Failed to convert line to overlap

[AoiKudoh]

Hi, Thank you very much for devloping PECAT!
I am trying to assemble the Nanopore reads using PECAT, and got error during correction step as: 2024-11-20 03:36:52 [ERROR] Failed to convert line to overlap
Could you help to solve the error?

Here is my command, cfgfile and the error messages.
pecat.pl unzip cfgfile

cfgfile:

project=XXXX
reads=/XXXX/XXXX.fastq.gz
genome_size=388000000
threads=16
cleanup=1
grid=local
prep_min_length=3000
prep_output_coverage=80
corr_iterate_number=1
corr_block_size=4000000000
corr_correct_options=
corr_filter_options=--filter0=l=5000:al=2500:alr=0.5:aal=5000:oh=3000:ohr=0.3
corr_rd2rd_options=-x ava-ont
corr_output_coverage=80
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=
phase_rd2ctg_options=-x map-ont -c -p 0.5 -r 1000
phase_use_reads=1
phase_phase_options=
phase_clair3_command=singularity exec --containall -B `pwd -P`:`pwd -P` clair3_v0.1-r12.sif /opt/bin/run_clair3.sh
phase_clair3_use_reads=0
phase_clair3_options=--platform=ont --model_path=/opt/models/ont_guppy5/  --include_all_ctgs
phase_clair3_rd2ctg_options=-x map-ont -w10 -k19 -c -p 0.5 -r 1000
phase_clair3_phase_options=--coverage lc=30 --phase_options icr=0.1:icc=6:sc=10 --filter i=70
phase_clair3_filter_options=--threshold=2500 --rate 0.05
asm2_assemble_options=
polish_map_options=-x map-ont
polish_filter_options=--filter0 oh=1000:ohr=0.1
polish_cns_options=
polish_medaka=
polish_medaka_command=singularity exec --containall -B `pwd -P`:`pwd -P` medaka_1.7.2--aa54076.sif medaka
polish_medaka_map_options=-x map-ont
polish_medaka_cns_options=--model r1041_e82_400bps_sup_g615

error messages:

2024-11-20 03:34:14 [INFO] Memory: 22264
2024-11-20 03:36:52 [ERROR] Failed to convert line to overlap 
   1395449	44147	35206	44132	-	389
/XXXX/scripts/crr0_correct_0.sh: line 16: 3053358 Aborted                 (core dumped) /XXXX/miniconda3/envs/pecat/share/pecat-0.0.3-0/bin/fsa_rd_correct /XXXX/1-correct/0/rd2rd.txt.sub.0.paf /XXXX/0-prepare/prepared_reads.fasta /XXXX/1-correct/0/corrected_reads_0.fasta.0 --output_directory=/XXXX/1-correct/0 --thread_size=16 --read_name_fname=/XXXX/1-correct/0/readname.core.0 --infos_fname /XXXX/1-correct/0/corrected_reads_0.fasta.0.infos
Plgd script end: 2024-11-20 03:36:52

Thank you for your help!

[lemene]

Hi @AoiKudoh
It seems an error occurred in the previous step. 1395449 44147 35206 44132 - 389 is not a complete line in PAF format. You can rerun the previous step as bellow:

$ xxx/scripts/crr0_split.sh
$ pecal.pl unzip cfg

If the issue persists, you will need to re-run the all vs all alignment using minimap2.

$ rm xxx/1-correct/0/*.paf
$ pecal.pl unzip cfg

[AoiKudoh]

Thank you for your help! I will try to rerun the previous step.