Closed rob123king closed 6 years ago
export PYTHONPATH=/home/data/bioinf_resources/programming_tools/falcontest/lib/python2.7
That PYTHONPATH is wrong, and it shouldn't be needed.
Anyway, you have to look into a task directory to learn why that task failed.
Exception: Some tasks are recently_done but not satisfied: set([Node(0-rawreads)
That means you need to look for a stderr
file somewhere under 0-rawreads/
. Usually, the problem is an immediately obvious integration problem.
I have installed falcon-unzip as below using the pre-compiled binaries and seems fine
How do I run the example data, what commands and config files to use? I can download the raw data from ENA using project codes below. Arabidopsis data: PRJNA314706 V. vinifera cv. Cabernet Sauvignon: PRJNA316730 I've downloaded the config files from below for a test run:
And changed the line in fc_unzip.cfg to below:
smrt_bin=/home/data/bioinf_resources/programming_tools/falcontest/bin/
I've downloaded the example assemblies file which comes with the config files used:
fc_run.cfg input.fofn
fc_unzip.cfg unzip.sh
Assume download the raw data and put paths in “input.fofn” but then how to start it..
I have downloaded the raw data for the arabidopsis assembly as a test first. I have updated the input.fofn file with locations and smrtanalysis/bin location in fc_unzip.cfg
The unzip.sh file first command has changed in the pre-built binaries. This is the file used in the paper to run start to finish but very first command I get an error. "This fc_track_reads.py" has become "fc_track_reads_htigs0.py" Change made but when run first command get the below error