My lab mate has been using bwa aln
to align a 21G fastq.gz
file to a dog reference genome using 31 threads. At first the generation speed of .sai
file was fast, writing 6GB a day and we estimate in 5 days it will complete. However, after writing the first 23 GB at a fast speed, it only write exactly 1 MB (1048576 bytes) every ten or twenty minutes, though CPU usage is still near 3100%.
Is there anything wrong? What is the structure of .sai
file? How long will it complete?
I am new to biostars but I have got help from the site many times before. Thanks everyone for sharing knowledge!