Is there any way to pass this Samtools error

Question

when I was trying to get the part of remote BAM file. The expected BAM file is not downloaded and the following error is encountered.

connect: Connection timed out  
[kftp_connect_file] 350 Restart position accepted (0).  
[main_samview] fail to open file for reading.

I command I used:

samtools view -b -o NA20542.chrom21.ILLUMINA.bwa.TSI.low_coverage.bam ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/NA20542/alignment/NA20542.chrom21.ILLUMINA.bwa.TSI.low_coverage.20100311.bam 21:20454259-20654259

what might be the problem? (I am not fully comfortable in reading/analyzing C code. ...samtools 0.1.7a) Is there any way that I could avoid this error?

Accepted Answer

The "Restart position" line means that you successfully connected to the FTP server for communication, but for some reason the connection timed out. This may be due to high traffic on the 1000genome server, and it not being able to handle as many request as it's getting at the time. You could try again later.

Additionally, there may be some sort of traffic restriction from your Internet service provider/IT department. If you talk to them, mention that your FTP connection is timing out on file transfer, but you are able to send FTP commands that don't involve file transfer (that's what the Restart position line means).

Is there any way to pass this Samtools error

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