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Old 01-25-2019, 04:41 AM   #663
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,015

I see that you are using samtools module as well. With that you can directly write BAM files no need to use SAM.

So let us try a modified command line and see what happens (I am going to assume that you have ~30G of RAM and 4 cores available for this job in command below and the two fastq files are in the current directory). dm3.fa is just a multi-fasta file of Drosophila chromosomes?

Code: -Xmx30g threads=4 ref=/users/chutfilz/data/chutfilz/Dm3_Index/dm3.fa in1=PoolCH-1_R1_001_val_1.fa.gz in2=PoolCH-1_R2_001_val_2.fa.gz out=PoolCH-1.bam ambig=random maxindel=10000 trd=t
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