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Old 09-06-2011, 04:25 PM   #1
tatinhawk
Martin
 
Location: Cambridge

Join Date: Dec 2009
Posts: 11
Default Problems Running Picard's ReorderSam

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
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Old 09-07-2011, 07:10 AM   #2
tatinhawk
Martin
 
Location: Cambridge

Join Date: Dec 2009
Posts: 11
Default

In case someone else had this problem I found the solution here:

https://sourceforge.net/mailarchive/...sg_id=27661567

Cheers,
Martin
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Old 08-25-2012, 12:41 PM   #3
Artur Jaroszewicz
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Thank you for posting the solution when you found it, Martin! I wish everyone would do this. You are the fairy godcoder of the internet.
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Old 08-26-2012, 07:57 PM   #4
tatinhawk
Martin
 
Location: Cambridge

Join Date: Dec 2009
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Default

Quote:
Originally Posted by Artur Jaroszewicz View Post
Thank you for posting the solution when you found it, Martin! I wish everyone would do this. You are the fairy godcoder of the internet.

No worries, I think is better to share the info and save the painstaking process of finding the solution to others... (if I already found one…) The solution here was to name the dictionary with the “.dict” extension as stated on the link.

Cheers Artur!
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