pb-cdunn / falcon-examples

Examples on branches, and a useful place for testing

FALCON-examples

Examples, with test-cases, and a useful place for testing

To run, first build FALCON and its dependencies, and set-up your environment. (See FALCON-integrate in GitHub.) Then:

make run-ecoli

We do not recommend piping the output, since if you need to stop early (with Ctrl-C aka KeyboardInterrupt), your program might be killed before it has time to qdel the outstanding jobs.

Environment

One way to set-up your environment is to use Python virtualenv. Before running these examples, activate your virtualenv in your shell or via FALCON-integrate.

Data

*.fofn

These are "files of filenames". Since they are in the repo, they should be relative paths. (Relative to the current directory when they are used. But that is wrong. It should be relative to their own location. TODO)

Files

The repo source is lightweight because it contains symlinks instead of the contents of large files. These are managed by git-sym.

git-sym

This separates big-file caching from revision-control. There are several alternatives:

data directories

Relying on git-sym, symlinks to the data are stored in data/ sub-directories. The files should point (relatively) into .git_sym/, which contains more symlinks to a cache directory. git_sym.makefile should include a rule to produce files for those symlinks.

falcon-examples's Issues

Falcon issues

Hi
We have some sequel I pacbio sequences, but we have troubles with SmartLink, so we decide to try another assembly source, we think FALCON can be a good solution for our bacterial long-read sequences, then we installed and follow the tutorial, but we have some issues that can't be solved. I will show the content of our configuration files and the issues that we had to get some advice and finally use the assembler.

Thanks for your attention!

Content of my "run_falcon_sh" file:

#!/bin/bash
#$ -S /bin/bash
#$ -N myJob
#$ -cwd
#$ -q myqueue

load dependencies

module load python/2.7.9 gcc/4.9.2

source build

cd /home/lorena/DOCTORADO/LGMB/33kpn/ensambladosCANU/33kpn62/Falc
source env.sh

navigate to job directory, directory containing input.fofn

cd/home/lorena/DOCTORADO/LGMB/33kpn/ensambladosCANU/33kpn62/Falc

run it!

/home/lorena/miniconda3/pkgs/fc_run_kp.cfg

Content of my fc_run.cfg file:
[General]
#job_type = SGE

list of fasta files

input_fofn = input.fofn

input type, raw or pre-assembled reads (preads, error corrected reads)

input_type = raw
#input_type = preads

The length cutoff used for seed reads used for error correction.

"-1" indicates FALCON should calculate the cutoff using

the user-defined genome length and coverage cut off

otherwise, user can specify length cut off in bp (e.g. 2000)

length_cutoff = 15000
genome_size = 6400000
#seed_coverage = 30

The length cutoff used for overalpping the preassembled reads

length_cutoff_pr = 12000

resource usage

jobqueue = bigmem

grid settings for...

daligner step of raw reads

sge_option_da = -pe smp 5 -q %(jobqueue)s

las-merging of raw reads

sge_option_la = -pe smp 20 -q %(jobqueue)s

consensus calling for preads

sge_option_cns = -pe smp 12 -q %(jobqueue)s

daligner on preads

sge_option_pda = -pe smp 6 -q %(jobqueue)s

las-merging on preads

sge_option_pla = -pe smp 16 -q %(jobqueue)s

final overlap/assembly

sge_option_fc = -pe smp 24 -q %(jobqueue)s

job concurrency settings for...

preassembly

pa_concurrent_jobs = 48

consensus calling of preads

cns_concurrent_jobs = 48

overlap detection

ovlp_concurrent_jobs = 48

daligner parameter options for...

https://dazzlerblog.wordpress.com/command-guides/daligner-command-reference-guide/

initial overlap of raw reads

pa_HPCdaligner_option = -v -B4 -t16 -e.70 -l1000 -s1000

overlap of preads

ovlp_HPCdaligner_option = -v -B4 -t32 -h60 -e.96 -l500 -s1000

parameters for creation of dazzler database of...

https://dazzlerblog.wordpress.com/command-guides/dazz_db-command-guide/

raw reads

pa_DBsplit_option = -x500 -s50

preads

ovlp_DBsplit_option = -x500 -s50

settings for consensus calling for preads

falcon_sense_option = --output_multi --min_idt 0.70 --min_cov 4 --max_n_read 200 --n_core 4

setting for filtering of final overlap of preads

overlap_filtering_setting = --max_diff 100 --max_cov 100 --min_cov 20 --bestn 10 --n_core 4

ISSUE showed when I try to run the script qsub run_falcon.sh:
There was an error running the SLURM sbatch command.
The command was:
'/usr/bin/sbatch -e run_falcon.sh.e%A -o run_falcon.sh.o%A run_falcon.sh 2>&1'
and the output was:
'sbatch: error: s_p_parse_file: unable to status file /etc/slurm-llnl/slurm.conf: No such file or directory, retrying in 1sec up to 60sec
sbatch: fatal: Unable to process configuration file