Failed to parse config "fc_run.cfg"
linshengnan2020 opened this issue · 1 comments
linshengnan2020 commented
hi , I ran the falcon and met an error. could you give me some advises, thank you very much !
the log
ffalcon-kit 1.8.1 (pip thinks "falcon-kit 1.8.1")
pypeflow 2.3.0
[INFO]Setup logging from file "None".
[INFO]$ lfs setstripe -c 12 /data/fg1/linsn/30_genome_asm/16_xubao/03_falcon >
[INFO]Apparently '/data/fg1/linsn/30_genome_asm/16_xubao/03_falcon' is not in lustre filesystem, which is fine.
[INFO]fc_run started with configuration falcon.cfg
[WARNING]Option contains flags with "_":
"falcon_sense_option=--output_multi --min_idt 0.70 --min_cov 4 --max_n_read 200 --n_core 18". Those should be "-", as in
"falcon_sense_option=--output-multi --min-idt 0.70 --min-cov 4 --max-n-read 200 --n-core 18". Auto-replaced.
[WARNING]Option contains flags with "_":
"overlap_filtering_setting=--max_diff 100 --max_cov 100 --min_cov 10 --bestn 10 --n_core 18". Those should be "-", as in
"overlap_filtering_setting=--max-diff 100 --max-cov 100 --min-cov 10 --bestn 10 --n-core 18". Auto-replaced.
[ERROR]Failed to parse config "falcon.cfg".
Traceback (most recent call last):
File "/data/fg1/linsn/miniconda3/envs/pb-assembly/lib/python3.7/site-packages/falcon_kit/mains/run1.py", line 52, in main1
config = run_support.parse_cfg_file(input_config_fn)
File "/data/fg1/linsn/miniconda3/envs/pb-assembly/lib/python3.7/site-packages/falcon_kit/run_support.py", line 151, in parse_cfg_file
update_defaults(config['General'])
File "/data/fg1/linsn/miniconda3/envs/pb-assembly/lib/python3.7/site-packages/falcon_kit/run_support.py", line 392, in update_defaults
clean_falcon_options(cfg)
File "/data/fg1/linsn/miniconda3/envs/pb-assembly/lib/python3.7/site-packages/falcon_kit/run_support.py", line 112, in clean_falcon_options
check_HPCdaligner_option(fc[dk])
File "/data/fg1/linsn/miniconda3/envs/pb-assembly/lib/python3.7/site-packages/falcon_kit/run_support.py", line 99, in check_HPCdaligner_option
raise Exception(msg)
Exception: HPC.daligner option "-dal" has changed to "-B".
Traceback (most recent call last):
File "/data/fg1/linsn/miniconda3/envs/pb-assembly/bin/fc_run", line 11, in <module>
load_entry_point('falcon-kit==1.8.1', 'console_scripts', 'fc_run')()
File "/data/fg1/linsn/miniconda3/envs/pb-assembly/lib/python3.7/site-packages/falcon_kit/mains/run1.py", line 706, in main
main1(argv[0], args.config, args.logger)
File "/data/fg1/linsn/miniconda3/envs/pb-assembly/lib/python3.7/site-packages/falcon_kit/mains/run1.py", line 52, in main1
config = run_support.parse_cfg_file(input_config_fn)
File "/data/fg1/linsn/miniconda3/envs/pb-assembly/lib/python3.7/site-packages/falcon_kit/run_support.py", line 151, in parse_cfg_file
update_defaults(config['General'])
File "/data/fg1/linsn/miniconda3/envs/pb-assembly/lib/python3.7/site-packages/falcon_kit/run_support.py", line 392, in update_defaults
clean_falcon_options(cfg)
File "/data/fg1/linsn/miniconda3/envs/pb-assembly/lib/python3.7/site-packages/falcon_kit/run_support.py", line 112, in clean_falcon_options
check_HPCdaligner_option(fc[dk])
File "/data/fg1/linsn/miniconda3/envs/pb-assembly/lib/python3.7/site-packages/falcon_kit/run_support.py", line 99, in check_HPCdaligner_option
raise Exception(msg)
Exception: HPC.daligner option "-dal" has changed to "-B".
the fc_run.cfg
[General]
#job_type=local
# list of files of the initial subread fasta files
input_fofn = input.fofn
genome_size = 600000000
input_type = raw
pwatcher_type = blocking
job_type = string
job_queue = bash -C ${CMD} >| ${STDOUT_FILE} 2>| ${STDERR_FILE}
#input_type = preads
# The length cutoff used for seed reads used for initial mapping
length_cutoff = 5000
# The length cutoff used for seed reads usef for pre-assembly
length_cutoff_pr = 4000
# overlapping options for Daligner
skip_check = true
skip_checks = true
stop_all_jobs_on_failure = false
pa_HPCdaligner_option = -v -dal4 -M32 -e.70 -l1000 -s1000
ovlp_HPCdaligner_option = -v -dal4 -M32 -h60 -e.96 -l500 -s1000
pa_DBsplit_option = -x500 -s400
ovlp_DBsplit_option = -x500 -s400
# error correction consensus options
falcon_sense_option = --output_multi --min_idt 0.70 --min_cov 4 --max_n_read 200 --n_core 18
# overlap filtering options
overlap_filtering_setting = --max_diff 100 --max_cov 100 --min_cov 10 --bestn 10 --n_core 18
# For job-submission options, see https://github.com/PacificBiosciences/FALCON/wiki/Configuration
# These are old-style, but should still work, for now.
sge_option_da = -l nodes=1:ppn=9 -q cu
sge_option_la = -l nodes=1:ppn=9 -q cu
sge_option_pda = -l nodes=1:ppn=9 -q cu
sge_option_pla = -l nodes=1:ppn=9 -q cu
sge_option_fc = -l nodes=1:ppn=9 -q cu
sge_option_cns = -l nodes=1:ppn=9 -q cu
pa_concurrent_jobs = 3
cns_concurrent_jobs = 3
ovlp_concurrent_jobs = 3
pb-cdunn commented
Exception: HPC.daligner option "-dal" has changed to "-B".
In the upstream repo, that option of HPC.daligner
changed. So you have to change these settings:
pa_HPCdaligner_option = -v -dal4 -M32 -e.70 -l1000 -s1000
ovlp_HPCdaligner_option = -v -dal4 -M32 -h60 -e.96 -l500 -s1000
from -dal
to -B