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comprna / RATTLE

Reference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing
GNU General Public License v3.0
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How can I cluster multiple Nanopore sequencing data together? #51

Open sheevivian opened 8 months ago

sheevivian commented 8 months ago

Dear developers, Many thanks for such a great tool! I have 32 fastq files sequenced from direct cDNA sequencing by nanopore, and compressed them into a fastq.gz file. When running the rattle cluster, it return Segmentation fault (core dumped). The commands are as shown below 1703841453272

But when I only use one of the 32 fastq files, it works normally. I use 392GB RAM with 56 cores, but I still can not run a command.

Or is there any other way to cluster all files together?

I hope you can help me understand how to proceed. Thanks in advance Vivian

eileen-xue commented 8 months ago

Hi Vivian,

The way you did for clustering is correct. And the problem is probably because RATTLE is running out of memory. Trying to increase the allocated RAM size or decrease the reads number should solve the problem.

Hope this helps. Eileen