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yatisht / usher

Ultrafast Sample Placement on Existing Trees
MIT License
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Docker UShER exits printing "Killed" #238

Closed rkdover closed 2 years ago

rkdover commented 2 years ago

Hi! Sorry if this is a non-issue but I could not figure out the cause so I thought I might as well set up an issue in case it is something. Using the docker build, I am attempting to follow the guide at https://usher-wiki.readthedocs.io/_/downloads/en/latest/pdf/, but I am encountering a weird error. All the preliminary steps (combining fasta files, alignment, vcf merging) are OK.

I am using the global phylogeny from https://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/UShER_SARS-CoV-2/ and using the command: usher -i ./ru/public-latest.all.masked.pb -v ./ru/merged_masked_all.vcf -d ./output/, and I am getting the following stdout:

root@ccf9f8a874d7:/HOME/usher# usher -i ./ru/public-latest.all.masked.pb -v ./ru/merged_masked_all.vcf -d ./output/
Initializing 1 worker threads.

Loading existing mutation-annotated tree object from file ./ru/public-latest.all.masked.pb
Killed
root@ccf9f8a874d7:/HOME/usher#

So the process exits printing "Killed" but without details as to why. There is no output, and no log files that I can see. docker stats indicates 1.2GiB of memory usage, of a maximum of 1.9GiB.

rkdover commented 2 years ago

I have the same issue in conda as well.

rkdover commented 2 years ago

Alright for anyone wondering, it was a resource problem. Increasing the memory available to the process let it run to completion. I run on very limited computing hardware and so the default was to use a more modest amount. I'll close this issue but perhaps some more verbose exception handling might be useful?