unable to close gaps using pacbio CCS reads

[shailij246]

Hi, I have a 2.8 GB genome in chromosomal scaffolds and I am trying to gap close using tgsgapcloser with PB CCS reads which are about 21 GB. Howerver, there are no gapclosed files generated.

Here is the command I used: tgsgapcloser --scaff jordan-sta3744-mb-hirise-fe9e409-10-2022hic_output.fasta --reads STS_CCS_m64047_230413_235222.ccs.fasta --output gapfilledSTS_PBCCS_ne_30May23 --ne --tgstype pb --thread 10 --g_check >pipe.log 2>pipe.err

also tried this to limit paf file size but it did not work: tgsgapcloser --scaff jordan-sta3744-mb-hirise-fe9e409-10-2022hic_output.fasta --reads STS_CCS_m64047_230413_235222.ccs.fasta --output gapfilledSTS_PBCCS_ne_30May23 --ne --minmap_arg '-x asm20 -K 80M' --tgstype pb --thread 10 --g_check >pipe.log 2>pipe.err

This is the error log:

• No error correction by --ne option
• TGS reads type is pb . MINIMAP2_PARAM is -x ava-pb MIN_IDY is 0.2 . MIN_MATCH is 200 .

INFO : Checking basic args & env end.

INFO : Step 1 , run TGSSeqSplit to split scaffolds into scaftigs(contigs). skip step1 since done_step1_tag exists

INFO : Step 1 , done .

INFO : Step 2 , skip TGSCandidate by --ne option.

INFO : Step 3 , skip error correction by --ne option.

INFO : Step 4 , gap filling ...

• Use STS_CCS_m64047_230413_235222.ccs.fasta as final TGS READS input.

FATAL : File gapfilledSTS_PBCCS_ne_30May23.contig does not exist !!! ! exit ... try -h/--help for usage.

I also tried gapclosing one chromosome at a time and it did not work either.

What am I doing wrong?

Thanks for your help, Shaili.

[shailij246]

Ok, this is resolved, I just needed to run it in a clean new directory.