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  • Jan 12 2021 17:17

    nellore on master

    adds deprecation note (compare)

  • Nov 30 2020 19:01
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  • Mar 04 2018 21:39
    nellore closed #86
abhinav
@nellore
oh, nm
yeah, mention @nellore if something else comes up
Julia di Iulio
@juliadiiulio_twitter
:thumbsup:
Julia di Iulio
@juliadiiulio_twitter

Hey @nellore, turns out that if I uncomment my credentials, the IAM role that was attached to my instance by devops is no longer working... (I talked to them, and this is why they had previously asked me to comment out my credentials in ~/.aws/credentials) which yield to the following error

*Errors encountered*
Job flow failed on Monday, Aug 21, 2017 at 10:38:37 PM UTC. Run time was 142.681 seconds.
Traceback (most recent call last):
File "app_main.py", line 75, in run_toplevel
File "/usr/local/raildotbio/rail-rna/dooplicity/emr_runner.py", line 285, in <module>
args.aws_exe, args.profile, args.region)
File "/usr/local/raildotbio/rail-rna/dooplicity/emr_runner.py", line 230, in run_job_flow

+ (' ensure that IAM roles are '

RuntimeError: (HTTP Error 400: Bad Request); ensure that IAM roles are configured properly. This may require talking to your AWS account admin. ...

Do you think there is a way to hack rail to prevent the previous error (the one that I got when I didn't have my credentials in ~/.aws/credentials) ? or does that sound difficult ?

abhinav
@nellore
are you launching an EMR cluster from an EC2 instance or from your laptop?
Julia di Iulio
@juliadiiulio_twitter
from an EC2 instance
abhinav
@nellore
hm, what happens when you run aws emr create-default-roles?
Julia di Iulio
@juliadiiulio_twitter

when the credentials are commented, it works and returns

[]

but when I don't comment the credentials, I get an error

An error occurred (AccessDenied) when calling the CreateRole operation

abhinav
@nellore
is that the default profile you're using?
Julia di Iulio
@juliadiiulio_twitter
hmm sorry but I am not sure I know, how can I check ?
abhinav
@nellore
on the EC2 instance, can you enter echo $AWS_ACCESS_KEY_ID
and let me know if it says anything, but not paste it?
Julia di Iulio
@juliadiiulio_twitter
it's blank (but I have my credentials commented again)
abhinav
@nellore
and in ~/.aws/credentials, just see if the commented-out lines are under [default]
blank, i see
Julia di Iulio
@juliadiiulio_twitter
yes they are
abhinav
@nellore
alright
can you do the following
(i'm following instructions here, modifying them slightly so rail might work)
export AWS_ACCESS_KEY_ID=curl http://169.254.169.254/latest/meta-data/iam/security-credentials/${instance_profile} | grep AccessKeyId | cut -d':' -f2 | sed 's/[^0-9A-Z]*//g'
grrr
``export AWS_ACCESS_KEY_ID=curl http://169.254.169.254/latest/meta-data/iam/security-credentials/${instance_profile} | grep AccessKeyId | cut -d':' -f2 | sed 's/[^0-9A-Z]*//g'````
``export AWS_ACCESS_KEY_ID=\curl http://169.254.169.254/latest/meta-data/iam/security-credentials/${instance_profile} | grep AccessKeyId | cut -d':' -f2 | sed 's/[^0-9A-Z]*//g'````
ugh
okay
you see the aws_access_key_id and secret_access_key lines there?
run those, except precede them with export, and make the variable names before the equals signs uppercase
then, keeping those lines in your credentials file commented
try running the rail-rna cluster launch command
there = from the link i sent you
Julia di Iulio
@juliadiiulio_twitter

hmmm from

curl http://169.254.169.254/latest/meta-data/iam/security-credentials/${instance_profile}

all I get is the ec2-role, there is no aws_access_key_id or secret_access_key that I can see

aaaaargh... I'm sorry for so much troubleshooting :(
abhinav
@nellore
no no, i'm learning too
a role was created for you
so you need to grab some temporary security credentials
read under Using Temporary Security Credentials with the AWS CLI
Julia di Iulio
@juliadiiulio_twitter
Okay!
abhinav
@nellore
run $ aws sts assume-role --role-arn arn:aws:iam::123456789012:role/role-name --role-session-name "RoleSession1" --profile IAM-user-name > assume-role-output.txt
except replace role-name with the name of the role given you
and IAM-user-name with your IAM user name
see if an access key id and secret access key are stored in assume-role-output
if so, then set the global variables AWS_ACCESS_KEY_ID and AWS_SECRET_ACCESS_KEY to them, and _now_try resubmitting the job flow
Julia di Iulio
@juliadiiulio_twitter
Okay let me try !
Julia di Iulio
@juliadiiulio_twitter

... now looks like the role devops gave me doesn't allow me to do "assume-role"

An error occurred (AccessDenied) when calling the AssumeRole operation: Not authorized to perform sts:AssumeRole

I will have to check with them tomorrow because they are gone for the day
I'll keep you posted

abhinav
@nellore
sounds good
Julia di Iulio
@juliadiiulio_twitter

Hi @nellore, I'm still waiting from devops for the elastic mode issue...
meanwhile for the local mode issue that I referred to yesterday

rail-rna_logs/align_reads/dp.reduce.log/1.0.log
Traceback (most recent call last):
File "app_main.py", line 75, in run_toplevel
File "/usr/local/raildotbio/rail-rna/rna/steps/align_reads.py", line 774, in <module>
no_polyA=args.no_polyA)
File "/usr/local/raildotbio/rail-rna/rna/steps/align_reads.py", line 465, in go
for is_reversed, name, qual in xpartition:
ValueError: expected length 3, got 2

when I open the respective preprocessed file in

rail-rna_logs/preprocess/push/1.0.gz
All of the reads (column 1 in that file) are at least 35 bp long, and so are the qualities (column 4 in that file). Is there anything else that could create this issue ?

I also get the following error a lot (for most of the run; btw locally, I'm running 4 samples at a time with around 50Mio reads per sample, PE 75bp initially before trimming, and I am using 8 thread per run).

*Errors encountered*
Streaming command "LC_ALL=C sort -T ./ -S 8000000 -k1,1 -t$'\t' -m /scratch/output/RNAseq/rail-rna_logs/align_reads/dp.tasks/4.* | /usr/local/raildotbio/pypy-2.5-linux_x86_64-portable/bin/pypy /usr/local/raildotbio/rail-rna/rna/steps/align_reads.py --bowtie-idx=/scratch/output/Genome/Index/Bowtie1/hg38_ERCC92 --bowtie2-idx=/scratch/output/Genome/Index/Bowtie2/hg38_ERCC92 --bowtie2-exe=/usr/local/raildotbio/bowtie2-2.2.7/bowtie2 --exon-differentials --partition-length=5000 --min-exon-size=9 --search-filter=1 --manifest=/scratch/output/RNAseq/manifest_20170808_local.txt --max-readlet-size=25 --readlet-interval=4 --capping-multiplier=1.1 --gzip-level 3 --index-count 400 --tie-margin 0 --verbose --scratch ./ --output-bam-by-chr --no-polyA -- 2>/scratch/output/RNAseq/rail-rna_logs/align_reads/dp.reduce.log/4.0.log" failed; exit level was 137.
Job flow failed on Tuesday, Aug 22, 2017 at 03:08:10 AM UTC. Run time was 15272.846 seconds.

and the rail-rna_logs/align_reads/dp.reduce.log/4.0.log is actually empty

Julia di Iulio
@juliadiiulio_twitter
just realized something that goes beyond my understanding :smile: : when I only run 1 set of 4 sample at a time locally on an ec2 instance, it seems like the run doesn't give error, while if I run several set of 4 samples in the same instance (but different directories), it looks like the chances of errors are very high.
The exact same set of 4 samples that gave me the error (ValueError: expected length 3, got 2) don't give the error anymore when they are the only set of samples run on the instance. There is also another confounding factor: the instance type is now different. Does any of this make sense to you ?