Racon aborting with 'core dumped' error

[lilypeck]

Hello

Firstly thanks for making this great tool.

Racon has run fine on some of my genomes, but then on others it is throwing up a strange error.

First i'm using minimap2 to create the sam file

minimap2 -ax map-ont ${INFILE}/assembly.fasta \
	/u/project/vlsork/ldpeck/longreads/fastq/${INFILE}_ALLpass.fastq.gz \
        > ${INFILE}/${INFILE}_haploid.sam

Then i'm feeding the sam file into racon

racon /u/project/vlsork/ldpeck/longreads/fastq/${INFILE}_ALLpass.fastq.gz \
         ${INFILE}/${INFILE}_haploid.sam ${INFILE}/assembly.fasta > ${INFILE}/${INFILE}_haploid.flye_r1.fa

[racon::Polisher::initialize] loaded target sequences 29.016455 s
[racon::Polisher::initialize] loaded sequences 669.493081 s
/work/UGE/8.6.4/n1036/job_scripts/6916368: line 32:  5780 Aborted                 (core dumped) racon /u/project/vlsork/ldpeck/longreads/fastq/${INFIL
E}_ALLpass.fastq.gz ${INFILE}/${INFILE}_haploid.sam ${INFILE}/assembly.fasta > ${INFILE}/${INFILE}_haploid.flye_r1.fa

Do you know what's causing this? I am running the script on a server with 200G virtual memory and it's only using ~100G, and there is lots of storage space so it's not running out of either these. I can't see another issue relating to this same error.

Thank you in advance

Lily

[JasperBruggema]

I'm currently running into the same issue.
Have you found a fix yet?