abra

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Exception in thread "main" java.lang.IllegalStateException: Unable to delete: abra_temp_dir at abra.ReAligner.init(ReAligner.java:1102) at abra.ReAligner.reAlign(ReAligner.java:121) at abra.ReAligner.run(ReAligner.java:1240) at abra.Abra.main(Abra.java:12) please help me!!!

lovelycatZ

Hi, I tested building on following 2 systems and get same resolve errors at bottom for build. 1. Centos 7 Apache Maven 3.6.3 (cecedd343002696d0abb50b32b541b8a6ba2883f) Maven home: /export/home/bwiley4/tools/apache-maven-3.6.3 Java version: 11.0.10,...

BJWiley233

Per email discussion, this is a Dockerfile that would build whatever the latest ABRA checked out of github.

alanhoyle

Is it possible to get the assembled contig?

2

Is it possible to get as output the assembled contig against which the realignment is done for each targeted region?

juberpatel

Change header in bam

1

Dear all, I have problems with header after realignment of abra tool. Do you have same problem? FixMateInformation doesn't work. Thank you Filip

FedikZe

Abra error

2

Hi, I am trying this tool to do realignment in a few regions, but got following error: java.lang.NegativeArraySizeException at java.lang.AbstractStringBuilder.(AbstractStringBuilder.java:64) at java.lang.StringBuffer.(StringBuffer.java:108) at abra.CompareToReference2.getSequence(CompareToReference2.java:400) at abra.KmerSizeEvaluator.getBases(KmerSizeEvaluator.java:44) at abra.KmerSizeEvaluator.identifyMinKmer(KmerSizeEvaluator.java:98) at abra.NativeAssembler.assembleContigs(NativeAssembler.java:273)...

yuhongning

Amplicon data

5

Hi Looks like a great tool I just wondered it will work with amplicon data. I seem to recall haplotype caller struggling with the lack of sequence diversity. Thanks Matt

mcgml

[Request] Replace System.out.print* statements with System.err.print* for stream compatibility

3

The output of ABRA is, unfortunately, not necessarily coordinate-sorted, such that I would prefer to replace any usage with one that piped to samtools #sort. In addition, it would be...

dnbaker

Error in Cadabra

4

Hi I realigned my reads using abra and wants to do somatic calling using Cadabra but keep having a problem and I do not understand why. Here is my command:...

GKerdivel

Exception in thread Error

2

ABRA version - 0.96 Platform - CentOS command used to run ABRA `java -Xmx4G -jar abra-0.96-SNAPSHOT-jar-with-dependencies.jar --in C26.bam --out C26.ABRA.bam --ref hs37d5.fa --targets Agilent_Nimblegen.bed --threads 4 --working temp_dir >abra.log 2>...

tinuthomas