Ankush Sharma
2017-Feb-03 11:19 UTC
[R] Error: long vectors (argument 1) are not supported in .Fortran
Hi all , I'm working on WGCNA on R-3.3.1 version to reconstruct gene -gene coexpression networks of 54000 probes in 230 samples on Load Sharing facility (Remote computing cluster). Despite memory at dispose, I'm encountering a error of allocation of memory at soft thresholding step or at TOM Similarity step. The problem of memory allocation at soft thresholding step was corrected by allocating the required memory using [bsub -R "rusage[mem=40000]". Error Message > # Turn adjacency into topological overlap> TOM = TOMsimilarity(adjacency);Error in TOMsimilarity(adjacency) : long vectors (argument 1) are not supported in .Fortran Calls: TOMsimilarity -> .C Execution halted Warning message: system call failed: Cannot allocate memory ?Is there a way to run build this TOMsimilarity matrix. ?Thanks ? Best Regards, ?Ankush Sharma,PhD Visiting CASyM Postdoctoral Research fellow (CASyM Consortium, EU-FP7) LISM, Institute of Clinical Physiology, Siena (Italy) ?Experimental Oncology Unit (UOS), ?I? ?nstitute of Clinical Physiology ?- National Research Council, ? Siena (IT) [[alternative HTML version deleted]]
Bert Gunter
2017-Feb-03 15:31 UTC
[R] Error: long vectors (argument 1) are not supported in .Fortran
Probably wrong list. Try the Bioconductor list instead. Cheers, Bert Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) On Fri, Feb 3, 2017 at 3:19 AM, Ankush Sharma <ankush.sak at gmail.com> wrote:> Hi all , > > I'm working on WGCNA on R-3.3.1 version to reconstruct gene -gene > coexpression networks of 54000 probes in 230 samples on Load Sharing > facility (Remote computing cluster). Despite memory at dispose, I'm > encountering a error of allocation of memory at soft thresholding step or > at TOM Similarity step. The problem of memory allocation at soft > thresholding step was corrected by allocating the required memory using [bsub > -R "rusage[mem=40000]". > > Error Message > > # Turn adjacency into topological overlap > >> TOM = TOMsimilarity(adjacency); > > Error in TOMsimilarity(adjacency) : > > long vectors (argument 1) are not supported in .Fortran > > Calls: TOMsimilarity -> .C > > Execution halted > > Warning message: > > system call failed: Cannot allocate memory > > > Is there a way to run build this TOMsimilarity matrix. > > > Thanks > > > > > > > Best Regards, > Ankush Sharma,PhD > Visiting CASyM Postdoctoral Research fellow (CASyM Consortium, EU-FP7) > LISM, Institute of Clinical Physiology, Siena (Italy) > Experimental Oncology Unit (UOS), > I > nstitute of Clinical Physiology > - National Research Council, > Siena (IT) > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.
Peter Langfelder
2017-Feb-03 17:32 UTC
[R] Error: long vectors (argument 1) are not supported in .Fortran
Just to set the record straight, WGCNA is a CRAN package. As to Ankush's question - the current WGCNA version does not support analysis of more than about 46300 nodes (probes) in one block. You have two options: 1. filter out some of the least-informative probes (e.g., probes with lowest mean expression or lowest variance); 2. use the "blockwise" approach as implemented in blockwiseModules. Set the maxBlockSize argument to say 40000, and the function will automatically split your data into 2 blocks and run the analysis in each block separately. The third option is to wait a few weeks (possibly months), I do have a WGCNA update in the works that __should__ work on blocks larger than 46300. Best, Peter On Fri, Feb 3, 2017 at 7:31 AM, Bert Gunter <bgunter.4567 at gmail.com> wrote:> Probably wrong list. Try the Bioconductor list instead. > > Cheers, > Bert > > > Bert Gunter > > "The trouble with having an open mind is that people keep coming along > and sticking things into it." > -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) > > > On Fri, Feb 3, 2017 at 3:19 AM, Ankush Sharma <ankush.sak at gmail.com> wrote: >> Hi all , >> >> I'm working on WGCNA on R-3.3.1 version to reconstruct gene -gene >> coexpression networks of 54000 probes in 230 samples on Load Sharing >> facility (Remote computing cluster). Despite memory at dispose, I'm >> encountering a error of allocation of memory at soft thresholding step or >> at TOM Similarity step. The problem of memory allocation at soft >> thresholding step was corrected by allocating the required memory using [bsub >> -R "rusage[mem=40000]". >> >> Error Message >> > # Turn adjacency into topological overlap >> >>> TOM = TOMsimilarity(adjacency); >> >> Error in TOMsimilarity(adjacency) : >> >> long vectors (argument 1) are not supported in .Fortran >> >> Calls: TOMsimilarity -> .C >> >> Execution halted >> >> Warning message: >> >> system call failed: Cannot allocate memory >> >> >> Is there a way to run build this TOMsimilarity matrix. >> >> >> Thanks >> >> >> >> >> >> >> Best Regards, >> Ankush Sharma,PhD >> Visiting CASyM Postdoctoral Research fellow (CASyM Consortium, EU-FP7) >> LISM, Institute of Clinical Physiology, Siena (Italy) >> Experimental Oncology Unit (UOS), >> I >> nstitute of Clinical Physiology >> - National Research Council, >> Siena (IT) >> >> [[alternative HTML version deleted]] >> >> ______________________________________________ >> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.