Error: SPAdes crashed during read correction

[kapsakcj]

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

[rec3141]

see #69 (comment)

[rrwick]

Since a couple people have now hit this problem, I may make a new Unicycler option --spades_tmp_dir so people don't have to hack the Unicycler code. It should be an easy addition that I can put into the next release.

Ryan

[kapsakcj]

The fix https://github.com/rrwick/Unicycler/issues/69#issuecomment-360305189 did in fact work for me. SPAdes read error correction ran fine I edited the python script. I think it would be a good little fix for the next release

[rec3141]

Hey Ryan, yes that would be great, and you might want to put a note in the docs on why that option is there (virtual box) and to note that it should be a vbox local directory

[rrwick]

See issue #69: the --spades_tmp_dir option is now in the development branch and will be in the next release.