011.extras_mito.fasta 6835866 base pairs. Using weight 17 mers for initial seeds Sorted mer list loaded successfully Sorted mer list loaded successfully Caught signal 11 Cleaning up and exiting! Temporary files deleted. In all of the above examples the output file is produced but is empty. Do I need any additional software or am I running it in a wrong way ? Please help me with this problem or give the contact to a person that can help. Bartlomiej Tomiczek Department of Genetics, Evolution and Environment University College London Darwin Building Gower Street London WC1E 6B United Kingdom ------------------------------------------------------------------------------ All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d _______________________________________________ Mauve-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mauve-users
