lmdu/krait

An ultrafast tool for genome-wide survey of microsatellites and primer design

krait's Issues

Error: Need more than 1 value to unpack error

Dear Dr Du,
For SSRs location, I got this error message. I use a gff file. Please, how can I solve this issue?

Problem in SSR finding

I am Gauravi Trivedi, I imported a sequence and GFF file in Krait. In order to find SSR, I clicked on "SSR" button without changing any parameters. Sequence got imported but the process of finding SSR is running without giving any output. If I click again on the SSR button, it pops up a text message saying "Task is still running". Can you please have a look at my issue and guide me through.
It will be really helpful.
Thank you

MacOS Security issues

Dear Lianming,

I downloaded the "Krait-v1.1.0-mac.tar.gz", unzipped and tried running Krait on a Macbook Pro OS = Catalina10.15.4. Unfortunately, I keep getting security pop-ups saying that the software could not be opened because the developer cannot be verified. An example:

“libopenblasp-r0.3.7.dylib” cannot be opened because the developer cannot be verified.

It first does this for "Krait" and then a similar warning pops up from Python and then it starts going through each "module" in the folder, giving a warning for each one. I can allow each particular module to run by giving it permission with my password, but then it just pops up with another warning for the next module - and there are many, many modules, which makes it very inconvenient.

Do you have any ideas for getting around this?

Perhaps if one could compile it from source, then these warnings wouldn't pop up, but I don't see any instructions for compiling from source in the manual/readme and I'm not sure how to do it. The Mac is running python2.7. Is that fine, or does it need python3?

Cheers
Deon

An error on searching Primers

I had an error on searching primers, see below.

My Krait version is 1.2.3.

Thank you in advance.

Primer location and export fasta

I'm using Krait v1.3.3.
I could not confirm the location of reverse primers without highlight colors, but the outputted reverse primer was actually included in the target sequence.
Curiously, it was highlighted when I analyzed the example file.
Perhaps, the complementary option did not work in the big data?

For another issue, there is no "Export Selected as Fasta" in File Menu.

Thank you in advance.

导入基因组fas格式后，点击SSRs出现错误

您好，为什么下载了最新版本14的krait分析基因组SSR，还是会出现这种情况，目前可以解决这个问题嘛，13.3版本的也是这种情况

Multithreading support?

The tool is wonderful and fast, but when I was using Krait to find the SSRs in the genome of Canis lupus famalaris, it seemed that it's running on a single thread. Is there any multithreading support?

Error with erroneous sequence data

When searching for SSRs in a large fasta file (with more than 250 000 sequences) I get the following error:

This is apparently triggered by erroneous sequence data, so far I traced back two sequences that did this, see attached files.

NODE_12838_length_70_cov_23.79.txt
NODE_42629_length_65_cov_2.692.txt

Krait installation on Mac with OS 11.6

I have attempted to install Krait using the mac os .dmg file and by direct install via source code. When using the .dmg file, the program installs but never launches (the error message is that the application isn't responding and force quit is required to terminate the program). When I install Krait via the source code in Terminal, everything works until the 'python3 main.py' command (nothing happens thereafter).

Any help you could provide would be most appreciated.

SSRs的search结果中type=2包括了本应该属于type=1的结果，造成重复统计

您好，我运行1.4.0版本发现统计的结果中SSRs的search结果中type=2包括了本应该属于type=1的结果，造成SSRs重复统计，如下图，具体的 view sequence 视图打开可以看到是单碱基重复。

Sudden die during statistical analysis

Thanks for your effort in renewed version. However v1.1.0 could search microsatellite loci successfully but suddenly die during statistical analysis. I found that the several libraries are incompatible in my environment (Ubuntu 18.04) when I run from terminal and so replaced some libraries in Krait folder. But the program still die after indicating "Could not find QtWebEngineProcess". Thank you in advance for fixing this problem.

Traceback error exporting data as .gff

I get this Error message every time I try to export my SSR data as a .gff file:

Traceback (most recent call last):
File "workers.py", line 113, in run
File "workers.py", line 592, in process
File "workers.py", line 585, in
File "utils.py", line 76, in format_to_gff
AttributeError: 'list' object has no attribute 'sequence'

What do I do to fix this so that I can export my data as a .gff file?

Mannul

The Manual.pdf is invalid, could you please update it.

errortraceback

Another error on searching primers

Hello,
Unfortunately, another error occurred on searching primers, attached the message.

All the best,

Import error

I get the following error while installing on Linux.
ImportError: /usr/lib/x86_64-linux-gnu/mesa/libGL.so.1: undefined symbol: drmGetDevices2
Kindly help

the standard motif and motif

Thank you very much for the krait software, but I can’t understand what the standard motif in the SSRs search results means. Can you explain?

Issue in "Primer"

After SSR search, I conducted Primer design, but facing the following error in both linux (Ubuntu) and Windows 10 (64bit). The result is truncated in hundred loci or a thousand, even I submitted few million loci. Also I could not export results after indication of this error.
Thx.

Traceback (most recent call last):
File "workers.py" line 82, in run
File "workers.py" line 413, in process
File "db.py", line 157, in begin
File "db.py", line 134, in query
File "c:\users\appveyor\appdata\local\temp\1\pip-req-build-pfvgtr\src\cursor.c", line 236, in resetcursor SQLError: SQLError: cannot start a transaction within a transaction

visual contrast bug affecting only Mac

Krait worked fine for me last week but now has a strange visual contrast bug. It still functions normally but I can't read any of the words on the table. I have restarted the computer and reinstalled Krait but it's still the same. Interestingly though, Krait still works fine on my windows laptop so problem only seems to affect Mac.

ubuntu 22.04 install Krait-v1.4.0-amd64.deb occur Segmentation fault

My real machine is Centos7, and I installed the image of Ubuntu 2204 through singularity. I installed Krait version 1.4.0 using deb in the image, but there was an error when opening it. The following is my opening process. Could you please help me find a solution. Thank you.

Singularity> ls -l /usr/lib/Krait/Krait
-rwxr-xr-x 1 root root 3156248 Jan 1 2023 /usr/lib/Krait/Krait
Singularity> ls -ltr /usr/lib/Krait/Krait
-rwxr-xr-x 1 root root 3156248 Jan 1 2023 /usr/lib/Krait/Krait
Singularity> ls -ltrh /usr/lib/Krait/Krait
-rwxr-xr-x 1 root root 3.1M Jan 1 2023 /usr/lib/Krait/Krait
Singularity> /usr/lib/Krait/Krait
QFactoryLoader::QFactoryLoader() checking directory path "/usr/lib/Krait/PySide2/Qt/plugins/platforms" ...
QFactoryLoader::QFactoryLoader() looking at "/usr/lib/Krait/PySide2/Qt/plugins/platforms/libqeglfs.so"
Found metadata in lib /usr/lib/Krait/PySide2/Qt/plugins/platforms/libqeglfs.so, metadata=
{
"IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",
"MetaData": {
"Keys": [
"eglfs"
]
},
"archreq": 0,
"className": "QEglFSIntegrationPlugin",
"debug": false,
"version": 331520
}

Got keys from plugin meta data ("eglfs")
QFactoryLoader::QFactoryLoader() looking at "/usr/lib/Krait/PySide2/Qt/plugins/platforms/libqlinuxfb.so"
Found metadata in lib /usr/lib/Krait/PySide2/Qt/plugins/platforms/libqlinuxfb.so, metadata=
{
"IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",
"MetaData": {
"Keys": [
"linuxfb"
]
},
"archreq": 0,
"className": "QLinuxFbIntegrationPlugin",
"debug": false,
"version": 331520
}

Got keys from plugin meta data ("linuxfb")
QFactoryLoader::QFactoryLoader() looking at "/usr/lib/Krait/PySide2/Qt/plugins/platforms/libqminimal.so"
Found metadata in lib /usr/lib/Krait/PySide2/Qt/plugins/platforms/libqminimal.so, metadata=
{
"IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",
"MetaData": {
"Keys": [
"minimal"
]
},
"archreq": 0,
"className": "QMinimalIntegrationPlugin",
"debug": false,
"version": 331520
}

Got keys from plugin meta data ("minimal")
QFactoryLoader::QFactoryLoader() looking at "/usr/lib/Krait/PySide2/Qt/plugins/platforms/libqminimalegl.so"
Found metadata in lib /usr/lib/Krait/PySide2/Qt/plugins/platforms/libqminimalegl.so, metadata=
{
"IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",
"MetaData": {
"Keys": [
"minimalegl"
]
},
"archreq": 0,
"className": "QMinimalEglIntegrationPlugin",
"debug": false,
"version": 331520
}

Got keys from plugin meta data ("minimalegl")
QFactoryLoader::QFactoryLoader() looking at "/usr/lib/Krait/PySide2/Qt/plugins/platforms/libqoffscreen.so"
Found metadata in lib /usr/lib/Krait/PySide2/Qt/plugins/platforms/libqoffscreen.so, metadata=
{
"IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",
"MetaData": {
"Keys": [
"offscreen"
]
},
"archreq": 0,
"className": "QOffscreenIntegrationPlugin",
"debug": false,
"version": 331520
}

Got keys from plugin meta data ("offscreen")
QFactoryLoader::QFactoryLoader() looking at "/usr/lib/Krait/PySide2/Qt/plugins/platforms/libqvnc.so"
Found metadata in lib /usr/lib/Krait/PySide2/Qt/plugins/platforms/libqvnc.so, metadata=
{
"IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",
"MetaData": {
"Keys": [
"vnc"
]
},
"archreq": 0,
"className": "QVncIntegrationPlugin",
"debug": false,
"version": 331520
}

Got keys from plugin meta data ("vnc")
QFactoryLoader::QFactoryLoader() looking at "/usr/lib/Krait/PySide2/Qt/plugins/platforms/libqwayland-egl.so"
Found metadata in lib /usr/lib/Krait/PySide2/Qt/plugins/platforms/libqwayland-egl.so, metadata=
{
"IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",
"MetaData": {
"Keys": [
"wayland-egl"
]
},
"archreq": 0,
"className": "QWaylandEglPlatformIntegrationPlugin",
"debug": false,
"version": 331520
}

Got keys from plugin meta data ("wayland-egl")
QFactoryLoader::QFactoryLoader() looking at "/usr/lib/Krait/PySide2/Qt/plugins/platforms/libqwayland-generic.so"
Found metadata in lib /usr/lib/Krait/PySide2/Qt/plugins/platforms/libqwayland-generic.so, metadata=
{
"IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",
"MetaData": {
"Keys": [
"wayland"
]
},
"archreq": 0,
"className": "QWaylandIntegrationPlugin",
"debug": false,
"version": 331520
}

Got keys from plugin meta data ("wayland")
QFactoryLoader::QFactoryLoader() looking at "/usr/lib/Krait/PySide2/Qt/plugins/platforms/libqwayland-xcomposite-egl.so"
Found metadata in lib /usr/lib/Krait/PySide2/Qt/plugins/platforms/libqwayland-xcomposite-egl.so, metadata=
{
"IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",
"MetaData": {
"Keys": [
"wayland-xcomposite-egl"
]
},
"archreq": 0,
"className": "QWaylandXCompositeEglPlatformIntegrationPlugin",
"debug": false,
"version": 331520
}

Got keys from plugin meta data ("wayland-xcomposite-egl")
QFactoryLoader::QFactoryLoader() looking at "/usr/lib/Krait/PySide2/Qt/plugins/platforms/libqwayland-xcomposite-glx.so"
Found metadata in lib /usr/lib/Krait/PySide2/Qt/plugins/platforms/libqwayland-xcomposite-glx.so, metadata=
{
"IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",
"MetaData": {
"Keys": [
"wayland-xcomposite-glx"
]
},
"archreq": 0,
"className": "QWaylandXCompositeGlxPlatformIntegrationPlugin",
"debug": false,
"version": 331520
}

Got keys from plugin meta data ("wayland-xcomposite-glx")
QFactoryLoader::QFactoryLoader() looking at "/usr/lib/Krait/PySide2/Qt/plugins/platforms/libqwebgl.so"
Found metadata in lib /usr/lib/Krait/PySide2/Qt/plugins/platforms/libqwebgl.so, metadata=
{
"IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",
"MetaData": {
"Keys": [
"webgl"
]
},
"archreq": 0,
"className": "QWebGLIntegrationPlugin",
"debug": false,
"version": 331520
}

Got keys from plugin meta data ("webgl")
QFactoryLoader::QFactoryLoader() looking at "/usr/lib/Krait/PySide2/Qt/plugins/platforms/libqxcb.so"
Found metadata in lib /usr/lib/Krait/PySide2/Qt/plugins/platforms/libqxcb.so, metadata=
{
"IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3",
"MetaData": {
"Keys": [
"xcb"
]
},
"archreq": 0,
"className": "QXcbIntegrationPlugin",
"debug": false,
"version": 331520
}

Got keys from plugin meta data ("xcb")
QFactoryLoader::QFactoryLoader() checking directory path "/usr/lib/Krait/platforms" ...
loaded library "/usr/lib/Krait/PySide2/Qt/plugins/platforms/libqxcb.so"
loaded library "Xcursor"
Segmentation fault
Singularity>

A crash occurred on searching SSR

I tried Krait v1.3.2, but it crashed without error messages on searching SSRs in a large fasta file (more than 300 000 sequences).
Thank you in advance.

view sequence无法打开

你好！
krait1.3.3版本，我用的windows软件界面。可以查找SSRs cSSRs iSSRs，但是得到的结果按照您发布的gif动画点击view sequence 无响应 。且mapping出现了错误图1，primer出现了错误图2。请问这三个问题如何解决呢？（图三是我的文件夹 第3个是我输入的fasta文件，第6个是mapping的软件）

Question for command line version of Krait？

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.

Primer design not working

SSR markers are identified but primer designing not working. Everytime you select any SSR marker, it shows the error
Here jcf7180029229335 is contig name
Traceback (most recent call last):
File "workers.py", line 113, in run
File "workers.py", line 457, in process
KeyError: 'jcf7180029229335 does not exist in fasta file'

Mapping SSR

One of the Reviewers raised a query "distribution of identified SSRs in different genomic regions". I tried to run on both Linux and Windows operating systems. Identification of SSRs and their statistical report was perfectly obtained but while analyzing annotation files no results were obtained. I downloaded the GFF, GTF, and GFF3 files from NCBI and Ensemble. Please guide me regarding this issue.  Thanking you

Error while mapping

help-Import Multiple FASTA Files

Hello, I would like to ask in the manual can enter multiple fasta sequence as shown in Figure 1, but I opened the interface, found that can only enter a sequence (Import fasta) Where is the input button for multiple sequences? Thank you!

n

searching error

Hi, I've just downloaded the newer version because I had gotten problems with importing GFF files and... now I cannot even analyze microsatellites: here what comes after I tried:

Mapping Error

您好，我在Mapping时报错，找不到解决办法，希望能得到您们的帮助。

Mapping Error

您好，我在Mapping时报错，找不到解决办法，希望能得到您们的帮助。

Filtering out Microsatellites for which Primers weren't generated

I'm using Krait to design primers for whole genomes. The genome sequences are present in scaffolds. Thus, if a microsatellite is present at the start or end of scaffold, the primer designing fails. I wish to filter out these failed microsatellites so as to combine microsatellite list and primer list. Deleting all the failed microsatellites manually is too much of a chore.

Execute Script Problem

Hi! I get an error (failure to execute script) when trying to launch the program.