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Old 01-17-2017, 12:07 PM   #48
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

Hi Jake,

The problem is the presence of spaces in your filepath. Try adding quotes:

java -ea -Xmx15000m -Xms15000m -cp /Users/DJV/programs/bbmap/current/ assemble.Tadpole in="/Users/DJV/Desktop/IN/150-P6-C9 assembled to HXB2 Nested Amplified Region.fastq" out=/Users/DJV/Desktop/Out/contigs.fa
Also, you need to add a filename to the output (e.g. /Users/DJV/Desktop/Out/contigs.fa). If using quotes does not work, try renaming the file with underscores rather than spaces. Do you know what your read length and approximate depth are? Tadpole's default kmer length is 31, but with sufficient depth and read length, you will get a better assembly with a longer kmer.
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