Intermittent problem with jbrowse text-index

[bbimber]

I have seen this intermittent problem locally (windows), and also in our TeamCity CI (linux and windows). I'm running a command like this:

/mnt/teamcity/work/5f343dad1177482/build/deploy/modules/jbrowse/external/jb-cli/cli-linux text-index --force --quiet --attributes Name,ID,gene_id,gene_name --file /mnt/teamcity/work/5f343dad1177482/build/deploy/files/JBrowseVerifyProject/@files/.jbrowse/resources/AB340AE2-FEC4-1039-9671-ADD9DBB5A1C0/AB340AE2-FEC4-1039-9671-ADD9DBB5A1C0fakeData.gff.gz

The error that happens is something like:

Error: ENOENT: no such file or directory, open
'/mnt/teamcity/temp/buildTmp/jbrowse-trix-sort-33244-1Oin84LV9tq0/0.tmp'
Code: ENOENT

It doesnt fail 100% of the time, but this isnt especially rare. Have you seen anything like this?

[cmdcolin]

have not seen that before...
can you run this with

DEBUG=*

as an environment variable?
on my machine that looks like

DEBUG=* jbrowse text-index ...

[cmdcolin]

also when you say windows is this Windows Subsystem for Linux or actual windows version of node?

[bbimber]

windows version. it's definitely intermittent, but it has happened on both OS

[cmdcolin]

i ran a script to repeat indexing the file 100s of times on some of our test data files, large and small but didn't yet see this

set -o errexit
for i in {1..1000}; do echo $i; jbrowse text-index --file volvox.sort.gff3.gz --quiet; done;

ran it on a larger file too

if you have any info on node version, data file, or debug info it may be useful

[bbimber]

i'll add the debug flag and see what happens

[cmdcolin]

thanks again for creating this bug, it should be fixed on main now