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sam2rma error while doing metagenomics analysis
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13 months ago
shashi • 0
India

hi everyone,

I doing metagenomics analysis using minimap2, MEGAN, Kronatools pipeline. i have done mapping of nanopore reads with minimap2 keeping reference nt.fa database which provide output .sam file.

The analysis was done in AWS ubuntu server 32RAM , 1TB storage

i have used sam2rma tool in megan to convert file format for further analysis like taxonomic classification, OTU etc.

but i got error "java.lang.ArrayIndexOutOfBoundsException" while running the command

./sam2rma -i /home/ubuntu/minimap2/barcode3_5_aligned.sam -lg -alg longReads -a2t nucl_acc2tax-Nov2018.abin.zip -v -o /home/ubuntu/megan/barcode_3_5_rmafile/

Below is the error which im getting

Caught: java.lang.ArrayIndexOutOfBoundsException 
at java.util.zip.Deflater.setInput(Deflater.java:204) 
at megan.io.Compressor.deflateString2ByteArray(Compressor.java:106) 
at megan.io.OutputWriter.writeString(OutputWriter.java:170) 
at megan.rma6.RMA6FileCreator.addQuery(RMA6FileCreator.java:128) 
at megan.rma6.RMA6FromBlastCreator.parseFiles(RMA6FromBlastCreator.java:249) 
at megan.tools.SAM2RMA6.createRMA6FileFromSAM(SAM2RMA6.java:328) 
at megan.tools.SAM2RMA6.run(SAM2RMA6.java:284) 
at megan.tools.SAM2RMA6.main(SAM2RMA6.java:64)

can anyone please help me to resolve the issue

Thank you

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