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    nellore on master

    adds deprecation note (compare)

  • Nov 30 2020 19:01
    Rimsk commented #85
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    nellore on master

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  • Dec 03 2018 15:25
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  • Mar 04 2018 21:39
    nellore closed #86
abhinav
@nellore
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 ?
abhinav
@nellore
everything you just said makes total sense
jk
that's super weird
abhinav
@nellore
okay, i think i need more details to help
@juliadiiulio_twitter
so you run rail on 4 samples in local mode on an EC2 instance
and everything is fine
abhinav
@nellore
then you run rail in local mode on the same EC2 instance with different output directories on S3, and everything is not fine?
can you paste the rail-rna commands you're running?
Julia di Iulio
@juliadiiulio_twitter

so the output directories are all on the EC2 instance.
but I open a screen (with > screen -S railrna)
and run let's say 2 different sets of 4 samples each one on a different screen and with different output directories

here is the command line I use :

smpl=smpl41to44
mcd /scratch/output/RNAseq/${smpl}/
deliverables=idx,tsv,bed,bam,bw,jx
rail-rna go local -m /scratch/output/RNAseq/${smpl}.txt \
--bowtie-idx /scratch/output/Genome/Index/Bowtie1/hg38_ERCC92 /scratch/output/Genome/Index/Bowtie2/hg38_ERCC92 \
-d ${deliverables} --verbose --num-processes 8 --scratch ./ --skip-bad-records --sort-memory-cap 8000000

if I then want to change the set of samples, I just change smpl=smpl41to44 to smpl=smpl45to48 and run the same command but on another screen.
where mcd is an alias for mkdir -p and cd

abhinav
@nellore
@juliadiiulio_twitter ok hm, so does the following thing happen: when you run on sample set A alone, you get no error, but when you run on sample set A at the same time as sample sets B and C on separate screens, the sample set A run returns an error? Or do different sample sets return errors consistently?
trying to figure out whether the errors are reproduced across runtime conditions
Julia di Iulio
@juliadiiulio_twitter
@nellore the first option is correct :
"when you run on sample set A alone, you get no error, but when you run on sample set A at the same time as sample sets B and C on separate screens, the sample set A run returns an error"
abhinav
@nellore
cry
that's no good
Julia di Iulio
@juliadiiulio_twitter
hahah I did a little inside :smile:
abhinav
@nellore
okay, we want to find out which line makes rail choke
which input line
this will require adding a line to align_reads.py
Julia di Iulio
@juliadiiulio_twitter
Oh no don't worry, it takes several hours before rail chokes, so I think for now I'll just run the set on different instances :)
abhinav
@nellore
would love to figure out why this happens
but i'd also like to know why you're running rail this way
rather than on all samples at once on EMR
Julia di Iulio
@juliadiiulio_twitter
oh ideally I would definitely run all samples at once on EMR
... it just that I am running into those permission issues on AWS, and devops didn't come back to me yet.. and I have to find a way to get the project going
abhinav
@nellore
sorry to hear you're having trouble!
how many samples are you analyzing in total?
Julia di Iulio
@juliadiiulio_twitter
but I agree, that would def be my first choice :)
abhinav
@nellore
and how many reads per sample?
Julia di Iulio
@juliadiiulio_twitter
96 samples
abhinav
@nellore
have you tried taking your credentials
Julia di Iulio
@juliadiiulio_twitter
~50mio reads
abhinav
@nellore
and launching the EMR job from your laptop?
that's the use case we were targeting
Julia di Iulio
@juliadiiulio_twitter
ha I did not !