error: unequal lengths in sequence and overlap file for sequence

[mattbird567]

Am trying to run Racon for the first time (currently running the below)

./racon -t 8 -q 30 -e 0.3 -m 8 -x -6 -g -8 -w 500 /path/to/illuminaR1.fastq /path/to/output.sam /path/to/assembly.fasta >output.fasta`

However, its returning the error [racon::Polisher::initialize] loaded target sequences 0.049634 s [racon::Polisher::initialize] loaded sequences 4.750742 s [racon::Overlap::transmute] error: unequal lengths in sequence and overlap file for sequence D00146:334:HCFWCBCXY:2:1101:1096:2019!

Any help would be great

[rvaser]

Hello, can you paste command which produced output.sam?

Best regards, Robert

[yinxingdechibang]

I entered the following command and got an error: Order： nohup /users/zhangx/miniconda3/bin/racon -t 20 /users/zhangx/data/fp/fpgenome/fp.contigs.fasta ONTmin_IT0.paf /users/zhangx/data/fp/purge_haplotigs/purged.fa > ONTmin_IT1.fasta 2>2.log& Mistake ： error: unequal lengths in sequence and overlap file for sequence 3c9e295c-2cb5-41ae-88d3-55f4f5896c22! I need your help urgently, thank you very much ！

[rvaser]

Hello, can you please paste the mapping/alignment command? You probably misplace the reads/reference file in the Racon command.

Best regards, Robert

[yinxingdechibang]

I am very happy to get your reply, the command for this step is:

(1) nohup /users/zhangx/miniconda3/bin/minimap2 -t 20 /users/zhangx/data/fp/purge_haplotigs/purged.fa /users/zhangx/data/fp/fpgenome/fp.contigs.fasta > ONTmin_IT0. paf 2> 1.log

(2) nohup /users/zhangx/miniconda3/bin/racon -t 20 /users/zhangx/data/fp/fpgenome/fp.contigs.fasta ONTmin_IT0.paf /users/zhangx/data/fp/purge_haplotigs/purged.fa > ONTmin_IT1.fasta 2> 2.log

Error in the second step. I looked at this sequence of errors reported in the file as follows :

What do you think I should do? Thank you very much

[rvaser]

Are you trying to polish contigs with reads or with the same (modified?) contigs? If second, there might be two sequences in purged.fa and fp.contigs.fasta which share the same name but have different lengths.

[yinxingdechibang]

Hello, sorry to bother you, "fp.contigs.fasta" is the original downloaded genome file, and "purged.fa" is the redundancies removed by the purge_dups software. So how do you think we should solve it? thank you very much！

------------------ 原始邮件 ------------------ 发件人: "isovic/racon" @.>; 发送时间: 2022年2月16日(星期三) 凌晨2:42 @.>; @.**@.>; 主题: Re: [isovic/racon] error: unequal lengths in sequence and overlap file for sequence (#162)

Are you trying to polish contigs with reads or with the same (modified?) contigs? If second, there might be two sequences in purged.fa and fp.contigs.fasta which share the same name but have different lengths.

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[rvaser]

Can you explain what you are trying to do?

[setshabaTaukobong]

Hi there, I am having a similar issue as the above:

[racon::Polisher::initialize] loaded target sequences 3.574446 s
[racon::Polisher::initialize] loaded sequences 33.367121 s
[racon::Overlap::transmute] error: unequal lengths in sequence and overlap file for sequence 2525deca-ece8-4652-8429-19ca02a0aeca!

I typed the following command for racon: racon -m 8 -x -8 -g -6 -w 500 -t 4 /home/staukobong/data/sample_id.trimmed.fastq /home/staukobong/data/sample_id.sam /home/staukobong/data/Assembled/00-assembly/draft_assembly.fasta > sample_idRac.fasta

And I used minimap2 to map my reads to the assembled genome: minimap2 -a -t 4 /home/staukobong/data/Assembled/00-assembly/draft_assembly.fasta /home/staukobong/data/sample_id.trimmed.fastq > sample_id.sam

Could I please get some assistance on this?