-e line 1

Ignoramus1 has asked for the wisdom of the Perl Monks concerning the following question:

Working on Windows 8 x64 system and continue to run into multiple errors. Copy of command prompt commands and errors listed bellow. Any help would be greatly appreciated.

C:\Desktop\MSP Project Working Folder\MSP-forward>perl tagcl eaner.pl -minlen 100 -nomatch 3 -verbose -64 -trim_within 100 -log -fastq msp898 3_F09R08.fastq -out tagcleaner_out/msp8983_F09R08_4M2_SWS6.15F -tag5 ACGCTCGACAA AAGCACATTTAATTCATTATCC -tag3 ATGAGTTTCTGGGGTGCTACTACAGTGCT

Can't find string terminator "'" anywhere before EOF at -e line 1.

ERROR: input file for -fastq is in UNKNOWN format not in FASTQ format. Try 'perl tagcleaner.pl -h' for more information. Exit program.

ERROR: Can't open file : No such file or directory

C:\Desktop\MSP Project Working Folder\MSP-forward>perl -e ta gcleaner.pl -minlen 100 -nomatch 3 -verbose -64 -trim_within 100 -log -fastq msp 8983_F09R08.fastq -out tagcleaner_out/msp8983_F09R08_4M2_SWS6.15F -tag5 ACGCTCGA CAAAAGCACATTTAATTCATTATCC -tag3 ATGAGTTTCTGGGGTGCTACTACAGTGCT

Can't locate inlen.pm in @INC (@INC contains:

C:/Strawberry/perl/site/lib C:/Str awberry/perl/vendor/lib C:/Strawberry/perl/lib .). BEGIN failed--compilation aborted.

C:\Desktop\MSP Project Working Folder\MSP-forward>perl -e "t agcleaner.pl -minlen 100 -nomatch 3 -verbose -64 -trim_within 100 -log -fastq ms p8983_F09R08.fastq -out tagcleaner_out/msp8983_F09R08_4M2_SWS6.15F -tag5 ACGCTCG ACAAAAGCACATTTAATTCATTATCC -tag3 ATGAGTTTCTGGGGTGCTACTACAGTGCT"

Number found where operator expected at -e line 1, near "minlen 100" (Do you need to predeclare minlen?)

Number found where operator expected at -e line 1, near "nomatch 3" (Do you need to predeclare nomatch?)

Number found where operator expected at -e line 1, near "trim_within 100" (Do you need to predeclare trim_within?)

syntax error at -e line 1, near "minlen 100"

Search pattern not terminated at -e line 1.

Comment on -e line 1

Replies are listed 'Best First'.
Re: -e line 1 by stevieb (Canon) on May 29, 2015 at 00:25 UTC
How are we to troubleshoot code issues when you haven't specified even a line of code of the script(s) you're trying to run? Not only that, it looks like you're mangling your command line repeatedly. Put together a single command string (the proper one), and combine it with the output in <code></code> tags. Do the same with the code in the script itself. -stevieb	[reply]
Re: -e line 1 by kensaigm (Hermit) on May 29, 2015 at 00:45 UTC
It would appear after looking at the author’s website that the standalone version is designed for *nix environments. I found the following listed. Hardware - Computer with a Linux/Unix or Mac OS X operating system There is an alternative version that uses a web interface that you might find more suited to your windows environment.	[reply]
Re: -e line 1 by 2teez (Vicar) on May 29, 2015 at 00:56 UTC
Hi Ignoramus1, Welcome to the Monastery. I think you might have to look at perlrun to start with. If you tell me, I'll forget. If you show me, I'll remember. if you involve me, I'll understand. --- Author unknown to me	[reply]
Re: -e line 1 by ikegami (Patriarch) on May 29, 2015 at 15:29 UTC
`-e` allows Perl code to be specified on the command line. `perl -e"perl code to execute here" args` [download] You're not doing that, so you shouldn't be using `-e` `perl file_containing_perl_code.pl args` [download]	[reply] [d/l] [select]