tigmint-make 'missing separator' error about arcs HOT 8 CLOSED

Thank you! Version 1.2.6 worked

from arcs.

Hi @juliadouglasf,

Hmm, that's a strange one - I'm having issues reproducing that behaviour on my side.

To confirm, do you see the missing separator error if you run:

make -f arcs/bin/share/tigmint-1.2.10-1/bin/tigmint-make version

What operating system are you using?

Thank you for your interest in ARCS and Tigmint!
Lauren

from arcs.

Thanks for your response, @lcoombe.

When I run that command, I get the version. Tigmint 1.2.10.

I'm using Linux.

from arcs.

Thanks @juliadouglasf - Ok, that should indicate that the file itself is OK.
Since we're troubleshooting the Tigmint step here, could you run the test that we supply in the Tigmint repository? https://github.com/bcgsc/tigmint/tree/master/tests

There's a README there that describes what to run, etc. If the test fails, please include the full standard out and error.

from arcs.

The test ran successfully, although the headers for test_contig.test_linkedreads.as0.65.nm5.molecule.size2000.dist50000.trim0.window1000.span20.breaktigs.fa are slightly different (e.g., >test-1::test:0-3051 instead of >test-1).

from arcs.

Ok great, so Tigmint is working fine.

There must be some issue with arcs-make then.
You have a couple options:

1. Run Tigmint first, then run ARCS using arcs-make (ie. instead of using the arcs-tigmint rule)
2. If you want to use arcs-make with the arcs-tigmint rule, it would help me for you to send me the full standard log and output you get when you launch the job, including the command.

from arcs.

Hi @juliadouglasf,

I was able to look into the issue further this morning, and think I found the source of your error. I have pushed a fix to master branch (#165) and will be doing a new release (v1.2.6) that incorporates the fix shortly.

from arcs.

Great, glad to hear that!

from arcs.