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zhangrengang avatar zhangrengang commented on August 27, 2024

Please use TE or LTR sequences instead of genome sequences. Here are examples to extract TE sequences from Repeatmakser and LTR_retriver outputs.

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zhangrengang avatar zhangrengang commented on August 27, 2024

The error:

Fatal exception (source file p7_pipeline.c, line 697):
Target sequence length > 100K, over comparison pipeline limit.
(Did you mean to use nhmmer/nhmmscan?)

is owned to the HMMer since v3.3.1 which has a design limit of 100K:

The comparison engine used by hmmsearch, hmmscan, phmmer, and jackhmmer has a design limit of 100K residues for target sequence length (usually protein sequences, sometimes RNA transcripts). Only nhmmer/nhmmscan are designed for searching arbitrary length genome sequences. That limit was not being enforced, and it was possible for a user to run hmmsearch inadvertently instead of nhmmer, which can cause numerical overflows and give infinite scores, among other problems. The comparison engine now exits with an error if the target sequence length is >100K.

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yongzhiyang2012 avatar yongzhiyang2012 commented on August 27, 2024

Thank you.
I have deleted the sequences that were longer than 100k and it worked.

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zhangrengang avatar zhangrengang commented on August 27, 2024

HMMer v3.3 can work with sequence length > 100K.

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