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BGI-Qingdao / TGS-GapCloser

A gap-closing software tool that uses long reads to enhance genome assembly.
GNU General Public License v3.0
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error: empty target sequences set! #80

Open Marison-1 opened 6 months ago

Marison-1 commented 6 months ago

Hi! I installed the TGS-gapcloser by conda,when I running this tools,I got an error report like this "[racon::Polisher::initialize] error: empty target sequences set!" in [.0.0.racon.log] file. And my command is as follow:

`Path_Scaff=/public-dss/share/gap_lab/MaYuSheng/Rice/LJY_lab/14Rice/Assembly/ragtag/ZKF5_hifi/scaffold_2/ragtag.scaffold.fasta Path_reads=/public-dss/share/gap_lab/MaYuSheng/Rice/LJY_lab/14Rice/Assembly/tgsGapCloser/ZKF5/reads/ZKF5.fasta Path_out=/public-dss/share/gap_lab/MaYuSheng/Rice/LJY_lab/14Rice/Assembly/tgsGapCloser/ZKF5/gapFill_2/ Path_racon=/public-supool/home/marison/micromamba/envs/racon/bin/racon

tgsgapcloser --scaff $Path_Scaff --reads $Path_reads --output $Path_out --racon $Path_racon --tgstype pb --minmap_arg '-x asm20' --thread 10 --r_round 1`

I wonder if there any details that I hadn't noticed! Thanks a lot!

smallfishcui commented 6 months ago

Hi, I got the same error message. Can you tell how you solved it? thanks!

adonis316 commented 6 months ago

Please check #79

Please check whether the file XXX.ont.fasta is empty. If XXX.ont.fasta is empty, then racon will not run since there are no long reads waiting to be corrected.

There could be many reasons that the XXX.ont.fasta is empty. Please check if there are gaps in the input scaffolds. Also check the file XXX.sub.filter.paf, which gives the mapping relationship of long reads against scaffolds.

Thanks, Mengyang