Comments (12)
from pggb.
Oh I didn't take the warning message so seriously, when I tested the test file! Now I know the problem! I will change to a computer with Intel core and try!
Thanks a lot! Also looking forward to the version that can support arm64!
from pggb.
from pggb.
Hi @zmz1988,
for me docker build --target binary -t ${USER}/pggb:latest .
works with the latest pggb
commit. The Dockerfile
itself is designed in a way to already have the GCC version incorporated that's required to compile seqwish
.
So my impression is that you maybe changed the Dockerfile
?
Did you just go for
git clone --recursive https://github.com/pangenome/pggb
cd pggb
docker build --target binary -t ${USER}/pggb:latest .
?
Or it could be your hardware does not support -mcx16
. But that seems very unlikely: https://superuser.com/questions/187254/how-prevalent-are-old-x64-processors-lacking-the-cmpxchg16b-instruction.
from pggb.
Hi @ekg @subwaystation , Thank you both for answering me!
I did exactly as suggested in the installation section of readme file. I never use docker before, so I had to install docker with the version of Mac with Apple chip. Then in my terminal, use the exact lines as showed above. I'm still so naive to understand how to change the docker file...
I checked my machine. After gcc --version
:
Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/4.2.1 Apple clang version 12.0.5 (clang-1205.0.22.11) Target: arm64-apple-darwin20.6.0 Thread model: posix InstalledDir: /Library/Developer/CommandLineTools/usr/bin
I also checked the options for the gcc command by typing gcc- help
in terminal, and I didn't find -mcx16
. So I guess that my machine does not support -mcx16
?
I tried to pull a gcc version in docker, but am still slowly learning how to do it...
from pggb.
Your local GCC should not affect the GCC when running the pggb
docker container.
Can you please try docker pull ghcr.io/pangenome/pggb:latest
followed by docker run -it -v ${PWD}/data/:/data ghcr.io/pangenome/pggb:latest "pggb -i /data/HLA/DRB1-3123.fa.gz -N -s 5000 -I 0 -p 80 -n 10 -k 8 -t 2 -v -L -o /data/out -m"
?
First you pull the already created docker image, then you run it with a test data set. Make sure that you cd
into the pggb
folder first!
from pggb.
I get an error. Please see the following:
MacBook-Pro-2 pggb % docker run -it -v ${PWD}/data/:/data ghcr.io/pangenome/pggb:latest "pggb -i /data/HLA/DRB1-3123.fa.gz -N -s 5000 -I 0 -p 80 -n 10 -k 8 -t 2 -v -L -o /data/out -m" WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested [wfmash::map] Reference = [/data/HLA/DRB1-3123.fa.gz] [wfmash::map] Query = [/data/HLA/DRB1-3123.fa.gz] [wfmash::map] Kmer size = 16 [wfmash::map] Window size = 2 [wfmash::map] Segment length = 5000 (read split disabled) [wfmash::map] Block length min = 15000 [wfmash::map] Alphabet = DNA [wfmash::map] Percentage identity threshold = 80% [wfmash::map] Mapping output file = //wfmash-s3ZAf5 [wfmash::map] Filter mode = 1 (1 = map, 2 = one-to-one, 3 = none) [wfmash::map] Execution threads = 2 [wfmash::skch::Sketch::build] minimizers picked from reference = 108363 terminate called after throwing an instance of 'std::overflow_error' what(): robin_hood::map overflow qemu: uncaught target signal 6 (Aborted) - core dumped Command terminated by signal 6 wfmash -X -s 5000 -l 15000 -N -p 80 -n 10 -k 16 -t 2 /data/HLA/DRB1-3123.fa.gz /data/HLA/DRB1-3123.fa.gz 0.34s user 0.01s system 101% cpu 0.35s total 22548Kb max memory
Is it related the memory issue that I don't have enough memory? I had to run it locally, as the cluster I use does not support docker...
from pggb.
Alright, now I get the problem. You have an ARM64
CPU architecture, but all our tools are build for the AMD64
architecture. No wonder you couldn't build seqwish
. It was because an instruction specifically for the AMD64
architecture was set.
Maybe a better way to approach this is tool by tool, first. Because we didn't test any of them on a ARM64
CPU architecture. I am afraid, non of the major developers has access to such a machine.
Get a more recent GCC and try to build https://github.com/ekg/wfmash, https://github.com/pangenome/smoothxg as instructed in the README.
If that works we can take a closer look at the seqwish
problem. But it might take some time to figure out some compiler errors.
Unfortunately, you can't install all the tools from Bioconda, because the ARM64
support is still pretty scarce there, too.
@ekg @AndreaGuarracino What do you think about ARM64
regarding pggb
and its tools?
from pggb.
We should support arm64!
Seems like Rust won't be there any time soon! rust-lang/rust#73908 (comment).
from pggb.
@zmz1988 Please tell us, if switching the machine architecture worked for you :)
from pggb.
@subwaystation Works smoothly in MacBook with Intel core i7!
Thanks a lot!!
from pggb.
Thanks for letting us know! Have fun building graphs ;)
The support of arm64 is not on a very close horizon, so I am closing this issue.
from pggb.
Related Issues (20)
- seqwish fails when `--output-dir` contains commas HOT 1
- Parameters optimization
- [help] My reference genome of a diploid organism is a primary assembly HOT 3
- Gradual increase of pan-genomes HOT 1
- computational efficiency of pggb HOT 3
- container creation failed
- Command terminated by signal 6 HOT 4
- Setting the poa-length-target(s)
- A null vcf file HOT 3
- what dose "consensus path" generated with parameter -Q mean HOT 2
- pggb: option requires an argument -- 'i' HOT 1
- the effect of `n_mappings`
- For aligning chromosomes of different species over 100MYA or div is it better to use .masked files?
- Memory size required to build large genomes HOT 14
- run without errors and outputs HOT 7
- erro about paf2net.py HOT 2
- Recommended practices for downstream analyses
- mismatched line lengths at line 3 within sequence
- PGGB singularity vg deconstruct not recognizing sample prefix
- Unable to generate giraffe indexes for PGGB graph
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 pggb.