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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
269 stars 49 forks source link

Segmentation fault after loading sequence #173

Closed cbirbes closed 3 years ago

cbirbes commented 3 years ago

Hello, I have been using racon for a very long time to polish my genomes, I even did a nextflow pipeline using racon without problems. Recently I have encountered a problem on a genome that I want to polish with CLR reads (usually I use ONT)

I am having the following problem:

racon::Polisher::initialize] loaded target sequences 12.395108 s
/var/spool/slurm/d/job21101485/slurm_script : ligne 7 : 102585 Segmentation fault  racon -t 20 longreads.rename.fq.gz map.polisher.sam offspring_raw.cgt.fa > assembly.racon3.fa

My command :

minimap2 -a -t 16 -x map-pb offspring_raw.cgt.fa ${reads} > map.polisher.sam

Racon 1.4.10
racon -t 20 longreads.rename.fq.gz map.polisher.sam offspring_raw.cgt.fa > assembly.racon3.fa

Ty for your help

rvaser commented 3 years ago

Hi Clement, can you try the same command with the newest version (1.4.13)? Also, can you paste the compilation commands you used? Running on cluster might be a problem if you compiled on one node and run on another.

Best regards, Robert

cbirbes commented 3 years ago

I'm not admin on the cluster I will ask for the version update, but i think Running on this cluster is not a problem, i did more than 100 polishing in the past year and 99% worked (sometimes memory problem, but nothing more)

I come back with more information soon !

rvaser commented 3 years ago

Was the executable compiled from source or are you using the conda version?

cbirbes commented 3 years ago

From source

rvaser commented 3 years ago

If you can recompile, use -Dspoa_optimize_for_portability=ON when running cmake. This might solve the problem. If not, try updating the version.

cbirbes commented 3 years ago

Ok, I tried several things but finally the error came from me. Small file notation error so I had a fastq file which was in fact a fasta ... so successive> and @, but each time with sequences and not qualities! Thank you for your help !