Error while running ABRA about abra

[mozack]

On what OS are you running?

[chisqr]

I am using CentOS release 6.7. I compiled the program on my end before doing the analysis. The binary version available from the website also does not work.

[chisqr]

Here is the output when I use a single thread:

Tue Sep 29 11:16:20 CDT 2015 : Processing region: 15_89398455_89398855
Abra JNI entry point v0.94, prefix: 15_89398455_89398855, read_length: 300, kmer_size: 65, min_node_freq: 2, min_base_qual: 60, min_edge_ratio 0.020000, debug: 1
Assembling: -> tmp1/15_89398455_89398855_contigs.fasta_k65
STOPPED_ON_REPEAT: 15_89398455_89398855
Done assembling(0): tmp1/15_89398455_89398855_contigs.fasta_k65, 0
Abra JNI entry point v0.94, prefix: 15_89398455_89398855, read_length: 300, kmer_size: 67, min_node_freq: 2, min_base_qual: 60, min_edge_ratio 0.020000, debug: 1
Assembling: -> tmp1/15_89398455_89398855_contigs.fasta_k67
STOPPED_ON_REPEAT: 15_89398455_89398855
Done assembling(1): tmp1/15_89398455_89398855_contigs.fasta_k67, 0
Abra JNI entry point v0.94, prefix: 15_89398455_89398855, read_length: 300, kmer_size: 69, min_node_freq: 2, min_base_qual: 60, min_edge_ratio 0.020000, debug: 1
Assembling: -> tmp1/15_89398455_89398855_contigs.fasta_k69
STOPPED_ON_REPEAT: 15_89398455_89398855
Done assembling(0): tmp1/15_89398455_89398855_contigs.fasta_k69, 0
Abra JNI entry point v0.94, prefix: 15_89398455_89398855, read_length: 300, kmer_size: 71, min_node_freq: 2, min_base_qual: 60, min_edge_ratio 0.020000, debug: 1
Assembling: -> tmp1/15_89398455_89398855_contigs.fasta_k71
STOPPED_ON_REPEAT: 15_89398455_89398855
Done assembling(0): tmp1/15_89398455_89398855_contigs.fasta_k71, 0
Abra JNI entry point v0.94, prefix: 15_89398455_89398855, read_length: 300, kmer_size: 73, min_node_freq: 2, min_base_qual: 60, min_edge_ratio 0.020000, debug: 1
Assembling: -> tmp1/15_89398455_89398855_contigs.fasta_k73
STOPPED_ON_REPEAT: 15_89398455_89398855
Done assembling(0): tmp1/15_89398455_89398855_contigs.fasta_k73, 0
Abra JNI entry point v0.94, prefix: 15_89398455_89398855, read_length: 300, kmer_size: 75, min_node_freq: 2, min_base_qual: 60, min_edge_ratio 0.020000, debug: 1
Assembling: -> tmp1/15_89398455_89398855_contigs.fasta_k75
STOPPED_ON_REPEAT: 15_89398455_89398855
Done assembling(0): tmp1/15_89398455_89398855_contigs.fasta_k75, 0
Abra JNI entry point v0.94, prefix: 15_89398455_89398855, read_length: 300, kmer_size: 77, min_node_freq: 2, min_base_qual: 60, min_edge_ratio 0.020000, debug: 1
Assembling: -> tmp1/15_89398455_89398855_contigs.fasta_k77
STOPPED_ON_REPEAT: 15_89398455_89398855
Done assembling(0): tmp1/15_89398455_89398855_contigs.fasta_k77, 0
Abra JNI entry point v0.94, prefix: 15_89398455_89398855, read_length: 300, kmer_size: 79, min_node_freq: 2, min_base_qual: 60, min_edge_ratio 0.020000, debug: 1
Assembling: -> tmp1/15_89398455_89398855_contigs.fasta_k79
STOPPED_ON_REPEAT: 15_89398455_89398855
Done assembling(1): tmp1/15_89398455_89398855_contigs.fasta_k79, 0
Abra JNI entry point v0.94, prefix: 15_89398455_89398855, read_length: 300, kmer_size: 81, min_node_freq: 2, min_base_qual: 60, min_edge_ratio 0.020000, debug: 1
Assembling: -> tmp1/15_89398455_89398855_contigs.fasta_k81
STOPPED_ON_REPEAT: 15_89398455_89398855
Done assembling(0): tmp1/15_89398455_89398855_contigs.fasta_k81, 0
Abra JNI entry point v0.94, prefix: 15_89398455_89398855, read_length: 300, kmer_size: 83, min_node_freq: 2, min_base_qual: 60, min_edge_ratio 0.020000, debug: 1
Assembling: -> tmp1/15_89398455_89398855_contigs.fasta_k83
STOPPED_ON_REPEAT: 15_89398455_89398855
Done assembling(0): tmp1/15_89398455_89398855_contigs.fasta_k83, 0
Abra JNI entry point v0.94, prefix: 15_89398455_89398855, read_length: 300, kmer_size: 85, min_node_freq: 2, min_base_qual: 60, min_edge_ratio 0.020000, debug: 1
Assembling: -> tmp1/15_89398455_89398855_contigs.fasta_k85
STOPPED_ON_REPEAT: 15_89398455_89398855
Done assembling(0): tmp1/15_89398455_89398855_contigs.fasta_k85, 0
Abra JNI entry point v0.94, prefix: 15_89398455_89398855, read_length: 300, kmer_size: 87, min_node_freq: 2, min_base_qual: 60, min_edge_ratio 0.020000, debug: 1
Assembling: -> tmp1/15_89398455_89398855_contigs.fasta_k87
STOPPED_ON_REPEAT: 15_89398455_89398855
Done assembling(0): tmp1/15_89398455_89398855_contigs.fasta_k87, 0
Abra JNI entry point v0.94, prefix: 15_89398455_89398855, read_length: 300, kmer_size: 89, min_node_freq: 2, min_base_qual: 60, min_edge_ratio 0.020000, debug: 1
Assembling: -> tmp1/15_89398455_89398855_contigs.fasta_k89
Done assembling(0): tmp1/15_89398455_89398855_contigs.fasta_k89, 6
Elapsed_msecs_in_NativeAssembler Region: 15_89398455_89398855 Length: 400 ReadCount: 404 Elapsed 2150 Assembled true 65
Tue Sep 29 11:16:22 CDT 2015 : Processing region: 15_89398655_89399055
Abra JNI entry point v0.94, prefix: 15_89398655_89399055, read_length: 300, kmer_size: 265, min_node_freq: 2, min_base_qual: 60, min_edge_ratio 0.020000, debug: 1
Assembling: -> tmp1/15_89398655_89399055_contigs.fasta_k265

A fatal error has been detected by the Java Runtime Environment:

SIGSEGV (0xb) at pc=0x00007fa07cf9646c, pid=93291, tid=140327268058880

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:

C [libAbra.so+0x2546c] is_node_in_list(node_, linked_node_)+0x25

Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again

An error report file with more information is saved as:

hs_err_pid93291.log

If you would like to submit a bug report, please visit:

http://bugreport.sun.com/bugreport/crash.jsp

The crash happened outside the Java Virtual Machine in native code.

See problematic frame for where to report the bug.

Aborted

[mozack]

Would you be able to provide a BAM snippet that reproduces the problem?

[chisqr]

Is this issue fixed in 0.95 ?

[mozack]

Thanks for your patience. One of the regions in this BAM file appears to have a long repeat, which caused the kmer size to increase beyond the max buffer size causing a buffer overrun. v0.96 should behave better.

I haven't run ABRA against reads of this length. Would be interested in hearing how it behaves for you in these cases. Not sure if assembly will give much additional context.

Please let me know if you run into any more issues.