Comments (7)
Hi HajkD,
Yes. I'd like to run all 300K elements against Dfam for the annotation purpose.
You indicate a good idea to take one representative rather than go through many sequences sharing homology. I will give a try.
Thanks!
from ltrpred.
Fatal exception (source file esl_hmm.c, line 198):
malloc of size -307968 failed
Aborted (core dumped)
Error running command:
It seems like you don't have enough memory to perform the search. I would recommend to use a computer with more RAM.
I hope this helps.
from ltrpred.
Thanks for that pointing out. I run it on 500G RAM machine with 32 cpu still getting the same error. I am not aware of how to allocate memory size to LTRpred in the parameterization options listed in the documentation.
Another challenge, is there a tweak to set up LTRpred to pick dfamscan from local installation or conda version which could help to test it in a server machine where one doesn't have admin privilege to install dfamscan in /usr/local/bin/?
from ltrpred.
Any suggestions on this, please?
from ltrpred.
Hi Sadik,
Since this is an issue coming from the dfamscan script provided by the Dfam community, I would suggest to contact them.
Alternatively, have you tried running the failed command? :
nhmmscan --noali -E 0.001 --dfamtblout /tmp/nXeK2iJYcP --cpu=16 dfam/Dfam.hmm /home/ltrpred/epo_ltrdigest/epo-ltrdigest_complete.fas
Maybe this yields more comprehensive error messages?
For me to understand, does the yeast
example from the documentation work for you on this machine or does it also fail? It clearly seems to be a memory assignment issue and now you would need to troubleshoot where this comes from in detail.
Regarding your question:
Another challenge, is there a tweak to set up LTRpred to pick dfamscan from local installation or conda version which could help to test it in a server machine where one doesn't have admin privilege to install dfamscan in /usr/local/bin/?
You can run the dfamscan.pl directly without sudo rights in any folder by typing:
perl dfamscan.pl -fastafile [[seq_file]] -hmmfile path/to/Dfam.hmm -dfam_outfile DfamAnnotation.out -E 1E-5 -cpu 16 --log_file logfile.txt --masking_thresh
I hope this helps.
Cheers,
Hajk
from ltrpred.
I am facing the same issue when feeding 300K sequences to LTRpred Dfam scan with 1TB RAM, 112 threads machine.
Fatal exception (source file esl_hmm.c, line 198):
malloc of size -148920 failed
If RAM is the limitation causing the fault by feeding so many sequences, is it possible to do Dfam nhmmscan by batch? (eg. scan 1-1000 sequences -> store the result in tmp -> scan 1001-2000 sequences ->store the result in tmp -> ....->combine the chunks to the final output.
from ltrpred.
Hi @a7032018
This is an excellent idea.
Do I understand correctly that LTRpred annotated 300k elements and you would like to run all 300k elements against Dfam?
By any chance, did you enable the TE family clustering option in LTRpred
to check whether some elements generate huge clusters and thus only a cluster representative (family member) needs to be hmmered against the Dfam? This could be an alternative option.
Regarding the batch Dfam scans I noted it down as feature request and will work on it when time permits.
from ltrpred.
Related Issues (20)
- Error in Join solo LTR Copy Number Estimation table HOT 3
- Seeking advice for my test case, test run output validation, and post-processing of files HOT 5
- R installation instructions need to be updated HOT 1
- Installation instructions of dependencies should be updated HOT 4
- Installation of dependencies fail - Docker wrapper needed HOT 9
- License in the repository is missing HOT 1
- Running LTRpred docker container in userspace with udocker HOT 6
- Small details on the vignette HOT 1
- Paper typo HOT 1
- How to fix this run error? HOT 6
- Issue with genome fasta header format
- Fasta header truncated in ltrdigest_tabout.csv
- "Error: Tibble columns must have compatible sizes" at Step 6 HOT 2
- Issue with running with singularity HOT 7
- Running LTRPred HOT 3
- Error: Column `cn_3ltr` must be length 48 (the number of rows) or one, not 0 HOT 1
- How to pull LTRpred in singularity HOT 1
- could not install biocLite.R HOT 2
- could LTRpred detect DIRS/DIRS in genome contigs? HOT 3
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from ltrpred.