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loneknightpy / idba

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what(): ShortSequence: Sequence is too long. #58

Open LukeSergey opened 3 years ago

LukeSergey commented 3 years ago

Hi,

I am new to the IDBAUD bioinformatics research. I came across with the following problem and hope anyone might help 👍 :

My code is:

!/bin/bash

SBATCH -t 80:00:00

SBATCH -N 1

SBATCH -c 8

SBATCH --mem=80G

module load IDBAUD/1.1.0

idba_ud -r A_S1_outmergefile.fa -o A_S1_assemblesample --num_threads 8 --mink 40 --maxk 120 --step 10

scontrol show job $SLURM_JOB_ID

The error message is (from the Slurm file): terminate called after throwing an instance of 'std::logic_error' what(): ShortSequence: Sequence is too long. /var/lib/slurmd/job64877788/slurm_script: line 9: 11279 Aborted

Thank you in advance for your kind help!

Best, Luke

MDSharma commented 1 year ago

Note that IDBA assemblers are designed for short reads (around 100bp). If you want to assemble paired-end reads with longer read length, please modify the constant kMaxShortSequence in src/sequence/short_sequence.h to support longer read length.