Michigan Imputation Server - Local docker image

Question

[batch_effect]

Hi,

Due to clinical data and not meeting the minimum sample of 20, I hope to use the Michigan Imputation Server locally via its' Docker image. I got couple of questions that I hope others can help:

• I tried to do this on MacBook Pro M2 without success. One of the errors that I'm not sure whether it was Java-related. Also, not sure whether the different CPU architecture of ARM64 M2 and the Intel-based Docker image was also the culprit?

2023-05-29 15:25:42 # A fatal error has been detected by the Java Runtime Environment: 2023-05-29 15:25:42 # 2023-05-29 15:25:42 # Internal Error (safepoint.cpp:310), pid=995, tid=0x000000402fb6d700 2023-05-29 15:25:42 # guarantee(PageArmed == 0) failed: invariant 2023-05-29 15:25:42 # 2023-05-29 15:25:42 # JRE version: OpenJDK Runtime Environment (8.0_222-b10) (build 1.8.0_222-8u222-b10-1~14.04-b10) 2023-05-29 15:25:42 # Java VM: OpenJDK 64-Bit Server VM (25.222-b10 mixed mode linux-amd64 compressed oops) 2023-05-29 15:25:42 # Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again

• Is it possible to run this Docker image on HPC? At the moment, submitting a job for the local Michigan Imputation Server is through the browser and require GUI to choose parameters.

Been stuck on this for 4 months, and desperate for advice.

Thanks.

Answer 1

[LauferVA]

Hi Ms. or Mr. Effect,

A couple ideas:

1) if its not working on the local docker image, have you tried uploading your data for imputation on their server?

2) have you contacted the support folks at Michigan? They are very good.

3) Re: running Docker on a HPC: In general Docker is not usable on HPCs. Part of the appeal for use of such a container is that it enables root access to the file system in which it exists, which results in unacceptable security risks to the HPC. As a result, others have created tools like singularity, which was created with use cases similar to genomics on HPCs in mind. I tried singularity a while back, and found it difficult to use, but it may have improved (last attempt was 18-24 months ago).

4) In general, if you have been stuck on this for 4 months, I recommend starting to pursue other approaches if the above do not work for you. There is more than one way to impute a cat