Error using samtools for downloading bam files
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7.6 years ago
Maria333 ▴ 20

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 • 1.9k views
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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...

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

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

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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).

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

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Can you post your code?

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