I have made a .tcl file to simulate Gossiping-based Ad Hoc Routing. When I try to run it using NS 2.35 I am getting the following error:
xgridsz=, ygridsz=
Sim.: utime/stime: 67 10 stack/heap: -4192 4591616
num_nodes is set 0
warning: Please use -channel as shown in tcl/ex/wireless-mitf.tcl
couldn't read file "": no such file or directory
while executing
"source.orig {}"
("uplevel" body line 1)
invoked from within
"uplevel source.orig [list $fileName]"
invoked from within
"if [$instance_ is_http_url $fileName] {
set buffer [$instance_ read_url $fileName]
uplevel eval $buffer
} else {
uplevel source.orig [list $fileName]
..."
(procedure "source" line 8)
invoked from within
"source $val(cp)"
(file "simAODVG.tcl" line 155)
The link of my tcl file is given below:
https://drive.google.com/file/d/0B1OEPsG0ILELSHhMQzZQdW5STW8/view?usp=sharing
How will I solve this?
Line 155 , "" :
couldn't read file "": no such file or directory
Answer : "" is defined in line 18 : set val(cp) [lindex $argv 1]
...... and argv 1 seems not to be defined anywhere ?
Related
I am writing a bwa mapping module using nextflow (dsl=2), modules/map_reads.nf to map single-end reads. When I execute this workflow it does not return error from the terminal and it also output bam files with the correct file names. However, I found that the bam files are not correctly mapped and I also found in .command.err an error:
[E::bwa_idx_load_from_disk] fail to locate the index files
I have checked the paths are correct and also execute shell command directly in terminal.
I appreciate any suggestions or solution to this problem.
modules/map_reads.nf
#!/usr/bin/env nextflow
nextflow.enable.dsl=2
process mapping {
conda 'envs/bwa.yml'
publishDir 'results/mapped', mode: 'copy'
input:
tuple val(sample_id), file(fastq)
file index
output:
tuple val(sample_id), file('*.bam')
script:
"""
bwa mem $index $fastq | samtools view -b - > ${sample_id}.bam
"""
}
workflow {
fastq_data = channel.fromPath( 'data/samples/*.fastq' ).map { file -> tuple(file.baseName, file) }
index = channel.fromPath( 'data/genome.fa' )
mapping( fastq_data, index )
}
Here is my directory structure:
envs/bwa.yml
name: bwa
channels:
- bioconda
- defaults
dependencies:
- bwa
- samtools=1.9
[E::bwa_idx_load_from_disk] fail to locate the index files
BWA MEM is expecting a number of index files to be provided with it's first argument, but you've only localized the genome FASTA file:
index = channel.fromPath( 'data/genome.fa' )
BWA MEM only requires the actual index files. I.e. it doesn't require the FASTA file (or FASTA index), so you can save some time and resources by skipping the localization of the FASTA (this is especially relevant if you localize from s3 for example, since the FASTA file is often a couple of gigabytes). Also ensure you use a value channel here, so that the channel can be used an unlimited number of times:
process mapping {
conda 'envs/bwa.yml'
publishDir 'results/mapped', mode: 'copy'
input:
tuple val(sample_id), path(fastq)
path bwa_index
output:
tuple val(sample_id), path("${sample_id}.bam")
script:
def idxbase = bwa_index[0].baseName
"""
bwa mem "${idxbase}" "${fastq}" | samtools view -b - > "${sample_id}.bam"
"""
}
workflow {
fastq_data = channel.fromPath( 'data/samples/*.fastq' ).map { file ->
tuple(file.baseName, file)
}
bwa_index = file( 'data/genome.fa.{,amb,ann,bwt,pac,sa}' )
mapping( fastq_data, bwa_index )
}
Also, the reason you didn't see an error on the command line is that, by default, the return value of a pipeline is the exit status of the last command. In your BWA MEM SAMtools pipeline, the last command (i.e. samtools) completes successfully and returns exit status zero. The option you want to add is called 'pipefail', man bash:
pipefail
If set, the return value of a pipeline is the value of the
last (rightmost) command to exit with a non-zero status, or zero if
all commands in the pipeline exit successfully. This option is
disabled by default.
Usually, you can just add the following to your nextflow.config to have it applied to all processes:
process {
shell = [ '/bin/bash', '-euo', 'pipefail' ]
}
I use windows 7 pro service pack 1.
I have the following code in the post build event :
SET VAR1=BLABLA
ECHO %VAR1% > Test.txt
It wont work. In the file, i get «command echo activated» (translated from french).
Embarcadero documentation says that i can use any valid dos command in those events.
If i just use :
ECHO BLABLA > Test.txt
It works, no problem. Is this a bug or there is a problem with % character ? % is an ascii char so i dont even know what could be the problem.
ty for your help.
% is used in cmd to delimit variablenames when the value of the variable is required, hence echo %var1% > test.txt will write the current value of the environment variable var1 to the file.
If var1 is not defined at the time, it will report the echo status (Echo is on/off`.
This can be circumvented by using echo(%var1% - the ( modifies echo's behaviour to not report the echo status if the arguments are resolved to nothing.
If you want to echo a literal % then you need to escape the % with another %. cmd normally uses ^ to escape symbols with a special meaning - % is the exception; %% to echo a literal %.
BTW - the space between the string to be echoed and the redirector will be output to the file. To prevent this, use > test.txt echo %var1% Note that > creates a file anew. >> will create or append if the file already exists. The space between the redirector and the filename is optional.
However, it's important when using batch to post exactly the code that's in use.
SET VAR1=BLABLA
ECHO %VAR1% > Test.txt
will work happily.
SET VAR1 = BLABLA
ECHO %VAR1% > Test.txt
will not because this latter code sets a variable named "var1Space"
On my 10.2.1 system, I've tried the code as published.
The actual code that's executed is
SET VAR1=BLABLA&ECHO %VAR1% > Test.txt
not
SET VAR1=BLABLA
ECHO %VAR1% > Test.txt
as shown in the "Build events commands" window.
This will not work because the entire line is executed as published on the "build events" page - SET VAR1=BLABLA&ECHO %VAR1% > Test.txt which will be interpreted by cmd after cmd performs its standard parsing routine.
cmd replaces any %var% with the actual value at parse time, not at run time hence as var1 has no value when the line SET VAR1=BLABLA&ECHO %VAR1% > Test.txt is parsed, the code is executed as SET VAR1=BLABLA&ECHO > Test.txt hence the problem encountered.
To cure this, you need to use
SET VAR1=BLABLA&call ECHO %%VAR1%% > Test.txt
where cmd will execute the parsed-ECHO command in a subshell. % is the escape character for % so the subshell executes ECHO %VAR1% > Test.txt after var1 has been set.
I'd suggest you raise this as a problem with EMBT. Batch commands cannot be strung together with & without side-effects. The code entered into the "Build events commands" window should be executed without reformatting - just written to a (temporary) batch file and the batch file then executed.
No doubt the eager downvoters will support the resolution of this problem.
my build steps:
cd $WORKSPACE
export TERM="linux"
. venv/bin/activate
pylint --rcfile=pylint.cfg $(find handlers -maxdepth 1 -name "*.py" -print) > pylint.log || exit 0
result of pylint.log:
************* Module handlers
C: 1, 0: Missing module docstring (missing-docstring)
C: 8, 0: Missing function docstring (missing-docstring)
************* Module handlers.foo
C: 1, 0: Black listed name "foo" (blacklisted-name)
C: 1, 0: Missing module docstring (missing-docstring)
C: 1, 0: Missing function docstring (missing-docstring)
E: 2,11: Undefined variable 'a' (undefined-variable)
E: 2,13: Undefined variable 'b' (undefined-variable)
Report
======
...
(the report continues with statistics by type, raw metrics, external dependencies)
the xml filename pattern for pylint is:
**/pylint.log
with the source path pattern being:
**/
Even after all this, and with pylint.log showing I have lint errors, the graph shows nothing.
any ideas how to get pylint and the violations plugin working nicely together?
it seems the correct pylint command is the following:
pylint --rcfile=pylint.cfg $(find handlers -maxdepth 1 -name "*.py" -print) --msg-template="{path}:{line}: [{msg_id}({symbol}), {obj}] {msg}" > pylint.log || exit 0
note the addition of the --msg-template param
I had this problem myself. I think it was a result of the way I installed the Violations plugin. It worked after restarting Jenkins:
$ sudo service jenkins restart
I created a file ~/mayhemnum.txt, I tried to add the line number of the word mayhem from the file /usr/share/dict/words as its only word. This was the command I used and it didn't work. I did check the correct line number for the word and its 5.
echo "5" > ~/mayhemnum.txt
echo 5 > ~/mayhemnum.txt
this was the correct command that worked
I can't figure out how to get my audio extractor script working via commandline arguments on ahk. I know the command line argument is correct, as I'm able to get it working through a batch file, but I keep getting the error below. I think I'm probably doing something wrong syntactically but I just can't figure out what.
I'd really appreciate any help. Thanks.
Error: the following variable name contains an illegal character"
channels=2,samplerate=44100}:standard{access="file",mux=dummy,dst="%A_LoopField%.mp3"}
Code:
fileselectfile, File_Name, M3
SplitPath, File_Name, name
Loop, parse, name, `n
if a_index = 2
{
msgbox, %A_LoopField%
Run, "C:\Program Files\VideoLAN\VLC\vlc.exe" "-I dummy -v %File_Name% :sout=#transcode{vcodec=none,acodec=mp3,ab=128,channels=2,samplerate=44100}:standard{access="file",mux=dummy,dst="%A_LoopField%.mp3"}"
}
Here is the original batch code if you're curious about the audio extraction function I was talking about
#ECHO OFF
REM Loop through files (Recurse subfolders)
REM Syntax
REM FOR /R [[drive:]path] %%parameter IN (set) DO command
REM
REM Key
REM drive:path : The folder tree where the files are located.
REM
REM set : A set of one or more files. Wildcards must be used.
REM If (set) is a period character (.) then FOR will
REM loop through every folder.
REM
REM command : The command(s) to carry out, including any
REM command-line parameters.
REM
REM %%parameter : A replaceable parameter:
REM in a batch file use %%G (on the command line %G)
FOR /R %%G IN (*.mp3) DO (CALL :SUB_VLC "%%G")
FOR /R %%G IN (*.mp3.mp*) DO (CALL :SUB_RENAME "%%G")
GOTO :eof
:SUB_VLC
SET _firstbit=%1
SET _qt="
CALL SET _newnm=%%_firstbit:%_qt%=%%
SET _commanm=%_newnm:,=_COMMA_%
REM echo %_commanm%
ECHO Transcoding %1
REM Here's where the actual transcoding/conversion happens. The next line
REM fires off a command to VLC.exe with the relevant arguments:
CALL "C:\Program Files\VideoLAN\VLC\vlc" -I dummy -v %1 :sout=#transcode{vcodec=none,acodec=mp3,ab=128,channels=2,samplerate=44100}:standard{access="file",mux=dummy,dst="%_commanm%.mp3"} vlc://quit
REM Having no SLEEP-esque command, we have to trick DOS/Windows into pausing
REM for a bit between encode ops - To give the host OS a chance to do what it
REM needs to - Via clever use of the PING utility:
REM (Thanks to http://www.computing.net/answers/programming/dos-command-for-wait-5-seconds/11192.html for the tip! :-)
PING -n 1 -w 10000 1.1.1.1 > NUL
GOTO :eof
:SUB_RENAME
SET _origfnm=%1
SET _endbit=%_origfnm:*.mp3=%
CALL SET _newfilenm=%%_origfnm:.mp3%_endbit%=.mp3%%
SET _newfilenm=%_newfilenm:_COMMA_=,%
COPY %1 %_newfilenm%
GOTO :eof
:eof
REM My own little addition to prevent the batch window from "vanishing" without
REM trace at the end of execution, as if a critical error had occurred.
PAUSE
Have you tried without the SplitPath, File_Name, name? I got rid of the error like this, but I don't know if it produces the result you want in the end.
I found the answer. I was making syntatical errors I just didn't have the knowledge to fix myself. The new RUN statement works perfectly.
Here is the newly revised script
fileselectfile, File_Name, M3
SplitPath, File_Name, name, dir, ext, name_no_ext, drive
StringReplace, File_Name, File_Name,`n, \
Loop, parse, name, `n
{if a_index = 2
msgbox, %A_LoopField%
Run % "C:\Program Files\VideoLAN\VLC\vlc.exe -I dummy -v """ File_Name """ :sout=#transcode{vcodec=none,acodec=mp3,ab=128,channels=2,samplerate=44100}:standard{access=""file"",mux=dummy,dst=""" A_LoopField ".mp3""} "
}