Process killed

[skrakau]

Hi @skrakau ,

I installed the package from conda. When I run the program, the process killed itself.

pureclip -i aligned.prepro.R2.bam -bai aligned.prepro.R2.bam.bai \
 -g ref.hg19.fa -iv 'chr1;chr2;chr3;' -nt 0 \
 -o PureCLIP.crosslink_sites.bed \
 -ts 6000 -mtc2 5000 -nta 0 -vv >> log_0817_v2

• snippets before process got killed log_0817_v2.txt

Simple linear regression (count <- kde): b0 = -0.168431 and b1 = 111.308 .
  Compute KDEs ...
  Estiamte Ns ... 1
Prior ML estimation of density distribution parameters using predefined cutoff ...
Initial gamma1: Run simplex algorithm using different start points.
updateThetaAndK... kMax: 1
Call GSL multimin solver nmsimplex2 ...

• pureclip version

pureclip - Protein-RNA interaction site detection 
==================================================
    pureclip [OPTIONS] <-i BAM FILE> <-bai BAI FILE> <-g GENOME FILE> <-o OUTPUT BED FILE>
    Try 'pureclip --help' for more information.

VERSION
    Last update: April 2019
    pureclip version: 1.3.1
    SeqAn version: 2.2.0

This (https://hub.docker.com/layers/ubuntu/library/ubuntu/xenial-20200706/images/sha256-e5ec578bd8c334d7c9849fd9bbaa78ec25f2b51b0bf7c9e18b1e9b7ca32d6681?context=explore) docker image.

Thanks.

Originally posted by @eric-yyjau in https://github.com/skrakau/PureCLIP/issues/11#issuecomment-675034144

[skrakau]

Hi @eric-yyjau, I opened a new issue, since I think this is a different problem. Are you sure that it was not killed from externally, e.g. because of the used resources? And why did you specify -nt 0 and -nta 0? I am not sure about the behaviour for non-positive values.

[eric-yyjau]

Hi @skrakau ,

Thank you for your reply. The commands with -nt 0 and -nta 0 is meant to limit the cpu resources used.

I actually tested the program under 2 environments. Under both environments I installed using conda.

1. A desktop with 32GB RAM and 12 cores.

No LSB modules are available.
Distributor ID:	Ubuntu
Description:	Ubuntu 16.04.6 LTS
Release:	16.04
Codename:	xenial

The following command works on my desktop.

pureclip -i aligned.prepro.R2.bam -bai aligned.prepro.R2.bam.bai \
-g ref.hg19.fa -iv 'chr1;chr2;chr3;' -nt 0 \
-o PureCLIP.crosslink_sites.bed \
-ts 6000 -mtc2 5000 -nta 0 -vv

2. A cluster with docker image. 2 cpu cores and 8 GB ram. dorowu/ubuntu-desktop-lxde-vnc Tags - Docker Hub https://hub.docker.com/r/dorowu/ubuntu-desktop-lxde-vnc/tags/

I ran the same command but failed at the line

Call GSL multimin solver nmsimplex2 ...

So I guess it is the issue of the GSL solver. I don't know if there's any dependency needed.

Thank you.

[eric-yyjau]

If possible, can you try to test under docker image to see if you can reproduce the bug? Thank you!

[skrakau]

Dependencies actually shouldn't be the problem, because a static build is used for bioconda. Not sure what could cause the problem here, sorry, but I also don't have the resources currently to look into other containers.