"--clib" flag error in intervalmiss

[tim-oconnor]

Hi Alex,

I'm looking forward to using Wengan on a handful Illumina + ONT assemblies in the near future. Before running my own data I tried the demo assembly, but ran into the following error at the intervalmiss stage. From <prefix>.im.err:

/gpfs/apps/haswell/software/gcc-6.2.0/wengan/0.2/bin/intervalmiss: unrecognized option `--clib'

This appears to come from this block int the .mk file:

test.wengan.MBC1.msplit.fa : test.wengan.contigs.disco.fa test.wengan1.fm.sam test.wengan.im.1.I500.fm.sam test.wengan.im.1.I1000.fm.sam test.wengan.im.1.I2000.fm.sam
    @echo "test.wengan1.fm.sam  0"  >  test.wengan.fms.sams.txt
    @echo "test.wengan.im.1.I500.fm.sam 1"  >>  test.wengan.fms.sams.txt
    @echo "test.wengan.im.1.I1000.fm.sam    1"  >>  test.wengan.fms.sams.txt
    @echo "test.wengan.im.1.I2000.fm.sam    1"  >>  test.wengan.fms.sams.txt
    /gpfs/apps/haswell/software/gcc-6.2.0/wengan/0.2/bin/intervalmiss -d 1 --clib 1  -t 8 -s test.wengan.fms.sams.txt -c  test.wengan.contigs.disco.fa -p  test.wengan 2>test.wengan.im.err >test.wengan.im.log

Do you have any idea what the issue might be and how to resolve it? I tried deleting the --clib argument but got a floating point exception. One bit of context is that installing wengan dependencies proved tricky on our cluster. The system admin built all the dependencies under gcc6 but discovardenovo with gcc4. I don't think this should affect intervalmiss, though.

Thanks for any help. Tim

[tim-oconnor]

Hi again,

I've been digging a bit and it looks like we may have an outdated version of intervalmiss. I looked through the source code and realized that the code for v0.1 of Wengan didn't have the clib argument.

I'm going to check in with my system administrator and see if we can get that updated. I'll update if/when I get things working.

Tim

[tim-oconnor]

Yep, just an outdated version. Sorry!