similar to: error in rsync protocol on large file

I just ran this again and got this error: leelab/NCBI_Data_old/GenBank/htg write failed on leelab/NCBI_Data_old/GenBank/htg : Error 0 rsync error: error in file IO (code 11) at receiver.c(243) Received signal 16. (no core) rsync error: received SIGUSR1 or SIGINT (code 20) at rsync.c(229) The command I am running is: /usr/local/bin/rsync -auv --delete --rsh=/usr/bin/ssh lpgfs104:/share/group/*

So basically I have made a HTML file with a table in it. Column 3 contains a GenBank number and is always proceeded by "=GenBank">". I want to read the file and return the number which comes directly after this (the contents of column 3). Ideally I would like to save this number as a string for use later in the script, but any help is good help. Been at this for HOURS and

Hi all, I am learning R by "doing". And this is my first post. I want to use R: 1- to fetch a DNA sequence from a databank (see bellow) and 2- store it as FASTA file. The problem: neither an error is prompted nor the fasta file is created. Testing the code (see bellow), I notice that everything works until the *"write.dna" *command - which is not creating the fasta file.

Hi, I am trying to work with the ape package, and there is one thing I am struggling with. When calling the *read.GenBank()* function, I can get it to work with an object created like this: *>x <- c("AY395554","AY611035", ...)* *>read.GenBank(x)* However, I am trying to use the function to fetch several hundred sequences at once. So I have been testing with small

Hi I am trying to read genbank est flat files. Is there any function in R to do that. I was looking for something similar to SeqIO.parse(input_handle, "genbank") in bioPython that convert the genebank sequence into fasta sequence. (One option is to call biopython from R but I am not familiar with python functions so I want to avoid that and I am keeping it as last resort) Thanks and

I suspect you meant WD <- "~/Documents/Scripting/R_Studio/Sequences/" but I am entirely unfamiliar with the packages you are using, and know nothing about what is on your hard drive. For future reference: A) Read the Posting Guide. This is a plain text email list, and your html formatting gets removed leaving a mess that is not always readable. B) Most frequent users of R

Dear R-helpers: thank your for your attention. i am a newer to R and i am doing some protein category classification based on the amino acid sequence.while i have some questions urgently. 1. any packages for analysis amino acid sequence 2. given two sequences "AAA" and "BBB",how can i combine them into "AAABBB" 3. based on "AAABBB",how can i get some

Anyone have any experience with MpiBlast and Lustre. We have MpiBlast-1.4.0-pio and lustre-1.6.3 and we are seeing some pretty poor performance with most of the mpiblast threads spending 20% to 50% of their time in disk wait. We have the genbank nt database split into 24 fragments (one for each of our OSTs, 3 per OSS). The individual fragments are not striped due to the

I'd isolate all that RAID stuff from your OS, so the root, /boot, /usr, /etc /tmp, /bin swap are on "normal" partition(s). I know I'm missing some directories, but the point is you should be able to unmount that RAID stuff to adjust it without crippling your system. https://www.howtogeek.com/117435/htg-explains-the-linux-directory-structure-explained/ ?On 6/27/19, 9:37 AM,

On Thu, 27 Jun 2019, Peda, Allan (NYC-GIS) wrote: > I'd isolate all that RAID stuff from your OS, so the root, /boot, /usr, /etc /tmp, /bin swap are on "normal" partition(s). I know I'm missing some directories, but the point is you should be able to unmount that RAID stuff to adjust it without crippling your system. > >

Hello! I don't know if there is some R-package able to associate ontology to a long list of GeneBank Name (a txt-tab file or an XML file), i.e. I would as output a formatted file with 4 columns (1:GeneBank Name 2,3,4:ontology). I know that I have to perform a mapping of genes, I got a look on AnnBuilder pkg, but I 've not idea from where to start. Some suggestion? Thanks in advance!

CRAN (and crantastic) updates this week New packages ------------ * Bergm (1.0) Alberto Caimo http://crantastic.org/packages/Bergm Functions implementing Bayesian estimation for exponential random graph models via exchange algorithm Updated packages ---------------- lmtest (0.9-26), logcondens (1.3.5), MTSKNN (0.0-4), pmml (1.2.21), r2lUniv (0.9.4), rattle (2.5.11), rgdal (0.6-23),

Hello list. The next days we are going to install Centos 7 on a new server, with 4*3Tb sata hdd as raid-5. We will use the graphical interface to install and set up raid. Do I have to consider anything before installation, because the disks are very large? Does the graphical use the parted to set/format the raid? I hope the above make sense. Thank you in advance. Nikos

Hi, I am a Ph.D. student from Québec, Canada. I’m a beginner with R and Bioconductor. Until now the only experience I have is in analyzing microarray data using affy and limma packages. Now I am trying to analyze Rat Gene 10 st arrays and I would like to run RMA analysis and Smyth moderated t test on those arrays. Since no cdf official package is available for those arrays, after reading many

Ape is an R package for "analyses of phylogenetics and evolution". The first version (0.1) has been released on 27 August 2002 and is available on CRAN. >From the 'Description' file of version 0.1: Ape provides functions for reading, and plotting phylogenetic trees in parenthetic format (standard Newick format), analyses of comparative data in a

Dear all, I am happy to announce that {geneviewer*}* v0.1.10 is now on CRAN. *{geneviewer}* is an R package for plotting gene clusters and transcripts. It imports data from GenBank, FASTA, and GFF files, performs BlastP and MUMmer alignments, and displays results on gene arrow maps. The package offers extensive customization options, including legends, labels, annotations, scales, colors,

Dear all, I am happy to announce that {geneviewer*}* v0.1.10 is now on CRAN. *{geneviewer}* is an R package for plotting gene clusters and transcripts. It imports data from GenBank, FASTA, and GFF files, performs BlastP and MUMmer alignments, and displays results on gene arrow maps. The package offers extensive customization options, including legends, labels, annotations, scales, colors,

Dear useRs, The seqinR package is a library of utilities to retrieve and analyse biological sequences. A new version of seqinR, seqinR 1.0-7, has been released on CRAN. Here is a summary of changes: o A new *experimental* function extractseqs() to download sequences thru zlib compressed sockets from an ACNUC server is released. Preliminary tests suggest that working with about 100,000

Dear useRs, The seqinR package is a library of utilities to retrieve and analyse biological sequences. A new version of seqinR, seqinR 1.0-7, has been released on CRAN. Here is a summary of changes: o A new *experimental* function extractseqs() to download sequences thru zlib compressed sockets from an ACNUC server is released. Preliminary tests suggest that working with about 100,000

BioInformatics Scientist Job Code: 10-TR25 Location: Cambridge, MA Description We are seeking a highly motivated, independent bioinformatics scientist to join a group of scientists, analysts and programmers to develop tools and methodologies for large-scale gene expression data analysis. The group supports a variety of research projects in target and drug discovery as well as biomarker