Falcon issues

[lcortesv12]

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