[Samtools-help] samtools view through ftp sometimes fails

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

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.