JBrowse issue

[zijian-yu]

I got this error from JBrowse, here is the stack trace:

Error
Error
../../../node_modules/@gmod/bgzf-filehandle/src/unzip.ts:31:15 (at i ()
../../../node_modules/@gmod/bgzf-filehandle/src/bgzFilehandle.ts:59:12 (at d._readAndUncompressBlock ()
../../../node_modules/@gmod/bgzf-filehandle/src/bgzFilehandle.ts:73:13 (at async d.read ()
../../../node_modules/@gmod/indexedfasta/src/indexedFasta.ts:189:8 (at async o._fetchFromIndexEntry ()
JBrowse 3.0.3

[cmdcolin]

that's a weird one. the error is weird being empty like this, but it this seems like maybe the fasta index isn't being parsed correctly.

I would check

a) that you have inputted the fasta, fai, and gzi correctly

b) check that your web server is NOT adding the "Content-Encoding: gzip" response header. jbrowse does NOT want this header added, and you will need to find the setting for your server that can turn this off, or use a different server if it is present

[cmdcolin]

can also try re-indexing the file e.g. unzipping, re-running bgzip -i file.fa and samtools faidx file.fa.gz