Error: SPAdes crashed during read correction #82
Description
Hi,
I ran into an issue while running Unicycler for the first time. I'm trying out a hybrid assembly using paired-end Illumina reads and MinION reads. I was wondering if anyone can help me get Unicycler running.
It appears that SPAdes crashed during the read error correction step and I was directed to the spades.log for information. I found the following:
=== Stack Trace ===
[0x408b5e]
[0x409a91]
[0x40d61b]
[0x4012fa]
[0x541e60]
[0x40668d]
Verification of expression '(intptr_t) MappedRegion != -1L' failed in function 'void MMappedWriter::reserve(size_t)'. In file '/spades/src/common/io/kmers/mmapped_writer.hpp' on line 92. Message 'mmap(2) failed. Reason: Invalid argument. Error code: 22'.
Verification of expression '(intptr_t) MappedRegion != -1L' failed in function 'void MMappedWriter::reserve(size_t)'. In file '/spades/src/common/io/kmers/mmapped_writer.hpp' on line 92. Message 'mmap(2) failed. Reason: Invalid argument. Error code: 22'.
hammer: /spades/src/common/io/kmers/mmapped_writer.hpp:92: void MMappedWriter::reserve(size_t): Assertion `(intptr_t) MappedRegion != -1L' failed.
== Error == system call for: "['/home/curtis/miniconda2/envs/unicyclerEnv/share/spades-3.10.1-0/bin/hammer', '/media/sf_sharedVMfolder/unicyclerTestrun/spades_assembly/read_correction/corrected/configs/config.info']" finished abnormally, err code: -6
After some googling, I think this may have to do with the fact that I'm running Unicycler on VirtualBox with Ubuntu 14.04. And my sequence files are located in a shared folder that I have setup between my host OS (windows) with the guest OS (Ubuntu 14.04). Does this have anything to do with it?
Best,
Curtis