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How much memory should Pindel be using on a 30x whole genome? With the smallest window size it is using a large amount of memory even when the log says it is processing a window with only 1000 reads.
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can you tell me your Pindel version? You could split calculation by 5MB per job. Sometimes there is extreme high coverage at a few small regions. This causes maximum memory usage going high.
Kai -
The version was 0.2.5a4, May 2 2014. We tried using the smallest window (.01) but still maxed out 30Gb of memory.Comment
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Is it possible to send me the log file or console output to my email [email protected]?Originally posted by Nick View PostComment
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The COVID-19 pandemic highlighted the need for proactive pathogen surveillance systems. As ongoing threats like avian influenza and newly emerging infections continue to pose risks, researchers are working to improve how quickly and accurately pathogens can be identified and tracked. In a recent SEQanswers webinar, two experts discussed how next-generation sequencing (NGS) and machine learning are shaping efforts to monitor viral variation and trace the origins of infectious...Yesterday, 11:48 AM -
This year’s Advances in Genome Biology and Technology (AGBT) General Meeting commemorated the 25th anniversary of the event at its original venue on Marco Island, Florida. While this year’s event didn’t include high-profile musical performances, the industry announcements and cutting-edge research still drew the attention of leading scientists.
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The biggest announcement was Roche stepping back into the sequencing platform market. In the years since...03-03-2025, 01:39 PM -
The human gut contains trillions of microorganisms that impact digestion, immune functions, and overall health1. Despite major breakthroughs, we’re only beginning to understand the full extent of the microbiome’s influence on health and disease. Advances in next-generation sequencing and spatial biology have opened new windows into this complex environment, yet many questions remain. This article highlights two recent studies exploring how diet influences microbial...02-24-2025, 06:31 AM
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