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a-ludi / dentist

Close assembly gaps using long-reads at high accuracy.
https://a-ludi.github.io/dentist/
MIT License
47 stars 6 forks source link

DALIGNER version #14

Closed EdHarry closed 3 years ago

EdHarry commented 3 years ago

Hi,

I'm getting a lot of LAcheck errors when I try running dentist (via singularity).

Your Snakefile reports the following message in the logs 

Duplicate LAs: can be fixed by LAsort from 2020-03-22 or later.

But your dependencies section in the README has DALIGNER (=2020-01-15) i.e. git brach c2b47da6b3c94ed248a6be395c5b96a4e63b3f63 (which is used in your docker recipe)

Is dentist tied to DALIGNER version 2020-01-15 or can the bug-fixed version from 2020-03-22 be used?

a-ludi commented 3 years ago

Hi,

the quick solution is simple: just issue export SKIP_LACHECK=1 before running Snakemake. If there are only "duplicate LAs" this will produce entirely correct results. As I have never seen any other error, this is pretty safe.

DENTIST is not itself tied to any specific daligner version but damapper is because it calls some of the auxiliary tools like LAsort and LAmerge. The versions specified in the README (and used in the container) are the most recent working combination.

EdHarry commented 3 years ago

Ok, I'll try disabling the LAchecks.

I'm assuming that any other errors that LAcheck would potentially catch would cause further downstream errors?

On Wed, 24 Mar 2021 at 12:32, Arne @.***> wrote:

Hi,

the quick solution is simple: just issue export SKIP_LACHECK=1 before running Snakemake. If there are only "duplicate LAs" this will produce entirely correct results. As I have never seen any other error, this is pretty safe.

DENTIST is not itself tied to any specific daligner version but damapper is because it calls some of the auxiliary tools like LAsort and LAmerge. The versions specified in the README (and used in the container) are the most recent working combination.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/a-ludi/dentist/issues/14#issuecomment-805783175, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHHI7IOAUDOTOQIRJC7YHHLTFHLXPANCNFSM4ZXD35UA .

a-ludi commented 3 years ago

I'm assuming that any other errors that LAcheck would potentially catch would cause further downstream errors?

I am afraid there is no guarantee for that in the optimized binaries included in the container. However, it is unlikely that there is any other error. You can check the corresponding log files logs/*alignment*.log for other errors if you like but LAcheck just stops after the issue so there is still a chance something went wrong.

I am sorry for this inconvenience. Actually, I asked the author of these tools to include the removal of duplicate LAs into LAsort which is mentioned in the message but as I explained the version became incompatible for other reasons. I really hope I can depart from damapper sometime in the future but for now it is the best option.

EdHarry commented 3 years ago

No problem, thanks for letting me know.

On Wed, 24 Mar 2021 at 14:15, Arne @.***> wrote:

I'm assuming that any other errors that LAcheck would potentially catch would cause further downstream errors?

I am afraid there is no guarantee for that in the optimized binaries included in the container. However, it is unlikely that there is any other error. You can check the corresponding log files logs/alignment.log for other errors if you like but LAcheck just stops after the issue so there is still a chance something went wrong.

I am sorry for this inconvenience. Actually, I asked the author of these tools to include the removal of duplicate LAs into LAsort which is mentioned in the message but as I explained the version became incompatible for other reasons. I really hope I can depart from damapper sometime in the future but for now it is the best option.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/a-ludi/dentist/issues/14#issuecomment-805857488, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHHI7IJCVOTSDL6XPJS722TTFHXZDANCNFSM4ZXD35UA .