Falcon is a heirarchical genome assembly process. It uses the following steps for generating a genome assembly from a set of sequencing reads:
cp /usr/local/apps/samples/falcon.tar . tar xvf falcon.tar cd falcon
bsub < bfalcon
should run the example which relies on the fc_run_ecoli_local.cfg which in this case used 64 GBytes of RAM and 16 cores. The bfalcon file consists of
#!/bin/ksh #BSUB -R span[ptile=16] #BSUB -n 16 #BSUB -q single_chassis #BSUB -W 2000 source /usr/local/apps/falcon/falcon.ksh fc_run.py fc_run_ecoli_local.cfg #BSUB -o out.%J #BSUB -e err.%J
The only files needed were the bfalcon and run_ecoli_local.cfg (along with input.fofn and the fasta files it points to), the other files and subdirectories were created running falcon. To run your own problem you'll need to modify the .cfg file.
A main problem in running the job was successfully specifiying the input files. The "file not found error" was not in the err.xxxxx file or in all.log, but in 0-rawreads/pwatcher.dir/stderr. I had to copy input.fofn (specified in the .cfg file) to the directory in which falcon was searching. Another problem was that the .sh files in 0-rawread were not created as executable.
cd 0-rawreads chmod +x *.sh
made the .sh files executable. This version of falcon links to python-2.7.13.
For more documentation on this example, see e coli falcon tutorial.
Falcon unzip is also part of the falcon tool chain, using files produced by a run of falcon. In the same directory as above (or tar up the directory /home/gwhowell/apps/samples/falcon/greg200k-sv2 and "tar xvf" to unpack it).
cd greg200k-sv2 rm -rf 0-rawreads rm -rf 1-preads_ovl rm -rf 2-asm-falcon rm -rf 3-unzip
bsub < bfalcon
will run falcon and recreate the first 3 of the above directories (log is logfalcon1 ). Then
bsub < bunfalcongives a run of falcon unzip, with log in all.log
This version used the default fc_unzip.cfg.
Last modified: March 23 2022 13:18:51.