Comments (14)
The details (such as they are) are in this comment in issue 549: #549 (comment)
As far as how to use the binary — download it and run it (giving an explicit path to where it is on your machine). Or put it in some directory that's defined in your $PATH, and run it (just using the binary's file name).
from pbbioconda.
What OS and kernel are you using?
from pbbioconda.
I have the same problem. Installed from bioconda earlier today. isoseq3 seems to segfault right away regardless of what's the rest of the command line looks like.
I installed this earlier today in a fresh conda environment.
isoseq3-3.8.2 h9ee0642_0 1.6 MB bioconda
Am trying to do perform the steps at https://isoseq.how/clustering/cli-workflow.html , but have been advised to use isoseq3 instead of isoseq. I successfully ran step 2 which uses lima. At step 3 I try isoseq3 refine and get the segfault.
uname -a
Linux fletony 4.19.0-21-amd64 #1 SMP Debian 4.19.249-2 (2022-06-30) x86_64 GNU/Linux
from pbbioconda.
I'm also seeing this again on a new machine, same as back in #549...
Output of uname
:
Linux 4.19.0-23-cloud-amd64 #1 SMP Debian 4.19.269-1 (2022-12-20) x86_64 GNU/Linux
from pbbioconda.
The solution from back then worked for me now (downloaded the binaries directly) but it would be really nice if the conda packages actually worked.
from pbbioconda.
Thanks @jamestwebber . Unfortunately the binary doesn't work for me. I just get "Illegal instruction" instead of a segfault.
from pbbioconda.
Illegal instructions means that you are using an ancient CPU that does not support SSE4.1
from pbbioconda.
@jamestwebber it's strange what conda did to the binary. I'll try to re-upload it...
from pbbioconda.
Illegal instructions means that you are using an ancient CPU that does not support SSE4.1
Inferring from what I see above, the conda package doesn't rebuild isoseq3, it merely loads a binary (am I correct?). In which case even if the conda package's isoseq3 didn't segfault, I'd still have the illegal instruction issue. Right?
As for why I was running on such an old CPU, I was running on the primary machine attached to disk where my sequenced data is. The only restriction I noticed (when I was reading installation instructions) was that I needed my bioconda environment to be python 2.7.
I need to ask, then, if I locate a machine that supports SSE4.1 should that be sufficient?
from pbbioconda.
For Iso-Seq, you don't need python. Just a machine that isn't older than from ~2007.
from pbbioconda.
@armintoepfer &J.
from pbbioconda.
The solution from back then worked for me now (downloaded the binaries directly) but it would be really nice if the conda packages actually worked.
since I'm getting a Segfault too, could we write here how we can go about downloading and then using the binaries directly? This sounds pretty magical but also mysterious!
Maybe it helps the next person who needs to download binaries too, but doesn't have the experience to know what's involved in this.
from pbbioconda.
But I would guess when the latest version number changes, you'd have to consider that when you download the binary.
from pbbioconda.
I have uploaded a new version. If that still segfaults, but not the github binary itself, then conda is corrupting the binary.
from pbbioconda.
Related Issues (20)
- Error while running Falcon HOT 1
- Cannot download Iso-Seq example data HOT 1
- filter HOT 1
- Lima failing to detect CCS data after Skera de-concatination & Bam2Fastq conversion HOT 1
- pigeon classification doesn't work (Chinese Hamster) HOT 5
- Segmentation fault (core dumped) when installing ilma. HOT 1
- isoseq correct is very sensitive for style of input HOT 1
- Isoseq3 cluster2 exits without error message
- isoseq3 collapse stops with fatal error map::at
- Generate HiFi reads
- iso-seq reads and pbfusion HOT 2
- identify transcripts with polyA tails
- IsoPhase on MAS-Iso-seq data for haplotyping
- isoseq for scRNA: duplicate molecules are kept
- isoseq for scRNA: UMI with homopolymers are not removed
- What can I do only with .fastq reads?
- isoseq groupdedup for variant analysis
- lima not outputting enough ZMWs - issue with primers or primer choice?
- What's the difference of = and X cigar of pbmm2? HOT 3
- PBSV system requirements 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 pbbioconda.