FALCON
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PacificBiosciences
Problem on the 0-rawreads process：
I ran FALCON to assemble a 700Mb genome using 60X raw pacbio reads. In order to avoid the duplicate error, I installed the latest DALIGNER in FALCON. However, my assembly always got stuck at the first rawreads process. There are 24 tasks failed, and 45 tasks unfinished. Then I checked the pwatcher.dir/stderr files with the following information:
raw_reads.56.raw_reads.24.N1: Duplicate overlap (1748840 vs 700961)
.....
raw_reads.9.raw_reads.56.N2: 104,472 all OK
raw_reads.9.raw_reads.56.N3: 110,434 all OK
2016-12-25 16:46:26,524 - root - DEBUG - CD: '/home/xinw/project/Brain_coral_new/Pacbio/denovo_assemble/assemble_22_Dec/0-rawreads/job_003c' -> '/home/xinw/project/Brain_coral_new/Pacbio/denovo_assemble/assemble_22_Dec/0-rawreads/job_003c'
2016-12-25 16:46:26,524 - root - DEBUG - CD: '/home/xinw/project/Brain_coral_new/Pacbio/denovo_assemble/assemble_22_Dec/0-rawreads/job_003c' -> '/home/xinw/project/Brain_coral_new/Pacbio/denovo_assemble/assemble_22_Dec/0-rawreads/job_003c'
2016-12-25 16:46:26,524 - root - CRITICAL - Error in /home/xinw/software/FALCON/FALCON-integrate/pypeFLOW/pypeflow/do_task.py with args="{'json_fn': '/home/xinw/project/Brain_coral_new/Pacbio/denovo_assemble/assemble_22_Dec/0-rawreads/job_003c/task.json',\n 'timeout': 60,\n 'tmpdir': None}"
Traceback (most recent call last):
File "/usr/lib/python2.7/runpy.py", line 174, in _run_module_as_main
"main", fname, loader, pkg_name)
File "/usr/lib/python2.7/runpy.py", line 72, in _run_code
exec code in run_globals
File "/home/xinw/software/FALCON/FALCON-integrate/pypeFLOW/pypeflow/do_task.py", line 190, in
real 183m14.040s user 650m58.448s sys 9m49.484s returned: 256
I am not sure it is the problem of "duplicate overlap". In the config file, i used the skip_checks = true, and update DALIGNER to the latest one, but it is still coming out these error.
SO anyone know what's the problem? how can i solve this? Thanks && Merry xmas
first, check if your rj_003c.sh contains the LACheck command, if so, either you did not really run from the update environment or the script is not updated.
Yes, I could still find LACheck. I downloaded and installed the FALCON-instegrate based on the easy way: export GIT_SYM_CACHE_DIR=~/.git-sym-cache # to speed things up git clone git://github.com/PacificBiosciences/FALCON-integrate.git cd FALCON-integrate
Here I downloaded the latest version of DALIGNER and executed the following commands
git checkout master # or whatever version you want make init source env.sh make config-edit-user make -j all make test # to run a simple one
I don't think it would be the update environment. Do I also need to update the FALCON? Thanks for the quick respond.
Hi, I have the same problem, did you solve it? By the way, I didn't do "make config-edit-user" as it would output follow error and I am running with virtualenv.
python -c 'import pip; print pip' || python get-pip.py --user
<module 'pip' from '/data7/Falcon/myVirtualenv/lib/python2.7/site-packages/pip/__init__.pyc'>
pip install --user --upgrade pip
Can not perform a '--user' install. User site-packages are not visible in this virtualenv.
makefile:47: recipe for target 'install-pip' failed
make[2]: *** [install-pip] Error 1
make[2]: Leaving directory '/data7/Falcon/FALCON-integrate/FALCON-make'
makefile:16: recipe for target 'all' failed
make[1]: *** [all] Error 2
make[1]: Leaving directory '/data7/Falcon/FALCON-integrate/FALCON-make'
makefile:19: recipe for target 'all' failed
make: *** [all] Error 2
The code of setting up Falcon:
mkdir myVirtualenv
python virtualenv/virtualenv.py -p python2.7 myVirtualenv
unset PYTHONPATH
source myVirtualenv/bin/activate
export GIT_SYM_CACHE_DIR=~/.git-sym-cache
git clone git://github.com/PacificBiosciences/FALCON-integrate.git
cd FALCON-integrate
git checkout master
make init
source env.sh
#make config-edit-user
make -j all
make test
I had run the pipeline successfully by adding "skip_check = true" in cfg as stated in https://github.com/PacificBiosciences/FALCON/issues/501.