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mourisl / Rcorrector

Error correction for Illumina RNA-seq reads
GNU General Public License v3.0
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Encountering Failed at Stage 1 error #39

Closed ablanchette23 closed 9 months ago

ablanchette23 commented 9 months ago

Hello! I am trying to run rcorrector on my 150-base pair paired-end reads and it was successful for all but one individual. For that individual I am getting the following error:

Screenshot 2023-11-28 111650

I tried redownloading these specific reads in case something had happened originally, but the files themselves are on par quality-wise as the other reads I have and they weren't truncated when I originally downloaded them. The FastQC for them doesn't show any glaring issues with the reads.

I don't know why this might be happening - especially with only one pair of reads. I don't think it's a memory issue since these aren't the largest file sizes I ran with rcorrector. Do you have any ideas? Thank you!

mourisl commented 9 months ago

I think this is a bug in jellyfish. If you have enough memory on your machine, you may consider changing the jellyfish's command in the wrapper "run-rcorrector" to directly count the k-mers without bloom filter.

ablanchette23 commented 9 months ago

I think this is a bug in jellyfish. If you have enough memory on your machine, you may consider changing the jellyfish's command in the wrapper "run-rcorrector" to directly count the k-mers without bloom filter.

Thank you! I tried again after increasing the amount of memory and that worked, so I didn't try disabling the bloom filter, but I appreciate the response!