masurca_scaffold.sh error

[shri1984]

Hi, I am trying to run masurca_scaffold.sh using two pacbio assemblies generated from some other assembler. I am using main assembly (closest to the estimated genome size) as -r and another assembly as -q. The run goes smoothly until I get an error at the scaffolding stage.

Illegal division by zero at find_repeats.pl line 43, line 145686. walking the scaffold graph failed

any idea what going on here?

[gitcruz]

Hi, Same problem here. After polishing, while creating the scaffold graph.

STDOUT [Wed Jul 21 21:11:09 CEST 2021] Aligning the reads to the contigs [Wed Jul 21 21:51:18 CEST 2021] Filtering alignments [Wed Jul 21 21:51:39 CEST 2021] Extracting reads for the patches [Wed Jul 21 21:54:07 CEST 2021] Creating scaffold links [Thu Jul 22 02:08:11 CEST 2021] Aligning the scaffolding sequences to the contigs [Thu Jul 22 02:09:25 CEST 2021] Creating scaffold graph and building scaffolds

STDERR Illegal division by zero at /home/devel/fcruz/bin/programs/MaSuRCA-4.0.4/bin/find_repeats.pl line 43, line 65474. [Thu Jul 22 02:09:27 CEST 2021] walking the scaffold graph failed

Any idea on how to fix this? We could look at some of the intermediate files to track it down.

Best, Fernando

[alekseyzimin]

Hi, this is solved in 4.0.5 release.

[gitcruz]

Okay, I missed that update. Thanks! F.

El mié., 1 sept. 2021 15:04, Aleksey Zimin @.***> escribió:

Hi, this is solved in 4.0.5 release.

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