search

lmdu / krait

An ultrafast tool for genome-wide survey of microsatellites and primer design
http://krait.biosv.com
GNU Affero General Public License v3.0
35 stars 9 forks source link

Question for command line version of Krait？ #17

Open Zjianglin opened 3 years ago

Zjianglin commented 3 years ago

Dear developers, Krait is really an excellent tool for STR detection. I'd like to know is there any version of command line version of Krait for us, because I want to analysis many genomes. In addition , I encountered many times crash down when I try to import a fasta file. The stderr output is 

(Krait:25246): Gtk-WARNING **: GModule (/usr/lib/x86_64-linux-gnu/gtk-3.0/3.0.0/immodules/im-fcitx.so) initialization check failed: GLib version too old (micro mismatch)

(Krait:25246): Gtk-WARNING **: Loading IM context type 'fcitx' failed

(Krait:25246): GLib-GIO-WARNING **: unknown schema extension 'd'

(Krait:25246): GLib-GIO-WARNING **: unknown schema extension 'd'

(Krait:25246): Gtk-WARNING **: GModule (/usr/lib/x86_64-linux-gnu/gtk-3.0/3.0.0/immodules/im-fcitx.so) initialization check failed: GLib version too old (micro mismatch)

(Krait:25246): Gtk-WARNING **: Loading IM context type 'fcitx' failed

(Krait:25246): Gtk-WARNING **: GModule (/usr/lib/x86_64-linux-gnu/gtk-3.0/3.0.0/immodules/im-fcitx.so) initialization check failed: GLib version too old (micro mismatch)

(Krait:25246): Gtk-WARNING **: Loading IM context type 'fcitx' failed

(Krait:25246): Gtk-WARNING **: GModule (/usr/lib/x86_64-linux-gnu/gtk-3.0/3.0.0/immodules/im-fcitx.so) initialization check failed: GLib version too old (micro mismatch)

(Krait:25246): Gtk-WARNING **: Loading IM context type 'fcitx' failed

(Krait:25246): Gtk-WARNING **: Error loading image 'file:///usr/share/themes/Ambiance/gtk-3.0/assets/button-active.png': Unable to load image-loading module: /usr/lib/x86_64-linux-gnu/gdk-pixbuf-2.0/2.10.0/loaders/libpixbufloader-png.so: /data/amax81t/packages/Krait/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/x86_64-linux-gnu/libpng16.so.16)

(Krait:25246): Gtk-WARNING **: Error loading image 'file:///usr/share/themes/Ambiance/gtk-3.0/assets/button.png': Unable to load image-loading module: /usr/lib/x86_64-linux-gnu/gdk-pixbuf-2.0/2.10.0/loaders/libpixbufloader-png.so: /data/amax81t/packages/Krait/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/x86_64-linux-gnu/libpng16.so.16)

(Krait:25246): Gtk-WARNING **: Error loading image 'file:///usr/share/themes/Ambiance/gtk-3.0/assets/button-disabled.png': Unable to load image-loading module: /usr/lib/x86_64-linux-gnu/gdk-pixbuf-2.0/2.10.0/loaders/libpixbufloader-png.so: /data/amax81t/packages/Krait/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/x86_64-linux-gnu/libpng16.so.16)

(Krait:25246): Gtk-WARNING **: Error loading image 'file:///usr/share/themes/Ambiance/gtk-3.0/assets/button-toolbar.png': Unable to load image-loading module: /usr/lib/x86_64-linux-gnu/gdk-pixbuf-2.0/2.10.0/loaders/libpixbufloader-png.so: /data/amax81t/packages/Krait/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/x86_64-linux-gnu/libpng16.so.16)

(Krait:25246): Gtk-WARNING **: Error loading image 'file:///usr/share/themes/Ambiance/gtk-3.0/assets/button-default-hover.png': Unable to load image-loading module: /usr/lib/x86_64-linux-gnu/gdk-pixbuf-2.0/2.10.0/loaders/libpixbufloader-png.so: /data/amax81t/packages/Krait/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/x86_64-linux-gnu/libpng16.so.16)

(Krait:25246): Gtk-WARNING **: Error loading image 'file:///usr/share/themes/Ambiance/gtk-3.0/assets/button-toolbar-active-focused.png': Unable to load image-loading module: /usr/lib/x86_64-linux-gnu/gdk-pixbuf-2.0/2.10.0/loaders/libpixbufloader-png.so: /data/amax81t/packages/Krait/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/x86_64-linux-gnu/libpng16.so.16)

(Krait:25246): GLib-GIO-WARNING **: unknown schema extension 'd'
double free or corruption (out)
Aborted (core dumped)

 Is there any required library or tools to be installed before? I'm looking forward to your reply. Thanks.
lmdu commented 3 years ago

I am sorry, there is no command version for krait. I am developing Krait2 which can process multiple genomes once time. I could not resolve the error above. I recommend you use windows version. It's more stable!

Zjianglin commented 3 years ago

Okay, thanks for your reply.

XWBarton commented 3 years ago

I am loving Krait but am just leaving a +1 for a command line version for Linux as my computing power is command line only and it takes a while to process large amounts of data locally.

lmdu commented 3 years ago

The command version is being developed. You can find it here stripy. I will release the first version in the next month.