-
Notifications
You must be signed in to change notification settings - Fork 0
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Part2 Freec as default: Cnv focal files update #2
Conversation
I can't remember with absolute certainty, but I think 32GB is enough to do it. |
Sorry for the delay,@jharenza @jaclyn-taroni I am having memory issues with this module 04-prepare-cn-file.R kills the docker. I tried to run the script line by line and it seems R/Docker gets killed/crashes at
I have tested with 15G in my local docker container and it gets killed so tried with 50G ec2 instance (t2.small with 12 CPUs) running docker as Weirdly I am getting this error on the ec2 instance while running
but not while running locally:
This is the mem distirbution within docker container:
I'm trying again with more memory will report back, more than happy to hear any suggestions. |
I unfortunately do not have any suggestions. I am going to tag @jashapiro who may have more insight. |
A |
Thank you @jashapiro! That fixed my issue with the ec2 errors, more some reason I was only looking at the cpu credits per hour 😅 |
hmm spoke too soon, still gets killed at 04 with : run-prepare-cn.sh: line 48: 7087 Killed Rscript --vanilla 04-prepare-cn-file.R --cnv_file ${scratch_dir}/consensus_seg_with_status.tsv --gtf_file $gtf_file --metadata $histologies_file --filename_lead "consensus_seg_annotated_cn" --seg on ec2 m5.2xlarge, 50 EBS |
I'd probably try going a bit bigger (e.g., |
Updating to m5a.4 helped, also I realized that I was using neutral calls copy_number as 3 which was discussed before and that was creating a larger file to annotate and output. But it is now updated to copy_number == NA as seen in 6096f54#diff-cb6603f5ac5cd549a5ff342ce8d9b950a72351ca92dbb16c3ccff1b58e3637cd Thank you for helping me figure this out! I've documented additional discussion about the output in AlexsLemonade#1010 |
Part4 Freec as default: Chromosome wide CNV plots per histology
Part3 Freec as default: Oncoprint update
Purpose/implementation Section
What scientific question is your analysis addressing?
We updated the consensus seg file creation in AlexsLemonade#987 to use freec CN calls as default. In this PR we will re-run
focal-cn-file-preparation
to identify changes in focal calls because of the update.What was your approach?
Just run run-prepare-cn.sh
What GitHub issue does your pull request address?
related to AlexsLemonade#964
Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.
Which areas should receive a particularly close look?
🚨 I couldn't complete the plotting in the module.
I haven't run this module before, so I started with having 12GB memory in docker which killed 04-prepare-cn-file.R. I increased that to 15G and re-run the 04,05,06 but it seems rna-expression-validation.R would need more than 15G.
Is this something that was seen before ?
Is there anything that you want to discuss further?
🚨
plots
are not complete for consensus calls because of the mem issue mentioned above.Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?
tables in
results
:Yesfigures in
plots
:NOResults
What types of results are included (e.g., table, figure)?
What is your summary of the results?
Comparing
consensus_seg_annotated_cn_autosomes.tsv.gz
generated in this branch with the v18 version the change logs are in:change_log.txt
column named
_latest
are from the file in the branch and_previous
is v18 release fileHere's a rough plot for status change (majority of the changes seem to be from loss to gain) reported in the change_log.txt above
Reproducibility Checklist
Documentation Checklist
README
and it is up to date.analyses/README.md
and the entry is up to date.