circlator stuck #188
Description
My circlator (Circlator version: 1.5.5) run with the following command was running for 3 days and then stopped and never continued. Here is the last part of the log file:
Command:
circlator all /opt/extern/bremen/symbiosis/jkiefer/HiFi/nematoda/Astomonema/trimmed/asm/hifiasm/hifiasm/out.bp.p_ctg.fa\
/opt/extern/bremen/symbiosis/jkiefer/HiFi/nematoda/Astomonema/trimmed/merged_trimmed.fastq.gz\
circlator_hifiasm --threads $NSLOTS --verbose
the log file:
syscall: samtools faidx /opt/extern/bremen/symbiosis/jkiefer/CAL23/PB/circlator_hifiasm/03.assemble.tmp.spades.77.rhln6v0r/contigs.fasta
[assemble] kmer N50
[assemble] 77 1329
[assemble] 87 399
[assemble] 97 194
[assemble] 107 4067
[assemble] 117 416
[assemble] 127 793
[assemble] using assembly with kmer 107
________________________________ Running merge ________________________________
Running command: bash run_nucmer.sh
Making ACT files from 00.input_assembly.fasta /opt/extern/bremen/symbiosis/jkiefer/CAL23/PB/circlator_hifiasm/03.assemble/contigs.fasta 04.merge.merge.iter.1.coords
samtools 1.19.2 /opt/share/software/bin/samtools
bwa 0.7.17 /opt/share/software/bin/bwa
syscall: bwa index -p 04.merge.merge.iter.2.bam.tmp.bwa_index 04.merge.merge.iter.2.merged.fasta
syscall: bwa mem -x pacbio -t 60 04.merge.merge.iter.2.bam.tmp.bwa_index 02.bam2reads.fasta | samtools view -F 0x0800 -T 04.merge.merge.iter.2.merged.fasta -b -o 04.merge.merge.iter.2.bam.tmp.unsorted.bam -
syscall: samtools sort -@ 4 -m 125M 04.merge.merge.iter.2.bam.tmp.unsorted.bam -o 04.merge.merge.iter.2.bam
syscall: samtools index 04.merge.merge.iter.2.bam
samtools 1.19.2 /opt/share/software/bin/samtools
spades 3.7.1 /opt/share/software/bin/spades.py
syscall: spades.py -s /opt/extern/bremen/symbiosis/jkiefer/CAL23/PB/circlator_hifiasm/04.merge.merge.iter.2.reads.fasta -o /opt/extern/bremen/symbiosis/jkiefer/CAL23/PB/circlator_hifiasm/04.merge.merge.iter.2.assembly.tmp.spades.127.eti_6tv6 -t 60 -k 127 --careful --only-assembler
syscall: samtools faidx /opt/extern/bremen/symbiosis/jkiefer/CAL23/PB/circlator_hifiasm/04.merge.merge.iter.2.assembly.tmp.spades.127.eti_6tv6/contigs.fasta
syscall: spades.py -s /opt/extern/bremen/symbiosis/jkiefer/CAL23/PB/circlator_hifiasm/04.merge.merge.iter.2.reads.fasta -o /opt/extern/bremen/symbiosis/jkiefer/CAL23/PB/circlator_hifiasm/04.merge.merge.iter.2.assembly.tmp.spades.117.0x3z7_g4 -t 60 -k 117 --careful --only-assembler
syscall: samtools faidx /opt/extern/bremen/symbiosis/jkiefer/CAL23/PB/circlator_hifiasm/04.merge.merge.iter.2.assembly.tmp.spades.117.0x3z7_g4/contigs.fasta
syscall: spades.py -s /opt/extern/bremen/symbiosis/jkiefer/CAL23/PB/circlator_hifiasm/04.merge.merge.iter.2.reads.fasta -o /opt/extern/bremen/symbiosis/jkiefer/CAL23/PB/circlator_hifiasm/04.merge.merge.iter.2.assembly.tmp.spades.107.9frhnio3 -t 60 -k 107 --careful --only-assembler
syscall: samtools faidx /opt/extern/bremen/symbiosis/jkiefer/CAL23/PB/circlator_hifiasm/04.merge.merge.iter.2.assembly.tmp.spades.107.9frhnio3/contigs.fasta
syscall: spades.py -s /opt/extern/bremen/symbiosis/jkiefer/CAL23/PB/circlator_hifiasm/04.merge.merge.iter.2.reads.fasta -o /opt/extern/bremen/symbiosis/jkiefer/CAL23/PB/circlator_hifiasm/04.merge.merge.iter.2.assembly.tmp.spades.97.1u1v59s_ -t 60 -k 97 --careful --only-assembler
syscall: samtools faidx /opt/extern/bremen/symbiosis/jkiefer/CAL23/PB/circlator_hifiasm/04.merge.merge.iter.2.assembly.tmp.spades.97.1u1v59s_/contigs.fasta
syscall: spades.py -s /opt/extern/bremen/symbiosis/jkiefer/CAL23/PB/circlator_hifiasm/04.merge.merge.iter.2.reads.fasta -o /opt/extern/bremen/symbiosis/jkiefer/CAL23/PB/circlator_hifiasm/04.merge.merge.iter.2.assembly.tmp.spades.87.04_chcus -t 60 -k 87 --careful --only-assembler
syscall: samtools faidx /opt/extern/bremen/symbiosis/jkiefer/CAL23/PB/circlator_hifiasm/04.merge.merge.iter.2.assembly.tmp.spades.87.04_chcus/contigs.fasta
syscall: spades.py -s /opt/extern/bremen/symbiosis/jkiefer/CAL23/PB/circlator_hifiasm/04.merge.merge.iter.2.reads.fasta -o /opt/extern/bremen/symbiosis/jkiefer/CAL23/PB/circlator_hifiasm/04.merge.merge.iter.2.assembly.tmp.spades.77.d8jls8k7 -t 60 -k 77 --careful --only-assembler
any idea how I can get circlator to finish?