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LuoGroup2023 / DeChat

Repeat and haplotype aware error correction in nanopore sequencing reads with DeChat
GNU General Public License v3.0
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malloc(): invalid size when producing recorrected.fa #5

Open melop opened 4 months ago

melop commented 4 months ago

Hello, I am trying to use dechat to correct ont R10.4.1 SUP reads (a mixture of N50=18kb of ~130Gb and N50=80kb ultra long of ~30Gb). The program produces about 95Gb of recorrected.fa, then threw an error :

malloc(): invalid size (unsorted) /var/spool/slurmd/job239412/slurm_script: line 10: 475996 Aborted (core dumped) dechat -i allreads.fq -o corrected -t $CPU

I have attached the full log for your information. log.txt.gz

LuoGroup2023 commented 4 months ago

Hello, I am trying to use dechat to correct ont R10.4.1 SUP reads (a mixture of N50=18kb of ~130Gb and N50=80kb ultra long of ~30Gb). The program produces about 95Gb of recorrected.fa, then threw an error :

malloc(): invalid size (unsorted) /var/spool/slurmd/job239412/slurm_script: line 10: 475996 Aborted (core dumped) dechat -i allreads.fq -o corrected -t $CPU

I have attached the full log for your information. log.txt.gz Hi，

I recently tested a raw ONT dataset, and dechat reported the same error. This issue is caused by a third-party library that dechat is using. I am working diligently to resolve it. In the meantime, you can try filtering your dataset (in my testing, I filtered out sequences shorter than 1000 bases, which allowed it to run successfully). I hope this can help you.

melop commented 4 months ago

Thank you! I will try this.

LuoGroup2023 commented 4 months ago

Thank you! I will try this. Hello，

The latest version of dechat has been uploaded, fixing potential errors encountered during the generation of recorrected.fa. Updates for the conda environment submissions will follow. You can compile locally to run the latest version of dechat.

melop commented 4 months ago

Using the old version, it encountered a "malloc(): corrupted top size" error, which looks different. I will try the new version.