Hi All,
I am trying to perform a local realignment of some BAM generated with Novoalign. I run the following commands:
Command 1:
novoalign -f reads.fastq.gz -c 2 -d Mosaik/reference -o SAM 2> reads.novoalign_logS0.txt | samtools view -S -b -q 1 - | samtools sort - reads
Command 2:
java -Xmx2g -jar /usr/local/bin/picard/SortSam.jar I=reads.bam O=readssorted.bam SO=coordinate
Command 3:
java -Xmx2g -jar /usr/local/bin/gatk/GenomeAnalysisTK.jar -I readssorted.bam -R Mosaik/reference.fasta -T RealignerTargetCreator -o forIndelRealigner.intervals
Command 4:
java -Xmx2g -jar /usr/local/bin/gatk/GenomeAnalysisTK.jar -I readssorted.bam -R Mosaik/reference.fasta -T IndelRealigner --targetIntervals forIndelRealigner.intervals -o realignedBam.bam
The RealignerTargetCreator (3) finishes successfully and creates the required file:
LASV-reference:52-53
LASV-reference:305-339
LASV-reference:439-519
However, when I run the last command (4) - IndelRealigner, I get the following error:
##### ERROR MESSAGE: File associated with name forIndelRealigner.intervals is malformed: Interval file could not be parsed in any supported format. caused by Failed to parse Genome Location string: LASV-reference:52-53
Any idea what might be the problem here? I have tried various things, but I always fail here.
My reference.dict looks like this:
@HD VN:1.0 SO:unsorted
@SQ SN:LASV-reference LN:3402 UR:file:/Users/kga/Desktop/Mosaik/reference.fasta M5:8a4c76005c28bef3f2775dbf6ffa2062
reference.fasta.fai:
LASV-reference 3402 89 3402 3403
Thanks very much,
Kristian
I am trying to perform a local realignment of some BAM generated with Novoalign. I run the following commands:
Command 1:
novoalign -f reads.fastq.gz -c 2 -d Mosaik/reference -o SAM 2> reads.novoalign_logS0.txt | samtools view -S -b -q 1 - | samtools sort - reads
Command 2:
java -Xmx2g -jar /usr/local/bin/picard/SortSam.jar I=reads.bam O=readssorted.bam SO=coordinate
Command 3:
java -Xmx2g -jar /usr/local/bin/gatk/GenomeAnalysisTK.jar -I readssorted.bam -R Mosaik/reference.fasta -T RealignerTargetCreator -o forIndelRealigner.intervals
Command 4:
java -Xmx2g -jar /usr/local/bin/gatk/GenomeAnalysisTK.jar -I readssorted.bam -R Mosaik/reference.fasta -T IndelRealigner --targetIntervals forIndelRealigner.intervals -o realignedBam.bam
The RealignerTargetCreator (3) finishes successfully and creates the required file:
LASV-reference:52-53
LASV-reference:305-339
LASV-reference:439-519
However, when I run the last command (4) - IndelRealigner, I get the following error:
##### ERROR MESSAGE: File associated with name forIndelRealigner.intervals is malformed: Interval file could not be parsed in any supported format. caused by Failed to parse Genome Location string: LASV-reference:52-53
Any idea what might be the problem here? I have tried various things, but I always fail here.
My reference.dict looks like this:
@HD VN:1.0 SO:unsorted
@SQ SN:LASV-reference LN:3402 UR:file:/Users/kga/Desktop/Mosaik/reference.fasta M5:8a4c76005c28bef3f2775dbf6ffa2062
reference.fasta.fai:
LASV-reference 3402 89 3402 3403
Thanks very much,
Kristian
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