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sanger-pathogens / circlator

A tool to circularize genome assemblies
http://sanger-pathogens.github.io/circlator/
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circlator stuck #188

Open jpinus opened 1 month ago

jpinus commented 1 month ago

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?