Search
Question: ShortRead internal: too many 'snap' entries
0
gravatar for Ramzi TEMANNI
7.9 years ago by
Ramzi TEMANNI150
Ramzi TEMANNI150 wrote:
Hi, I'm using the following function to extract a subselection of reads based on their ID from a FastQ file: extract.reads.fq<-function(dir,fq.file,id.list) { rfq <- readFastq(dir, pattern=fq.file) tmp=extract.id(rfq) sv.reads=rfq[which(id.list%in%tmp)] writeFastq(sv.reads, paste("sv_",fq.file,sep="")) } The function works well but for one file i got the following error : Error in .local(dirPath, pattern, ...) : ShortRead internal: too many 'snap' entries Tried to google it but nothing is coming out, anyone encoutred this error ? Thanks in advance for your help. ---------------------------------------------------------------- Kind regards / Met vriendelijke groet, Mohamed-Ramzi Temanni, ---------------------------------------------------------------- [[alternative HTML version deleted]]
ADD COMMENTlink modified 7.9 years ago by Martin Morgan ♦♦ 21k • written 7.9 years ago by Ramzi TEMANNI150
0
gravatar for Martin Morgan
7.9 years ago by
Martin Morgan ♦♦ 21k
United States
Martin Morgan ♦♦ 21k wrote:
Hi -- Ramzi TEMANNI wrote: > Hi, > I'm using the following function to extract a subselection of reads based on > their ID from a FastQ file: > extract.reads.fq<-function(dir,fq.file,id.list) > { > rfq <- readFastq(dir, pattern=fq.file) > tmp=extract.id(rfq) > sv.reads=rfq[which(id.list%in%tmp)] > writeFastq(sv.reads, paste("sv_",fq.file,sep="")) > } > > The function works well but for one file i got the following error : > Error in .local(dirPath, pattern, ...) : > ShortRead internal: too many 'snap' entries Probably the format of the one file is causing problems -- maybe a missing new line after the last file record? Can you post the result of sessionInfo(), and if the format of the file is not obviously wrong can you make it available to me? Martin > Tried to google it but nothing is coming out, anyone encoutred this error ? > > Thanks in advance for your help. > > > > > ---------------------------------------------------------------- > Kind regards / Met vriendelijke groet, > Mohamed-Ramzi Temanni, > ---------------------------------------------------------------- > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-sig-sequencing mailing list > Bioc-sig-sequencing at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
ADD COMMENTlink written 7.9 years ago by Martin Morgan ♦♦ 21k
Hi Martin, Thanks for your reply. I've take a look at the file and you are right the problem arise of an abnormal termination of the conversion from scarf to fastq on that file. problem corrected and things are running smooth now. Have a nice day. Regards, Ramzi ---------------------------------------------------------------- On Wed, Jan 6, 2010 at 9:30 AM, Martin Morgan <mtmorgan@fhcrc.org> wrote: > Hi -- > > Ramzi TEMANNI wrote: > > Hi, > > I'm using the following function to extract a subselection of reads based > on > > their ID from a FastQ file: > > extract.reads.fq<-function(dir,fq.file,id.list) > > { > > rfq <- readFastq(dir, pattern=fq.file) > > tmp=extract.id(rfq) > > sv.reads=rfq[which(id.list%in%tmp)] > > writeFastq(sv.reads, paste("sv_",fq.file,sep="")) > > } > > > > The function works well but for one file i got the following error : > > Error in .local(dirPath, pattern, ...) : > > ShortRead internal: too many 'snap' entries > > Probably the format of the one file is causing problems -- maybe a > missing new line after the last file record? > > Can you post the result of sessionInfo(), and if the format of the file > is not obviously wrong can you make it available to me? > > Martin > > > > Tried to google it but nothing is coming out, anyone encoutred this error > ? > > > > Thanks in advance for your help. > > > > > > > > > > ---------------------------------------------------------------- > > Kind regards / Met vriendelijke groet, > > Mohamed-Ramzi Temanni, > > ---------------------------------------------------------------- > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioc-sig-sequencing mailing list > > Bioc-sig-sequencing@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > > > -- > Martin Morgan > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > [[alternative HTML version deleted]]
ADD REPLYlink written 7.9 years ago by Ramzi TEMANNI150
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 326 users visited in the last hour