JBrowse

Troubleshooting

Setup.sh "Installing perl prerequisites" fails for me, why?

Inspect your setup.log

If for example it says

version.c:30:16: fatal error: db.h: No such file or directory

Then run

sudo apt-get install libdb-dev

Then re-run setup.sh

If you see errors for XML::Parser

sudo apt-get install libexpat1-dev

Then re-run setup.sh

Also make sure you use "./setup.sh" or "bash setup.sh", do not use "sh setup.sh"

Should I be worried about the error "Building and installing legacy wiggle format (superceded by BigWig tracks)...failed"?

This error is often due to some system issues about compiling libraries like libpng, and for all intents and purposes can be ignored, as it is only used in wig-to-json.pl and this is superceded by directly reading BigWig files (no conversion step needed)

You can follow these instructions for how to setup a BigWig file if needed http://gmod.org/wiki/JBrowse_FAQ#How_do_I_set_up_a_BigWig_file.3F

I see a message that says "Congratulations, JBrowse is on the web" but I don't see my genome

This message normally means that jbrowse is setup but a genome hasn't been loaded or located correctly

You can continue by running

bin/prepare-refseqs.pl --fasta yourfile.fa

Then reload the page and your genome should be available.

Note: If the red box on the "Congratulations page" shows a different message than just 404 on seq/refSeqs.json, then report the error to github or the mailing list with as much detail about your setup as possible.

What is this error during setup.sh "No such file or directory at /loader/0x13517b30/App/cpanminus/script.pm line 224."

This can normally be fixed by deleting ~/.cpanm

It may be due to conflict between jbrowse's own cpanm and your system cpanm, but it should not be too problematic.

Generally deleting ~/.cpanm is harmless, it is a "build" directory (generally ~/perl5 is the local::lib directory, and in jbrowse's case, it actually uses an alternate local::lib directory named extlib inside the jbrowse directory to ensure ease-of-install)

What is "Integer overflow error"?

From what we have seen, the "Integer overflow error" sometimes appears on BigWig tracks when your webserver is not configured correctly. It seems to be due to errors with a "reverse proxy" or something not forwarding the data properly.

Therefore, it is most likely not due to corrupted bigwig files or jbrowse bugs, but more probably, due to your server's configuration.

Why do I get a popup saying "Error reading from name store"?

This error basically says the "search function" from generate-names.pl isn't working. You can try a couple things to fix the error

  1. Refresh your browser (especially in Apollo, where session can expire)
  2. Re-run generate-names.pl
  3. Re-run generate-names.pl --hashBits 16 (manually specifying the hashBits can fix error sometimes)
  4. Re-run generate-names.pl with --completionLimit 0 which disables autocomplete and makes index smaller
  5. Make sure that the fields you are indexing (e.g. Name or ID) don't contain full text descriptions (they should be symbols or identifiers, the default hash search won't index keywords but rather match prefixes)

Note if there are continued troubles, you can try an alternative search engine, such as jbrowse_elasticsearch (an experimental plugin) https://github.com/cmdcolin/jbrowse_elasticsearch/

What is this error message "Argument isn't numeric in addition (+)" loading GFF3?

If you get an error similar to this:

_Argument "-" isn't numeric in addition (+) at
/Library/WebServer/Documents/scbrowse/JBrowse-1.12.0/bin/../src/perl5/Bio/JBrowse/FeatureStream/GFF3_LowLevel.pm
line 32, <$f> line 44611._

Make sure your GFF3 is tab delimited

It keeps showing "too much data" on my track. How do I fix it and make my track display?

Increase maxFeatureScreenDensity to a higher value. This value is by default 0.5 but if you allow a higher "density" of features, set it to 6 for example and the message should disappear.

I get the error "Too much data...chunk size xxxxx exceeds chunkSizeLimit"

Several things can happen to cause this (generally on VCF of BAM tracks)

  1. You actually have exceeded the chunkSize during regular loading of data. You might see one specific block/region out of your whole track is giving this error. In this case, simply increase it.
  2. Your data is actually fairly sparse so when it first starts up, the "stats estimation routine", which "doubles" the region it searches in until it gets enough data, is failing. If it doubles too many times, then the chunk will become large and then hit the limit. In JBrowse 1.12.3 a "statsTimeout" configuration was introduced to avoid these doublings from consuming too much area.

I set a value in my config file but it isn't working. Why not?

Some things to check:

  • Don't add quotes around numerical values in your JSON config files e.g. trackList.json. Numbers can remain unquoted. Booleans can too. Functions are included in quotes though, because those are evaluated at runtime.
  • Also don't add quotes around even the strings in the .conf config files e.g. jbrowse.conf or tracks.conf files. So use defaultTracks=mytrack1,mytrack2 not defaultTracks="mytrack1,mytrack2"
  • Clear your cache. JSON is often cached pretty strongly. The .conf are cached even more. And, additionally, if there is a syntax issue with your JSON, it will try and use an older version oftentimes until you clear cache.

Also note: specifically with regards to the "defaultTracks" parameter, defaultTracks is overridden by the users cookies and the &tracks= parameter in the URL, so to test whether defaultTracks works, clear you cookies and visit without &tracks in the url. Use alwaysOnTracks or forceTracks if you want to have it turn on despite cookies/URL.

I get the error "Too many open files opening bucket log" with generate-names.pl

If you get the error such as this

Too many open files opening bucket log /path/to/your/data/names/00f/6.json.log at perl5/lib/perl5/Bio/JBrowse/HashStore.pm line 197, <$fh> line 85.

Then try increasing number of files available

ulimit -n 1000

The default can sometimes be as low as 256 (view with ulimit -a)

How do I fix the "Not a BAM file" issue?

This is normally due to a module called mime_magic being enabled on your Apache server. Two options for fixing this are 1. disable mime_magic or 2. configuring custom file types with AddType in your apache configuration. See JBrowse_Configuration_Guide#Apache_Configuration_Note for recommended fixes.

What is the error "invalid BGZF header" on my VCF files?

Your server is misconfigured for VCF.GZ files, and this can be due to it thinking that it should set "Content-Encoding: gzip" on the your .vcf.gz files. Your webserver should actually NOT put "Content-Encoding: gzip" on your VCF.GZ files. If you think you have this problem, can try using "curl -I" to view the headers that your server is putting on your VCF.GZ file.

Note: this issue can be confusing to research about, especially the "Content-Encoding: gzip" issue, because most information on the web typically says that it should put "Content-Encoding: gzip" on gzip data, and this header implies that the client should decompress the content itself, however JBrowse does not want this to happen because VCF.gz files are a special type of gzip, specifically, bgzip, so it is manually decompressed by JBrowse javascript code.

My track doesn't display the gene names, but I expected it to. Why not?

If you have a very dense track with many features, JBrowse might decide to hide the labels to save space, but you can force them to display again by adding this to your trackList.json

"style":{"labelScale": 0.01}

This says that the label will be displayed when the zoom level is greater than 0.01 regardless of how many features are there. The value 0.01 is measured in pixels per base pair, at max zoom level, there are 25 pixels per base pair for example, and when zoomed out farther, each base takes up less space, hence 0.01 will display the feature names always if you are reasonably zoomed in.

You can also change maxHeight to a larger value to make the track taller and see more features.

Why does my track keep saying "Loading"?

This normally means some javascript code for handling the track has crashed. Check your javascript console for clues on how to fix it. Add a github issue if it represents a real bug!

Note: you should use the "-dev" packages for debugging, i.e. JBrowse-1.11.6-dev.zip as opposed to for example JBrowse-1.11.6.zip, because the -dev package contains "un-minified" source code and more readable javascript console messages

My CanvasFeatures don't show up with subfeatures, why not?

If your GFF does not follow this structure

gene->mRNA->exon+CDS

Then you need to add extra configuration

Specifically, if it is "transcript" instead of "mRNA" (which is common for Ensembl GFF for example), then you must set

"transcriptType": "transcript"

Also, if you only have "exon" and no "CDS", then you need to set the subParts config (the default settings assumes that both exons and CDS exist, so if there are only exons, like in a cufflinks output file, then you need this)

"subParts": "exon"

If your GFF does not include UTR, but the UTR can be "implied" from the difference between the exon and CDS boundaries, then you can use this on your track type to enable them

"impliedUTRs": true

If your GFF file has features with this structure

match -> match_part

This only has two levels, you might consider just setting the "Segments" glyph

"glyph": "JBrowse/View/FeatureGlyph/Segments"

The segments glyph accepts all subfeatures, so match and match_part structure is fine.

Note: the tips above only apply for CanvasFeatures tracks

My HTMLFeatures don't show up with subfeatures, why not?

HTMLFeatures generally load data at the "transcript" level. This means that they should be loaded with something similar to --type mRNA when using flatfile-to-json.pl in order to see the transcript subfeatures

flatfile-to-json.pl --type mRNA --gff your_genes.gff --trackLabel MyTrack

This means that it loads the features where mRNA would be in column 3 of your GFF. If it was an Ensembl GFF, you might use instead --type transcript

Note that this also loses the information about the "parent" gene feature however, so it might be worth loading an additional track at the gene level like

flatfile-to-json.pl --type gene --gff your_genes.gff

This track will not display the transcript and exon subfeatures, but instead just show a box where the gene is, so this is commonly called a "gene spans" track

Note: If you would like a track that displays with the transcript subfeatures, you can use the CanvasFeatures type track (i.e. load with flatfile-to-json.pl --type gene --trackType CanvasFeatures ...)

Why are my subfeatures being displayed as separate features?

Your GFF should use proper ID and Parent relations. Your subfeatures do not need to themselves have IDs if they have no further subfeatures, but they must have a Parent pointing to the Parent's ID

Note that it should be spelled Parent, not PARENT

I get the error "Building and installing legacy bam-to-json.pl support (superseded by direct BAM tracks) ... failed"

If you get the error "Building and installing legacy bam-to-json.pl support (superseded by direct BAM tracks) ... failed. See setup.log file for error messages. If you really need bam-to-json.pl (most users don't), try reading the Bio-SamTools troubleshooting guide at https://metacpan.org/source/LDS/Bio-SamTools-1.33/README for help getting Bio::DB::Sam installed."

Then note:

  • This error message can be ignored. It refers only to not being able to run a small outdated feature of jbrowse.
  • If you want to fix it, the issue might refer to a conflict with the system version of samtools. Uninstall your system samtools and then re-run setup.sh (notably homebrew samtools causes this step to fail)
  • Again, this only refers to bam-to-json.pl, which converts entire BAM files to json. It is better to use the add-bam-track.pl which simply can read BAM files directly from the server with no conversion.

After I load my track it appears in the tracklist, but the track appears empty

This can happen if the chromosome names from your track don't match the names from your reference genome.

Try and make sure the chromosome names from your evidence tracks match the chromosome names from the reference genome fasta.

My BigWig file is producing an error related to DataView or jDataView

Examples of error messages

  • RangeError: Offset is outside the bounds of the DataView (Chrome)
  • Error: jDataView length or (byteOffset+length) value is out of bounds (Firefox)
  • RangeError: Out of bounds access (Safari)
  • RangeError: Argument 1 accesses an index that is out of range (Firefox)

Check that

  • The file that you are using is actually the right filetype (i.e. maybe it is a textfile, but you are giving it a bigwig file extension)
  • The webserver you are using allows Range HTTP headers (apache, nginx, etc should allow this by default)
  • That you aren't simply opening up your index.html without a webserver i.e. using <file:///> protocol (which will not allow accessing byte-range Range HTTP requests and cause this error)
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