That is not Perl. The membrane-thin wrapper of Perl serves literally no purpose. That is nothing but shell code. If you write the loop inside shell you'll save so much trouble and CPU time.
I too made this error when first learning to program in Perl and shell. Learn a little more shell and it will make more sense.
You can also split across multiple lines for readability by putting backslash-newline wherever you need to split it.
Code:
while read LINE
do
echo perl table_annovar.pl -vcfinput "$LINE" humandb/ -buildver hg19 -arg '-hgvs',,,,, -remove -protocol \
IDP.refGene,avsnp147,popfreq_all_20150413,spidex,dbnsfp33a,clinvar_20161128 \
-operation g,f,f,f,f,f -otherinfo -nastring .
done < target.txt
Remove the echo once you've tested and made sure it does what you want.
Last edited by Corona688; 02-02-2017 at 11:32 AM..
Hi,
while running the perl script i am getting this error message ,
Day '' out of range 1..31 at rsty.sh line 44
what do iam missing in the script, any suggestion
#!/usr/bin/perl
use Time::Local;
my $wday = $ARGV;
my $month = $ARGV;
# convert the month shortname into 0-11 number
if... (4 Replies)
This just started happening.
I use the rcp command to copy a file from one server to another.
Now when I use the command, every other time I execute the exact same command I get the error: remshd: login correct
Example:
1. rcp testfile server2:/db/tmp (Work ok, verified file... (6 Replies)
so in unix this command works works and shows me a list of directories
find . -name \*.xls -exec dirname {} \; | sort -u | > list.txt
but when i try running a perl script to run this command
my $query = 'find . -name \*.xls -exec dirname {} \; | sort -u | > list.txt';... (2 Replies)
I have a script which outputs some timing data a line at a time. There are approx. 10 lines echoed, each line looks something like this:
0.741 http://checkip.dyndns.org 94.170.119.226Since I needed to add all the values in the first column, I piped the output to grep, matching and printing the... (7 Replies)
Hi All,
This command works when I type it on but when I run the batch file it doesn't..any ideas why?
attrib.exe * | find /c /v "" >filecount.txt (1 Reply)
Hi
I have an ftp script which works fine when i execute through a test scheduler(UC4), but when i run it through the prod scheduler(UC4), it hungs indefinetely, when we cancel the job and re-run it it works perfectly fine. here is the code,, any idea why this is happening ????
... (1 Reply)
I would like to be able to display the local time (or anytime for that matter) when I run Xentop in batch mode. Is that possible? (In other words, when I look back at the data, I want to be able to tell what time that the output was displayed). (2 Replies)
I ran this script yesterday (in the background)
/usr/bin/nohup myfilelocation/myscriptname.sh &
the script worked perfectly.
i ran it today (also in the background) and just sat there. So i killed it and ran it normally and it worked perfectly.
Anyone suggest why it just sat there and... (8 Replies)
Discussion started by: twinion
8 Replies
LEARN ABOUT LINUX
qrerun
QRERUN(P) POSIX Programmer's Manual QRERUN(P)
NAME
qrerun - rerun batch jobs
SYNOPSIS
qrerun job_identifier ...
DESCRIPTION
To rerun a batch job is to terminate the session leader of the batch job, delete any associated checkpoint files, and return the batch job
to the batch queued state. A batch job is rerun by a request to the batch server that manages the batch job. The qrerun utility is a user-
accessible batch client that requests the rerunning of one or more batch jobs.
The qrerun utility shall rerun those batch jobs for which a batch job_identifier is presented to the utility.
The qrerun utility shall rerun batch jobs in the order in which their batch job_identifiers are presented to the utility.
If the qrerun utility fails to process any batch job_identifier successfully, the utility shall proceed to process the remaining batch
job_identifiers, if any.
The qrerun utility shall rerun batch jobs by sending a Rerun Job Request to the batch server that manages each batch job.
For each successfully processed batch job_identifier, the qrerun utility shall have rerun the corresponding batch job at the time the util-
ity exits.
OPTIONS
None.
OPERANDS
The qrerun utility shall accept one or more operands that conform to the syntax for a batch job_identifier (see Batch Job Identifier ).
STDIN
Not used.
INPUT FILES
None.
ENVIRONMENT VARIABLES
The following environment variables shall affect the execution of qrerun:
LANG Provide a default value for the internationalization variables that are unset or null. (See the Base Definitions volume of
IEEE Std 1003.1-2001, Section 8.2, Internationalization Variables for the precedence of internationalization variables used to
determine the values of locale categories.)
LC_ALL If set to a non-empty string value, override the values of all the other internationalization variables.
LC_CTYPE
Determine the locale for the interpretation of sequences of bytes of text data as characters (for example, single-byte as opposed to
multi-byte characters in arguments).
LC_MESSAGES
Determine the locale that should be used to affect the format and contents of diagnostic messages written to standard error.
LOGNAME
Determine the login name of the user.
ASYNCHRONOUS EVENTS
Default.
STDOUT
None.
STDERR
The standard error shall be used only for diagnostic messages.
OUTPUT FILES
None.
EXTENDED DESCRIPTION
None.
EXIT STATUS
The following exit values shall be returned:
0 Successful completion.
>0 An error occurred.
CONSEQUENCES OF ERRORS
In addition to the default behavior, the qrerun utility shall not be required to write a diagnostic message to standard error when the
error reply received from a batch server indicates that the batch job_identifier does not exist on the server. Whether or not the qrerun
utility waits to output the diagnostic message while attempting to locate the job on other servers is implementation-defined.
The following sections are informative.
APPLICATION USAGE
None.
EXAMPLES
None.
RATIONALE
The qrerun utility allows users to cause jobs in the running state to exit and rerun.
The qrerun utility is a new utility, vis-a-vis existing practice, that has been defined in this volume of IEEE Std 1003.1-2001 to correct
user-perceived deficiencies in the existing practice.
FUTURE DIRECTIONS
None.
SEE ALSO
Batch Environment Services
COPYRIGHT
Portions of this text are reprinted and reproduced in electronic form from IEEE Std 1003.1, 2003 Edition, Standard for Information Technol-
ogy -- Portable Operating System Interface (POSIX), The Open Group Base Specifications Issue 6, Copyright (C) 2001-2003 by the Institute of
Electrical and Electronics Engineers, Inc and The Open Group. In the event of any discrepancy between this version and the original IEEE
and The Open Group Standard, the original IEEE and The Open Group Standard is the referee document. The original Standard can be obtained
online at http://www.opengroup.org/unix/online.html .
IEEE /The Open Group 2003 QRERUN(P)