User: xiaoyanli82

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Posts by xiaoyanli82

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Comment: C: Realignertargetcreator Error: Not Enough Memory
... The reason for this maybe too many contigs of my references, thanks for all your answers! ...
written 6.3 years ago by xiaoyanli820
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Comment: C: Realignertargetcreator Error: Not Enough Memory
... I tried without the -rbs 10000000 argument, the same error was report. And I also realigned the same bam file to the CDS region of my reference genome, the program succeed. The reason maybe my reference is too large which is above 4G of wheat draft genome. ...
written 6.3 years ago by xiaoyanli820
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Comment: C: Realignertargetcreator Error: Not Enough Memory
... (GATK) v2.5-2-gf57256b ...
written 6.3 years ago by xiaoyanli820
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Comment: C: Realignertargetcreator Error: Not Enough Memory
... I missed the GenomeAnalysis.jar when i edit the post, sorry , and I have added in the post ...
written 6.3 years ago by xiaoyanli820
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Realignertargetcreator Error: Not Enough Memory
... Hi, everyone I use GATK to realignment the bam files, which is about 400M, the command I ues is : java -Xmx24g -jar GenomeAnalysis.jar -T RealignerTargretCreator -rbs 10000000 -R ref.fa -I sample.bam -o sample.realigner.intervals After running 1h, the program exit with this error report: ER ...
gatk memory written 6.3 years ago by xiaoyanli820
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Comment: C: Picard Markduplicates Error: Requested Array Size Exceeds Vm Limit
... I tried again following your suggestion, the problem was fixed, thank you very much! ...
written 6.4 years ago by xiaoyanli820
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Comment: C: Picard Markduplicates Error: Requested Array Size Exceeds Vm Limit
... Yes, the system has 1024g RAM. ...
written 6.4 years ago by xiaoyanli820
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Comment: C: Picard Markduplicates Error: Requested Array Size Exceeds Vm Limit
... The linux system has 1024g RAM ...
written 6.4 years ago by xiaoyanli820
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Picard Markduplicates Error: Requested Array Size Exceeds Vm Limit
... Hi, everyone, I am working with wheat exome data, which are Illumina PE 100 reads. I analysed the data followed the GATK pipeline. Read were aligned to references using BWA and the BAM files were sorted by samtools. But when I tried to mark PCR dupication using Picard, I got error: java -Xms16g - ...
picard markduplicates written 6.4 years ago by xiaoyanli820 • updated 6.4 years ago by Jordan1.1k
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Answer: A: Cigar And Sequence Length Are Inconsistent In Sam File
... I tried my data using the latest version and the problem is fixed, thank you Michael Dondrup. ...
written 6.4 years ago by xiaoyanli820

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