Question: Error using samtools for downloading bam files
0
gravatar for Maria333
4.4 years ago by
Maria33310
European Union
Maria33310 wrote:

Hi,

I was just trying to run my typical script which downloaded a lot of regions I wanted before, but it stopped all of a sudden presenting the following errors at two different times:

1)

227 Entering Passive Mode (193,62,192,8,185,217).
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[main_samview] fail to read the header from "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00119/alignment/HG00119.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam".

2)  EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[main_samview] fail to read the header from "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00123/alignment/HG00123.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam"

Does anyone have any idea? The strange thing is that each of the times I ran the code, it presented as errors different bam files which were downloaded before.  I looked online but everyone says I should ignore these kind of errors.. 

Any help would be really appreciated.

Thank you 

 

 

 

samtools bams • 1.3k views
ADD COMMENTlink written 4.4 years ago by Maria33310
1

You'll always get the EOF message with FTP, it's hard-coded. I've been meaning to make a pull request to prevent that in fact...

ADD REPLYlink written 4.4 years ago by Devon Ryan91k

Thank you..So do you suggest that I should continue running the code until it's fixed?

ADD REPLYlink written 4.4 years ago by Maria33310

At least for (2) yes. I don't remember (1) also occurring, though I'll check real quick.

ADD REPLYlink written 4.4 years ago by Devon Ryan91k

I don't get (1). So perhaps you have a networking issue or are using a different version. Make sure you're using the most recent version (1.2 or 1.2.1 I think).

ADD REPLYlink written 4.4 years ago by Devon Ryan91k

Thank you for that. It seems everything's fine with the code.. Don't know what's happening.. 

ADD REPLYlink written 4.3 years ago by Maria33310

Can you post your code?

ADD REPLYlink modified 4.4 years ago • written 4.4 years ago by PoGibas4.8k
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