[Error] Failed to run correcting reads 0, crr0

[dmacguigan]

Hello,

I am running PECAT v.0.0.3 to correct reads on a SLURM cluster. Here is my config file.

project=Emac_PECAT
reads=/vscratch/grp-tkrabben/MacGuigan/rawNanoporeData/Emac/Emac.cell1.passed.fastq
genome_size=800000000
threads=20
cleanup=1
grid=slurm:12
grid_options= --reservation=ubhpc-future --qos=general-compute --partition=general-compute --account=tkrabben --time=72:00:00 --mem=100G
prep_min_length=7000
prep_output_coverage=60
corr_iterate_number=1
corr_block_size=1000000000
corr_correct_options=--score=weight:lc=16 --aligner edlib --filter1 oh=1000:ohr=0.01 --candid>
corr_filter_options=--filter0=l=7000:al=3500:alr=0.5:aal=10000:oh=5000:ohr=0.3
corr_rd2rd_options=-x ava-ont
corr_output_coverage=60
phase_method = 0
polish_medaka = 0
#align_block_size=4000000000
#align_rd2rd_options=-X -g3000 -w30 -k19 -m100 -r500
#align_filter_options=--filter0=l=5000:aal=6000:aalr=0.5:oh=3000:ohr=0.3 --task=extend --filter1=oh=300:ohr=0.03
#asm1_assemble_options=
#phase_method=0
#phase_rd2ctg_options=-x map-ont -c -p 0.5 -r 1000
#phase_use_reads=1
#phase_phase_options= --coverage lc=30 --phase_options icr=0.2:icc=6:sc=8
#phase_filter_options= --threshold=1000
#asm2_assemble_options=
#polish_use_reads=0
#polish_filter_options= --filter0 oh=1000:ohr=0.1
#polish_map_options = -x map-ont -k19 -w10
#polish_cns_options =

I was able to complete the alignment portion of pecat.pl correct. However, I then encountered the following error message.

2023-10-07 03:04:17 [Error] Failed to run correcting reads 0, crr0

If we look at the log file for one of the "correct" scripts, we see the following syntax error.

(flye-2.9.2) dmacguig@vortex-future:~/vscratch/MacGuigan/rawNanoporeData/Emac/PECAT/Emac_PECAT/scripts$ cat crr0_correct_0.sh.log
Plgd script start: 2023-10-07 03:02:59
/var/spool/slurmd/job13661441/slurm_script: line 6: syntax error near unexpected token `newline'
/var/spool/slurmd/job13661441/slurm_script: line 6: `  /projects/academic/tkrabben/modules_KrabLab/easybuild/2023.01/software/Core/miniconda3/22.11.1-1/envs/PECAT/share/pecat-0.0.3-0/bin/fsa_rd_correct /vscratch/grp-tkrabben/MacGuigan/rawNanoporeData/Emac/PECAT/Emac_PECAT/1-correct/0/rd2rd.txt.sub.0.paf /vscratch/grp-tkrabben/MacGuigan/rawNanoporeData/Emac/PECAT/Emac_PECAT/0-prepare/prepared_reads.fasta /vscratch/grp-tkrabben/MacGuigan/rawNanoporeData/Emac/PECAT/Emac_PECAT/1-correct/0/corrected_reads_0.fasta.0 --output_directory=/vscratch/grp-tkrabben/MacGuigan/rawNanoporeData/Emac/PECAT/Emac_PECAT/1-correct/0 --thread_size=20  --read_name_fname=/vscratch/grp-tkrabben/MacGuigan/rawNanoporeData/Emac/PECAT/Emac_PECAT/1-correct/0/readname.core.0 --infos_fname /vscratch/grp-tkrabben/MacGuigan/rawNanoporeData/Emac/PECAT/Emac_PECAT/1-correct/0/corrected_reads_0.fasta.0.infos --score=weight:lc=16 --aligner edlib --filter1 oh=1000:ohr=0.01 --candid>'

Any suggestion on how to fix this?

Thanks! Dan

[lemene]

Hi, @dmacguigan The parameter corr_correct_options is incomplete.

corr_correct_options =--score=weight:lc=16 --aligner edlib --filter1 oh=1000:ohr=0.01 --candid>

It should be

corr_correct_options =--score=weight:lc=16 --aligner edlib --filter1 oh=1000:ohr=0.01

or

corr_correct_options=--score=weight:lc=16 --aligner edlib --filter1 oh=1000:ohr=0.01 --candidate n=400:f=20

[dmacguigan]

Ah thank you @lemene, that line was accidentally truncated when copying an older config file. Read correction is running fine now.