Error reading from name store.

[man4ish]

Hi,

I am getting pop up window erroe message when i start the browser.

Error reading from name store.

Following is tranks.conf file.

{ "tracks" : [ { "chunkSize" : 20000, "storeClass" : "JBrowse/Store/Sequence/StaticChunked", "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-", "type" : "SequenceTrack", "label" : "DNA", "category" : "Reference sequence", "key" : "Reference sequence" }, { "style" : { "className" : "feature" }, "key" : "GeneId", "storeClass" : "JBrowse/Store/SeqFeature/NCList", "trackType" : null, "urlTemplate" : "tracks/GeneId/{refseq}/trackData.json", "compress" : 0, "type" : "FeatureTrack", "label" : "GeneId" }, { "style" : { "className" : "feature" }, "key" : "RefGene", "storeClass" : "JBrowse/Store/SeqFeature/NCList", "trackType" : null, "urlTemplate" : "tracks/RefGene/{refseq}/trackData.json", "compress" : 0, "type" : "FeatureTrack", "label" : "RefGene" }, { "style" : { "className" : "feature" }, "key" : "DGV", "storeClass" : "JBrowse/Store/SeqFeature/NCList", "trackType" : null, "urlTemplate" : "tracks/DGV/{refseq}/trackData.json", "compress" : 0, "type" : "FeatureTrack", "label" : "DGV" }, { "style" : { "className" : "feature" }, "key" : "snp138", "storeClass" : "JBrowse/Store/SeqFeature/NCList", "trackType" : null, "urlTemplate" : "tracks/snp138/{refseq}/trackData.json", "compress" : 0, "type" : "FeatureTrack", "label" : "snp138" }, ], "names" : { "url" : "names/", "type" : "Hash" }, "formatVersion" : 1 }

How can i fix such issue?

[cmdcolin]

This error basically indicates a problem when generate-names.pl was run. You can try to re-run generate-names.pl on your data directory. In some cases, running "generate-names.pl --hashBits 16" can fix it too.

[man4ish]

I ran with following command but still same error.

sudo perl bin/generate-names.pl --hashBits 16 WARNING: No feature names found for indexing, only reference sequence names will be indexed.

This is new setup where i have just reference sequence only but still i am gettting same error popup window.

[cmdcolin]

@man4ish I would recommend not using sudo. You should fix your permissions on your data directory "chown -R manish:manish data" or similar, and then run these commands without sudo. You can also see in your http error log if the files are being given permission denied.

[man4ish]

I changed permission also

-rwxrwxrwx 1 manish manish 7003 18 14:10 setup.sh drwxrwxrwx 4 manish manish 4096 18 14:10 sample_data -rwxrwxrwx 1 manish manish 3803 18 14:10 README.md drwxrwxrwx 8 manish manish 4096 18 14:10 plugins -rwxrwxrwx 1 manish manish 253 18 14:10 package.json -rwxrwxrwx 1 manish manish 2962 18 14:10 Makefile.PL -rwxrwxrwx 1 manish manish 33634 18 14:10 LICENSE -rwxrwxrwx 1 manish manish 299 18 14:10 jbrowse_conf.json -rwxrwxrwx 1 manish manish 2893 18 14:10 jbrowse.conf -rwxrwxrwx 1 manish manish 97 18 14:10 INSTALL -rwxrwxrwx 1 manish manish 4823 18 14:10 index.html drwxrwxrwx 2 manish manish 4096 18 14:10 img drwxrwxrwx 5 manish manish 4096 18 14:10 docs drwxrwxrwx 2 manish manish 4096 18 14:10 css -rwxrwxrwx 1 manish manish 2145 18 14:10 compat_121.html drwxrwxrwx 2 manish manish 4096 18 14:10 browser -rwxrwxrwx 1 manish manish 112142 18 14:10 release-notes.txt drwxrwxrwx 10 manish manish 4096 14:13 src drwxrwxrwx 5 manish manish 4096 7 22:42 extlib drwxrwxrwx 6 manish manish 4096 7 22:48 samtools-0.1.20 drwxrwxrwx 8 manish manish 4096 7 22:49 blib -rwxrwxrwx 1 manish manish 60808 8 00:16 Makefile -rwxrwxrwx 1 manish manish 2582 8 00:16 MYMETA.json -rwxrwxrwx 1 manish manish 1504 8 00:16 MYMETA.yml -rwxrwxrwx 1 manish manish 0 8 00:17 pm_to_blib -rwxrwxrwx 1 manish manish 32139 11 20:17 setup.log drwxrwxrwx 2 manish manish 4096 14 19:41 bin -rwxrwxrwx 1 manish manish 3147288982 17 19:09 genome.fa drwxrwxrwx 5 manish manish 4096 7 23:04 data

Command for generating name:

perl bin/generate-names.pl --hashBits 16

But still same error

[man4ish]

Is there anything that i need to change?

[nathandunn]

Just grasping at things: 1 - what are the permissions for the name-store in JBrowse (vs the other served documents)? . . unlikely to be the error, but an easy fix if so 2 - are you seeing any errors reported in your apache log or the console?

[man4ish]

Following is permisson for names store.

-rwxrwxrwx 1 manish manish 0 17 19:22 tracks.conf drwxrwxrwx 27 manish manish 4096 17 19:22 seq drwxrwxrwx 3 manish manish 4096 1 18:51 tracks -rwxrwxrwx 1 manish manish 782 7 23:25 trackList.json drwxrwxr-x 2 manish manish 4096 7 23:25 names

I just checked in console.

[](not well-formed jbrowse.conf:1:2 no element found tracks.conf:1:1 Use of getAttributeNode() is deprecated. Use getAttribute() instead. dojo.js:171:494 Object { message: "Unable to load http://localhost/jbr…", stack: ".cache["dojo/errors/create"]/</</d@…", response: Object, status: 404, responseText: "<!DOCTYPE HTML PUBLIC "-//IETF//DTD…", xhr: XMLHttpRequest } dojo.js:360:282

Object { message: "Unable to load http://localhost/jbr…", stack: ".cache["dojo/errors/create"]/</</d@…", response: Object, status: 404, responseText: "<!DOCTYPE HTML PUBLIC "-//IETF//DTD…", xhr: XMLHttpRequest })

[man4ish]

Pls help me in fixing in this issue as i am stuck in my project.

[cmdcolin]

If you want, you can just remove this from trackList.json

"names" : { "url" : "names/", "type" : "Hash" },

And the error will go away

The search functionality won't be enabled, but there are not any features being indexed apparently, so in that case it does not change anything

[man4ish]

This solves the problem but not sure later hash-name is needed or not?

[cmdcolin]

It won't cause any problems really without it enabled.

If you want to enable searching, you can re-run generate-names.pl, and hopefully have better luck. Feel free to re-open the issue when then happens!