Entering edit mode
7.6 years ago
biomagician
▴
410
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.
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:
Looks like a reference to the The Hitchhiker's Guide to the Galaxy.
the contents of the file
ecoli.gkpStore.BUILDING.err
may have more info on the error.One of the .err files says:
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:
There are errors but I don't know how to fix them.
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