Before trying to assemble sequence data, I get a file size estimate for my raw READ1/READ2 files by running the command ls -l -h from the directory the files are in. The output looks something like this:
-rwxrwxrwx# 1 catharus2021 staff 86M Jun 11 15:03 pluvialis-dominica_JJW362-READ1.fastq.gz
-rwxrwxrwx# 1 catharus2021 staff 84M Jun 11 15:03 pluvialis-dominica_JJW362-READ2.fastq.gz
For a previous run using the identical command, but a different batch of data, the output was as such:
-rwxr-xr-x 1 catharus2021 staff 44M Mar 16 2018 lagopus_lagopus_alascensis_JJW1970_READ1.fastq.gz
-rwxr-xr-x 1 catharus2021 staff 52M Mar 16 2018 lagopus_lagopus_alascensis_JJW1970_READ2.fastq.gz
It doesn't seem to be affecting any downstream commands, but does anyone know why the strings at the very beginning (-rwxrwxrx# vs. -rwxr-xr-x) are different? I assume that they're permissions flags, but google has been less-than-informative when I try to type those in and search.
Thanks in advance for your time.
The coding describes who can access a file in which way. It is oredred:
owner - group - world
rwxr-xr-x
user can read, write and execute
group can only read and execute
world can only read and execute
This prevents that other people can overwrite your data. If you change to
rwxrwxrwx
Everybody can overwrite your data.
Related
I am looking for a way to show the results of the file "tcp-variants-comparison.cc" under ns3 (3.28) used with Ubuntu 18.04.
I found here an old topic from 2013, but it seems not to work correctly in my current environment.
P.S: I am a newbie in ns3, so i will appreciate any help.
regards
cedkhader
Running ./waf --run "tcp-variants-comparison --tracing=1" yields the following files:
-rw-rw-r-- 1 112271415 Aug 5 15:52 TcpVariantsComparison-ascii
-rw-rw-r-- 1 401623 Aug 5 15:52 TcpVariantsComparison-cwnd.data
-rw-rw-r-- 1 1216177 Aug 5 15:52 TcpVariantsComparison-inflight.data
-rw-rw-r-- 1 947619 Aug 5 15:52 TcpVariantsComparison-next-rx.data
-rw-rw-r-- 1 955550 Aug 5 15:52 TcpVariantsComparison-next-tx.data
-rw-rw-r-- 1 38 Aug 5 15:51 TcpVariantsComparison-rto.data
-rw-rw-r-- 1 482134 Aug 5 15:52 TcpVariantsComparison-rtt.data
-rw-rw-r-- 1 346427 Aug 5 15:52 TcpVariantsComparison-ssth.data
You can use other command line arguments to generate the desired output, see list below.
Program Arguments:
--transport_prot: Transport protocol to use: TcpNewReno, TcpHybla, TcpHighSpeed, TcpHtcp, TcpVegas, TcpScalable, TcpVeno, TcpBic, TcpYeah, TcpIllinois, TcpWestwood, TcpWestwoodPlus, TcpLedbat [TcpWestwood]
--error_p: Packet error rate [0]
--bandwidth: Bottleneck bandwidth [2Mbps]
--delay: Bottleneck delay [0.01ms]
--access_bandwidth: Access link bandwidth [10Mbps]
--access_delay: Access link delay [45ms]
--tracing: Flag to enable/disable tracing [true]
--prefix_name: Prefix of output trace file [TcpVariantsComparison]
--data: Number of Megabytes of data to transmit [0]
--mtu: Size of IP packets to send in bytes [400]
--num_flows: Number of flows [1]
--duration: Time to allow flows to run in seconds [100]
--run: Run index (for setting repeatable seeds) [0]
--flow_monitor: Enable flow monitor [false]
--pcap_tracing: Enable or disable PCAP tracing [false]
--queue_disc_type: Queue disc type for gateway (e.g. ns3::CoDelQueueDisc) [ns3::PfifoFastQueueDisc]
--sack: Enable or disable SACK option [true]
in ns3.36.1 I used this command
./ns3 run examples/tcp/tcp-variants-comparison.cc -- --tracing=1
and output look like this
TcpVariantsComparison-ascii
TcpVariantsComparison-cwnd.data
TcpVariantsComparison-inflight.data
TcpVariantsComparison-next-rx.data
TcpVariantsComparison-next-tx.data
TcpVariantsComparison-rto.data
TcpVariantsComparison-rtt.data
TcpVariantsComparison-ssth.data
I'm learning how to develop Kde Plasma 5 plasmoids, and testing it with a small widget, consistent of just two qmls. I read some information sources, like https://techbase.kde.org or https://api.kde.org/frameworks/ and created a package structure and sources for my test plasmoid, which looks like this:
$ ls -lR test
test:
total 8
drwxr-xr-x 3 alberto alberto 4096 nov 26 14:28 contents
-rw-r--r-- 1 alberto alberto 459 nov 26 14:28 metadata.desktop
test/contents:
total 4
drwxr-xr-x 2 alberto alberto 4096 nov 26 14:33 ui
test/contents/ui:
total 8
-rw-r--r-- 1 alberto alberto 275 nov 26 14:28 main.qml
-rw-r--r-- 1 alberto alberto 465 nov 26 14:33 RootContainer.qml
The RootContainer is just the fullRepresentation of the widget, and contains only a label with the text "prueba1". So, as i read in the documentation, i used the command plasmapkg2 to install the widget as follows:
$ plasmapkg2 --install test
pluginname: "org.matrixland.test"
Generated "/home/xxx/.local/share/plasma/plasmoids//kpluginindex.json" ( 3 plugins)
/home/xxx/Programación/proyectos/plasmoides/test instalado con éxito
Then, i can use it in the kde desktop and everything is fine. It is shown in the desktop, with the text label.
But now, if i change the text of the label, "prueba2", and i remove and reinstall the plugin as follows
$ plasmapkg2 --remove test
Constructing a KPluginInfo object from old style JSON. Please use kcoreaddons_desktop_to_json() for "" instead of kservice_desktop_to_json() in your CMake code.
Calling KPluginInfo::property("X-KDE-PluginInfo-Name") is deprecated, use KPluginInfo::pluginName() in "/usr/lib/x86_64-linux-gnu/qt5/plugins/plasma/packagestructure/plasma_packagestructure_share.so" instead.
Constructing a KPluginInfo object from old style JSON. Please use kcoreaddons_desktop_to_json() for "" instead of kservice_desktop_to_json() in your CMake code.
Calling KPluginInfo::property("X-KDE-PluginInfo-Name") is deprecated, use KPluginInfo::pluginName() in "/usr/lib/x86_64-linux-gnu/qt5/plugins/plasma/packagestructure/plasma_packagestructure_share.so" instead.
Generated "/home/xxx/.local/share/plasma/plasmoids//kpluginindex.json" ( 2 plugins)
/home/xxx/Programación/proyectos/plasmoides/test desinstalado con éxito
>xxx#eleanor:~/Programación/proyectos/plasmoides$ plasmapkg2 --install test
pluginname: "org.matrixland.test"
Generated "/home/alberto/.local/share/plasma/plasmoids//kpluginindex.json" ( 3 plugins)
/home/alberto/Programación/proyectos/plasmoides/test instalado con éxito
If now, i add it again to the desktop, i see the old text instead of the new one. I checked in the /home/xxx/.local/share/plasma/plasmoids/org.matrixland.test directory that the source is up to date and refreshed, so i can't guess why am i obtaining the old text instead of the new one.
Obviously my problem is that none of the changes i make in the qml is reflected in the widget, not only text changes. I don't know if i am doing something wrong, or if i must do anything else to update the widget. Can anybody help me with that?
This is because the old QML is "cached" still. You'll need to restart plasmashell in order to see the changes.
killall plasmashell; kstart5 plasmashell
I used this script to reinstall applets when I want to test live. When I want to test quickly though, I'll use plasmoidviewer with:
plasmoidviewer -a package -l bottomedge -f horizontal
like in this script.
I'm looking at modifying a backup script that has been setup for me on my server. The script currently runs each morning to backup all of my domains under the /var/www/vhosts/ directory and I'd like to have it run only four times per week (Sun, Tue, Thu, Sat) instead of daily, if possible. I'm relatively new to the scripting language/commands and was wondering if someone might be able to help me with this? Here is the current script:
umask 0077
BPATH="/disk2/backups/vhosts_backups/`date +%w`"
LOG="backup.log"
/bin/rm -rf $BPATH/*
for i in `ls /var/www/vhosts` on
do
tar czf $BPATH/$i.tgz -C /var/www/vhosts $i 2>>$BPATH/backup.log
done
Thank you,
Jason
To answer my own question (in case it could benefit anyone else), it turns out that the backup script was scheduled through crontab, and that's what needed the adjustment. I did crontab -e and modified the 4th field below from an * to "0,2,4,6" (for Sun, Tue, Thu, Sat).
5 1 * * 0,2,4,6 /root/scripts/vhosts_backup.sh
I'm using SQLite and a php application that runs in background. I have blocked the application using (Ctrl-c) and I just noticed that i have database.sqlite and database.sqlite-journal.
At the moment, How can I remove -journal file without compromising the database?
Thank you!
P.S. SQLite version 3.7.9
EDIT:
-rw-r--r--. 1 damiano damiano 51M 8 mar 18.15 test.sqlite2
-rw-r--r--. 1 damiano damiano 2,6K 8 mar 18.15 test.sqlite2-journal
[damiano#localhost backup]$ sqlite3 test.sqlite2
SQLite version 3.7.13 2012-06-11 02:05:22
Enter ".help" for instructions
Enter SQL statements terminated with a ";"
sqlite>
[damiano#localhost backup]$ ls -lh
-rw-r--r--. 1 damiano damiano 51M 8 mar 18.15 test.sqlite2
-rw-r--r--. 1 damiano damiano 2,6K 8 mar 18.15 test.sqlite2-journal
[damiano#localhost backup]$
Execute this command:
sqlite3 test.sqlite2 vacuum
It will make your database as small as possible and apply possible outstanding transactions or rollbacks in -journal file (and remove it in process). You can actually execute any other transaction that does something (but simply connect/disconnect is NOT enough), but vacuum seems like easiest approach.
Just open the database (with your program or with the sqlite3 command-line tool).
SQLite will then roll back the changes of your interrupted transaction and afterwards remove the journal.
How does dump create the incremental backup? It seems I should use the same file name when I create a level 1 dump:
Full backup:
dump -0aLuf /mnt/bkup/backup.dump /
and then for the incremental
dump -1aLuf /mnt/bkup/backup.dump /
What happens if I dump the level 1 to a different file:
dump -1aLuf /mnt/bkup/backup1.dump /
I am trying to understand how dump keeps track of the changes. I am using a ext3 file system.
This is my /etc/dumpdates:
# cat /etc/dumpdates
/dev/sda2 0 Wed Feb 13 10:55:42 2013 -0600
/dev/sda2 1 Mon Feb 18 11:41:00 2013 -0600
My level 0 for this system was around 11GB and then I ran level 1 today and I used the same filename and the size was around 5 GB.
I think I figured out the issue. It looks like dump adds information in the file so it knows when the previous level occurred.
Level 0 backup
# file bkup_tmp_0_20130220
bkup_tmp_0_20130220: new-fs dump file (little endian), This dump Wed Feb 20 14:29:31 2013, Previous dump Wed Dec 31 18:00:00 1969, Volume 1, Level zero, type: tape header, Label my-label, Filesystem /tmp, Device /dev/sda3, Host myhostname, Flags 3
Level 1 backup, after some change
# file bkup_tmp_1_20130220
bkup_tmp_1_20130220: new-fs dump file (little endian), This dump Wed Feb 20 14:30:48 2013, Previous dump Wed Feb 20 14:29:31 2013, Volume 1, Level 1, type: tape header, Label my-label, Filesystem /tmp, Device /dev/sda3, Host myhostname, Flags 3