abra2
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mozack
ABRA2
On a Ubuntu base image, if I try to use the precompiled `abra2-2.24.jar`, using command: ``` java -jar abra2-2.24.jar --in input.bam --out out.abra.bam --ref reference.fa --threads 2 --tmpdir /tmp ```...
Hi, Abra is being picked up by a log4j vulnerability detection tool. I would guess the threat level is low (not web based), but am not sure. Is there any...
This my command: `java -Xmx1000g -jar /.../abra2-2.24-0/abra2.jar --sa --cons --amq 32 --in in.bam --out out.bam --ref ~/.../XENLA_9.2_genome.fa --threads 50 --targets /.../X9.2_opt_SORTED.bed --tmpdir /.../tmp > abra_s10.log` After running for 30min to...
Hello, the pipeline I am working on use in parrallele consensus (based on unique molecular index) or classical non consensus reads. So for a sample, I have in the same...
Hello, I have abra2 integrated in a snakemake workflow for variant calling and it usually does a great job. With my current dataset on Maniok esculenta, however, Abra2 exits with...
This corrects a broken link, adds a couple of other links, and adds some formatting to the readme.
Hi Lisle, I'm applying Abra2 to rna data in which the read lengths vary dramatically from the first record to the last. I noticed in the Abra logs that it...
Once I try to run ABRA2, I get the following error. Would you please look into it? Thanks. cmd=java -Xmx16G -jar target/abra2-2.19-jar-with-dependencies.jar --in /path_to/filesample_dedupSort.bam --out /path_to/filesample_abraRealign.bam --ref /path_to/hg19.fasta --threads 8...
My bed file with its one-line header made abra2 crash with the following error: Loading target regions from : target.bed Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 1 at abra.RegionLoader.load(RegionLoader.java:49) at abra.ReAligner.getRegions(ReAligner.java:1347)...
