Re: [Jalview-discuss] Problems installing and then running Jalview on Windows 10
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:foreverem...@gmail.com] On Behalf Of James Procter > Sent: Tuesday, October 18, 2016 1:09 PM > To: Kausik Datta <kdat...@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] > > >> 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
Re: [Jalview-discuss] Problems installing and then running Jalview on Windows 10
Hi again Kausik. Thanks for sending the images - these helped clarify whats going on. I'll just take each of your steps in turn... On 17/10/2016 16:31, Kausik Datta wrote: > 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. -- --- 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
Re: [Jalview-discuss] Problems installing and then running Jalview on Windows 10
...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. https://www.youtube.com/watch?v=RdbcdZZUDHg whilehttp://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-boun...@jalview.org > <jalview-discuss-boun...@jalview.org> on behalf of Kausik Datta > <kdat...@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.bar...@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 ___ Jalview-discuss mailing list Jalview-discuss@jalview.org http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
Re: [Jalview-discuss] Problems installing and then running Jalview on Windows 10
Dear Kausik. On 17/10/2016 08:54, Mungo Carstairs (Staff) wrote: > 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=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. -- --- 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
Re: [Jalview-discuss] Problems installing and then running Jalview on Windows 10
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-boun...@jalview.org <jalview-discuss-boun...@jalview.org> on behalf of Kausik Datta <kdat...@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
