[Error] No gap can be closed

[Bank-tidy]

Hello, Thank you for developing a very useful tool,I have some doubts about using the tool, so I woulld like to ask you for advice:

The contigs I entered using the -g parameter are contigs assembled by hifiasm, not the original sequencing fastq files. The -d parameter genome is the conitgs assembled by hifiasm and then the ragtag is mounted on the reference genome. Is this correct?

• These are my eight gaps areas：

Type    Shape   Chr Start   End color
gap box 1   34169914    34170013    ff7f00
gap box 1   34334335    34334434    ff7f00
gap box 1   34407737    34407836    ff7f00
gap box 1   34524188    34524287    ff7f00
gap box 7   69516260    69516359    ff7f00
gap box 7   69567308    69567407    ff7f00
gap box 8   60420099    60420198    ff7f00
gap box 9   33288797    33288896    ff7f00

• This is my script：

python3 /public1/home/yinhang/software/apps/quarTeT/quartet.py GapFiller -d ${hifiasm_genome} -g ${hifiasm_contigs} -t 60 -p tomato_gap

• This is my error：

[Info] Paramater: draftgenomefile=~/tomato_t2t_N0.fasta, gapclosercontigfilelist=[~/SL50_hifiasm_all.fa'], flanking=5000, minalignmentlength2=1000, minalignmentidentity2=0.4, maxfillinglen=1000000, prefix=tomato_gap, threads=60, minimapoption=-x asm5 -t 60, overwrite=False, enablejoin=False, joinonly=False
[Info] Getting gaps flanking sequence...
[Info] gapfilling with SL50_hifiasm_all.fa...
[Info] Running minimap2...
[Info] Analysising Alignments...
[Info] All files processed.
[Error] No gap can be closed.

Looking forward to your reply, Best wishes

[Echoring]

Are you using contigs from hifiasm to close gaps in a genome assembled by the same contigs? These same contigs cannot provide information that can be used to close the gaps. You should use sequences from other source to do this. (e.g. raw reads, ONT, other contig assembly tools) Meanwhile, quarTeT currently not support fastq format. If you want to use raw reads to close the gaps, you should change them to fasta format.

[Bank-tidy]

Thank you for your suggestion, so I used hifi_reads, ONT_reads, NGS_reads1, NGS_reads2 at the same time, but unfortunately an error was reported during the operation. Do you have any suggestions to solve this error?

error:

slurmstepd: error: Detected 1 oom-kill event(s) in StepId=3167.batch cgroup. Some of your processes may have been killed by the cgroup out-of-memory handler.

my shell:

python3 /public1/home/yinhang/software/apps/quarTeT/quartet.py GapFiller -d ${genome} -g ${hifi_reads} ${ONT_reads} ${NGS_reads1} ${NGS_reads2} -t 60 -p tomato_gap

Looking forward to your reply, Best wishes！

[Echoring]

This error is not reported by quarTeT, but your computer. Seems your computer is out of memory. Meanwhile, NGS reads is too short to give information for gapclosing. Use longer assembly.

[Bank-tidy]

Thanks for your suggestion！ I'll try it again