Development version of Easyfig
This is the updated version of Easyfig, migrated from Sourceforge.
Easyfig is a Python application for creating comparison figures. It is freely available under a GPLv3 license.
The main site for Easyfig is now here.
Please visit files to download Easyfig binaries.
Please visit the wiki for a comprehensive manual including tutorials and installation instructions.
The Easyfig plots use a color gradient to specify the degree of similarity between the compared genome regions.
It is possible to specifiy the color for minimum and maximum points, but it is not possible to define a specific minimum value for calculating the gradient (only the minimum identity which should be considered as a BLAST hit). Instead Easyfig just assumes the minimum similarity observed in the current blast-comparisons as minimum value.
While this can often be quite convenient, it makes it difficult to compare separate images created with Easyfig (comparing different subsets of sequences, where the observed minimum BLAST similarity may change).
Would it be possible to add an option to manually specify a distinct minimum value for the Color gradient in the "BLAST Options" menu?
I am trying to plot synteny of 12 genes present in a pathogenicity cluster identified in my bacterial species and want to compare it with six other bacterial species (already available genomes). However I am not able to get the plots.
I have so far:
Done a local tblastx using my pathogenicity genes (12 genes) as query and other available bacterial species (6 genomes) as subject (one at a time) to generate 6 tblastx output tables (outfmt 6).
Used the tblastx output as input blast files for easyfig and fasta files of query genes and blast hits as input annotation files for easyfig.
All it gives me just three straight lines. I understand I am doing something wrong here.
I have following questions:
Can I use unannotated fasta files under annotation files or I have to use only .gb files?
Do I get only top blast hits from mt blast output or use the blast output as such under blast files in easyfig. In the current form my blast output file has multiple hits against the each gene.
If I have to use .gb files then do the gb files have to be specific to the gene coordinates extracted from the whole genome gb file?
Is windows and linux version the same in terms of features that are used to generate the figure?
Could you please look into my files and suggest. If you can then I will share my files with you and it will be a great help.
Thank you
GA
I have the latest version of OSX (version 10.14.6), with the easy fig 2.2 the buttons were empty. I wonder what is wrong?
Regards
Lynx
orfs are there but no blast hits drawn between them....and there should be.
no_blast_hits.pptx
Hello,
I am using EasyFig version 2.2.2 for Mac OSX. For some GenBank files (for example this one: http://www.ncbi.nlm.nih.gov/nuccore/NC_009348.1), EasyFig cannot draw the features (CDS, tRNA ...).
Is there something wrong (particularities) with this GenBank file? I tried on Windows and I have the same issue.
Thank you!
Hello! I've been trying to troubleshoot EasyFig for my Mac but have had little success. When I downloaded the mac version and tried to open it with python/python launcher, it didn't allow me to click them as an option. So, I tried simply launching the EasyFig.py script within the directory that contained all the files for the Mac download and it worked....partially. There appears to be an issue with the GUI but I'm not entirely sure outside of that. I've attached an image of what I'm currently seeing (even after resizing the window, which was a suggestion from a few years ago). Any and all help would be greatly appreciated!
Thanks and enjoy your day,
A.J
I created the picture(picture2),but no comparing like piecture 1
Hello,
I am using easyfig to draw GC-content plots. I annotate 2kb regions (one annotation per file) in 3mb scaffolds and save them as gb files. These files work alright except two- the annotations are not detected by easyfig. Simialr files give me the plots. Is there anything that I am doing wrong? any thoughts?
I didn't see it in the manual, but it should be noted that dashes in file names will produce the following error. Running .exe on Win10.
Exception in thread Thread-3:
Traceback (most recent call last):
File "C:\Users\mjsul_000\Documents\GitHub\build\Easyfig\out00-PYZ.pyz\threading", line 810, in __bootstrap_inner
File "C:\Users\mjsul_000\Documents\GitHub\build\Easyfig\out00-PYZ.pyz\threading", line 763, in run
File "", line 9732, in makeFigure2
File "", line 6913, in drawsvg
File "", line 5729, in getArrows
ValueError: need more than 1 value to unpack
Exception in thread Thread-4:
Traceback (most recent call last):
File "C:\Users\mjsul_000\Documents\GitHub\build\Easyfig\out00-PYZ.pyz\threading", line 810, in __bootstrap_inner
File "C:\Users\mjsul_000\Documents\GitHub\build\Easyfig\out00-PYZ.pyz\threading", line 763, in run
File "", line 9701, in dotdotdot
AttributeError: App instance has no attribute 'theminblast'
Hi there,
I'm hoping someone can help me resolve an issue with BLAST files when trying to create a figure.
I am using a Windows 64-bit machine. I have downloaded the latest version of ncbi-blast-2.12.0+-win64. I have shown the software where the blast executables are on my computer through the "choose blast location" button. After adding two GenBank files, I will click "generate blastn files" and I will see two files be created in the working directory, namely: "1.easyfig.fa" and "2.easyfig.fa". Then, in the Blast Files tab, there will be a file ending in "/12.easyfig.out".
However, when finally clicking "create figure", an error message pops up saying: "A selected file does not exist". Also, within the working directory, there is no file ending in "/12.easyfig.out".
I was wondering if there was anything I could do to fix this?
Thank you for your help!
I would like to analyze 10 prophage genomes (gbk format) and each gbk file has ~120kb. I added a colour feature to each gbk file manually, say, /colour=7 based on the genbank file provided in the example. The blastn output files generated well, however, when I clicked the create figure section, it takes very long time and the figure was not generated. I don't really know that whether the program on the progress or struck or it doesn't prompt any error messages too. What will be the possible reasons for this troubleshooting and how can I fix this issue? Please help!!
Hello,
I am trying to use EasyFig to compare two gene clusters. I have the gene clusters in two genbank files. I want to reverse some of the gene arrows in each genbank file. However, when I try to use subregions to do this, I can only select one subregion per genbank file. The figure ends up being only the reversed arrow. How can I reverse the gene arrow (subregion) but still keep the other features (gene arrows) from the genbank file?
Thanks for your help in advance.
I was working well the whole day but when I tried to compare 3 genebank files,suddenly it generate blastn files but not blastx files anymore. When I clicked crate blastx file, if re-creates the blastn files again. Does anyone know how to solve? please , thanks in advance
Hi,
Can anyone suggest me to change or present the of the ORF in the picture? I added the code presented in the example 1 and 2 such as /colour=10. However, nothing was changed in the picture. Thanks in advance.
Best regards,
Oof
Hi everyone,
I have triangles appearing in Fetaure Labels (please see picture). Does anyone knows how to remove them? I am wondering if this is something wrong in the genebank files... However, for the same file I have Features appearing with and without the rectangles...
Many thanks,
Nelson
I have been trying to use easyfig to compare multiple sequences of different strains. I have been having multiple issues so far and was hoping for some help. The first attempt was with easyfig version 2.3 and downloaded the blast file win.64.exe. I was able to draw a figure, however, it was showing inconsistencies between two computers running the same sequences. Comparison between two sequences showed the presence of a gene in both that was not in fact present in one of the sequences.
I was advised to download version 2.2 because of errors others have had using version 2.3. Downloading the same blast file the error that now occurs is either a message saying that no file available (indicating no blast file out being produced) or when it works and the drawing of the figure is produced there is no identity shown only the sequences with the arrows of the two sequences. Someone please help I've spent a day working on this an need to get to the other part of my project.
Hello there! Thanks for this very useful tool.
I am new to using Easyfig. My aim is to compare some bacterial genomes and identify sites of mutations or alterations. The genomes are same bacteria, but one is wildtype and the other is an evolved variant. After WGS, I obtained the sequences in fasta formats. I have also performed annotation for the two genomes.
My question is what do I upload in the Blast files column? In the annotation files, I uploaded the annotation files in genebank format; correct?
Kindly help! Thank you very much.
1.Input / output file path cannot have space bar
2.After downloading blast, try opening easyfig_ 2.2.5_ win/makeblastdb.exe，If you are prompted that the 'vcruntime140. DLL' file is missing，You can go to this website ‘https://support.microsoft.com/zh-cn/help/2977003/the-latest-supported-visual-c-downloads’ Download the latest visual c++. After the installation is complete, try opening again makeblastdb.exe. If there is no error prompt, it indicates that the problem has been solved.
Hi,
I'm having trouble to draw exons for CDS that are in reverse direction. In my genbank files, exons are defined as follows:
join(complement(59762..60896),complement(60948..60968))
Only the last exon (the one on the left) of my reverse genes and the dashes joining the different exons of the genes are displayed.
It works well for exons in the forward genes defined as follows:
join(49140..49167,49241..50136)
I am using the python script 2.2.3
Do you know what is wrong?
Thank you,
Best,
Flora
Hello,
Can anyone help me with the Easyfig 2.2.2 program. I have downloaded the program, I am using a windows 64bit computer, I have had a go at the examples but when it comes to generating a figure for my work I run into some issues.
I am aiming to compare a series of bacterial sequences (approx 23kb in length) to assess which genes are conserved in my regions of interest.
I have added the annotation files but when I go to add the blast files I run into problems.
I have manually downloaded blast onto my computer as doing it automatically didn't seem to work. When I go to 'add a blast file' I'm not too sure what I am suppose to add?
I go into program files, find the NCBI folder, click on blast-2.6.0+, then do I go into the bin folder? Which files am I suppose to add? When I try say blastn and try to generate a figure it tells me too few blast files?
I am very new to this and I would greatly appreciate anyone's advice.
Thanks :)
Hey there! First, thank for developing this very nice and useful tool and for keeping it updated.
This is not an issue per se, but I was wondering if there is a easy way to increase the number of characters of the feature labels, which are currently limited to 10 characters. The problem is that some labels nowadays have more characters (e.g. something like I204_006840) and thus, by excluding the last character, Easyfig prints out the same label for consecutive genes (10 genes in this case). Also, I would be nice if the labels could be added to all tracks when comparing multiple genomes rather than just the top and/or bottom genomes. Thanks.
Hello,
I have uploaded the same DNA sequence to the Easyfig software (.gbk files) with different names to test the graphical representation. Instead of 100% similarity I got some areas where the similarity is below 100%.
Can anyone explain this? If it is the very same sequence it should give 100% similarity for the whole sequence, and a graphical representation with 100% similarity...
Thanks in advance,
Nelson
Hello,
I got the following error when invoking Easyfig from the command line on Linux. The Easyfig version that I am using is "Version 2.2.2 10.08.2015". Could you help me to figure out what might cause this error?
python /home/yjx/Programs/Easyfig/Easyfig.py -o test -blastn chrI.embl 1 40850 R chrI.embl 179930 219929
Traceback (most recent call last):
File "/home/yjx/Programs/Easyfig/Easyfig.py", line 10988, in
inlist = genBlast(templist, cutlist)
NameError: name 'genBlast' is not defined
Thanks!
Best,
Jia-Xing
In some places the version is 2.1.0 (the GitHub tag) and others just 2.1 (the tarballs and app name). Please be consistent and use 2.1.0 throughout.
See Semantic Versioning.
Hi,
I'm using Ubuntu 20 LTS and I'm trying to run Easyfig. Once that I've already submitted the files (both gff and blast) and press create figure it does not do anything. It just display the "cancel figure" message but it does not show the "creating figure" message in the orange box
Any recommendation?
Not sure this is an issue as I am not fluent with python. To seek help to get it run in my Debian machine.
Same error message with both ran from source code and binary, which is:
Exception in thread Thread-1:
Traceback (most recent call last):
File "/home/mjsull/scripts/build/Easyfig/out00-PYZ.pyz/threading", line 810, in __bootstrap_inner
File "/home/mjsull/scripts/build/Easyfig/out00-PYZ.pyz/threading", line 763, in run
File "<string>", line 9721, in makeFigure2
File "<string>", line 6029, in draw
File "<string>", line 5918, in getArrows
MemoryError
Exception in thread Thread-2:
Traceback (most recent call last):
File "/home/mjsull/scripts/build/Easyfig/out00-PYZ.pyz/threading", line 810, in __bootstrap_inner
File "/home/mjsull/scripts/build/Easyfig/out00-PYZ.pyz/threading", line 763, in run
File "<string>", line 9701, in dotdotdot
AttributeError: App instance has no attribute 'theminblast'
Any help is greatly appreciated.
-Yifang
When I using the Colour the coding-sequence (CDS) features function by manually adding one /colour feature qualifier to my GenBank file (i.e. /colour=16), the genes after I would like to change the colour disappeared in the final image. For example, I would like to change the tenth gene into the red colour, but the genes from the eleventh to the last cannot be displayed any more. The demo data works fine with me to change the colour.
Windows 7, 64 bit computer, Experience with computers: could not write a line of code to safe my life.
I wish to compare two sequences about 57 Kb in size for my paper.
I have exported my annotated files from CLC and saved them as both .gbk and .fa
I downloaded the EasyFig 2.2.2 and extracted it into a folder in My Documents
The program can run and I can easily add my sequences by pressing the [Add feature file] button.
When I press [Generate blastn Files] or [Download BLAST automatically] it starts downloading BLAST, but gets stuck after download is complete with the message "Downloading ...Complete, Extracting file...". After a while the black window reads:
So I decided to download BLAST manually, the program suggests I download ncbi-blast-2.7.1+-win64.exe. I install it in the default C:\Program Files\NCBI
I install BLAST and restart the EasyFig application. Again I load in the files and goes into [Blast]->[Choose BLAST Location], I find the C:\Program Files\NCBI\blast-2.7.1+\bin
Now I'm ready to generate so I press [Generate blastn Files], I now have to choose a location. I select same folder as where my sequences are in My Documents
Then I press save as and choose my folder in My Documents again
After I name the file an error pops up [A selected file does not exist [OK] ]
I know my folder names may contain spaces or my paths are pretty long. A new version 2.2.3 is added but I don't know what to do with a .py file
I believe a tutorial where we have to generate the BLAST files ourselves would be a very nice addition to the wiki
Help is much appreciated
When I using the Colour the coding-sequence (CDS) features function by manually adding one /colour feature qualifier to my GenBank file (i.e. /colour=10), the genes after I would like to change the colour disappeared in the final image. For example, I would like to change the tenth gene into the red colour, but the genes from the eleventh to the last cannot be displayed any more. The demo data works fine with me to change the colour.
Hello,
I find Easyfig very convenient to represent a comparison between 2 or more sequences in a linear space.
I wonder if it is (or will?) be possible to upload features in other formats: e.g. annotation in gff3/bed format, nucmer/any table alignment, and so on. If not, do you know of any other tool to visualize alignments and annotations between regions of a genome? possibly that will work also well above 5 Mb - I work with eukayotic genomes.
Also, is there a maximum genome size that the tool can work with?
thanks,
Dario
Line 11197 in 11e3996
Should be
mineval = float(sys.argv[i+1])
Good day,
I have downloaded and extracted Easyfig_2.2.2_linux.tar.gz from https://mjsull.github.io/Easyfig/files.html.
When I run Easyfig on the command line I get the following message:
Fontconfig warning: line 5: unknown element "its:rules"
Fontconfig warning: line 6: unknown element "its:translateRule"
Fontconfig error: line 6: invalid attribute 'translate'
Fontconfig error: line 6: invalid attribute 'selector'
Fontconfig error: line 7: invalid attribute 'xmlns:its'
Fontconfig error: line 7: invalid attribute 'version'
Fontconfig warning: line 9: unknown element "description"
Fontconfig warning: "/etc/fonts/conf.d/10-hinting-slight.conf", line 4: unknown element "its:rules"
Fontconfig warning: "/etc/fonts/conf.d/10-hinting-slight.conf", line 5: unknown element "its:translateRule"
Fontconfig error: "/etc/fonts/conf.d/10-hinting-slight.conf", line 5: invalid attribute 'translate'
Fontconfig error: "/etc/fonts/conf.d/10-hinting-slight.conf", line 5: invalid attribute 'selector'
Fontconfig error: "/etc/fonts/conf.d/10-hinting-slight.conf", line 6: invalid attribute 'xmlns:its'
Fontconfig error: "/etc/fonts/conf.d/10-hinting-slight.conf", line 6: invalid attribute 'version'
Fontconfig warning: "/etc/fonts/conf.d/10-hinting-slight.conf", line 8: unknown element "description"
Fontconfig warning: "/etc/fonts/conf.d/10-scale-bitmap-fonts.conf", line 4: unknown element "its:rules"
Fontconfig warning: "/etc/fonts/conf.d/10-scale-bitmap-fonts.conf", line 5: unknown element "its:translateRule"
Fontconfig error: "/etc/fonts/conf.d/10-scale-bitmap-fonts.conf", line 5: invalid attribute 'translate'
Fontconfig error: "/etc/fonts/conf.d/10-scale-bitmap-fonts.conf", line 5: invalid attribute 'selector'
Fontconfig error: "/etc/fonts/conf.d/10-scale-bitmap-fonts.conf", line 6: invalid attribute 'xmlns:its'
Fontconfig error: "/etc/fonts/conf.d/10-scale-bitmap-fonts.conf", line 6: invalid attribute 'version'
Fontconfig warning: "/etc/fonts/conf.d/10-scale-bitmap-fonts.conf", line 8: unknown element "description"
Fontconfig warning: "/etc/fonts/conf.d/11-lcdfilter-default.conf", line 4: unknown element "its:rules"
Fontconfig warning: "/etc/fonts/conf.d/11-lcdfilter-default.conf", line 5: unknown element "its:translateRule"
Fontconfig error: "/etc/fonts/conf.d/11-lcdfilter-default.conf", line 5: invalid attribute 'translate'
Fontconfig error: "/etc/fonts/conf.d/11-lcdfilter-default.conf", line 5: invalid attribute 'selector'
Fontconfig error: "/etc/fonts/conf.d/11-lcdfilter-default.conf", line 6: invalid attribute 'xmlns:its'
Fontconfig error: "/etc/fonts/conf.d/11-lcdfilter-default.conf", line 6: invalid attribute 'version'
Fontconfig warning: "/etc/fonts/conf.d/11-lcdfilter-default.conf", line 8: unknown element "description"
Fontconfig warning: "/etc/fonts/conf.d/20-unhint-small-vera.conf", line 4: unknown element "its:rules"
Fontconfig warning: "/etc/fonts/conf.d/20-unhint-small-vera.conf", line 5: unknown element "its:translateRule"
Fontconfig error: "/etc/fonts/conf.d/20-unhint-small-vera.conf", line 5: invalid attribute 'translate'
Fontconfig error: "/etc/fonts/conf.d/20-unhint-small-vera.conf", line 5: invalid attribute 'selector'
Fontconfig error: "/etc/fonts/conf.d/20-unhint-small-vera.conf", line 6: invalid attribute 'xmlns:its'
Fontconfig error: "/etc/fonts/conf.d/20-unhint-small-vera.conf", line 6: invalid attribute 'version'
Fontconfig warning: "/etc/fonts/conf.d/20-unhint-small-vera.conf", line 8: unknown element "description"
Fontconfig warning: "/etc/fonts/conf.d/30-metric-aliases.conf", line 4: unknown element "its:rules"
Fontconfig warning: "/etc/fonts/conf.d/30-metric-aliases.conf", line 5: unknown element "its:translateRule"
Fontconfig error: "/etc/fonts/conf.d/30-metric-aliases.conf", line 5: invalid attribute 'translate'
Fontconfig error: "/etc/fonts/conf.d/30-metric-aliases.conf", line 5: invalid attribute 'selector'
Fontconfig error: "/etc/fonts/conf.d/30-metric-aliases.conf", line 6: invalid attribute 'xmlns:its'
Fontconfig error: "/etc/fonts/conf.d/30-metric-aliases.conf", line 6: invalid attribute 'version'
Fontconfig warning: "/etc/fonts/conf.d/30-metric-aliases.conf", line 8: unknown element "description"
Fontconfig warning: "/etc/fonts/conf.d/40-nonlatin.conf", line 4: unknown element "its:rules"
Fontconfig warning: "/etc/fonts/conf.d/40-nonlatin.conf", line 5: unknown element "its:translateRule"
Fontconfig error: "/etc/fonts/conf.d/40-nonlatin.conf", line 5: invalid attribute 'translate'
Fontconfig error: "/etc/fonts/conf.d/40-nonlatin.conf", line 5: invalid attribute 'selector'
Fontconfig error: "/etc/fonts/conf.d/40-nonlatin.conf", line 6: invalid attribute 'xmlns:its'
Fontconfig error: "/etc/fonts/conf.d/40-nonlatin.conf", line 6: invalid attribute 'version'
Fontconfig warning: "/etc/fonts/conf.d/40-nonlatin.conf", line 8: unknown element "description"
Fontconfig warning: "/etc/fonts/conf.d/45-generic.conf", line 4: unknown element "its:rules"
Fontconfig warning: "/etc/fonts/conf.d/45-generic.conf", line 5: unknown element "its:translateRule"
Fontconfig error: "/etc/fonts/conf.d/45-generic.conf", line 5: invalid attribute 'translate'
Fontconfig error: "/etc/fonts/conf.d/45-generic.conf", line 5: invalid attribute 'selector'
Fontconfig error: "/etc/fonts/conf.d/45-generic.conf", line 6: invalid attribute 'xmlns:its'
Fontconfig error: "/etc/fonts/conf.d/45-generic.conf", line 6: invalid attribute 'version'
Fontconfig warning: "/etc/fonts/conf.d/45-generic.conf", line 8: unknown element "description"
Fontconfig warning: "/etc/fonts/conf.d/45-latin.conf", line 4: unknown element "its:rules"
Fontconfig warning: "/etc/fonts/conf.d/45-latin.conf", line 5: unknown element "its:translateRule"
Fontconfig error: "/etc/fonts/conf.d/45-latin.conf", line 5: invalid attribute 'translate'
Fontconfig error: "/etc/fonts/conf.d/45-latin.conf", line 5: invalid attribute 'selector'
Fontconfig error: "/etc/fonts/conf.d/45-latin.conf", line 6: invalid attribute 'xmlns:its'
Fontconfig error: "/etc/fonts/conf.d/45-latin.conf", line 6: invalid attribute 'version'
Fontconfig warning: "/etc/fonts/conf.d/45-latin.conf", line 8: unknown element "description"
Fontconfig warning: "/etc/fonts/conf.d/49-sansserif.conf", line 4: unknown element "its:rules"
Fontconfig warning: "/etc/fonts/conf.d/49-sansserif.conf", line 5: unknown element "its:translateRule"
Fontconfig error: "/etc/fonts/conf.d/49-sansserif.conf", line 5: invalid attribute 'translate'
Fontconfig error: "/etc/fonts/conf.d/49-sansserif.conf", line 5: invalid attribute 'selector'
Fontconfig error: "/etc/fonts/conf.d/49-sansserif.conf", line 6: invalid attribute 'xmlns:its'
Fontconfig error: "/etc/fonts/conf.d/49-sansserif.conf", line 6: invalid attribute 'version'
Fontconfig warning: "/etc/fonts/conf.d/49-sansserif.conf", line 8: unknown element "description"
Fontconfig warning: "/etc/fonts/conf.d/50-user.conf", line 4: unknown element "its:rules"
Fontconfig warning: "/etc/fonts/conf.d/50-user.conf", line 5: unknown element "its:translateRule"
Fontconfig error: "/etc/fonts/conf.d/50-user.conf", line 5: invalid attribute 'translate'
Fontconfig error: "/etc/fonts/conf.d/50-user.conf", line 5: invalid attribute 'selector'
Fontconfig error: "/etc/fonts/conf.d/50-user.conf", line 6: invalid attribute 'xmlns:its'
Fontconfig error: "/etc/fonts/conf.d/50-user.conf", line 6: invalid attribute 'version'
Fontconfig warning: "/etc/fonts/conf.d/50-user.conf", line 8: unknown element "description"
Fontconfig warning: "/etc/fonts/conf.d/51-local.conf", line 4: unknown element "its:rules"
Fontconfig warning: "/etc/fonts/conf.d/51-local.conf", line 5: unknown element "its:translateRule"
Fontconfig error: "/etc/fonts/conf.d/51-local.conf", line 5: invalid attribute 'translate'
Fontconfig error: "/etc/fonts/conf.d/51-local.conf", line 5: invalid attribute 'selector'
Fontconfig error: "/etc/fonts/conf.d/51-local.conf", line 6: invalid attribute 'xmlns:its'
Fontconfig error: "/etc/fonts/conf.d/51-local.conf", line 6: invalid attribute 'version'
Fontconfig warning: "/etc/fonts/conf.d/51-local.conf", line 8: unknown element "description"
Fontconfig warning: "/etc/fonts/conf.d/60-generic.conf", line 4: unknown element "its:rules"
Fontconfig warning: "/etc/fonts/conf.d/60-generic.conf", line 5: unknown element "its:translateRule"
Fontconfig error: "/etc/fonts/conf.d/60-generic.conf", line 5: invalid attribute 'translate'
Fontconfig error: "/etc/fonts/conf.d/60-generic.conf", line 5: invalid attribute 'selector'
Fontconfig error: "/etc/fonts/conf.d/60-generic.conf", line 6: invalid attribute 'xmlns:its'
Fontconfig error: "/etc/fonts/conf.d/60-generic.conf", line 6: invalid attribute 'version'
Fontconfig warning: "/etc/fonts/conf.d/60-generic.conf", line 8: unknown element "description"
Fontconfig warning: "/etc/fonts/conf.d/60-latin.conf", line 4: unknown element "its:rules"
Fontconfig warning: "/etc/fonts/conf.d/60-latin.conf", line 5: unknown element "its:translateRule"
Fontconfig error: "/etc/fonts/conf.d/60-latin.conf", line 5: invalid attribute 'translate'
Fontconfig error: "/etc/fonts/conf.d/60-latin.conf", line 5: invalid attribute 'selector'
Fontconfig error: "/etc/fonts/conf.d/60-latin.conf", line 6: invalid attribute 'xmlns:its'
Fontconfig error: "/etc/fonts/conf.d/60-latin.conf", line 6: invalid attribute 'version'
Fontconfig warning: "/etc/fonts/conf.d/60-latin.conf", line 8: unknown element "description"
Fontconfig warning: "/etc/fonts/conf.d/65-fonts-persian.conf", line 34: unknown element "its:rules"
Fontconfig warning: "/etc/fonts/conf.d/65-fonts-persian.conf", line 35: unknown element "its:translateRule"
Fontconfig error: "/etc/fonts/conf.d/65-fonts-persian.conf", line 35: invalid attribute 'translate'
Fontconfig error: "/etc/fonts/conf.d/65-fonts-persian.conf", line 35: invalid attribute 'selector'
Fontconfig error: "/etc/fonts/conf.d/65-fonts-persian.conf", line 36: invalid attribute 'xmlns:its'
Fontconfig error: "/etc/fonts/conf.d/65-fonts-persian.conf", line 36: invalid attribute 'version'
Fontconfig warning: "/etc/fonts/conf.d/65-nonlatin.conf", line 4: unknown element "its:rules"
Fontconfig warning: "/etc/fonts/conf.d/65-nonlatin.conf", line 5: unknown element "its:translateRule"
Fontconfig error: "/etc/fonts/conf.d/65-nonlatin.conf", line 5: invalid attribute 'translate'
Fontconfig error: "/etc/fonts/conf.d/65-nonlatin.conf", line 5: invalid attribute 'selector'
Fontconfig error: "/etc/fonts/conf.d/65-nonlatin.conf", line 6: invalid attribute 'xmlns:its'
Fontconfig error: "/etc/fonts/conf.d/65-nonlatin.conf", line 6: invalid attribute 'version'
Fontconfig warning: "/etc/fonts/conf.d/65-nonlatin.conf", line 8: unknown element "description"
Fontconfig warning: "/etc/fonts/conf.d/69-unifont.conf", line 4: unknown element "its:rules"
Fontconfig warning: "/etc/fonts/conf.d/69-unifont.conf", line 5: unknown element "its:translateRule"
Fontconfig error: "/etc/fonts/conf.d/69-unifont.conf", line 5: invalid attribute 'translate'
Fontconfig error: "/etc/fonts/conf.d/69-unifont.conf", line 5: invalid attribute 'selector'
Fontconfig error: "/etc/fonts/conf.d/69-unifont.conf", line 6: invalid attribute 'xmlns:its'
Fontconfig error: "/etc/fonts/conf.d/69-unifont.conf", line 6: invalid attribute 'version'
Fontconfig warning: "/etc/fonts/conf.d/70-no-bitmaps.conf", line 4: unknown element "its:rules"
Fontconfig warning: "/etc/fonts/conf.d/70-no-bitmaps.conf", line 5: unknown element "its:translateRule"
Fontconfig error: "/etc/fonts/conf.d/70-no-bitmaps.conf", line 5: invalid attribute 'translate'
Fontconfig error: "/etc/fonts/conf.d/70-no-bitmaps.conf", line 5: invalid attribute 'selector'
Fontconfig error: "/etc/fonts/conf.d/70-no-bitmaps.conf", line 6: invalid attribute 'xmlns:its'
Fontconfig error: "/etc/fonts/conf.d/70-no-bitmaps.conf", line 6: invalid attribute 'version'
Fontconfig warning: "/etc/fonts/conf.d/70-no-bitmaps.conf", line 8: unknown element "description"
Fontconfig warning: "/etc/fonts/conf.d/80-delicious.conf", line 4: unknown element "its:rules"
Fontconfig warning: "/etc/fonts/conf.d/80-delicious.conf", line 5: unknown element "its:translateRule"
Fontconfig error: "/etc/fonts/conf.d/80-delicious.conf", line 5: invalid attribute 'translate'
Fontconfig error: "/etc/fonts/conf.d/80-delicious.conf", line 5: invalid attribute 'selector'
Fontconfig error: "/etc/fonts/conf.d/80-delicious.conf", line 6: invalid attribute 'xmlns:its'
Fontconfig error: "/etc/fonts/conf.d/80-delicious.conf", line 6: invalid attribute 'version'
Fontconfig warning: "/etc/fonts/conf.d/90-synthetic.conf", line 4: unknown element "its:rules"
Fontconfig warning: "/etc/fonts/conf.d/90-synthetic.conf", line 5: unknown element "its:translateRule"
Fontconfig error: "/etc/fonts/conf.d/90-synthetic.conf", line 5: invalid attribute 'translate'
Fontconfig error: "/etc/fonts/conf.d/90-synthetic.conf", line 5: invalid attribute 'selector'
Fontconfig error: "/etc/fonts/conf.d/90-synthetic.conf", line 6: invalid attribute 'xmlns:its'
Fontconfig error: "/etc/fonts/conf.d/90-synthetic.conf", line 6: invalid attribute 'version'
Fontconfig error: Cannot load default config file
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
/usr/bin/google-chrome-stable: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /lib/x86_64-linux-gnu/libpng16.so.16)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
makeblastdb: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
blastn: /home/allison/Programs/Easyfig_2.2.2_linux/libz.so.1: version `ZLIB_1.2.9' not found (required by /usr/lib/ncbi-blast+/libxcompress.so)
It does, however run the GUI. I have chosen the Blast location, and the program will create and save the Blast output files correctly the first time, but after that it does not save the .out files to the directory.
Can you please help me resolve this issue?
I have attached a screenshot of the error message.
Kind regards,
Allison
I want to show the cds comparison results of two genomes , but I do not know how to prepare the input blast file for easyfig. I have tried using blastp results as input but It seems not right.
Hello,
I have just started using EasyFig and the example 2 in the handy tutorial is exactly what i want to achieve, i have several STEC sample and am looking to compare thier prophage regions to the sakai reference. However, when i try to add in the phage annotations to my GBK files i can't seem to get Easy Fig to recgnoise them. As far as i'm away i am adding them in at the same place as the example files but cannot get them to show as purple squares as they do in the example.
Any help would be greatly appreciated!
Many thanks, Matt
http://mjsull.github.io/Easyfig/files.html contains links to version 2.2.2 which generates some errors like #5. Could you update the links to 2.2.3?
Good day,
I installed Easyfig v 2.2.2 for Linux on my Ubuntu machine. I am running the GUI of Easyfig. I downloaded blast automatically, and it worked perfectly for two test runs.
Now it is creating and saving the 1.easyfig.fa and 2.easyfig.fa files, but not the 12.easyfig.out file (although it shows this file in the "Blast files" window of the GUI.
When I try to create a figure, it says that "a selected file does not exist", which I assume is the 12.easyfig.out file.
Any help to get this resolved would be much appreciated.
Kind regards,
Allison
Hello,
I was trying to run Easyfig on Ubuntu 20.04 LTS but I had many problems
a) BLAST+ was not working well
b) I was not having output files
c) Stopped moments after starting
So this is what I did:
I hope this can help!
Hi, when I chose to show gene annotations on top of the figure. Only fist 10 letters of the gene's name were shown. How can I make it show the full name?
Hi,
I'm using EasyFig V2.2.2 (the latest release obtained from your "Downloads" section).
It works fine in GUI-mode, but when I try to run EasyFig from the commandline like this:
Easyfig -o prelim_easyfig.bmp -blastn -filter myfasta1.fasta myfasta2.fasta
I get this error:
Traceback (most recent call last):
File "<string>", line 10988, in <module>
NameError: name 'genBlast' is not defined
This problem was reported already in Issue #2, but the poster said that this issue only occured in the official release, not in the most current github-version.
Therefore I tried to clone the github-version instead. However, in that case I only get an "Easyfig.py" and an "setup.py" file. None of them seem to run on my System (Linux Ubuntu 14.04).
Error when running "setup.py":
File "setup.py", line 4, in <module>
from cx_Freeze import setup, Executable
ImportError: No module named cx_Freeze
Error when running "EasyFig.py":
Traceback (most recent call last):
File "Easyfig.py", line 11452, in <module>
root = Tk()
File "/usr/lib/python2.7/lib-tk/Tkinter.py", line 1767, in __init__
self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use)
_tkinter.TclError: Can't find a usable init.tcl in the following directories:
/tmp/staden-generic-root/lib/tcl8.6 /usr/lib/tcl8.6 /lib/tcl8.6 /usr/library /library /tcl8.6.1/library /tcl8.6.1/library
This probably means that Tcl wasn't installed properly.
How do I Install the current github-version?
Would it be possible to exchange the current release in the "Download" section by a version where this bug is fixed (GUIs can be nice, but I would like to automize this task by including it in my shell scripts)?
EDIT:
The same problem also occurs when running the released Python-version "Easyfig.py" from your Download-section:
File "/home/john/Downloads/Easyfig.py", line 10988, in <module>
inlist = genBlast(templist, cutlist)
NameError: name 'genBlast' is not defined
Hi Mitchell,
I am trying to use Easyfig binary to depict syntenic blocks across plant genomes. Given that most genes comprise many introns tblastx across the genome nucleotide sequences does not generate the gene-to-gene alignments that I am aiming for but rather produces many small alignments representing individual exons.
Is there a way to generate blastp alignments based on the translated proteins?
Thanks for your advice
I have compared two plasmid sequences that are almost identical (0 SNPs identified by snippy and progressiveMAUVE). Also, alignment of the sequences in CLC and MEGA have shown a perfect alignment except the first 1031 bp, which are only present in one of the plasmids. However, in the figure created by EasyFig, several differences are indicated. Any idea what has happened? I have tried to take a look at the .out file from BLAST, and it seems that some regions are compared several times etc. Could this be the reason fro the errors in the figure? Any suggestions on how to solve this? :)
When I open Easyfig, it will open many interactive interface continually and automatically, like Create Figure, Add folder, and others.I have downloaded the latest version 2.2.5，also has the same problem and appear this window.
Does anyone know how to solve it？Thanks very much.
Sometimes appear these words：
Runt1me Error1
Program D:\F 列M3\Easyfig_22.3_win\Easyfig.exe
This application has requested the Runtime to terminate it in an unusual way,
Please contact the application's support team for more information.
Hi,
I have been trying to use Easyfig2.1 (the latest version has in our experience not cooperated as well with our hardware - running on Windows 10) to generate some alignments. I add genbank annotation files and click to generate blastn files, which works okay and the files appear in the UI. I then go to create the figure but consistently get an error message stating 'A selected file does not exist', referring to the blast files because when I run without any of those files it is okay.
I am trying to figure out the problem but have failed to make any progress. I have tried going to the file location stated in the UI (once generated, the file path is shown in the UI for each blast file), but there are no easyfig files in that pathway with the same name. The UI name is "C:/Users/pathway/12.easyfig.out" etc but in the folder all that is generated is files with the name 1.easyfig.fa, 2.easyfig,fa etc.
Do you have any suggestions? Any help would be greatly appreciated!
I have attached some images which hopefully illustrate my issue a little more. The console image is of when the blastn is running.
Best,
Hello,
I have downloaded EasyFig 2.2.4. I am using BLAST+ version 2.2.3 32-bit windows. I am on windows 10. When I compare two embl formatted files that have annotation and sequence, I get only the fasta files created, but no comparison files. Please advice.
Thanks
Abhijit
I have a genome contig of about 30 kbp that I did an annotation using RAST and I downloaded as EMBL and also as Genbank file to compare with a plasmid in the NCBI database. When I insert the EMBL file or the Genbank file and the reference plasmid (NCBI) in easyfig, I got only the genes as arrows in the reference plasmid and my sequence appears as a black line without the arrows. How can I add the arrows as genes by using a RAST annotation?
Thanks in advance!
Hi,
I encountered a very strange issue while using Easyfig_2.2.5_win version, my windows version is 1809, and I did not install any python related packages. But when I open Easyfig, it will open interactive interface continually and automatically, like Create Figure, Add folder, and others.
Please help to clarify this issue.
Many thanks!
Lucas
Hey there! First of all, let me thank you for this great tool and for still keeping it updated after a long time.
I am using Easyfig to generate multiple figures for multiple sets of genomes. Since I am doingthis with a custom script that calls Easyfig at the end to generate the images, it's a bit hard to keep track of the identity of the genomes included in each image and, more importantly, which genome is which one within one image.
For example, I would really like to have the respective genome ID (or file name, which in my case is the ID) printed to the left of each genome "line" in the final image. Is there an Easyfig feature that does something like this? If not, it would be really great if this could be added in the future.
Hi,
I'm trying to generate Blast files using EasyFig (2.2.2) but I am unable to do so. I've restarted EasyFig, downloaded Blast manually but EasyFig still cannot locate the Blast location and perform Blast. I wonder if it is possible to perform Blast online and download the output files to use this as the Blast files?
Best,
Liyana
The Easyfig version listed under download on the webpage (which is the first hit you get when you google the tool) is outdated and still contains the error reported in Issue #2 :
Traceback (most recent call last):
File "<string>", line 10988, in <module>
NameError: name 'genBlast' is not defined
Maybe the download section of that page should directly refer to this github-page instead?
When adjusting the rectangle feature's (rect) outline thickness (genet), only the left and bottom segments of the rectangle are adjusted. The right and top remain at default thickness (1 pixel).
Observed at both CLI and GUI.
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