Problems installing and then running Jalview on Windows 10

Please help.

  1. I have 32-bit Java JRE v.1.8.0_101 on my Windows 10 x64 machine.

  2. So I downloaded the 32 bit installer without the VM.

  3. Trying to install kept giving me Windows error 2 in loading Java VM.

  4. I bypassed the error by running from a command prompt: install-jalview.exe LAX_VM “C:\Program Files (x86)\Java\jre1.8.0_101\bin\java.exe”

  5. The installation would start and then fail with an error message about –i switch re GUI

  6. So, I tried: install-jalview.exe LAX_VM “C:\Program Files (x86)\Java\jre1.8.0_101\bin\java.exe” –i gui

  7. The installation went through this time. I was asked to specify a folder for installation, which I did.

  8. The installation was finished with a note that there were errors.

Now I find that none of the Java .jar executables in the created Jalview program folder work. None. Double-clicking on them returns no action at all.

I checked my Java by double-clicking an unrelated .jar file I had (a statistical applet) and it worked as usual.

I must be doing something wrong; can someone please help?

I cannot use the web-based version, because my FASTA files are large and I am running out of memory (I tried).

Thanks in advance,

Kausik

Kausik Datta, M.Sc., Ph.D.

Senior Research Specialist

Johns Hopkins University School of Medicine

Division of Infectious Disease

720 Rutland Ave, Ross Bldg. Rm. 1064

Baltimore, MD 21205

Lab Ph. (410) 614-9140

P Please consider the environment before printing this email.

Hello Kausik,

As a workaround, are you able to edit the jnlp file that is downloaded for Jalview Webstart to increase max-heap-size say to 2G? And run from the command line with javaws.

Someone will follow up on the Installer error (who is not on a mini iPad in a remote corner of the Scottish Highlands).

Regards,

Mungo

···

________________________________
From: jalview-discuss-bounces@jalview.org <jalview-discuss-bounces@jalview.org> on behalf of Kausik Datta <kdatta1@jhmi.edu>
Sent: 14 October 2016 19:01:11
To: jalview-discuss@jalview.org
Subject: [Jalview-discuss] Problems installing and then running Jalview on Windows 10

Please help.

1. I have 32-bit Java JRE v.1.8.0_101 on my Windows 10 x64 machine.
2. So I downloaded the 32 bit installer without the VM.
3. Trying to install kept giving me Windows error 2 in loading Java VM.
4. I bypassed the error by running from a command prompt: install-jalview.exe LAX_VM “C:\Program Files (x86)\Java\jre1.8.0_101\bin\java.exe”
5. The installation would start and then fail with an error message about –i switch re GUI
6. So, I tried: install-jalview.exe LAX_VM “C:\Program Files (x86)\Java\jre1.8.0_101\bin\java.exe” –i gui
7. The installation went through this time. I was asked to specify a folder for installation, which I did.
8. The installation was finished with a note that there were errors.

Now I find that none of the Java .jar executables in the created Jalview program folder work. None. Double-clicking on them returns no action at all.

I checked my Java by double-clicking an unrelated .jar file I had (a statistical applet) and it worked as usual.

I must be doing something wrong; can someone please help?

I cannot use the web-based version, because my FASTA files are large and I am running out of memory (I tried).

Thanks in advance,

Kausik

Kausik Datta, M.Sc., Ph.D.
Senior Research Specialist
Johns Hopkins University School of Medicine
Division of Infectious Disease
720 Rutland Ave, Ross Bldg. Rm. 1064
Baltimore, MD 21205
Lab Ph. (410) 614-9140
P Please consider the environment before printing this email.

The University of Dundee is a registered Scottish Charity, No: SC015096

Dear Kausik.

As a workaround, are you able to edit the jnlp file that is downloaded for Jalview Webstart to increase max-heap-size say to 2G? And run from the command line with javaws.

You can do this automatically with this link:

http://www.jalview.org/services/launchApp?Version=Release&jvm-max-heap=2G

1. I have 32-bit Java JRE v.1.8.0_101 on my Windows 10 x64 machine.

OK.

6. So, I tried: install-jalview.exe LAX_VM “C:\Program Files

(x86)\Java\jre1.8.0_101\bin\java.exe” –i gui

7. The installation went through this time. I was asked to

specify a folder for installation, which I did.
This sounds good...

8. The installation was finished with a note that there were errors.

The installer creates a log containing errors - this should be in the
directory where you unpacked install-jalview.exe

Now I find that none of the Java .jar executables in the created

Jalview program folder work. None. Double-clicking on them returns no
action at all.

That's not surprising. The install anywhere version creates a
Jalview.exe which you should run to launch the program. If the
installation was successful (which it may not have been) then the
runnable program should have the Jalview logo.

I cannot use the web-based version, because my FASTA files are large

and I am running out of memory (I tried).

As Mungo suggested - using the webstart + custom memory setting route is
the way forward here. We're working on a smoother way of launching
Jalview with specific memory settings, but for the moment, the launchApp
URL is the easiest way.

Let us know how you get on, Kauskik.
Jim.

···

On 17/10/2016 08:54, Mungo Carstairs (Staff) wrote:

--
-------------------------------------------------------------------
Dr JB Procter, Jalview Coordinator, The Barton Group
Division of Computational Biology, School of Life Sciences
University of Dundee, Dundee DD1 5EH, UK.
+44 1382 388734 | www.jalview.org | www.compbio.dundee.ac.uk

...yes, try the webstart version and edit the .jnlp file to increase the
heap size. It is usually more reliable to install Jalview this way
rather than through the InstallAnywhere method.

Once you have installed Jalview through webstart you can start it from
the .jnlp file when you are not connected to the web.

The section of the "Launching Jalview" Video at around 2 minutes
explains about the .jnlp file. How to launch the multiple sequence alignment viewer Jalview on your PC or MAC - YouTube

while http://www.jalview.org/jvmmemoryparams.html

gives some instructions on where to edit the .jnlp file.

I typically have mine set to 8 gigabytes since I have a 16 GB memory
computer.

I hope this helps,

Geoff.

···

On 17/10/2016 08:54, Mungo Carstairs (Staff) wrote:

Hello Kausik,

As a workaround, are you able to edit the jnlp file that is downloaded for Jalview Webstart to increase max-heap-size say to 2G? And run from the command line with javaws.

Someone will follow up on the Installer error (who is not on a mini iPad in a remote corner of the Scottish Highlands).

Regards,

Mungo

________________________________
From: jalview-discuss-bounces@jalview.org <jalview-discuss-bounces@jalview.org> on behalf of Kausik Datta <kdatta1@jhmi.edu>
Sent: 14 October 2016 19:01:11
To: jalview-discuss@jalview.org
Subject: [Jalview-discuss] Problems installing and then running Jalview on Windows 10

Please help.

1. I have 32-bit Java JRE v.1.8.0_101 on my Windows 10 x64 machine.
2. So I downloaded the 32 bit installer without the VM.
3. Trying to install kept giving me Windows error 2 in loading Java VM.
4. I bypassed the error by running from a command prompt: install-jalview.exe LAX_VM “C:\Program Files (x86)\Java\jre1.8.0_101\bin\java.exe”
5. The installation would start and then fail with an error message about –i switch re GUI
6. So, I tried: install-jalview.exe LAX_VM “C:\Program Files (x86)\Java\jre1.8.0_101\bin\java.exe” –i gui
7. The installation went through this time. I was asked to specify a folder for installation, which I did.
8. The installation was finished with a note that there were errors.

Now I find that none of the Java .jar executables in the created Jalview program folder work. None. Double-clicking on them returns no action at all.

I checked my Java by double-clicking an unrelated .jar file I had (a statistical applet) and it worked as usual.

I must be doing something wrong; can someone please help?

I cannot use the web-based version, because my FASTA files are large and I am running out of memory (I tried).

Thanks in advance,

Kausik

Kausik Datta, M.Sc., Ph.D.
Senior Research Specialist
Johns Hopkins University School of Medicine
Division of Infectious Disease
720 Rutland Ave, Ross Bldg. Rm. 1064
Baltimore, MD 21205
Lab Ph. (410) 614-9140
P Please consider the environment before printing this email.

The University of Dundee is a registered Scottish Charity, No: SC015096
_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss

--
Geoff Barton | Professor of Bioinformatics | Head of Division of Computational Biology
School of Life Sciences | University of Dundee, Scotland, UK | g.j.barton@dundee.ac.uk
Tel: +44 1382 385860 | www.compbio.dundee.ac.uk | twitter: @gjbarton

The University of Dundee is registered Scottish charity: No.SC015096

The University of Dundee is a registered Scottish Charity, No: SC015096

Hi again Kausik.

Thanks for sending the images - these helped clarify whats going on.
I'll just take each of your steps in turn...

Sadly, still no joy. My machine is a Core i7 with 16GB RAM, and yet, modifying the max-heap to 2048M didn't work for the jalview.jnlp file (I tried up to 4096M; I even tried increasing the initial heap to 500M). I downloaded the 2GB launchApp.jnlp from your website. Upon double-clicking it, I got the usual Java prompts and then it failed to start.

It's very easy to make a mistake in the JNLP file. Failure to start
(with an error message hidden away somewhere in the console) is the
usual symptom.

I put in http://www.jalview.org in my Java security exception list, but that didn't help.

You should not need to do this. We use a fully trusted certificate to
sign Jalview when launched from www.jalview.org.

Just to be sure, I recommend you remove any exceptions concerning
www.jalview.org before continuing. These might affect the security check.

In my Process Manager, I see that upon opening the launchApp.jnlp, the Java jp2launcher.exe starts up (screenshot), and then shuts down on its own. Opening the jalview.jnlp starts javaws.exe, which also shuts down on its own. I have attached the two .jnlp files I tried to use.

The shutdown suggests that there was an error in the jnlp file
downloaded. Taking a look at your launchApp.jnlp file, nothing appears
to be wrong, but we have seen some odd behaviour in the past with this,
so rather than debug the files you sent, I'd like you to try the following:

1. First - enable the Java webstart console (under the 'Advanced' tab of
your Java preferences)

2. Open the 'Command Prompt' app (you should be able to just hit the
launcher menu and type 'Command' ..)..

3. Type the following - exactly as shown:
javaws "http://www.jalview.org/services/launchApp?jvm-max-heap=7G"

On hitting return, you should see a Java webstart dialog open and the
Jalview desktop start to download and launch Jalview. Check your memory
settings by enabling Tools->Show Memory Usage.

If this doesn't work, try changing '7' to '3', and repeat.

Lastly, if things still dont work, if the Java web start console is
displayed, please copy and paste any messages into a file and send them
to me. If you also get an 'Application failed to launch' dialog then
also send me the 'Wrapped exception' output.. which gives the reason why
the webstart launch failed.

Jim.

···

On 17/10/2016 16:31, Kausik Datta wrote:

--
-------------------------------------------------------------------
Dr JB Procter, Jalview Coordinator, The Barton Group
Division of Computational Biology, School of Life Sciences
University of Dundee, Dundee DD1 5EH, UK.
+44 1382 388734 | www.jalview.org | www.compbio.dundee.ac.uk

I am happy to report that the Alignment -> Mafft with Defaults (prior to the redundancy removal) works exactly as expected. Thank you. This is what I am trying to achieve.

What I next needed to see is whether this pipeline can handle a FASTA file with similar AND dissimilar sequences in it. Unfortunately, Jalview tried to align all sequences in it, introducing gaps in the middle (naturally) which threw off the redundancy removal process also. I was able to partially remedy this by creating groups of similar sequences, but then I had to do the alignment & redundancy for each group separately.

This would be impossible to do from a large FASTA file that I have, with 430,000+ sequences and about 250MB in size.

What I have come to realize is that there is probably no single program that can help me do what I am trying to achieve: remove redundancies from a large FASTA file. So I shall use Jalview differently, as a quick check for short chunks of sequences.

Provided the memory issue is resolved. (My last email to you, titled "memory issue".)

Thank you for your most kind and patient help.

Best regards,
Kausik

···

-----Original Message-----
From: Jim Procter [mailto:foreveremain@gmail.com] On Behalf Of James Procter
Sent: Tuesday, October 18, 2016 1:09 PM
To: Kausik Datta <kdatta1@jhmi.edu>
Subject: Re: [Jalview-discuss] Problems installing and then running Jalview on Windows 10

Hi Kausik - I'm very glad that you've found a way that works ! (sleep is hard for me when I know there are Jalview users out there with problems!).

I'll again take your questions in turn. As I guess you'd prefer, I've not cc'ed the discussion list.

On 18/10/2016 17:41, Kausik Datta wrote:

gi>152212369|gb|ABS31340.1| beta-tubulin, partial [Aspergillus
gi>152212369|gb|acanthosporus]

<snip>

The last four sequences, under different accessions, are 100%
identical peptides. The first one, a larger peptide, contains the
entire sequence of the last four in it. I want to refine my FASTA file
to eliminate the replicate sequences post hoc.

OK. Before I go into your questions, let me suggest this workflow:
1. Use one of the alignment services on your imported sequence set (Webservice->Alignment->Mafft With Defaults should work fine).
2. Use Remove Redundancies as before. It should work as expected.

Now to explain why this works... your question:

(a) The sequence alignment for all five sequences start at position
1. Which is why Jalview might be missing (at least the graphical
representation) that all 5 of these proteins are identical. It thinks
the first sequence is off by an amino acid (an ‘S’ stands out)

Jalview only does what you tell it - except for a few defaults. In this case, you've given Jalview a set of unaligned sequences in a FASTA file, where for each sequence, no start position was specified, so Jalview has assigned position 1 to the first residue in each sequence, and shown them with out any gaps, since none were present in the initial file.

(b) I pressed Control+D to remove the redundancies. It removed
sequences 3-5, leaving 1 and 2 – which, clearly, it considers separate
sequences. QUESTION: Is it possible to have Jalview recognize that the
smaller peptide is actually a part of the larger peptide?

See my suggested workflow. The Redundancy dialog computes percent-identity between sequences based on the current alignment, rather than the unaligned pair. We've got an outstanding enhancement about this (see http://issues.jalview.org/browse/JAL-514), but it has not yet been implemented.

(c) When I try to export the output to FASTA (attached temp2.fasta
file), it seems to retain the trailing gap marks (----) which will
likely cause issues if I try to use this FASTA file for any downstream
search process. QUESTION: Is it possible to eliminate these trailing
‘-‘ character gap markers from the generated FASTA file?

It looks like you have 'Pad Gaps' enabled by default. If this is a one-off procedure, then first select 'Edit->Pad Gaps' to untick it, and then select 'Edit->Remove all gaps' to remove all the '-' symbols. You should then be able to export the file.

If you want to disable pad-gaps for all new alignments, you can disable 'Pad Gaps' via the 'Editing' panel in your Jalview's Preferences (Tools->Preferences).

Hope this helps ! Let me know if you have any more questions.
Jim.

PS. May I send a modified version of this email to Jalview-discuss for the benefit of other people on the list ?

Hi Kausik.

What I next needed to see is whether this pipeline can handle a FASTA file with similar AND dissimilar sequences in it. Unfortunately, Jalview tried to align all sequences in it, introducing gaps in the middle (naturally) which threw off the redundancy removal process also. I was able to partially remedy this by creating groups of similar sequences, but then I had to do the alignment & redundancy for each group separately.

This does sound like a limitation with the percent-identity measure
used, since it calculates the degree of similarity including gapped
columns (something that Jalview has done from the beginning). For 100%
identity, however, it is actually unlikely to matter, since for any
reliable alignment algorithm, sequence fragments will be aligned in the
same way as the full length sequences.

Could you give us a little more background ? If it is purely about
removing 'identical' fragments, then the '100%' removal will work
because a subsequence and its full length counterpart will be 100%
identical regardless.

What I have come to realize is that there is probably no single program that can help me do what I am trying to achieve: remove redundancies from a large FASTA file.

You may be correct here - Jalview's redundancy removal function was only
designed for use in comparative analsis. There are some standard methods
for performing this filtering, of course (it's a common step for any
sequencing pipeline) - but again, it depends what you you are trying to
achieve !

Does anyone else have any suggestions to help Kausik ?
Jim.

···

On 18/10/2016 19:33, Kausik Datta wrote:

--
-------------------------------------------------------------------
Dr JB Procter, Jalview Coordinator, The Barton Group
Division of Computational Biology, School of Life Sciences
University of Dundee, Dundee DD1 5EH, UK.
+44 1382 388734 | www.jalview.org | www.compbio.dundee.ac.uk

Hello,

CD-HIT can remove redundancies from sequence files, the sequences do not need to be aligned.
http://weizhongli-lab.org/cdhit_suite/cgi-bin/index.cgi?cmd=cd-hit

Andreas

···

-----Original Message-----
From: jalview-discuss-bounces@jalview.org [mailto:jalview-discuss-
bounces@jalview.org] On Behalf Of Jim Procter
Sent: 19 October 2016 07:47
To: jalview-discuss@jalview.org
Subject: [Jalview-discuss] Redundancy removal for large sets of sequences [was
Re: Problems installing and then running Jalview on Windows 10 ]

Hi Kausik.

On 18/10/2016 19:33, Kausik Datta wrote:

What I next needed to see is whether this pipeline can handle a FASTA file

with similar AND dissimilar sequences in it. Unfortunately, Jalview tried to align
all sequences in it, introducing gaps in the middle (naturally) which threw off
the redundancy removal process also. I was able to partially remedy this by
creating groups of similar sequences, but then I had to do the alignment &
redundancy for each group separately.
This does sound like a limitation with the percent-identity measure used, since
it calculates the degree of similarity including gapped columns (something that
Jalview has done from the beginning). For 100% identity, however, it is actually
unlikely to matter, since for any reliable alignment algorithm, sequence
fragments will be aligned in the same way as the full length sequences.

Could you give us a little more background ? If it is purely about removing
'identical' fragments, then the '100%' removal will work because a
subsequence and its full length counterpart will be 100% identical regardless.

What I have come to realize is that there is probably no single program that

can help me do what I am trying to achieve: remove redundancies from a large
FASTA file.
You may be correct here - Jalview's redundancy removal function was only
designed for use in comparative analsis. There are some standard methods for
performing this filtering, of course (it's a common step for any sequencing
pipeline) - but again, it depends what you you are trying to achieve !

Does anyone else have any suggestions to help Kausik ?
Jim.

--
-------------------------------------------------------------------
Dr JB Procter, Jalview Coordinator, The Barton Group Division of Computational
Biology, School of Life Sciences University of Dundee, Dundee DD1 5EH, UK.
+44 1382 388734 | www.jalview.org | www.compbio.dundee.ac.uk

_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss

Dear Kausik,

I'm glad you got Jalview working for you. It is not really the best
tool for removing redundancy from large sets of sequences. There are a
variety of different ways to do this depending on what you mean by
"redundancy". We've used "blastclust" on a couple of projects and it
did what we needed, but it may not be the best for your problem.

Anyway, there are quite a few solutions out there as this is a common
problem - hopefully you can find something that works for you and then
use Jalview to visualise the results!

All the best,

Geoff.

···

On 18/10/2016 19:33, Kausik Datta wrote:

I am happy to report that the Alignment -> Mafft with Defaults (prior to the redundancy removal) works exactly as expected. Thank you. This is what I am trying to achieve.

What I next needed to see is whether this pipeline can handle a FASTA file with similar AND dissimilar sequences in it. Unfortunately, Jalview tried to align all sequences in it, introducing gaps in the middle (naturally) which threw off the redundancy removal process also. I was able to partially remedy this by creating groups of similar sequences, but then I had to do the alignment & redundancy for each group separately.

This would be impossible to do from a large FASTA file that I have, with 430,000+ sequences and about 250MB in size.

What I have come to realize is that there is probably no single program that can help me do what I am trying to achieve: remove redundancies from a large FASTA file. So I shall use Jalview differently, as a quick check for short chunks of sequences.

Provided the memory issue is resolved. (My last email to you, titled "memory issue".)

Thank you for your most kind and patient help.

Best regards,
Kausik

-----Original Message-----
From: Jim Procter [mailto:foreveremain@gmail.com] On Behalf Of James Procter
Sent: Tuesday, October 18, 2016 1:09 PM
To: Kausik Datta <kdatta1@jhmi.edu>
Subject: Re: [Jalview-discuss] Problems installing and then running Jalview on Windows 10

Hi Kausik - I'm very glad that you've found a way that works ! (sleep is hard for me when I know there are Jalview users out there with problems!).

I'll again take your questions in turn. As I guess you'd prefer, I've not cc'ed the discussion list.

On 18/10/2016 17:41, Kausik Datta wrote:

gi>152212369|gb|ABS31340.1| beta-tubulin, partial [Aspergillus
gi>152212369|gb|acanthosporus]

<snip>

The last four sequences, under different accessions, are 100%
identical peptides. The first one, a larger peptide, contains the
entire sequence of the last four in it. I want to refine my FASTA file
to eliminate the replicate sequences post hoc.

OK. Before I go into your questions, let me suggest this workflow:
1. Use one of the alignment services on your imported sequence set (Webservice->Alignment->Mafft With Defaults should work fine).
2. Use Remove Redundancies as before. It should work as expected.

Now to explain why this works... your question:

(a) The sequence alignment for all five sequences start at position
1. Which is why Jalview might be missing (at least the graphical
representation) that all 5 of these proteins are identical. It thinks
the first sequence is off by an amino acid (an ‘S’ stands out)

Jalview only does what you tell it - except for a few defaults. In this case, you've given Jalview a set of unaligned sequences in a FASTA file, where for each sequence, no start position was specified, so Jalview has assigned position 1 to the first residue in each sequence, and shown them with out any gaps, since none were present in the initial file.

(b) I pressed Control+D to remove the redundancies. It removed
sequences 3-5, leaving 1 and 2 – which, clearly, it considers separate
sequences. QUESTION: Is it possible to have Jalview recognize that the
smaller peptide is actually a part of the larger peptide?

See my suggested workflow. The Redundancy dialog computes percent-identity between sequences based on the current alignment, rather than the unaligned pair. We've got an outstanding enhancement about this (see http://issues.jalview.org/browse/JAL-514), but it has not yet been implemented.

(c) When I try to export the output to FASTA (attached temp2.fasta
file), it seems to retain the trailing gap marks (----) which will
likely cause issues if I try to use this FASTA file for any downstream
search process. QUESTION: Is it possible to eliminate these trailing
‘-‘ character gap markers from the generated FASTA file?

It looks like you have 'Pad Gaps' enabled by default. If this is a one-off procedure, then first select 'Edit->Pad Gaps' to untick it, and then select 'Edit->Remove all gaps' to remove all the '-' symbols. You should then be able to export the file.

If you want to disable pad-gaps for all new alignments, you can disable 'Pad Gaps' via the 'Editing' panel in your Jalview's Preferences (Tools->Preferences).

Hope this helps ! Let me know if you have any more questions.
Jim.

PS. May I send a modified version of this email to Jalview-discuss for the benefit of other people on the list ?
_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss

--
Geoff Barton | Professor of Bioinformatics | Head of Division of Computational Biology
School of Life Sciences | University of Dundee, Scotland, UK | g.j.barton@dundee.ac.uk
Tel: +44 1382 385860 | www.compbio.dundee.ac.uk | twitter: @gjbarton

The University of Dundee is registered Scottish charity: No.SC015096

The University of Dundee is a registered Scottish Charity, No: SC015096