Closed shaobinzhong closed 4 years ago
This is documented in issue #1093 and others. You have quite deep coverage, over 200x, so there isn't enough memory to load all the overlaps. The solution ins #1093 should work (batMemory=32
or batMemory=64
). Canu 1.8 is also quite old and newer versions would downsample your input data automatically to avoid this error.
Hello Canu team,
I used Canu v1.8 to assembly PacBio reads generated for a fungus (36 Mb in size). The total reads are 133 Gb. I wanted to determine the minimum number of reads for good assembly, so I partitioned the total reads into a number of files (a, b, c, and so on) each having about 6-7 Gb of reads. Then I run canu with a, a+b, a+b+c, a+b+c+d, ......I got the assemblies with reads from one file, two files or three files combined. However, when I run the same program with reads combined from four or more files, I got the error "Bogart failed, retry". The log is attached here:
Please let me know what should I do to solve the problem?
Thanks.
Shaobin