Re: [Samtools-help] samtools view through ftp sometimes fails

[Josep I. L. L. <jos...@in...>]

In case anybody is interested, I finally realized that the error is in
the 1000genomes servers, which have a hard time to attend too many
requests of sliced data from a bam file. So, I followed the
recommendation in the following link:

http://seqanswers.com/forums/showthread.php?t=13866

Basically, I did not request to download more than one region at a time,
and I introduced a delay of 2 seconds before requesting the following
region. And it worked.


El dv 29 de 06 de 2012 a les 08:34 +0200, en/na Josep Ignasi Lucas Lledo
va escriure:
> Hello,
> 
> I was very happy to realize that samtools view can read remote files
> through ftp. I am downloading some reads from aligned bam files from the
> 1000 genomes project, and I realized that every once in a while samtools
> view fails to open a bam file.
> 
> The commands that I am using are the following:
> 
>    samtools view ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/$j $REGIONS
> 
>    samtools view -f 4 ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/$j
> 
>    samtools view -H ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/$j
> 
> 
> The errors or warnings that I am getting are:
> 
>    [main_samview] truncated file.
> 
>    [kftp_connect_file] 200 Switching to Binary mode.
> 
>    [main_samview] fail to open
> "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/pilot2_high_cov_GRCh37_bams/data/NA12878/alignment/NA12878.chrom1.ILLUMINA.bwa.CEU.high_coverage.20100311.bam" for reading.
> 
>    [kftp_connect_file] 227 Entering Passive Mode (193,62,193,8,42,120).
> 
>    [kftp_connect_file] 350 Restart position accepted (0).
> 
>    [bam_index_load] fail to load BAM index.
> 
> If I try to read the remote files that gave the error again, eventually,
> they work. Is it normal for this to happen? Is there a way to prevent
> the failure?
> 
> Thank you.
> 
> Ignasi.
> 
> 
> 
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