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Genomic refseq track not displaying correctly in 1.10.6 in fresh install #363

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jriethoven opened this issue Oct 10, 2013 · 5 comments

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@jriethoven
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commented Oct 10, 2013

In a fresh install of JBrowse 1.10.6, after loading genomic scaffolds, the DNA sequence is not displaying correctly (actually shows HTML/Javascript).

Can be seen here:

http://bioinformatics.unl.edu/jjtest/JBrowse-1.10.6/?loc=scaffold1%3A862565..862637&tracks=DNA&highlight=

Copying data stores from previous versions (1.10.4 and 1.10.5) into data directory will fix the issue.

Maybe related, maybe not: the trackList.json has no line breaks in them anymore in the fresh install:

[pow@JBrowse-1.10.6]# cat data/trackList.json
{"tracks":[{"chunkSize":20000,"storeClass":"JBrowse/Store/Sequence/StaticChunked","urlTemplate":"seq/{refseq_dirpath}/{refseq}-","type":"SequenceTrack","label":"DNA","key":"Reference sequence"}],"formatVersion":1}[pow@tunare JBrowse-1.10.6]#

@rbuels

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commented Oct 10, 2013

There are two different things going on here:

  1. Your reference sequences seem to not have been completely formatted. Did prepare-refseqs.pl report any errors when you ran it? If not, could you send me the file you loaded the reference sequences from?
  2. Your web server seems to be misconfigured. When a sequence chunk file is missing, instead of returning the correct 404 status code when JBrowse tries to fetch it, it gives a 302 and redirects to http://bioinformatics.unl.edu/error404.html (which succeeds with a 200 OK), which JBrowse tries to display as the sequence chunk (the HTML from error404.html is what you see in the sequence boxes). This behavior isn't compatible with JBrowse; when a file is not found, your web server needs to, at some point, return a 404 status. It would probably fix things if you just made error404.html be served with an HTTP 404 status code.
@rbuels

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commented Oct 10, 2013

But number 1 in the response above is the promixate problem.

@jriethoven

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commented Oct 11, 2013

The problem is indeed in the prepare-refseqs.pl part:

(1.10.6 browser but with 1.10.4 generated store, same FASTA file):

[root@tunare seq]# pwd
/var/www/chlorella_browser/JBrowse/data/seq
[root@tunare seq]# find . | wc -l
3693

(1.10.6. fresh browser, utilizing the 1.10.6 prepare-refseq.pl, same FASTA file):
[root@tunare seq]# pwd
/var/www/jjtest/JBrowse-1.10.6/data/seq
[root@tunare seq]# find . | wc -l
1123

Running prepare-refseq.pl in 1.10.6 fresh:
[root@tunare JBrowse-1.10.6]# pwd
/var/www/jjtest/JBrowse-1.10.6
[root@tunare JBrowse-1.10.6]# bin/prepare-refseqs.pl --fasta /var/www/chlorella_browser/data/raw/UNL0001HC_assembly.fa
[root@tunare JBrowse-1.10.6]#

I can't see anything wrong in the FASTA file - I have forwarded the file via mail to you.

The number of main directories in data/seq are the same for both instances, 241 excluding the refSeqs.json. The fresh 1.10.6 however as fewer files in most directories, e.g.

./222
./222/50e
./222/50e/88
./222/50e/88/scaffold211-0.txt
./222/50e/88/scaffold211-1.txt

as compared to 1.10.4/5:

./222
./222/50e
./222/50e/88
./222/50e/88/scaffold211-0.txt
./222/50e/88/scaffold211-5.txt
./222/50e/88/scaffold211-3.txt
./222/50e/88/scaffold211-6.txt
./222/50e/88/scaffold211-1.txt
./222/50e/88/scaffold211-2.txt
./222/50e/88/scaffold211-4.txt

Actually, 1.10.6 prepare-refseqs.pl only generated -0.txt and -1.txt files, while 1.10.4/5 have a lot more:

[root@tunare seq]# pwd
/var/www/jjtest/JBrowse-1.10.6/data/seq
[root@tunare seq]# find . | grep -e '-2'
[root@tunare seq]#

vs. (1.10.4/5):

[root@tunare seq]# pwd
/var/www/chlorella_browser/JBrowse/data/seq
[root@tunare seq]# find . | grep -e '-2'
./864/183/23/scaffold167-2.txt
./864/183/23/scaffold167-20.txt
./864/183/23/scaffold167-21.txt
[remainder snipped]

Just to be sure, I checked permissions (both are run as root), environment, and disk space (231GB avail).

@rbuels

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commented Oct 11, 2013

Where is the file? I don't see anything in my email.

@jriethoven

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commented Oct 11, 2013

Hi Robert,

Tried to send it to you but the file was too big – I have placed it for download here:

http://bioinformatics.unl.edu/chlorella/UNL0001HC_assembly.fa.gz

From: Robert Buels [mailto:notifications@github.com]
Sent: Friday, October 11, 2013 9:42 AM
To: GMOD/jbrowse
Cc: jriethoven
Subject: Re: [jbrowse] Genomic refseq track not displaying correctly in 1.10.6 in fresh install (#363)

Where is the file? I don't see anything in my email.


Reply to this email directly or view it on GitHub #363 (comment) .

@rbuels rbuels closed this in 5b0b9c5 Oct 11, 2013

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