sam2rma error while doing metagenomics analysis
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
• 1,609 views
•
link
updated
by
WouterDeCoster
•
written
by
shashi •
•
written
by
shashi •
0 answers
No answers yet.
Log in to answer this question.
For posting screenshots you should take a look at How to add images to a Biostars post
But posting error messages as an image is not helpful as these cannot be searched using e.g. google. Rather, post the full error here and use the formatting buttons (the 101010 button) for your commands and structured text blocks.
Hi thanks for information i have updated the Post thanks
I added code markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:
Thanks for the information