errors with dnadiff but not nucmer, is it because of installation?

[HuJane]

Dear gmarcais, I have downloaded mummer-3.9.4alpha.tar.gz by wget, untar and installed it as instructions. It looks fine. But when I ran dnadiff (with or without full path) some errors were appeared while no errors if ran nucmer. Do you know the reason? My commands: dnadiff -h nucmer -h nucmer --prefix mum_analysis/Normal_vs_DDEX.dnadiff Normal/Normal.contigs.fasta DDEX/DDEX.contigs.fasta dnadiff -d mum_analysis/Normal_vs_DDEX.dnadiff.delta

[HuJane]

The same as mummerplot:

[hujie@YanfaCenter01 bin]$ mummerplot /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 19: use: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 20: use: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 21: use: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 22: use: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 24: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 25: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 30: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 31: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 32: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 35: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 36: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 37: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 39: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 41: =: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 42: =: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 43: =: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 47: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 48: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 49: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 50: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 53: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 54: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 55: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 56: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 57: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 59: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 61: =: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 62: =: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 63: =: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 64: =: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 65: =: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 66: =: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 67: =: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 72: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 73: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 74: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 75: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 76: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 77: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 78: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 79: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 80: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 81: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 82: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 83: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 84: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 85: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 86: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 87: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 88: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 89: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 90: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 92: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 93: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 94: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 95: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 96: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 97: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 98: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 100: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 102: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 106: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 108: my: command not found /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 109: syntax error near unexpected token newline' /home/hujie/software/mummer-3.9.3alpha/bin/mummerplot: line 109: USAGE: mummerplot [options] '

[HuJane]

Hi, the problem was solved by add 'perl' before the command: [hujie@YanfaCenter01 bin]$ perl mummerplot

USAGE: mummerplot [options]

Try 'mummerplot -h' for more information. [hujie@YanfaCenter01 bin]$ perl dnadiff

USAGE: dnadiff [options] or dnadiff [options] -d

Try 'dnadiff -h' for more information.