Target sequence length > 100K, over comparison pipeline limit.

[lyuchengmarvin]

Description of bug

Hi,

I am trying to run the biosynthetic mode with the flag --bio, but the log indicates that one of my contigs exceeds the 100K limit for HMM scans. I would like to learn ways to work around this problem. Please let me know how to resolve this issue. Thank you!

Best,

Marvin

spades.log

ND-78.log

params.txt

params.txt

SPAdes version

SPAdes genome assembler v4.0.0

Operating System

Linux 8.10

Python Version

Python 3.10.18

Method of SPAdes installation

Installed on the HPC, so not sure.

No errors reported in spades.log

• Yes

[asl]

Unfortunately there is no way to workaround this limit now – it is built into HMMER...

[lyuchengmarvin]

Sadness:( Is there a way to split the contigs into smaller ones? Marvin Yu-Cheng Lin Ph.D. Candidate, Vincent Denef Lab <https://websites.umich.edu/~vdenef/> Department of Ecology and Evolutionary Biology University of Michigan, Ann Arbor, MI Anton Korobeynikov ***@***.***>於 2025年12月7日 週日，17:57寫道：

…

*asl* left a comment (ablab/spades#1546) <#1546 (comment)> Unfortunately there is no way to workaround this limit – this is built into HMMER... — Reply to this email directly, view it on GitHub <#1546 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BCSRYKTPUUWXXSO4B5G5B2D4ASWFBAVCNFSM6AAAAACOKEQQPGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTMMRTGY4DQOJSGU> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[1dayac]

Hello Marvin!
We never encountered this issue before, are you able to share this dataset with us, so will be able to come up with a fix for that

Thanks,
Dmitry