Comments (4)
Are you able to provide another BAM snippet that reproduces the problem?
from abra.
Here's one more
--
Abra JNI entry point v0.96, prefix: X_140994966_140995366, read_length: 101, kmer_size: 47, min_node_freq: 2, min_base_qual: 60, min_edge_ratio 0.020000, debug: 1, max_nodes: 9000
Assembling: -> abra_temp_dir/X_140994966_140995366_contigs.fasta_k47
STOPPED_ON_REPEAT: X_140994966_140995366
Done assembling(0): abra_temp_dir/X_140994966_140995366_contigs.fasta_k47, 0
Abra JNI entry point v0.96, prefix: X_140994966_140995366, read_length: 101, kmer_size: 49, min_node_freq: 2, min_base_qual: 60, min_edge_ratio 0.020000, debug: 1, max_nodes: 9000
Assembling: -> abra_temp_dir/X_140994966_140995366_contigs.fasta_k49
STOPPED_ON_REPEAT: X_140994966_140995366
Done assembling(0): abra_temp_dir/X_140994966_140995366_contigs.fasta_k49, 0
Abra JNI entry point v0.96, prefix: X_140994966_140995366, read_length: 101, kmer_size: 51, min_node_freq: 2, min_base_qual: 60, min_edge_ratio 0.020000, debug: 1, max_nodes: 9000
Assembling: -> abra_temp_dir/X_140994966_140995366_contigs.fasta_k51
Done assembling(1): abra_temp_dir/X_140994966_140995366_contigs.fasta_k51, 2
Elapsed_msecs_in_NativeAssembler Region: X_140994966_140995366 Length: 400 ReadCount: 460 Elapsed 794 Assembled true 23
Done assembling(3): abra_temp_dir/X_77244911_77245471_contigs.fasta_k17, 1033
Elapsed_msecs_in_NativeAssembler Region: X_77244911_77245471 Length: 560 ReadCount: 1241 Elapsed 2347 Assembled true 17
Clock time in Assembly: 475
Fri Nov 13 03:49:40 CST 2015 : Aligning contigs
Running: [bwa mem -t 14 /reference/gatk/bundle/2.8/human_g1k_v37_decoy.fasta abra_temp_dir/all_contigs.fasta > abra_temp_dir/all_contigs.sam]
A fatal error has been detected by the Java Runtime Environment:
SIGSEGV (0xb) at pc=0x00007fd32595b5fe, pid=38053, tid=140544852342528
JRE version: Java(TM) SE Runtime Environment (8.0_20-b26) (build 1.8.0_20-b26)
Java VM: Java HotSpot(TM) 64-Bit Server VM (25.20-b23 mixed mode linux-amd64 compressed oops)
Problematic frame:
V [libjvm.so+0x8e35fe] SR_handler(int, siginfo_, ucontext_)+0x3e
An error report file with more information is saved as:
--
I am using the binaries provided here, should I compile them myself and try ?
from abra.
I am running abra with 14 threads and using jdk1.8.0_20
from abra.
14 threads and java 1.8 should be fine.
The error message, unfortunately is not very informative.
You could try compiling yourself, however the fact that some samples succeed leads me to believe that might not help.
from abra.
Related Issues (20)
- Excessive run time HOT 2
- [fwrite] Remote I/O error HOT 5
- polyA/polyT/lowcomplexity region realignments for single ended reads HOT 3
- Exception in thread Error HOT 2
- Error in Cadabra HOT 4
- [Request] Replace System.out.print* statements with System.err.print* for stream compatibility HOT 3
- Amplicon data HOT 5
- xlC compatibility - C++ STL referenced in .c files HOT 4
- hidden dependency on bwa mem HOT 2
- Abra error HOT 2
- Change header in bam HOT 1
- Is YA tag deterministic? HOT 4
- Abra will realign duplicates? HOT 5
- Testing practices HOT 2
- Abra processes unique reads? HOT 2
- Is it possible to get the assembled contig? HOT 2
- No contigs assembled: no space left on device HOT 1
- abra2 error java.lang.NumberFormatException HOT 3
- build issue
- java.lang.IllegalStateException
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 abra.