Damapper command fails

Question

Damapper command fails

olekto opened this issue 4 years ago · 7 comments

Hi,
thank you for dentist, it is an intriguing tool.

However, it is a bit annoying for me. I keep getting errors like the one below, without any useful information.

damapper: Command Failed:
              LAmerge  -a reference.reads.439 /cluster/work/users/olekto/tmp/damapper.81025/reference.reads.439.R@.S.las

Or

LAmerge: Did not write all records to reference.reads.426 (8035)

damapper: Command Failed:
              LAmerge  -a reference.reads.426 /tmp/damapper.69457/reference.reads.426.R@.S.las

I wondered if the tmp dir was too small, so I set that to a shared folder that can contain multiple terabytes, so I doubt that is the issue anymore.

Some partitions go through fine, however, it is only a handful before one throws an error.

Is there a way to get more useful debugging information? So that I can know how the commands fail and can address that issue?

Thank you.

Sincerely,
Ole

Answer 1 · 2020-07-21T20:25:32.000Z

Hi Ole,

I am aware of this bug but have not found a solution, yet. Also, the author of damapper/daligner is informed about the bug.

I encountered this particular bug only recently, so I am positive it can be resolved by a certain combination of versions of damapper and LAmgere (contained in daligner package). I will probably find a quick fix until the end of this week and keep you updated.

Answer 2 · 2020-07-23T08:31:40.000Z

So, the bug is introduced by a new feature in LAsort that removes duplicates automatically while sorting. Damapper will probaly need some adjustments.

For the time being, I resorted to using LAsort as of 2020-01-15.

Answer 3 · 2020-07-23T08:49:18.000Z

This should be documented in the dependencies section of the README.

Answer 4 · 2020-07-23T09:56:55.000Z

Documentation added. I will keep this issue open as a reminder that this might get a proper fix sometime in the future.

Answer 5 · 2020-07-23T17:52:53.000Z

Great,
thank you Arne.

Ole

Answer 6 · 2020-10-09T17:02:41.000Z

In the dentist readme, daligner >=2020-07-27. I have daligner/2020.07.27 and dentist is still failing on:

damapper: Command Failed:
LAmerge -a XX.raw_subreads.308 /local/bgfs/cassie.newman/5138508/damapper.94044/XX.raw_subreads.308.R@.S.las

Should I just use daligner version 2020-01-15?

Answer 7 · 2020-10-15T08:19:20.000Z

@cassondranewman Sorry, for the late answer. Yes, please try the version 2020-01-15 of daligner.