search

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
261 stars 48 forks source link

3146 Killed error #185

Open yu878 opened 3 years ago

yu878 commented 3 years ago

Hi there,

I have tried racon to do polishing of my data, although I got the following error. [racon::Polisher::initialize] loaded target sequences 10097.802500 s [racon::Polisher::initialize] loaded sequences 19.091033 s bash: line 11: 3146 Killed

I found a similar issue, but I don't know what the problem is. How can I solve it?

The command I use was this. racon -t 8 wtdbg_TE.fa TE_bowtie.sam TE.fq > TE_racon.fasta

Best regards, Yu

isovic commented 3 years ago

Hi Yu, Does the computer you are using have enough RAM to store all the data you are loading with Racon?

Best regards, Ivan.

yu878 commented 3 years ago

Hi Ivan,

Thank you for your replying. I think there is enough RAM to store them, but I also tried racon-wrapper and got another error like the following.

[RaconWrapper::run] preparing data with rampler [RaconWrapper::run] total number of splits: 2714 [RaconWrapper::run] processing data with racon [racon::Polisher::initialize] loaded target sequences 1.836208 s [racon::Polisher::initialize] loaded sequences 17.155740 s [racon::Polisher::initialize] loaded overlaps 10015.492108 s [racon::Overlap::find_breaking_points] error: overlap is not transmuted! [racon::Overlap::find_breaking_points] error: overlap is not transmuted! [racon::Overlap::find_breaking_points] error: overlap is not transmuted! [racon::Overlap::find_breaking_points] error: overlap is not transmuted!

Did this error occur due to the limits of RAM or another problem?

Best regards, Yu

rvaser commented 3 years ago

Hi Yu, error overlap is not transmuted means you run the command wrong. Run racon (or racon_wrapper) with racon <reads> <overlaps> <backbone>. In your first command racon -t 8 wtdbg_TE.fa TE_bowtie.sam TE.fq > TE_racon.fasta you passed the reads and backbone the other way around, although the first error indicates that you run out of memory.

Best regards, Robert

yu878 commented 3 years ago

Hi Robert,

Thank you for your replying. I tried racon -t 8 TE_racon.fasta TE.fq > TE_bowtie.sam and got an error again like following. [RaconWrapper::run] preparing data with rampler [RaconWrapper::run] total number of splits: 0 [RaconWrapper::run] error: unable to find split target sequences!

I am not sure why this error happened. For TE.fq, I used Illumina short read. I am sorry for my poor understanding but hope you can help me.

Best regards, Yu

rvaser commented 3 years ago

Can you check out what is the length of the biggest contig in TE_racon.fasta? If not, check out the file size, divide id by 3 and use that number instead of <put length here>. Use the wrapper like this:

racon_wrapper -t 8 --split <put length here> TE.fq TE_bowtie.sam TE_racon.fasta > result.fasta
yu878 commented 3 years ago

Hi Robert,

I tried it by using the number of the length of the biggest contig, but I also got the same error.

[RaconWrapper::run] preparing data with rampler [RaconWrapper::run] total number of splits: 0 [RaconWrapper::run] error: unable to find split target sequences!

I hope you could help me to solve this error.

Best regards, Yu