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sanger-pathogens / iva

de novo virus assembler of Illumina paired reads
http://sanger-pathogens.github.io/iva/
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Tests fail with KMC 2.3 from Homebrew on OS X #63

Open satta opened 8 years ago

satta commented 8 years ago

The testsuite (python3 setup.py test) fails when using KMC 2.3 (from Homebrew) on OS X 10.11:

[...]
Test run_trimmomatic ... ok
test_process_seeds (seed_processor_test.TestSeedProcessor)
Test process_seeds ... The following command failed with exit code 1
bash run_kmc.sh

The output was:

*
Error: Cannot open temporary file /Users/satta/foss/iva/tmp.run_kmc.4rxfrvg2/kmc_00253.bin

The following command failed with exit code 1
bash run_kmc.sh

The output was:

*
Error: Cannot open temporary file /Users/satta/foss/iva/tmp.run_kmc.8_00xctz/kmc_00253.bin

This error is apparently from KMC itself, all the previous temporary files have length zero. All dependencies are also installed from Homebrew.

It has to be noted that the tests work fine on Linux when KMC 2.3 is used. This may be an OS X quirk.

sdwfrost commented 8 years ago

I also get this error on OSX when using KMC 2.1.1, pre-compiled from here as well as the latest pull from GitHub (f090276855a3f7c0b14e9f3abc8c99d3213247b3).

martinghunt commented 8 years ago

Sorry for the slow reply. This dropped off my radar...

I've put in an issue for this in the KMC repo (refresh-bio/KMC/issues/12).

My mac is running 10.8.5, and it works, so looks like a Mac version specific issue sometime after 10.8.5. @sdwfrost what OSX version do you have?

satta commented 8 years ago

Based on the hint from upstream (see link above), it might help increasing the open file limit using ulimit to 2048. This solved the problem for me.

sdwfrost commented 6 years ago

This worked for me too i.e.

ulimit -n 2048; iva {options}