I've got some contigs from an assembly using ABySS that I want to align with a related genome. If I try running mauve I get the following:
OS name is: Mac OS X arch: x86_64 Executing: /Applications/Mauve.app/Contents/MacOS/progressiveMauve --output=ABySS test --output-guide-tree=ABySS test.guide_tree --backbone-output=ABySS test.backbone /Users/guy/CP001918-20.gbk /Users/guy/Ecl13047-contigs.fa Storing raw sequence at /var/folders/22/22Fli5j6G6OGbn0txlgpGk+++TI/-Tmp-/rawseq3797.000 Sequence loaded successfully. /Users/guy/CP001918-20.gbk 5598796 base pairs. Storing raw sequence at /var/folders/22/22Fli5j6G6OGbn0txlgpGk+++TI/-Tmp-/rawseq3797.001 Sequence loaded successfully. /Users/guy/Ecl13047-contigs.fa 6221099 base pairs. Using weight 15 mers for initial seedsERROR! gap character encountered at genome sequence position 2903159 Creating sorted mer list Create time was: 2 seconds. Creating sorted mer list Input sequences must be unaligned and ungapped! Caught signal 11 Cleaning up and exiting! Temporary files deleted. Exited with error code: 11 The file "Ecl13047-contigs.fa" seems to be the culprit, but I can find no internal gap characters in any of the 4887 contigs. However, the sequences in the fasta are unwrapped (ABySS doesn't support wrapped fasta sequences in either input or output), and the longest such entry is 62225 bp. If I wrap the sequences at 80 characters/line -- and then clean up some inadvertantly wrapped definition lines that are also absurdly long -- mauve has no problems. Is there a maximum line length being assumed? Thanks, Guy ------------------------------------------------------------------------------ This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
