In OS X 10.14 (Mojave) we have installed Open JDK 12.0.1 (confirmed with java - version) and Artemis (3692:32994) repeatedly says "This application requires that Java 9 or later be installed on your computer." Java path is correct.

Tried on 2 Macs, one of which had never seen Java or Artemis. Same error.

Any hints?

Hi,

After a first unsuccessful attempt to install Artemis for Windows (I did try to install Java 11 first), I installed Artemis via Bioconda, following the instructions:
http://sanger-pathogens.github.io/Artemis/Artemis/

It seems everything worked, however, I can't run 'art'.

'art' is not recognized as an internal or external command,
operable program or batch file.

How can I solve this?

Thank you

Hi,
I'm really pleased to see that artemis is moving into a conda package but there seems to be a problem with the current version. Looks like conda only supports up to Java version 8 (?). I'm seeing the following error when I run 'conda install -c bioconda artemis':

Collecting package metadata: done
Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

• artemis -> openjdk[version='>=9']

Current channels:

• https://conda.anaconda.org/bioconda/osx-64
• https://conda.anaconda.org/bioconda/noarch
• https://repo.anaconda.com/pkgs/main/osx-64
• https://repo.anaconda.com/pkgs/main/noarch
• https://repo.anaconda.com/pkgs/free/osx-64
• https://repo.anaconda.com/pkgs/free/noarch
• https://repo.anaconda.com/pkgs/r/osx-64
• https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

https://anaconda.org

and use the search bar at the top of the page.

AND for 'conda search openjdk':

Loading channels: done

Name Version Build Channel

openjdk 8.0.121 0 pkgs/free
openjdk 8.0.121 1 pkgs/free
openjdk 8.0.152 h393ad39_1 pkgs/main
openjdk 8.0.152 he2ab291_0 pkgs/main

I try to click the blast in artemis, but always no response. The version 12.0 in my old computer works. The new version and old version do not woke on my new computer and on my lab member's. What setting should I change? Thank you.

Hi, I'm trying Artemis for the first time on Mac OS 10.14 (Mojave).

It was successfully installed but on running ./art the introductory window appears and then freezes. The following thrown exception is shown in the terminal: "This version of Mac OS X does not support the Apple EAWT. ApplicationEvent handling has been disabled (java.lang.ClassNotFoundException: com.apple.eawt.ApplicationListener)" (full stack trace attached)

Does this mean the Artemis GUI can't be used on the latest Mac OS? Or can I install something to bypass this error? Thanks

Stack_trace.txt

Instead it is truncated to 2 decimals.
Artemis 18.0.3 on Windows
example:
ftp://ftp.sanger.ac.uk/pub/resources/coursesandconferences/Online_Courses/Course3/data/Mycobacterium_leprae_TN_v1.embl
for the pseudogene ML0421 it shows 55.72% instead of 55.73% ((127 + 92) / 393 = 55.7251908... %) and for the pseudogene gnd2 it shows 56.23% instead of 56.24% ((333 + 235) / 1010 = 56.237623762... %)

I'm trying to open some bam files in the DNA plotter.
The bam files contain extracellular DNA sequences aligned to the reference genome. the bamview window of the artemis software let me visualize coverage of the genome, but I'd like to depict it in the whole genome representation of the DNAplotter.
I've tried to convert bamfiles into different formats but no success.
Is there a format that can be read by DNAplotter that also contains the coverage information?

Thank you

running act -help will print the help, but return 1 as a return code.

It should return 0

$ act -help; echo $?
SYNOPSIS
       Artemis Comparison Tool (ACT): Genome Comparison Tool
USAGE
        act [options] <SEQUENCE_1> <COMPARISON_1_2> <SEQUENCE_2> ...
OPTIONS
        SEQUENCE                   An EMBL, GenBank, FASTA, or GFF3 file
        FEATURE                    An Artemis TAB file, or GFF file
        COMPARISON                 A BLAST comparison file in tabular format

        -options FILE              Read a text file of options from FILE
        -chado                     Connect to a Chado database (using PGHOST, PGPORT, PGDATABASE, PGUSER environment variables)

        -Dblack_belt_mode=?         Keep warning messages to a minimum [true,false]
        -DuserplotX=FILE[,FILE2]    For sequence 'X' open one or more userplots
        -DloguserplotX=FILE[,FILE2] For sequence 'X' open one or more userplots, take log(data)
        -DbamX=FILE[,FILE2,...]     For sequence 'X' open one or more BAM, CRAM, VCF, or BCF files
        -Dchado="h:p/d?u"           Get ACT to open this CHADO database
        -Dread_only                 Open CHADO database read-only
EXAMPLES
        % act
        % act af063097.embl af063097_v_b132222.crunch b132222.embl
        % act -Dblack_belt_mode=true -Dbam1=MAL_0h.bam -Dbam2=MAL_7h.bam,var.raw.new.bcf
        % act -Duserplot2=/pathToFile/userPlot

HOMEPAGE
        http://www.sanger.ac.uk/science/tools/artemis-comparison-tool-act

1

I have just installed artemis via bioconda. When I start act, it exits, showing the errors below:

(base) [zyw@localhost pkgs]$ act
Starting ACT with arguments: -mx2g -ms100m -noverify --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.util=ALL-
UNNAMED -Djdbc.drivers=org.postgresql.Driver -Dartemis.environment=UNIX Unrecognized option: --add-opens=java.base/java.lang=ALL-UNNAMED
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.

How can I fix it?

When I run jannovar-cli-0.18.jar annotate-vcf , I got some problems.

The exception is:
Extending header with INHERITANCE...
Exception in thread "main" java.lang.NullPointerException
at de.charite.compbio.jannovar.mendel.filter.GeneWiseMendelianAnnotationProcessor.put(GeneWiseMendelianAnnotationProcessor.java:115)
at de.charite.compbio.jannovar.mendel.filter.CoordinateSortingChecker.put(CoordinateSortingChecker.java:46)
at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)
at java.util.stream.ReferencePipeline$11$1.accept(ReferencePipeline.java:373)
at java.util.Iterator.forEachRemaining(Iterator.java:116)
at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151)
at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.forEachOrdered(ReferencePipeline.java:423)
at de.charite.compbio.jannovar.cmd.annotate_vcf.AnnotateVCFCommand.run(AnnotateVCFCommand.java:133)
at de.charite.compbio.jannovar.Jannovar.main(Jannovar.java:62)

I try to debug it but I hardly read it because of the long relationship or chain. So I search for help here.

Commandline is:
java -Xms4G -Xms4G -jar ~/tools/jannovar/jannovar-cli-0.18.jar annotate-vcf -d ~/tools/jannovar/data/hg19_refseq.ser -i partital.vcf -o ped_result_v2.vcf --pedigree-file ../../lung_cancer.ped

After I search from google, I guess it is the problem from my vcf inputed.

So I want to know what the situation will cause this error. Thank you.

Hi!
When I try to install the latest version it tells me I need Java 9+ to use it. However, the highest version I can access for Mac OSX on java.com page is 8. Do you have any suggestion on how to solve this?
Best wishes,
k

Hello when I double click on the .jar file I get the error:

Error: A JNI error has occurred, please check your installation and try again

This is on a windows 10 machine, can someone please help me?

Thanks

I'm using Artemis 18.0.1 on Windows 10 with Java version "1.8.0_241".
I see this error across two machines with the same specifications and with multiple .gbk/.fasta files

I search for a given sequence, and it claims to have found it, but the highlighted string does not match the search query

Next, I attempted to 'View the bases of selection as Fasta'

This shows the same result as the query. The issue appears to be in the display of the DNA Viewer!

A similar problem: I use the navigator to go to base 5606. It's unclear from the DNA Viewer what this base is since the highlighted area doesn't clearly highlight a single base, but it appears to be a 'T'

Now, I select that base as fasta:
And it says it's a G

Artemis alredy can handle opening two seperate genbanks in seperate windows.
However if a multi-genbank file (multiple genbanks concatenated into a single file, seperated by file-end symbols "//") is opened, only the first contig is viewed. All other contigs are ignored.

As it is common practice to handle and store fragmented genomes and genomes with multiple replicons as multi-genbanks, it would be highly convenient if Artemis could recognize and handle such files.

Hi,

I am wondering if anyone has came across the same issue.
For example:
I edit this gene to remove the last exon only by changing the "Location" entry, copying the ranges in the exon "Location" entry and correcting the mRNA/gene "Location" entry:

Then I save the file with Ctrl+S

When I reopen the same gff file, the gene model is fragmented.

It seems that when saving to the original file Artemis is removing the ID of the gene and the whole model collapses.

Are there any suggestions on how to avoid this?

Thanks

I am trying to build the version 18.1.0 on FreeBSD using maven-3.6.3.
The build fails:

[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  14.474 s
[INFO] Finished at: 2020-01-19T12:21:34-08:00
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal on project artemis: Could not resolve dependencies for project uk.ac.sanger:artemis:jar:18.1.0: The following artifacts could not be resolved: com.ibatis:ibatis:jar:2.3.4.726, com.sshtools:j2ssh-core:jar:0.2.9, org.emboss:jemboss:jar:1.0, org.biojava:biojava:jar:1.6: Could not find artifact com.ibatis:ibatis:jar:2.3.4.726 in central (https://repo.maven.apache.org/maven2) -> [Help 1]
[ERROR] 
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException
*** Error code 1

Hi,

Starting from version 18.2.0, I see, in pom.xml:

@{surefireArgLine}
-Dlog4j.configurationFile=file:${project.build.testOutputDirectory}/log4j.properties

in the definition of the properties of the surefire plugin. Yet, by doing so, the second definition erases the first one, so that the whole @{surefireArgLine} is skipped.

Using
@{surefireArgLine} -Dlog4j.configurationFile=file:${project.build.testOutputDirectory}/log4j.properties
instead fixes this.

Regards,

Pierre

Hi,

In Artemis, Graph: Add User Plot will not open a file with brackets in the name: filename snps.depth (1).gz

(This file had the (1) appended when it was re-downloaded to mac).

Edited to add: the file also won't open with just the space in it (without the (1)) and also with a different name, e.g. snps.dept.gz, but will if these are changed to the (correct) name snps.depth.gz

Artemis (release 16.0.0) on Mac (Sierra 10.12.1)

Thanks!

Hi,
I am using Artemis on Windows 10. After saving file using "Save An Entry As ..." and adding name to the file, I tried to open the file using Artemis, but failed to do so. The error message I received is: "read failed: entry contains no sequence". What could be the reason behind this error? What would the solution be?

FYI - it seems all the MacOS files got into the tar file:

artemis/
artemis/._act
artemis/act
artemis/._art
artemis/art
artemis/artemis_sqlmap/
artemis/._bamview
artemis/bamview
artemis/._dnaplotter
artemis/dnaplotter
artemis/etc/
artemis/images/
artemis/lib/
artemis/._Makefile
artemis/Makefile
artemis/org/
artemis/._README.md
artemis/README.md
artemis/._setenv
artemis/setenv
artemis/uk/
artemis/uk/ac/
artemis/uk/ac/sanger/
artemis/uk/ac/sanger/artemis/
artemis/uk/ac/sanger/artemis/._.project
artemis/uk/ac/sanger/artemis/.project
artemis/uk/ac/sanger/artemis/Action.class
artemis/uk/ac/sanger/artemis/._Action.java
artemis/uk/ac/sanger/artemis/Action.java
artemis/uk/ac/sanger/artemis/ActionController.class
artemis/uk/ac/sanger/artemis/._ActionController.java
artemis/uk/ac/sanger/artemis/ActionController.java
artemis/uk/ac/sanger/artemis/ActionVector.class
artemis/uk/ac/sanger/artemis/._ActionVector.java
artemis/uk/ac/sanger/artemis/ActionVector.java
artemis/uk/ac/sanger/artemis/AlignMatch.class
artemis/uk/ac/sanger/artemis/._AlignMatch.java
artemis/uk/ac/sanger/artemis/AlignMatch.java

Does Artemis work correctly under open source JDKs/JREs such as OpenJDK or Corretto?

Oracle now requires organizations/businesses to license their Java JDK.

I hope everyone is doing well through these tough times.

As shown in the attached image (which may not be a good example) I have encountered a case where when loading a fully annotated gff file to an ACT comparison view, only a small part of the annotation is shown.
I initially thought that this is due to the comparison file limits but I can see that the comparison actually covers the full length.

Has anyone seen something like this before and what does it imply? What could I have been doing wrong here ?

NB: When the genome is visualized with Artemis it is clearly annotated throughout until the end but with ACT only a small portion is seen.

I really look forward to your contributions.

Hi, I'm sure this is a very naive problem, but once I download Artemis on my Windows 10 machine and then extract the files, I don't see any .jar files for atremis.jar or act.jar. I can't figure out what's going wrong. Downloading Artemis from github doesn't seem to produce a "artemis-windows-release-{version}.zip" folder but rather produces a "Artemis-master" folder which seems to lac the necessary .jar files to effectively use Artemis. Any help resolving this would be greatly appreciated.

Thanks!

I have the appropriate java version and previously used Artemis version 18.0.2. I have now deleted that version and downloaded the new one but Artemis is not starting on my windows. When I open artemis.jar file, it asks me how I want to open this file and shows applications in my laptop to open it, Please guide me on how to solve this issue. Thank you.

Is it possible install Artemis on Server platform like Fedora? or cluster-like platform?

The documentation that explains how to increase memory doesn't actually explain how to pass the argument when starting Artemis. All it says is:

-Xmsn -Xmxn

Use -Xmsn to specify the initial size, in bytes, of the memory allocation pool. This value must be a multiple of 1024 greater than 1MB. Append the letter k or K to indicate kilobytes, or m or M to indicate megabytes.

Use -Xmxn to specify the maximum size, in bytes, of the memory allocation pool. This value must a multiple of 1024 greater than 2MB. Append the letter k or K to indicate kilobytes, or m or M to indicate megabytes.

When I try to start Artemis by passing a maximum memory size argument, this is what prints to the screen:

./art -Xmx20g
Starting Artemis with arguments: -mx2g -ms100m -noverify --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.util=ALL-UNNAMED -Djdbc.drivers=org.postgresql.Driver -Dartemis.environment=UNIX  -Xmx20g
Exception in thread "Thread-0" java.lang.NullPointerException
	at uk.ac.sanger.artemis.j2ssh.SshFileManager.getSftpClient(SshFileManager.java:92)
	at uk.ac.sanger.artemis.j2ssh.SshFileManager.access$000(SshFileManager.java:47)
	at uk.ac.sanger.artemis.j2ssh.SshFileManager$SshGet.run(SshFileManager.java:419)
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
	at uk.ac.sanger.artemis.j2ssh.SshFileManager$SshGet.getByteArray(SshFileManager.java:444)
	at uk.ac.sanger.artemis.j2ssh.SshFileManager.getFileContents(SshFileManager.java:378)
	at uk.ac.sanger.artemis.components.filetree.FileList.getFileContents(FileList.java:146)
	at uk.ac.sanger.artemis.components.filetree.RemoteFileNode.getFileContents(RemoteFileNode.java:327)
	at uk.ac.sanger.artemis.util.RemoteFileDocument.getInputStream(RemoteFileDocument.java:115)
	at uk.ac.sanger.artemis.io.DocumentEntryFactory.makeDocumentEntry(DocumentEntryFactory.java:86)
	at uk.ac.sanger.artemis.components.EntryFileDialog.getEntryFromFileHelper(EntryFileDialog.java:242)
	at uk.ac.sanger.artemis.components.EntryFileDialog.getEntryFromFile(EntryFileDialog.java:299)
	at uk.ac.sanger.artemis.components.ArtemisMain.readArgsAndOptions(ArtemisMain.java:419)
	at uk.ac.sanger.artemis.components.ArtemisMain$10.run(ArtemisMain.java:795)
	at java.desktop/java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:313)
	at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:770)
	at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:721)
	at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:715)
	at java.base/java.security.AccessController.doPrivileged(Native Method)
	at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85)
	at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:740)
	at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
	at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
	at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
	at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
	at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)

Additionally, a pop up window shows up indicating "File not found -Xmx20g". When I click "OK" to dismiss the pop up window, a new window pops up and appears to be an SSH initiation window, as this window asks for login credentials for a hostname and a default port 22.

Any suggestions on how to pass the memory argument to Artemis?

Hi,
I wonder how to prepare the wiggle file for Artemis v16.0.0?

I used bam2wig in Augustus to convert bam to wig, as follows:

track name=paragon.vs.Bac3DLv2.NnoN.f.bam type=wiggle_0
variableStep chrom=ctg00006_001_A08.flt500_scaffold_1
585 1
586 1
587 1
588 1
589 2
590 2
591 2
592 2
593 2
594 2

but when I add user plot..., it showed some error: error while reading user data: uk.ac.sanger.artemis.io.ReadFormatException: the base position (7840) is greater than the sequence length:
7840 6

when I change to another scaffolds, it would show the similar error but different base num. I guess Artemis try to add all the wiggle to current chr/scaffold.

Or did I use a wrong way to add wiggle plot? What the right way.

The IGV did not report any error to my wiggle file. that's a little strange?

F

Hi

I'm trying to load a set of VCF files into Artemis for Mac. I've produced the VCF v4.1 files using FreeBayes and they have been phased using BEAGLE.

After using the Read BAM/VCF and select my files, nothing happens. Any clues of what might be the error or if this is a known issue?

Thanks in advance

Hi,

pom.xml does not mention htsjdk in the dependencies, although it is called in the code. I suggest adding

in the dependencies part.

Best,
Pierre

Just installed Artemis 18.0.3 on OSX 10.15.7 with the Java 15.0.2 and get the "This application requires that Java 9 or later be installed".

Java was installed via brew.

(I can get Artemis to run if I run the ./art script from the command line)

Dear,

I was wondering if there is support for reading annotations/features from BED(12) format?.
If not, are there any plans to include this in the artemis tool?

thx in advance,

Hi,
I did not manage to install Artemis with mvn
Do you know why I get this error ?

`bla@linne:~/Software/Artemis$ mvn -e clean package
[INFO] Error stacktraces are turned on.
[INFO] Scanning for projects...
[INFO]
[INFO] ------------------------< uk.ac.sanger:artemis >------------------------
[INFO] Building Artemis 18.1.0
[INFO] --------------------------------[ jar ]---------------------------------
[INFO]
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ artemis ---
[INFO] Deleting /home/rigou/Software/Artemis/target
[INFO]
[INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-maven-3) @ artemis ---
[INFO]
[INFO] --- maven-install-plugin:2.5.2:install-file (install-biojava-jar) @ artemis ---
[INFO] pom.xml not found in biojava.jar
[INFO] Installing /home/rigou/Software/Artemis/lib/biojava.jar to /home/rigou/.m2/repository/org/biojava/biojava/1.6/biojava-1.6.jar
[INFO] Installing /tmp/mvninstall8209771311433696208.pom to /home/rigou/.m2/repository/org/biojava/biojava/1.6/biojava-1.6.pom
[INFO]
[INFO] --- maven-install-plugin:2.5.2:install-file (install-jemalign-jar) @ artemis ---
[INFO] pom.xml not found in jemAlign.jar
[INFO] Installing /home/rigou/Software/Artemis/lib/jemAlign.jar to /home/rigou/.m2/repository/org/emboss/jemboss/1.0/jemboss-1.0.jar
[INFO] Installing /tmp/mvninstall2291838399772923129.pom to /home/rigou/.m2/repository/org/emboss/jemboss/1.0/jemboss-1.0.pom
[INFO]
[INFO] --- maven-install-plugin:2.5.2:install-file (install-j2ssh-core-jar) @ artemis ---
[INFO] pom.xml not found in j2ssh-core.jar
[INFO] Installing /home/rigou/Software/Artemis/lib/j2ssh-core.jar to /home/rigou/.m2/repository/com/sshtools/j2ssh-core/0.2.9/j2ssh-core-0.2.9.jar
[INFO] Installing /tmp/mvninstall94387948769839764.pom to /home/rigou/.m2/repository/com/sshtools/j2ssh-core/0.2.9/j2ssh-core-0.2.9.pom
[INFO]
[INFO] --- maven-install-plugin:2.5.2:install-file (install-ibatis-jar) @ artemis ---
[INFO] pom.xml not found in ibatis-2.3.4.726.jar
[INFO] Installing /home/rigou/Software/Artemis/lib/ibatis-2.3.4.726.jar to /home/rigou/.m2/repository/com/ibatis/ibatis/2.3.4.726/ibatis-2.3.4.726.jar
[INFO] Installing /tmp/mvninstall5370814239589167909.pom to /home/rigou/.m2/repository/com/ibatis/ibatis/2.3.4.726/ibatis-2.3.4.726.pom
[INFO]
[INFO] --- properties-maven-plugin:1.0.0:read-project-properties (load-external-properties) @ artemis ---
[INFO] Quiet processing - ignoring properties cannot be loaded from File: /home/rigou/Software/Artemis/maven.properties
[INFO]
[INFO] --- maven-antrun-plugin:1.8:run (updating-software-version-number) @ artemis ---
[INFO] Executing tasks

main:
[INFO] Executed tasks
[INFO]
[INFO] --- jacoco-maven-plugin:0.8.2:prepare-agent (pre-unit-test) @ artemis ---
[INFO] Skipping JaCoCo execution because property jacoco.skip is set.
[INFO]
[INFO] --- maven-resources-plugin:3.0.2:resources (default-resources) @ artemis ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 35 resources
[INFO]
[INFO] --- maven-resources-plugin:3.0.2:copy-resources (copy-property-files) @ artemis ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 37 resources
[INFO]
[INFO] --- maven-resources-plugin:3.0.2:copy-resources (copy-icons-folder) @ artemis ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 5 resources
[INFO]
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ artemis ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 585 source files to /home/rigou/Software/Artemis/target/classes
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 2.827 s
[INFO] Finished at: 2020-01-30T17:34:03+01:00
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.8.0:compile (default-compile) on project artemis: Fatal error compiling: invalid flag: --release -> [Help 1]
org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.8.0:compile (default-compile) on project artemis: Fatal error compiling
at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:215)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:156)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:148)
at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:117)
at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:81)
at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build (SingleThreadedBuilder.java:56)
at org.apache.maven.lifecycle.internal.LifecycleStarter.execute (LifecycleStarter.java:128)
at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:305)
at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:192)
at org.apache.maven.DefaultMaven.execute (DefaultMaven.java:105)
at org.apache.maven.cli.MavenCli.execute (MavenCli.java:956)
at org.apache.maven.cli.MavenCli.doMain (MavenCli.java:288)
at org.apache.maven.cli.MavenCli.main (MavenCli.java:192)
at sun.reflect.NativeMethodAccessorImpl.invoke0 (Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke (NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke (DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke (Method.java:498)
at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced (Launcher.java:282)
at org.codehaus.plexus.classworlds.launcher.Launcher.launch (Launcher.java:225)
at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode (Launcher.java:406)
at org.codehaus.plexus.classworlds.launcher.Launcher.main (Launcher.java:347)
Caused by: org.apache.maven.plugin.MojoExecutionException: Fatal error compiling
at org.apache.maven.plugin.compiler.AbstractCompilerMojo.execute (AbstractCompilerMojo.java:1140)
at org.apache.maven.plugin.compiler.CompilerMojo.execute (CompilerMojo.java:188)
at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo (DefaultBuildPluginManager.java:137)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:210)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:156)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:148)
at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:117)
at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:81)
at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build (SingleThreadedBuilder.java:56)
at org.apache.maven.lifecycle.internal.LifecycleStarter.execute (LifecycleStarter.java:128)
at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:305)
at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:192)
at org.apache.maven.DefaultMaven.execute (DefaultMaven.java:105)
at org.apache.maven.cli.MavenCli.execute (MavenCli.java:956)
at org.apache.maven.cli.MavenCli.doMain (MavenCli.java:288)
at org.apache.maven.cli.MavenCli.main (MavenCli.java:192)
at sun.reflect.NativeMethodAccessorImpl.invoke0 (Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke (NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke (DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke (Method.java:498)
at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced (Launcher.java:282)
at org.codehaus.plexus.classworlds.launcher.Launcher.launch (Launcher.java:225)
at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode (Launcher.java:406)
at org.codehaus.plexus.classworlds.launcher.Launcher.main (Launcher.java:347)
Caused by: org.codehaus.plexus.compiler.CompilerException: invalid flag: --release
at org.codehaus.plexus.compiler.javac.JavaxToolsCompiler.compileInProcess (JavaxToolsCompiler.java:173)
at org.codehaus.plexus.compiler.javac.JavacCompiler.performCompile (JavacCompiler.java:174)
at org.apache.maven.plugin.compiler.AbstractCompilerMojo.execute (AbstractCompilerMojo.java:1129)
at org.apache.maven.plugin.compiler.CompilerMojo.execute (CompilerMojo.java:188)
at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo (DefaultBuildPluginManager.java:137)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:210)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:156)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:148)
at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:117)
at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:81)
at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build (SingleThreadedBuilder.java:56)
at org.apache.maven.lifecycle.internal.LifecycleStarter.execute (LifecycleStarter.java:128)
at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:305)
at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:192)
at org.apache.maven.DefaultMaven.execute (DefaultMaven.java:105)
at org.apache.maven.cli.MavenCli.execute (MavenCli.java:956)
at org.apache.maven.cli.MavenCli.doMain (MavenCli.java:288)
at org.apache.maven.cli.MavenCli.main (MavenCli.java:192)
at sun.reflect.NativeMethodAccessorImpl.invoke0 (Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke (NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke (DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke (Method.java:498)
at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced (Launcher.java:282)
at org.codehaus.plexus.classworlds.launcher.Launcher.launch (Launcher.java:225)
at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode (Launcher.java:406)
at org.codehaus.plexus.classworlds.launcher.Launcher.main (Launcher.java:347)
Caused by: java.lang.IllegalArgumentException: invalid flag: --release
at com.sun.tools.javac.api.JavacTool.processOptions (JavacTool.java:206)
at com.sun.tools.javac.api.JavacTool.getTask (JavacTool.java:156)
at com.sun.tools.javac.api.JavacTool.getTask (JavacTool.java:107)
at com.sun.tools.javac.api.JavacTool.getTask (JavacTool.java:64)
at org.codehaus.plexus.compiler.javac.JavaxToolsCompiler.compileInProcess (JavaxToolsCompiler.java:125)
at org.codehaus.plexus.compiler.javac.JavacCompiler.performCompile (JavacCompiler.java:174)
at org.apache.maven.plugin.compiler.AbstractCompilerMojo.execute (AbstractCompilerMojo.java:1129)
at org.apache.maven.plugin.compiler.CompilerMojo.execute (CompilerMojo.java:188)
at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo (DefaultBuildPluginManager.java:137)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:210)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:156)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:148)
at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:117)
at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:81)
at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build (SingleThreadedBuilder.java:56)
at org.apache.maven.lifecycle.internal.LifecycleStarter.execute (LifecycleStarter.java:128)
at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:305)
at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:192)
at org.apache.maven.DefaultMaven.execute (DefaultMaven.java:105)
at org.apache.maven.cli.MavenCli.execute (MavenCli.java:956)
at org.apache.maven.cli.MavenCli.doMain (MavenCli.java:288)
at org.apache.maven.cli.MavenCli.main (MavenCli.java:192)
at sun.reflect.NativeMethodAccessorImpl.invoke0 (Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke (NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke (DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke (Method.java:498)
at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced (Launcher.java:282)
at org.codehaus.plexus.classworlds.launcher.Launcher.launch (Launcher.java:225)
at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode (Launcher.java:406)
at org.codehaus.plexus.classworlds.launcher.Launcher.main (Launcher.java:347)
[ERROR]
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR]
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
`

Thank you !

Hi,
I am a new Artemis user here. I experienced an error whenever I tried to save files. The error message I received was "error while saving: java.io.FileNotFoundException: File_Name (Access is denied). Has anyone experienced this before? How did you solve it?

Hi, I was wondering if it possible to fix the way the frames are ordered in each respective window; so that the reverse frames are either mirrored or in the same order as the forward frames?

Hi all,

I'm new to this subject, and I guess I have a very basic question.

I have my transposon mutant library, and I want to visualize the mapped transposon insertions to the reference genome via DNAplotter (Artemis).

I need the circular plot to be like the attached picture from the literature (where the red lines represent the transposon insertions).

In my case, I can only visualize the reference genome in DNAplotter because it is in EMBL format, but I could not import the transposon insertions to the polt.

The reason may be that non of the output files from BioTradis pipeline are in EMBL, GFF or GENBANK format (the mapped output files of transposon insertions are in BAM and fq.gz). Therefore, could anyone help or suggest how can I visualize the transposon insertions to the reference genome in DNAplotter.

Thanks in advance,

while trying to open the artemis.jar file they are asking for the password, is there any password like that to open the archive.

Dear developer,

I can not use Artemis in my red hat linux system. The error is as follows. Can you help to figure out the reason? Thank you very much.

[root@ts-rd350 Artemis-master]# ./art
Starting Artemis with arguments: -mx2g -ms100m -noverify -Djdbc.drivers=org.postgresql.Driver -Dartemis.environment=UNIX
错误: 找不到或无法加载主类 uk.ac.sanger.artemis.components.ArtemisMain

[root@ts-rd350 Artemis-master]# make
CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/ExternalProgramMonitor.java
/bin/sh: javac: 未找到命令
make: *** [uk/ac/sanger/artemis/ExternalProgramMonitor.class] 错误 127

As you may already be aware, a log4j 2.x vulnerability was identified last week (https://nvd.nist.gov/vuln/detail/CVE-2021-44228). Using the scanning tool from https://github.com/mergebase/log4j-detector , it appears that Artemis v18.1 uses an impacted version of log4j.

log4j-detector output:
artemis\act.jar contains Log4J-2.x >= 2.0-beta9 (< 2.10.0) VULNERABLE :-(
artemis\artemis.jar contains Log4J-2.x >= 2.0-beta9 (< 2.10.0) VULNERABLE :-(
artemis\bamview.jar contains Log4J-2.x >= 2.0-beta9 (< 2.10.0) VULNERABLE :-(
artemis\dnaplotter.jar contains Log4J-2.x >= 2.0-beta9 (< 2.10.0) VULNERABLE :-(

If this is correct, are there any plans to update Artemis to use a patched version of log4j? Thank you.

Hi all
According to their instructions, it accepts a variety of file format types including GFF3.
Hence I used GFF3 files for DNAplotter.
The example of GFF3 is shown below.

##gff-version 3
##gff generated with Blast2GO
##Number of FASTA deflines: 3990
6 AUGUSTUS gene 706 4825 0.14 + . ID=6.g1; seqName=6.g1; HintSupport=0
6 AUGUSTUS mRNA 706 4825 0.14 + . ID=6.g1.t1; Parent=6.g1; seqName=6.g1; HintSupport=0
6 AUGUSTUS transcription_start_site 706 706 . + . Parent=6.g1.t1; seqName=6.g1; HintSupport=0
6 AUGUSTUS exon 706 825 . + . Parent=6.g1.t1; seqName=6.g1; HintSupport=0
6 AUGUSTUS exon 3777 4048 . + . Parent=6.g1.t1; seqName=6.g1; HintSupport=0
6 AUGUSTUS start_codon 3783 3785 . + 0 Parent=6.g1.t1; seqName=6.g1; HintSupport=0
6 AUGUSTUS intron 4049 4163 0.36 + . Parent=6.g1.t1; seqName=6.g1; HintSupport=0
6 AUGUSTUS intron 4219 4305 0.97 + . Parent=6.g1.t1; seqName=6.g1; HintSupport=0
6 AUGUSTUS CDS 3783 4048 0.47 + 0 ID=6.g1.t1.cds; Parent=6.g1.t1; seqName=6.g1; HintSupport=0
6 AUGUSTUS CDS 4164 4218 0.36 + 1 ID=6.g1.t1.cds; Parent=6.g1.t1; seqName=6.g1; HintSupport=0
6 AUGUSTUS exon 4164 4218 . + . Parent=6.g1.t1; seqName=6.g1; HintSupport=0
6 AUGUSTUS CDS 4306 4575 0.94 + 0 ID=6.g1.t1.cds; Parent=6.g1.t1; seqName=6.g1; HintSupport=0
6 AUGUSTUS exon 4306 4825 . + . Parent=6.g1.t1; seqName=6.g1; HintSupport=0
6 AUGUSTUS stop_codon 4573 4575 . + 0 Parent=6.g1.t1; seqName=6.g1; HintSupport=0
6 AUGUSTUS transcription_end_site 4825 4825 . + . Parent=6.g1.t1; seqName=6.g1; HintSupport=0

I tried to visualize this gff3 file, however, got the error messages:

while reading from Blast2GO_gff_1.gff: gene can't have seqName as a qualifier
while reading from Blast2GO_gff_1.gff: gene can't have HintSupport as a qualifier
while reading from Blast2GO_gff_1.gff: mRNA can't have score as a qualifier
while reading from Blast2GO_gff_1.gff: transcription_start_site is not a valid key
while reading from Blast2GO_gff_1.gff: start_codon is not a valid key
while reading from Blast2GO_gff_1.gff: stop_codon is not a valid key
while reading from Blast2GO_gff_1.gff: transcription_end_site is not a valid key

best,

Hi. I am working on a PC running Windows 10. I have updated Java and downloaded and unpacked the Artemis zip files. The .jar files do nothing when I click on them. I have tried telling my PC to run .jar files with Java but all that happens now when I click on artemis.jar is a command line box opens and instantly closes, then nothing.

Hi,
I used gubbins in my whole genome alignment containing 9 whole genome sequences of _Helicobacter pylori. _ When I tried to view .gff and .embl file onto any sequence from the alignment in Artemis, there is an error message like this:
read failed: one of the features in the entry has out of range location: 1623848..1624333
Can you please help me fix this ?

Recently, we have noticed that whether or not the global average is displayed with user plots depends on the file format of the plot data. In particular, global averages are displayed for data that is formatted using, for want of better terminology, format number 1 described in the user manual ("one line per base and one or more columns of...") and is not displayed with format number 3 ("indexed tab delimited file").

We aren't sure whether this is a bug or an undocumented restriction.

We can provide sample data and or screenshots, if that would be helpful.

Thanks for all of your great work!

I note the JAR file for art, act, dnaplotter and bamview seem to be all the same.

I have entry points for the first 3, but can you tell me what it is for bamview?

    inreplace bin/"art", '"$@"', 'uk.ac.sanger.artemis.components.ArtemisMain "$@"'
    inreplace bin/"act", '"$@"', 'uk.ac.sanger.artemis.components.ActMain "$@"'
    inreplace bin/"dnaplotter", '"$@"', 'uk.ac.sanger.artemis.circular.DNADraw "$@"'

I am getting the following error when I run art in an environment. I am new to using environments and am not sure if it changes anything or not. I installed using bioconda.

Error: Could not find or load main class uk.ac.sanger.artemis.components.ArtemisMain
Caused by: java.lang.ClassNotFoundException: uk.ac.sanger.artemis.components.ArtemisMain

Hi,

I am working on the Debian packaging of Artemis.

I have written .metainfo files for the 4 executables built by Artemis in order to feed AppStream, which [enhances] the metadata available about software components in the Linux and free-software ecosystem (see [0]). AppStream allows to get relevant metadata about applications in the software centers of various distributions (Debian, Ubuntu, ....).

I am providing those 4 files I have written to you, please follow [1]. If you find this relevant, you can modify them and include them in your repository as:

• they might be useful to other distributions;
• if you fiil them (instead of me), the contents should be more accurate and useful to users.

Hoping this helps,

Pierre

[0] https://freedesktop.org/software/appstream/docs/chap-AppStream-About.html#about-whatis
[1] https://salsa.debian.org/med-team/artemis/-/tree/master/debian/metainfo

I have a multi-FastA file containing 18 genomic scaffolds. I also have a GFF containing gene features for all of the scaffolds. However, Artemis appears to be mapping all gene features to each and every scaffold.

The screencap below shows:

• Green box highlights different scaffold names in the gene GFF

• Red arrow shows Artemis currently viewing "Scaffold_01"

• Green arrows show gene GFF coordinates from different scaffolds are listed in the Artemis Scaffold_01 features list, even though only one of the gene features actually belongs in Scaffold_01

Any thoughts on what is happening here and/or how to correct this?

I just use Bamview and downloaded it in both linux (redhat) and window. In the linux, it could not be opened. In the window (10), it could be opened but closed automatically when loading a bam file.

Error message in linux: fanx@im-drc2-141mn4 ~]$ java -jar BamView_v1.2.11.jar
log4j:WARN No appenders could be found for logger (uk.ac.sanger.artemis.components.alignment.BamView).
log4j:WARN Please initialize the log4j system properly.
Exception in thread "main" java.lang.IllegalArgumentException: invalid range properties
at javax.swing.DefaultBoundedRangeModel.(DefaultBoundedRangeModel.java:102)
at javax.swing.JScrollBar.(JScrollBar.java:158)
at uk.ac.sanger.artemis.components.alignment.BamView.addBamToPanel(BamView.java:2398)
at uk.ac.sanger.artemis.components.alignment.BamView.(BamView.java:381)
at uk.ac.sanger.artemis.components.alignment.BamView.main(BamView.java:4394)

Can you help to solve this issue? Thanks

• While opening a current bacterial genome GenBank (Full) file I get the following warning:
  regulatory is not a valid key
• Given that this is a freshly downloaded GenBank file I was wondering if this feature must be added to Artemis?
  Thank You

It appears that \n is left in the manifest files instead of the newline?

$ art
Starting Artemis with arguments: -mx2g -ms100m -noverify -Djdbc.drivers=org.postgresql.Driver -Dartemis.environment=UNIX  
Error: Could not find or load main class uk.ac.sanger.artemis.components.ArtemisMain\nPermissions: all-permissions

FreeBSD 11.1

$ java -version
openjdk version "1.8.0_172"
OpenJDK Runtime Environment (build 1.8.0_172-b11)
OpenJDK 64-Bit Server VM (build 25.172-b11, mixed mode)