Originally posted by skatrinli
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Code:
stats.sh in=foo bar.fa Exception in thread "main" java.lang.RuntimeException: Unknown parameter bar.fa at jgi.AssemblyStats2.<init>(AssemblyStats2.java:166) at jgi.AssemblyStats2.main(AssemblyStats2.java:39)
Code:
stats.sh in="foo bar.fa" Exception in thread "main" java.lang.RuntimeException: Unknown parameter bar.fa at jgi.AssemblyStats2.<init>(AssemblyStats2.java:166) at jgi.AssemblyStats2.main(AssemblyStats2.java:39)
Code:
stats.sh in="foo\ bar.fa" A C G T N IUPAC Other GC GC_stdev NaN NaN NaN NaN NaN NaN NaN NaN 0.0000 Main genome scaffold total: 0 Main genome contig total: 0 Main genome scaffold sequence total: 0.000 MB Main genome contig sequence total: 0.000 MB NaN% gap Main genome scaffold N/L50: 0/0 Main genome contig N/L50: 0/0 Main genome scaffold N/L90: 0/0 Main genome contig N/L90: 0/0 Max scaffold length: 0 Max contig length: 0 Number of scaffolds > 50 KB: 0 % main genome in scaffolds > 50 KB: 0.00% Minimum Number Number Total Total Scaffold Scaffold of of Scaffold Contig Contig Length Scaffolds Contigs Length Length Coverage -------- -------------- -------------- -------------- -------------- --------
The exact way to deal with spaces is system-specific. In the normal Windows shell you can just use quotes; in Linux bash it looks like you need quotes and an escape character (backslash); in Windows under a Linux emulator I'm not entirely sure. The easiest thing to do is to put files in a path that does not have any spaces (so, not in My Documents, but in C:\data\ or something like that.)
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