Hi Fei Shi, It looks like your auto_blast.pl is not set up to run on Windows. Those are UNIX system commands that it's erroring on (rm, cp, cat).
On Tue, Aug 18, 2009 at 3:39 PM, Fei Shi<justfly2...@gmail.com> wrote: > Hi, Dear perl experts: > > I am a new hand of perl. I use perl because I am trying to use a > package called "miRDeep". I install the activeperl 5.10 for windows. Then I > used the MS DOS to try perl. > > But there is an error coming out when I tried to run this command > their demo: "perl auto_blast.pl 454_aligned.fa precursors. fa-b > > signatures". > > The error message is as follows: > Copying subject file 'cp' is not recognized as an internal or external > command, operable program or batch file. > formatting subject file [NULL_Caption] ERROR: Could not open > blast_dir_temp/file_subject > > Blasting query file against subject file > [NULL_Caption] WARNING: readdb: wrong version of formatdb was used to make > database blast_dir_temp/file_subject. > [NULL_Caption] WARNING: bartel_100023_x1: readdb: wrong version of formatdb > was used to make database blast_dir_temp/file_subject. > Parsing blast output: > 'cat' is not recognized as an internal or external command, > operable program or batch file. > 'cat' is not recognized as an internal or external command, > operable program or batch file. > 'cat' is not recognized as an internal or external command, > operable program or batch file. > 'rm' is not recognized as an internal or external command, > operable program or batch file. > 'rm' is not recognized as an internal or external command, > operable program or batch file. > > But I think the perl code "auto_blast.pl" is tested maturely by the author > of the package so I am suspicious that there may be something wrong with my > system? > The MS DOS is 5.1.2600 by windows XP. I wonder if the above error message > due to this or other reasons? I really appreciate if someone can point me > out of this and give me a clue of the problem. > > Thank you very much for your time. > > Sincerely, > Fei > > _______________________________________________ > Perl-Win32-Users mailing list > Perl-Win32-Users@listserv.ActiveState.com > To unsubscribe: http://listserv.ActiveState.com/mailman/mysubs > > _______________________________________________ Perl-Win32-Users mailing list Perl-Win32-Users@listserv.ActiveState.com To unsubscribe: http://listserv.ActiveState.com/mailman/mysubs
