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sequencing / isaac_aligner

Isaac Genome Alignment Software
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Memory error #1

Closed Benhgift closed 11 years ago

Benhgift commented 11 years ago

Hi, I'm getting a memory error when running this on a 256GB memory machine with 16 cores. The aligner is ran with 12 threads and 128gb mem as parameters. The error: 

2013-09-01 22:47:33     [7f850f23b700]  Saving 2626550564 bytes of sorted data for bin "/runs/run192mem12thread/Temp/bin-00000006-00000025.dat"
2013-09-01 22:47:33     [7f850f23b700]  ERROR: Thread: 18 also caught an exception: /illumina/isaac_aligner-master/src/c++/lib/build/Build.cpp(831): Throw in function void isaac::build::Build::saveBuffer(const std::vector<char>&, std::ostream&, const isaac::bam::BamIndexPart&, isaac::bam::BamIndex&, const boost::filesystem::path&)
Dynamic exception type: boost::exception_detail::clone_impl<isaac::common::IoException>
std::exception::what: Failed to write bgzf block of 2626550564 bytes into bam stream

2013-09-01 22:47:36     [7f8508430700]  WARNING: Holding up processing of bin: "/runs/run192mem12thread/Temp/bin-00000006-00000026.dat" until 17172851258 bytes of allowed memory is available.
come-raczy commented 11 years ago

This is not a memory error but an IO exception while writing the BAM file. It is difficult to tell for sure the exact root cause as the relevant parts of the log file are missing, but it is almost certain that there isn't enough space on the file system.

Benhgift commented 11 years ago

The machine has 5TB free though. I could be wrong but the whitepaper doesn't seem to mention the suggested amount of free space. Is there full documentation posted somewhere?

The entirety of the Temp folder generated by Isaac only takes 600GB, could Isaac really need >5TB?

come-raczy commented 11 years ago

5TB should be way more than enough. Would you mind getting the latest version (from today) and try again. If you still have all the temps, the '--start-from Last' command line option should work. If it still fails, I would need the log file.