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. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#242 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB34KVJSCPEMA6FU547GC2DT7YQEZANCNFSM5AG4RY2A> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.