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isovic / racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:
https://github.com/lbcb-sci/racon
MIT License
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unequal length error #224

Open iremdnzl opened 1 year ago

iremdnzl commented 1 year ago

Hi, I have multiple samples and I'm following the same scripts for all of them. Just one sample gave this error:

This is minimap2: minimap2 -a -x map-ont /media/idnzl/HDD/REFERENCES/GCA_023856395.1_Psun_UM_1.1_genomic.fa all_reads.fastq > Sample_alignment.sam

This is what I run: racon -m 8 -x 6 -g -8 -w 500 -t 4 all_reads.fastq Sample_alignment.sam /media/idnzl/HDD/REFERENCES/GCA_023856395.1_Psun_UM_1.1_genomic.fa > RACON/racon_Sample.fasta This is what I get:

[racon::Polisher::initialize] loaded target sequences 11.305067 s
[racon::Polisher::initialize] loaded sequences 2.537877 s
[racon::Overlap::transmute] error: unequal lengths in sequence and overlap file for sequence ec458864-7c3c-492e-afa8-2a9f7fbe5bef!

Do you have any suggestions? Cheers,

rvaser commented 1 year ago

The error unequal lengths indicates that the FASTA/Q files you used in minimap2 and the ones passed to racon have differences (offending read is ec458864-7c3c-492e-afa8-2a9f7fbe5bef). Did you by any chance change the files between minimap2 and racon runs or passed the wrong input?

Best regards, Robert