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Przemol / seqplots

:chart_with_upwards_trend:SeqPlots - An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps.
http://przemol.github.io/seqplots
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cannot load vector #36

Closed YannisKokkito closed 6 years ago

YannisKokkito commented 6 years ago

Dear Sir/Madam,

I am trying to use Seqplots for creating a heatmap from BAM files (12) made with HISAT2 and a homo sapiens hg38.91 gtf file. From the first readout it gives me a cannot load vector 3.9 GB and the connection to the server is lost. Can you please advice?

All the best,

Yannis

Przemol commented 6 years ago

It seems that the size of your data exceeds the specs of your computer.

You need to run SeqPlots on 64bit OS with more than 4GB of operating memory.

YannisKokkito commented 6 years ago

It seems that you need to reply a bit faster. Also, I have been using 64bit OS with 8gb of RAM

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-------- Original message -------- From: Przemyslaw Stempor notifications@github.com Date: 13/09/2018 23:06 (GMT+02:00) To: Przemol/seqplots seqplots@noreply.github.com Cc: Ioannis Kokkinopoulos i.kokkinopoulos@qmul.ac.uk, Author author@noreply.github.com Subject: Re: [Przemol/seqplots] cannot load vector (#36)

It seems that the size of your data exceeds the specs of your computer.

You need to run SeqPlots on 64bit OS with more than 4GB of operating memory.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Przemol/seqplots/issues/36#issuecomment-421135730, or mute the threadhttps://github.com/notifications/unsubscribe-auth/Ai2obCdudOnHWk1Ly5K2Bd2C0tqgoh_sks5uarrUgaJpZM4SItwe.

Przemol commented 6 years ago

You need ~4GB of free operating memory, not total.

It's a general issue with your R/hardware setup. You can read more here: https://stat.ethz.ch/R-manual/R-devel/library/base/html/Memory-limits.html

If you still have problems read relevant topics/ask for help here: http://r.789695.n4.nabble.com/R-help-f789696.html