Rsamtools scanBam error

[yuchioj]

Dear all,

I got this problem when using Rsamtools to get data from 1000 Genome Project.

na19240url="ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/pilot_data/data/NA19240/alignment/NA19240.chrom6.SLX.maq.SRP000032.2009_07.bam"
which <- GRanges(seqnames ="6", ranges = IRanges(1e+05, 110000))
p <- ScanBamParam(which = which)
na19240bam <- scanBam(na19240url, param = p)

This is exactly the same as is in the manual however it led to errror:

Error in open.BamFile(BamFile(file, index), "rb") : 
  failed to open SAM/BAM file
  file: 'ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/pilot_data/data/NA19240/alignment/NA19240.chrom6.SLX.maq.SRP000032.2009_07.bam'
In addition: Warning messages:
1: In open.BamFile(BamFile(file, index), "rb") : gethost: 11004
2: In open.BamFile(BamFile(file, index), "rb") : select time-out
3: In open.BamFile(BamFile(file, index), "rb") :
  [kftp_connect_file] 350 Restarting at 0. Send STORE or RETRIEVE to initiate transfer

I thought it was because I didn't index it. Hence I downloaded the .bai file and retried:

download.file("ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/pilot_data/data/NA19240/alignment/NA19240.chrom6.SLX.maq.SRP000032.2009_07.bam.bai","NA19240.chrom6.SLX.maq.SRP000032.2009_07.bam.bai")
na19240bam <- scanBam(na19240url, index="NA19240.chrom6.SLX.maq.SRP000032.2009_07.bam", param = p)

Still the same error. Anyone knows why? Thanks!

Yuchioj

[yuchioj]

update:

ran the first code on server and it went through... really not sure why...