Hello everyone,
I've been trying to use Picrad's ReorderSam.jar tool to sort one BAM file, because I want to use it later with GATK. But, every time that I try to sort the file I get the following error:
"2011-09-07 00:02:48 ReorderSam No reference sequence dictionary found. Aborting. You can create a sequence dictionary for the reference fasta using CreateSequenceDictionary.jar.
[Wed Sep 07 00:02:48 GMT 2011] net.sf.picard.sam.ReorderSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1012269056"
I have already created a dictionary as requested using CreateSequenceDictionary.jar and stored it on the same folder as the reference.
However, despite I have created the dictionary, I keep getting the same error message.
The commands that I used to call the run the .jar files are:
CreateSequenceDictionary.jar
"/usr/java/latest/bin/java -d64 -jar /share/apps/picard-tools-1.52/CreateSequenceDictionary.jar R= /share/Tepehuan/Genomes/Homo_sapiens/GRC37Homo_sapiens/Masked/GRCh37_hg19_masked.fa O= GRCh37_hg19_masked.fa.bai"
ReorderSam.jar
" /usr/java/latest/bin/java -d64 -jar /share/apps/picard-tools-1.52/ReorderSam.jar I= MP1_2_merged_clara_20110404_bwa_filtered_aln_paired.bam_sorted.bam O= MP1_2_merged_clara_20110404_bwa_filtered_aln_paired.bam_GATK_sorted.bam REFERENCE= /share/Tepehuan/Genomes/Homo_sapiens/GRC37Homo_sapiens/Masked/GRCh37_hg19_masked.fa"
Also, I have already tried with different extension suffixes for CreateSequenceDictionary.jar output file and I have already verified that my BAMfile has headers (i.e. @SQ SN:gi|224589801|ref|NC_000010.10| LN:135534747 lines)
Thank you very much!!
Martin
I've been trying to use Picrad's ReorderSam.jar tool to sort one BAM file, because I want to use it later with GATK. But, every time that I try to sort the file I get the following error:
"2011-09-07 00:02:48 ReorderSam No reference sequence dictionary found. Aborting. You can create a sequence dictionary for the reference fasta using CreateSequenceDictionary.jar.
[Wed Sep 07 00:02:48 GMT 2011] net.sf.picard.sam.ReorderSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1012269056"
I have already created a dictionary as requested using CreateSequenceDictionary.jar and stored it on the same folder as the reference.
However, despite I have created the dictionary, I keep getting the same error message.
The commands that I used to call the run the .jar files are:
CreateSequenceDictionary.jar
"/usr/java/latest/bin/java -d64 -jar /share/apps/picard-tools-1.52/CreateSequenceDictionary.jar R= /share/Tepehuan/Genomes/Homo_sapiens/GRC37Homo_sapiens/Masked/GRCh37_hg19_masked.fa O= GRCh37_hg19_masked.fa.bai"
ReorderSam.jar
" /usr/java/latest/bin/java -d64 -jar /share/apps/picard-tools-1.52/ReorderSam.jar I= MP1_2_merged_clara_20110404_bwa_filtered_aln_paired.bam_sorted.bam O= MP1_2_merged_clara_20110404_bwa_filtered_aln_paired.bam_GATK_sorted.bam REFERENCE= /share/Tepehuan/Genomes/Homo_sapiens/GRC37Homo_sapiens/Masked/GRCh37_hg19_masked.fa"
Also, I have already tried with different extension suffixes for CreateSequenceDictionary.jar output file and I have already verified that my BAMfile has headers (i.e. @SQ SN:gi|224589801|ref|NC_000010.10| LN:135534747 lines)
Thank you very much!!
Martin
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