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jasperlinthorst / reveal

Graph based multi genome aligner
MIT License
45 stars 3 forks source link

test fails #19

Closed VidJa closed 6 years ago

VidJa commented 6 years ago

after a succesful installation reveal align tests/1a.fa tests/1b.fa fails on step 2 reveal rem tests/1a.fa tests/1b.gfa -m20 -o prg.gfa 03/15/2018 12:03:03 PM Reading fasta: tests/1a.fa ... 03/15/2018 12:03:03 PM Reading graph: tests/1b.gfa ... 03/15/2018 12:03:03 PM No paths defined in GFA, exit.

jasperlinthorst commented 6 years ago

Sorry about that... it should be fixed now. Thanks for letting me know!

Jasper

ThijsMaas commented 6 years ago

Still the same test fail..

reveal align tests/1a.fa tests/1b.fa | sh 03/16/2018 03:44:52 PM Auto determined minchainsum to 663 03/16/2018 03:44:52 PM Assembly consists of 1 contigs. 03/16/2018 03:44:52 PM Using chains to layout the assembly. 03/16/2018 03:44:52 PM Found 1 chains for contig: An19_A_niger_CBS_513_88_0 03/16/2018 03:44:52 PM The following parts of contigs could not be placed anywhere on the reference sequence. 03/16/2018 03:44:52 PM 100.00% (96465 out of 96465) of the assembly was placed with respect to the reference. 03/16/2018 03:44:53 PM Loading input... 03/16/2018 03:44:53 PM Reading fasta: tests/1a.fa ... 03/16/2018 03:44:53 PM Reading graph: tests/1b.gfa ... 03/16/2018 03:44:53 PM No paths defined in GFA, exit.

jasperlinthorst commented 6 years ago

Just to be sure... Did you do a new git 'pull' or 'clone'? I just did and things seem to work for me.

ThijsMaas commented 6 years ago

I removed the installed files and the cloned repository, cloned a new one and installed. Do I need to do something differently?

VidJa commented 6 years ago

Might it be a documentation issue? reveal align tests/1a.fa tests/1b.fa | sh fails reveal align tests/1a.fa tests/1f.fa | sh passes

ThijsMaas commented 6 years ago

That works for me as well.

jasperlinthorst commented 6 years ago

No, this shouldn't be a documentation issue... both should work.

Can you run:

"reveal transform tests/1a.fa tests/1b.fa -o test.gfa"

Then use grep to see if there's a path line in test.gfa:

"grep "^P" test.gfa"

There should be, if not, the 'reveal' command is still pointing to the old version and there's a problem with the setup script...

Let me know.

ThijsMaas commented 6 years ago

There is no path line in test.gfa, only a header (H) and 1 big segment (S)

jasperlinthorst commented 6 years ago

I'd suggest a clean installation on a different environment, as this has to be a version problem, which I can not reproduce. This problem was most likely due to a bug which is fixed in the current master branch. If for some reason the installation fails to update the old version of reveal that is installed on your system, then its very hard for me to help without knowing the specifics of your environment... If you really can't figure out where things go wrong with the installation, write me an email with the specifics of your environment and I'll see if I can assist with that: jasper.linthorst@gmail.com

ThijsMaas commented 6 years ago

Tried it again on a different environment and it's working now, thanks.