I have used Trimmomatic-0.39 few times already for trimming some sequencing data. This time I tried the option -baseout as stated in the manual but it does not recognise it as a valid option and the command does not run. If I run the command, as I usually I do with all the output files listed, it works though.
I type in the command line:
java -jar trimmomatic-0.39.jar PE -phred33 -trimlog trimmed_file18_log.log -baseout file18.fastq.gz file18-R1.fastq.gz file18-R2.fastq.gz ILLUMINACLIP:NexteraPE-PE.fa:2:30:10 MAXINFO:25:0.2 MINLEN:20
What I get back is:
Unknown option -baseout file18.fastq.gz
Usage:
PE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-summary <statsSummaryFile>] [-quiet] [-validatePairs] [-basein <inputBase> | <inputFile1> <inputFile2>] [-baseout <outputBase> | <outputFile1P> <outputFile1U> <outputFile2P> <outputFile2U>] <trimmer1>...
or: .....
I get back the same error message even if I move the '-baseout file18.fastq.gz' option after '...jar PE' and before the list of all the other options.
I use the Linux kernel style in my C code, even though it's not related to the kernel. Running checkpatch.pl produces ERROR: Missing Signed-off-by: line(s). How to ignore it?
To intentionally silence the ERROR: Missing Signed-off-by: line(s) one can pass the --no-signoff parameter, e.g.:
git show | checkpatch.pl --no-tree --no-signoff
This can also be added on a new line to the .checkpatch.conf file to avoid having to type it.
Whenever I start Atom it opens two files, one called:
ATOM_DISABLE_SHELLING_OUT_FOR_ENVIRONMENT=false
And the other one:
/usr/bin/atom
It's really annoying and I don't understand how to fix it. From what I understand it is some sort of environment configuration bug, but I can't find what's causing it.
I am going to make several assumptions. You are running on Ubuntu and you've installed Atom via Snap.
If these assumptions are correct the cause of the issue is a misconfigured application menu item from the Snap package author.
To fix it you just need to run this command:
sudo sed -i 's/Exec=env BAMF_DESKTOP_FILE_HINT=\/var\/lib\/snapd\/desktop\/applications\/atom_atom.desktop \/snap\/bin\/atom ATOM_DISABLE_SHELLING_OUT_FOR_ENVIRONMENT=false \/usr\/bin\/atom %F/Exec=env BAMF_DESKTOP_FILE_HINT=\/var\/lib\/snapd\/desktop\/applications\/atom_atom.desktop ATOM_DISABLE_SHELLING_OUT_FOR_ENVIRONMENT=false \/snap\/bin\/atom %F/' /var/lib/snapd/desktop/applications/atom_atom.desktop
TL;DR {
Here is a detailed explanation of what's causing the issue and what the command above does. It may be useful if the file has been changed since the answer was written.
The actual cause for the bug is that this menu item file:
/var/lib/snapd/desktop/applications/atom_atom.desktop
It has a typo in it and what should be environment variables are set after calling
the atom executable, resulting in Atom treating it as arguments in the form of
files that it should open.
# ▼ Executable ▼ Not an environment variable ▼ Not an executable
Exec=env BAMF_DESKTOP_FILE_HINT=/var/lib/snapd/desktop/applications/atom_atom.desktop /snap/bin/atom ATOM_DISABLE_SHELLING_OUT_FOR_ENVIRONMENT=false /usr/bin/atom %F
It should instead be:
# ▼ Environment variable ▼ Environment variable ▼ Executable
Exec=env BAMF_DESKTOP_FILE_HINT=/var/lib/snapd/desktop/applications/atom_atom.desktop ATOM_DISABLE_SHELLING_OUT_FOR_ENVIRONMENT=false /snap/bin/atom %F
The solution above uses sed to search and replace the file and fix the issue.
}
NOTE: The command will work until the Snap author updates the menu item file (.desktop) when hopefully the issue would have been resolved.
I'm getting this on the console in a QML app:
QFont::setPointSizeF: Point size <= 0 (0.000000), must be greater than 0
The app is not crashing so I can't use the debugger to get a backtrace for the exception. How do I see where the error originates from?
If you know the function the warning occurs in (in this case, QFont::setPointSizeF()), you can put a breakpoint there. Following the stack trace will lead you to the code that calls that function.
If the warning doesn't include the name of the function and you have the source code available, use git grep with part of the warning to get an idea of where it comes from. This approach can be a bit of trial and error, as the code may span more than one line, etc, and so you might have to try different parts of the string.
If the warning doesn't include the name of the function, you don't have the source code available and/or you don't like the previous approach, use the QT_MESSAGE_PATTERN environment variable:
QT_MESSAGE_PATTERN="%{function}: %{message}"
For the full list of variables at your disposal, see the qSetMessagePattern() docs:
%{appname} - QCoreApplication::applicationName()
%{category} - Logging category
%{file} - Path to source file
%{function} - Function
%{line} - Line in source file
%{message} - The actual message
%{pid} - QCoreApplication::applicationPid()
%{threadid} - The system-wide ID of current thread (if it can be obtained)
%{qthreadptr} - A pointer to the current QThread (result of QThread::currentThread())
%{type} - "debug", "warning", "critical" or "fatal"
%{time process} - time of the message, in seconds since the process started (the token "process" is literal)
%{time boot} - the time of the message, in seconds since the system boot if that can be determined (the token "boot" is literal). If the time since boot could not be obtained, the output is indeterminate (see QElapsedTimer::msecsSinceReference()).
%{time [format]} - system time when the message occurred, formatted by passing the format to QDateTime::toString(). If the format is not specified, the format of Qt::ISODate is used.
%{backtrace [depth=N] [separator="..."]} - A backtrace with the number of frames specified by the optional depth parameter (defaults to 5), and separated by the optional separator parameter (defaults to "|"). This expansion is available only on some platforms (currently only platfoms using glibc). Names are only known for exported functions. If you want to see the name of every function in your application, use QMAKE_LFLAGS += -rdynamic. When reading backtraces, take into account that frames might be missing due to inlining or tail call optimization.
On an unrelated note, the %{time [format]} placeholder is quite useful to quickly "profile" code by qDebug()ing before and after it.
I think you can use qInstallMessageHandler (Qt5) or qInstallMsgHandler (Qt4) to specify a callback which will intercept all qDebug() / qInfo() / etc. messages (example code is in the link). Then you can just add a breakpoint in this callback function and get a nice callstack.
Aside from the obvious, searching your code for calls to setPointSize[F], you can try the following depending on your environment (which you didn't disclose):
If you have the debugging symbols of the Qt libs installed and are using a decent debugger, you can set a conditional breakpoint on the first line in QFont::setPointSizeF() with the condition set to pointSize <= 0. Even if conditional breakpoints don't work you should still be able to set one and step through every call until you've found the culprit.
On Linux there's the tool ltrace which displays all calls of a binary into shared libs, and I suppose there's something similar in the M$ VS toolbox. You can grep the output for calls to setPointSize directly, but of course this won't work for calls within the lib itself (which I guess could be the case when it handles the QML internally).
Here is a basic script with getopt command and assigned variables.
If someone were to type in
MyScript -a
with no words or numbers added after the -a, then an error message would pop up! The same happens if you replace -a with any other assigned variables. If I wanted no error message to appear, how would I go about doing this?
Hints/advice is preferred over a simply strict answer!
From the bash manual:
getopts can report errors in two ways. If the first character of optstring is a colon, silent error reporting is used. In normal operation diagnostic messages are printed when invalid options or missing option arguments are encountered. If the variable OPTERR is set to 0, no error messages will be displayed, even if the first character of optstring is not a colon.
Since you tag the question with Unix and don't mention bash, you may or may not be so lucky, but the answer is to read the manual page carefully.