I am trying to run SOAPdenovo for the first time. I launched it a few days ago and it seems to be running fine. There are no errors. This was the command:
I feel like it's taking too long. What really worries me is the progress meter in the log file:
The last update is for 34.7 billion reads. However, the input FASTQs only contain 370 million reads combined. What would cause such a discrepancy? Are the reads reported not the same thing as the reads from the FASTQs?
Code:
SOAPdenovo-63mer all \ -s config.config \ -p 10 \ -R \ -o graph \ -V hawkeye \ 1>ass.log.txt 2>ass.err.txt
Code:
Version 2.04: released on July 13th, 2012 Compile Jul 9 2013 11:57:16 ******************** Pregraph ******************** Parameters: pregraph -s config.config -p 10 -R -o graph In config.config, 1 lib(s), maximum read length 150, maximum name length 256. 10 thread(s) initialized. Import reads from file: FASTQ/lane_NoIndex_L000_R1_001.fastq.gz Import reads from file: FASTQ/lane_NoIndex_L000_R2_001.fastq.gz --- 100000000th reads. --- 200000000th reads. --- 300000000th reads. ... ... --- 34500000000th reads. --- 34600000000th reads. --- 34700000000th reads.
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