I'm running cat on AWS nodes. I'm having several problems:
First, when I tried to launch toil, it timed out connecting to the flatcar AMI server. So I set the flatcar AMI to: ami-08870dfc70c8d6fe4.
Second, it looks like docker won't mount any of the directories I created. I ran docker outside of cat, and still had this problem. For example:
docker run -v /catjobs:/catjobs -u 0:0 -i -t --rm quay.io/ucsc_cgl/cat:latest /bin/bash
results in an empty /catjobs. The only way I could work around this, is to put my catjobs directory in /var/tmp. It seems to mount those directories, but not the ones I create. I checked permissions and am running as root, so didn't see a problem there.
Third, the biggest problem I have is I'm getting the following error.
INFO: Informed scheduler that task Chaining_False_True_True_1fdbe7409d has status FAILED
GenerateHints also failed, but I don't see any other useful messages or information. I've also looked in the luigi_logs but I don't see what went wrong.
I've run:
luigid --background --logdir luigi_logs```
and my CAT command is:
Hi,
I'm running cat on AWS nodes. I'm having several problems:
First, when I tried to launch toil, it timed out connecting to the flatcar AMI server. So I set the flatcar AMI to: ami-08870dfc70c8d6fe4.
Second, it looks like docker won't mount any of the directories I created. I ran docker outside of cat, and still had this problem. For example:
docker run -v /catjobs:/catjobs -u 0:0 -i -t --rm quay.io/ucsc_cgl/cat:latest /bin/bashresults in an empty /catjobs. The only way I could work around this, is to put my catjobs directory in /var/tmp. It seems to mount those directories, but not the ones I create. I checked permissions and am running as root, so didn't see a problem there.
Third, the biggest problem I have is I'm getting the following error.
INFO: Informed scheduler that task Chaining_False_True_True_1fdbe7409d has status FAILEDGenerateHints also failed, but I don't see any other useful messages or information. I've also looked in the luigi_logs but I don't see what went wrong.
I've run:
luigi \ --module cat RunCat \ --hal="mMolNig1.hal" \ --ref-genome="hg38" \ --config="cat.config" \ --work-dir="cat-mMolNig1" \ --out-dir="cat-mMolNig1-out" \ --workers=3 \ --maxCores=8 \ --augustus \ --augustus-pb \ --augustus-cgp \ --assembly-hub \ --batchSystem mesos \ --zone "us-east-1a" \ --nodeTypes "m6a.8xlarge,c6a.8xlarge,c6a.16xlarge,r6a.8xlarge" \ --provisioner aws \ --maxNodes 20