I have been using Sequenceserver successfully for years. However, the switch to 1.0.4 seems to have broken it on my server. When I load the program, it opens a browser window that never is able to find the page. When I close the browser window, the command line lists an error: WARN: tilt autoloading ‘tilt/erb’ is a non thread-safe way; explicit require ‘tilt/erb’ suggested. I don’t know if this is what is causing the loading issue, but I haven’t been able to explicitly require tilt - I’ve tried both “-r tilt” and “-r (path to tilt)” to no avail. Please help! We use sequenceserver almost everyday.
Thanks,
Matt
Hey Matthew,
It’s unlikely that tilt warning is causing the issue.
Could it be similar to Mark’s issue discussed here - https://groups.google.com/forum/#!topic/sequenceserver/KYzks65XHgo
If not, I will need some details from you to debug this. Could you run SS in debug mode (sequenceserver -D), try accessing it in browser and and post me the log?
– Priyam
Pryiam,
Thanks for getting back to me. It doesn’t look like Mark’s issue is the same as mine. However, when I run SS in debug mode, it is visible to all my web browsers. Below is the output that is generated when I start the program and and access it from the web. Any thoughts?
Thanks,
Matt
root@blast1:~# sequenceserver -D
[2015-05-28 14:06:14] DEBUG Reading configuration file: /home/matt/.sequenceserver.conf.
[2015-05-28 14:06:14] DEBUG Will use NCBI BLAST+ at: /home/matt/.sequenceserver/ncbi-blast-2.2.30+/bin
[2015-05-28 14:06:14] DEBUG Will use BLAST+ databases at: /home/matt/blast_databases
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Astasia_curvata_March2014assembly’ at ‘/home/matt/blast_databases/ACU_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Colacium_vesiculosum’ at ‘/home/matt/blast_databases/CVS.cdna_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Colacium_vesiculosum_March2014assembly’ at ‘/home/matt/blast_databases/CVS_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Cryptoglena_skujai’ at ‘/home/matt/blast_databases/Crysk.cdna_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Cryptoglena_skujai_March2014assembly’ at ‘/home/matt/blast_databases/Crysk_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Diplonema_sp’ at ‘/home/matt/blast_databases/DI2.cdna_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Diplonema_sp_March2014assembly’ at ‘/home/matt/blast_databases/DI2_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Diplonema_ambulator’ at ‘/home/matt/blast_databases/DIA.cdna_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Diplonema_ambulator_March2014assembly’ at ‘/home/matt/blast_databases/DIA_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Diplonema_papillatum’ at ‘/home/matt/blast_databases/DIP.cdna_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Diplonema_papillatum_March2014assembly’ at ‘/home/matt/blast_databases/DIP_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Dimastigella_trypaniformis’ at ‘/home/matt/blast_databases/DMT.cdna_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Dimastigella_trypaniformis_March2014assembly’ at ‘/home/matt/blast_databases/DMT_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Discoplastis_spathirhyncha’ at ‘/home/matt/blast_databases/DSP.cdna_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Discoplastis_spathirhyncha_March2014assembly’ at ‘/home/matt/blast_databases/DSP_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Distigma_proteus’ at ‘/home/matt/blast_databases/Dpro.cdna_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Distigma_proteus_March2014assembly’ at ‘/home/matt/blast_databases/Dpro_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Entosiphon_sp’ at ‘/home/matt/blast_databases/ENTO.cdna_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Entosiphon_sp_March2014assembly’ at ‘/home/matt/blast_databases/ENTO_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Euglena_sanguinea_March2014assembly’ at ‘/home/matt/blast_databases/ESA_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Eutreptia_viridis’ at ‘/home/matt/blast_databases/EVIR.cdna_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Euglenaria_anabaena_UTEX373_March2014assembly’ at ‘/home/matt/blast_databases/Eana_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Euglenaria_anabaena_UTEX373’ at ‘/home/matt/blast_databases/Eavm.cdna_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Euglena_clara’ at ‘/home/matt/blast_databases/Eclra.cdna_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Euglena_clara_March2014assembly’ at ‘/home/matt/blast_databases/Eclra_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Euglena_gracilis’ at ‘/home/matt/blast_databases/Egr.cdna_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Euglena_gracilis_March2014assembly’ at ‘/home/matt/blast_databases/Egr_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Euglena_hiemalis’ at ‘/home/matt/blast_databases/Ehiem.cdna_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Euglena_hiemalis_March2014assembly’ at ‘/home/matt/blast_databases/Ehiem_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Euglenaformis_proxima’ at ‘/home/matt/blast_databases/Eprox.cdna_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Euglenaformis_proxima_March2014assembly’ at ‘/home/matt/blast_databases/Eprox_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Euglena_stellata’ at ‘/home/matt/blast_databases/Est1U.cdna_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Euglena_stellata_March2014assembly’ at ‘/home/matt/blast_databases/Est1U_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Eutreptiella_braarudii’ at ‘/home/matt/blast_databases/Etblr.cdna_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Eutreptiella_braarudii_March2014assembly’ at ‘/home/matt/blast_databases/Etlbr_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Euglena_gracilis_GenBank_ESTs’ at ‘/home/matt/blast_databases/Euglena_gracilis_ESTs_Genbank.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Euglena_viridis’ at ‘/home/matt/blast_databases/Eugvir.cdna_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Euglena_viridis_March2014assembly’ at ‘/home/matt/blast_databases/Eugvir_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Eutreptia_viridis_March2014assembly’ at ‘/home/matt/blast_databases/Evir_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Lepocinclis_playfairiana’ at ‘/home/matt/blast_databases/Lplay.cdna_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Lepocinclis_playfairiana_March2014assembly’ at ‘/home/matt/blast_databases/Lplay_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Lepocinclis_tripteris’ at ‘/home/matt/blast_databases/Ltrip.cdna_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Lepocinclis_tripteris_March2014assembly’ at ‘/home/matt/blast_databases/Ltrip_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Menoidium_bibacillatum_March2014assembly’ at ‘/home/matt/blast_databases/MEB_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Monomorphina_parapyrum’ at ‘/home/matt/blast_databases/Mpy.cdna_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Monomorphina_parapyrum_March2014assembly’ at ‘/home/matt/blast_databases/Mpy_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Petalomonas_cantuscygni’ at ‘/home/matt/blast_databases/PCT.cdna_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Petalomonas_cantuscygni_March2014assembly’ at ‘/home/matt/blast_databases/PCT_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Peranema_sp’ at ‘/home/matt/blast_databases/PER.cdna_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Peranema_sp_March2014assembly’ at ‘/home/matt/blast_databases/PER_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Pyramimonas_parkeae’ at ‘/home/matt/blast_databases/PYRAMI_G-454AllContigs_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Phacus_inflexus’ at ‘/home/matt/blast_databases/Pinf.cdna_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Phacus_inflexus_March2014assembly’ at ‘/home/matt/blast_databases/Pinf_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Ploeotia_oblonga’ at ‘/home/matt/blast_databases/Plobl.cdna_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Ploeotia_oblonga_March2014assembly’ at ‘/home/matt/blast_databases/Plobl_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Phacus_orbicularis’ at ‘/home/matt/blast_databases/Porbc.cdna_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Phacus_orbicularis_March2014assembly’ at ‘/home/matt/blast_databases/Porbc_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Rhynchopus_sp’ at ‘/home/matt/blast_databases/RHX.cdna_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Rhynchopus_sp_March2014assembly’ at ‘/home/matt/blast_databases/RHX_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Rhynchopus_euleeides’ at ‘/home/matt/blast_databases/RP1.cdna_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Rhynchopus_euleeides_March2014assembly’ at ‘/home/matt/blast_databases/RP1_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Rhabdomonas_costata’ at ‘/home/matt/blast_databases/Rcost.cdna_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Rhabdomonas_costata_March2014assembly’ at ‘/home/matt/blast_databases/Rcost_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Strombomonas_accuminata’ at ‘/home/matt/blast_databases/Sacc.cdna_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Strombomonas_acuminata_March2014assembly’ at ‘/home/matt/blast_databases/Sacc_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Trachelomonas_ellipsoidalis’ at ‘/home/matt/blast_databases/TEL.cdna_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Trachelomonas_ellipsoidalis_March2014assembly’ at ‘/home/matt/blast_databases/TEL_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Trachelomonas_volvocina’ at ‘/home/matt/blast_databases/Tvcna.cdna_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Found nucleotide database ‘Trachelomonas_volvocina_March2014assembly’ at ‘/home/matt/blast_databases/Tvcna_renamed_contigs.fasta’
[2015-05-28 14:06:14] DEBUG Will use 1 threads to run BLAST.
[2015-05-28 14:06:14] WARN Will listen on all interfaces (0.0.0.0). Consider using 127.0.0.1 (–host option).
[2015-05-28 14:06:14] INFO WEBrick 1.3.1
[2015-05-28 14:06:14] INFO ruby 2.0.0 (2013-02-24) [x86_64-linux]
[2015-05-28 14:06:14] INFO WEBrick::HTTPServer#start: pid=6199 port=80
** SequenceServer is ready.
Go to http://localhost:80 in your browser and start BLASTing!
Press CTRL+C to quit.
[2015-05-28 14:06:33] DEBUG {}
WARN: tilt autoloading ‘tilt/erb’ in a non thread-safe way; explicit require ‘tilt/erb’ suggested.
localhost - - [28/May/2015:14:06:33 EDT] “GET / HTTP/1.1” 200 45369
localhost - - [28/May/2015:14:06:33 EDT] “GET /css/bootstrap.min.css HTTP/1.1” 200 92175
localhost - - [28/May/2015:14:06:33 EDT] “GET /css/font-awesome.min.css HTTP/1.1” 200 23739
localhost - - [28/May/2015:14:06:33 EDT] “GET /js/underscore.min.js HTTP/1.1” 200 15626
localhost - - [28/May/2015:14:06:33 EDT] “GET /css/custom.css HTTP/1.1” 200 7720
localhost - - [28/May/2015:14:06:33 EDT] “GET /js/webshims/polyfiller.js HTTP/1.1” 200 15749
localhost - - [28/May/2015:14:06:33 EDT] “GET /js/jquery.min.js HTTP/1.1” 200 95931
localhost - - [28/May/2015:14:06:33 EDT] “GET /js/sequenceserver.js HTTP/1.1” 200 23276
localhost - - [28/May/2015:14:06:33 EDT] “GET /js/d3.v3.min.js HTTP/1.1” 200 146751
localhost - - [28/May/2015:14:06:33 EDT] “GET /js/jquery-ui.min.js HTTP/1.1” 200 24916
localhost - - [28/May/2015:14:06:33 EDT] “GET /js/sequenceserver.blast.js HTTP/1.1” 200 6007
localhost - - [28/May/2015:14:06:33 EDT] “GET /js/jquery.t.js HTTP/1.1” 200 14264
localhost - - [28/May/2015:14:06:33 EDT] “GET /js/bootstrap.min.js HTTP/1.1” 200 29616
localhost - - [28/May/2015:14:06:33 EDT] “GET /js/sequence.js HTTP/1.1” 200 193572
localhost - - [28/May/2015:14:06:33 EDT] “GET /js/webshims/shims/styles/shim.css HTTP/1.1” 200 12195
localhost - - [28/May/2015:14:06:33 EDT] “GET /js/webshims/shims/form-core.js HTTP/1.1” 200 5560
localhost - - [28/May/2015:14:06:33 EDT] “GET /fonts/fontawesome-webfont.woff?v=4.3.0 HTTP/1.1” 200 71508
[2015-05-28 14:06:34] DEBUG {}
localhost - - [28/May/2015:14:06:34 EDT] “GET /favicon.ico HTTP/1.1” 404 551
[2015-05-28 14:06:34] DEBUG {}
localhost - - [28/May/2015:14:06:34 EDT] “GET /js/webshims/shims/form-validation.js HTTP/1.1” 200 17130
localhost - - [28/May/2015:14:06:34 EDT] “GET /favicon.ico HTTP/1.1” 404 551
localhost - - [28/May/2015:14:06:34 EDT] “GET /js/webshims/shims/plugins/jquery.ui.position.js HTTP/1.1” 200 6495
Pryiam,
Additionally, in debug mode it seems to be working properly. I don’t know if this helps.
Matt
Matthew,
What happens if you remove -D flag? Does it show up in browser then?
Could you tell me how do you typically run SequenceServer (which is when it doesn’t show up in browser)? Do you launch it on boot? How?
– Priyam
Priyam,
If I remove the -D flag, it doesn’t load at all in the browser. In order to run sequenceserver, I run the following 3 commands from the command line.
sudo bash
source /home/matt/.rvm/scripts/rvm
sequenceserver
Thanks,
Matt
This is weird.
The only differences between debug (-D) and production (default) mode are that:
-
SequenceServer loads concatenated, minified JavaScript and CSS files in production, but individual, un-minified files in debug mode.
-
SequenceServer tries to open localhost:4567 in browser in production mode.
So you can continue to run SequenceServer with -D switch to work around this problem. But I would really like to understand what is the issue here. Since I’m not able to reproduce this on my system or any of my test beds, please could you tell me a bit more?
Are you behind a firewall? Which browser are you using? How long do you wait for SequenceServer to load in browser?
Can you Right click → Inspect Element → Console (or Ctrl - Shift - J or Cmd - Opt - J) and see if there’s an error message there? And lastly, what does running ‘curl localhost:4567’ produce? Is it an error or a longish HTML page? (All this when running SequenceServer without the -D flag.)
Which version of SequenceServer did you upgrade from?
– Priyam
Pryiam,
I’m glad to know that I can run sequenceserver in debug mode while we are trying to fix this, that alleviates some of my stress.
OK, onto your questions:
I do run this behind a firewall. The computer that is running it uses Firefox (it’s running on a server partition with Ubuntu OS), and I’ve tried accessing it from a remote computer with Safari. I never timed how long I let it try to load in the browser, but probably 5-10 minutes - I essentially tried to access and walked away for a while.
when I call sequenceserver, it gives me the following error in the terminal: (process:12772): GLib-CRITICAL **: g_slice_set_config: assertion ‘sys_page_size == 0’ failed, but nothing in the console of the web browser. When I try to use curl in the web browser console it tells me that curl is not defined. Also, I am using port 80, not port 4567, so that I can access it from other computers.
Thanks for your help,
Matt
I forgot to mention, I upgraded from 1.0.3
Hmm. When you earlier said “it opens a browser window that never is able to find the page”, did you mean Firefox says “Unable to connect”?
Did you also happen to upgrade the OS on your server while you upgraded to SequenceServer 1.0.4?
Does it work if you remove ‘xdg-utils’ package from your server? (and invoke SequenceServer without the -D switch)
– Priyam
Priyam,
What happens is that when I call up sequenceserver, it opens a Firefox window and the tab says connecting with a “loading" wheel that turns forever (perpetual motion?).
However, what I found this morning is that if I keep the Firefox window open, I can’t connect in from a remote machine. BUT, if I just close the automatically opened Firefox window that is trying to connect, I am able to connect just fine from a remote machine. I’m not exactly sure why, but it’s at least working correctly now.
I had run OS updates prior to the issue that occurred. I also ran OS updates again this morning. I’m not sure if the OS updates from today fixed the issue, or if I just didn’t previously try killing the Firefox window before trying to connect from an outside computer.
Hope this helps,
Matt
This is helpful. Thanks. SequenceServer uses ‘xdg-open’ command on Linux (from xdg-utils package on Debian family) and ‘open’ command on OSX to automatically load itself in browser on launch. Somehow xdg-open is interfering with SequenceServer’s server - though I’m not sure exactly how it’s getting in the way.
While it’s quite likely that a prior OS upgrade broke things, I don’t think that updating Ubuntu today morning fixed the issue. A fix would mean SequenceServer loads in browser on launch.
I’m opening an issue to track this. But I’m not really sure what can be done from SequenceServer’s end to fix this. Perhaps call xdg-open in a separate thread so the main server thread doesn’t get blocked. In any case, I would like to wait and see if a future OS upgrade fixes this first.
Please could you let us know if a future OS upgrade automatically fixes this?
– Priyam
Will do. I run updates once a month, so I’ll keep you informed monthly if this gets fixed. Thanks Again for all your help!
Cheers!
Matt
Hello Matthew,
I have the exact same problem with my server. Did you manage to find a solution?
Thanks in advance,
Michael.
Michael,
I was able to fix the issue, and it was an easy fix. When you start up sequenceserver, it automatically launches a web browser. I found that if I just closed the automatically launched web browser, sequenceserver worked without an issue.
Hope this helps,
Matt
I am using a virtual machine to run the server and i want to be able to start it automatically on boot. But unfortunately this issue is preventing me from doing that.
Thanks anyway,hope this issue could be resolved without this workaround that you suggested.
Cheers,
Michael.
Hi Michael,
Please could you update to 1.0.8 and let me know if that fixes the issue for you or not?
(just released - https://groups.google.com/forum/#!topic/sequenceserver/ZMHX4qgcyqY)
Thanks.
— Priyam
Hi Priyam,
Updated to 1.0.8 and now it works!
Thanks a bunch!!
Michael.
Super! Thanks for verifying.