HG00096.xxx.bam is no more

[darked89]

Hello,

seems that ppl @ftp.1000genomes.ebi.ac.uk moved from bam format and left only cram files in this directory:
/vol1/ftp/data/HG00096/alignment/

Also downloading > 15Gb file (CRAM is +14Gb) using ftp can take long time. The 100genomes project provides an access with Aspera client: http://www.1000genomes.org/faq/how-download-files-using-aspera

Hope it helps,

Darek Kedra

[davidonlaptop]

I am not sure to understand what you're trying to express. Do you have a specific problem with ADAM or our docker image for ADAM ?

[darked89]

Sorry, I should have been more precise. I have attempted to run Docker image for ADAM. One of the examples (Download a larger BAM) relies on downloading file mentioned above. File do not exist. Obviously one can get another BAM from another location, but then we add an extra variable.

Best,

DK

[davidonlaptop]

Hum you're right, it seems the BAM file is gone. I'm pretty sure there was a file at that URL before though. I've randomly checked at random folders, but I only found CRAM files.

I am not sure if ADAM supports CRAM files.

[darked89]

Fixed: the 1000genomes ppl changed the location. Now it is:
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00096/alignment/
And the selected file (HG00096.chrom20.ILLUMINA.bwa.GBR.low_coverage.20120522.bam) is just 300Mb, so no need to mess around with Aspera.

[davidonlaptop]

Thanks Darek! I'll have a look
On Jul 9, 2015 4:28 PM, "Darek K." [email protected] wrote:

Fixed: the 1000genomes ppl changed the location. Now it is:
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00096/alignment/
And the selected file
(HG00096.chrom20.ILLUMINA.bwa.GBR.low_coverage.20120522.bam) is just 300Mb,
so no need to mess around with Aspera.

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[davidonlaptop]

I am moving the instructions with your corrected path to a new issue (see #4), and I'll delete it from the main README.