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alekseyzimin / masurca

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Masurca issue mega-reads pass 1 failed #200

Open marco91sol opened 3 years ago

marco91sol commented 3 years ago

Dear all,

I am using Masurca for hybrid genome assembly through its conda version.

I ran masurca config.txt and I received the following error (image attached) image

How I could solve this issue?

Thanks for your support!

alekseyzimin commented 3 years ago

Hello, please check your Illumina data, there is an error in the fastq header. The mega-reads failed most likely because of not enough free memory, how much free RAM do you have?

marco91sol commented 3 years ago

These are the values at the moment:

MiB Mem : 515615.4 total, 239152.4 free, 109026.5 used, 167436.5 buff/cache MiB Swap: 0.0 total, 0.0 free, 0.0 used. 403300.1 avail Mem

alekseyzimin commented 3 years ago

Should be enough fo 1.8gbp genome. You can re-generate assemble.sh and re-run. Make sure you have disk space available as well. The code that failed is solid, there have been no reports of failures.

On Fri, Dec 18, 2020 at 9:30 AM marco91sol notifications@github.com wrote:

These are the values at the moment:

MiB Mem : 515615.4 total, 239152.4 free, 109026.5 used, 167436.5 buff/cache MiB Swap: 0.0 total, 0.0 free, 0.0 used. 403300.1 avail Mem

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-- Dr. Alexey V. Zimin Associate Research Scientist Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA (301)-437-6260 website http://ccb.jhu.edu/people/alekseyz/ blog http://masurca.blogspot.com