Canu: failed with exit code 134

Question

[biomagician]

Dear all,

I am trying to reproduce the Canu example here: http://canu.readthedocs.io/en/latest/quick-start.html

I've downloaded the data here:

canu -p ecoli -d output/assembly genomeSize=4.8m -pacbio-raw output/reads/pacbio/ecoli/p6.25x.fastq

and now I am running:

canu -p ecoli -d output/assembly genomeSize=4.8m -pacbio-raw output/reads/pacbio/ecoli/p6.25x.fastq

but I get this error:

 cd correction
    /usr/local/Cellar/canu/1.5/Darwin-amd64/bin/gatekeeperCreate \
      -minlength 1000 \
      -o ./ecoli.gkpStore.BUILDING \
      ./ecoli.gkpStore.gkp \
    > ./ecoli.gkpStore.BUILDING.err 2>&1
sh: line 4: 30328 Abort trap: 6           /usr/local/Cellar/canu/1.5/Darwin-amd64/bin/gatekeeperCreate -minlength 1000 -o ./ecoli.gkpStore.BUILDING ./ecoli.gkpStore.gkp > ./ecoli.gkpStore.BUILDING.err 2>&1

-- Finished on Mon Jun  5 18:24:23 2017 (lickety-split) with 126.644 GB free disk space
----------------------------------------
ERROR:
ERROR:  Failed with exit code 134.  (rc=34304)
ERROR:
================================================================================
Don't panic, but a mostly harmless error occurred and Canu stopped.

Can anybody help me, please?

Thanks.

c.

[WouterDeCoster]

I added code markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

Don't panic, but a mostly harmless error occurred

Looks like a reference to the The Hitchhiker's Guide to the Galaxy.

[h.mon]

the contents of the file ecoli.gkpStore.BUILDING.err may have more info on the error.

[biomagician]

One of the .err files says:

dyld: Library not loaded: /usr/local/opt/gcc/lib/gcc/6/libgomp.1.dylib
  Referenced from: /usr/local/Cellar/canu/1.5/Darwin-amd64/bin/gatekeeperCreate
  Reason: image not found

[biomagician]

Based on this: https://github.com/Homebrew/homebrew-science/issues/5585

I have rebuilt canu from source using

brew reinstall homebrew/science/canu

I got this message:

==> Reinstalling homebrew/science/canu 
==> Downloading https://github.com/marbl/canu/archive/v1.5.tar.gz
Already downloaded: /Users/cr517/Library/Caches/Homebrew/canu-1.5.tar.gz
==> make -C src
Last 15 lines from /Users/cr517/Library/Logs/Homebrew/canu/01.make:
compilation terminated.
In file included from AS_UTL/AS_UTL_stackTrace.C:34:0:
/private/tmp/canu-20170605-3454-1ajmv8v/canu-1.5/src/AS_global.H:75:10: fatal error: stdio.h: No such file or directory
 #include <stdio.h>
          ^~~~~~~~~
compilation terminated.
make: *** [/private/tmp/canu-20170605-3454-1ajmv8v/canu-1.5/Darwin-amd64/obj/libcanu.a/AS_UTL/bitEncodings.o] Error 1
make: *** [/private/tmp/canu-20170605-3454-1ajmv8v/canu-1.5/Darwin-amd64/obj/libcanu.a/AS_UTL/AS_UTL_stackTrace.o] Error 1
In file included from AS_UTL/AS_UTL_alloc.H:37:0,
                 from AS_UTL/AS_UTL_alloc.C:34:
/private/tmp/canu-20170605-3454-1ajmv8v/canu-1.5/src/AS_global.H:75:10: fatal error: stdio.h: No such file or directory
 #include <stdio.h>
          ^~~~~~~~~
compilation terminated.
make: *** [/private/tmp/canu-20170605-3454-1ajmv8v/canu-1.5/Darwin-amd64/obj/libcanu.a/AS_UTL/AS_UTL_alloc.o] Error 1

READ THIS: http://docs.brew.sh/Troubleshooting.html

There are errors but I don't know how to fix them.

[h.mon]

Did you READ THIS: http://docs.brew.sh/Troubleshooting.html? Your problem is very likely listed under "Check for common issues".

Hint: search for fatal error: stdio.h: No such file or directory macosx

Answer 1

[biomagician]

#### Install canu ####
# http://canu.readthedocs.io/en/latest/quick-start.html
# https://github.com/marbl/canu
system('brew install homebrew/science/canu')
# It seems that canu needs gnuplot
system('brew install gnuplot')
# [https://github.com/Homebrew/homebrew-science/issues/5585][1]
system('brew reinstall homebrew/science/canu --build-from-source > output/software/canuBuildFromSource.txt')
# [https://stackoverflow.com/questions/19580758/gcc-fatal-error-stdio-h-no-such-file-or-directory][2]
system('xcode-select --install')
#### Follow the instructions to install Xcode developer tools
system('brew reinstall homebrew/science/canu --build-from-source')
### canu command works!

Thanks folks! Thanks to h.mon's comments I was able to fix the problem and install canu. The details above.