Unable to download reference data

melnel000 commented 2 years ago

Hi

I am having an issue when trying to download the reference data. This is the error message I am receiving:

wget https://nci.space/_projects/clinsv_b38/refdata-b38_v1.0.tar --2022-06-09 20:30:01-- https://nci.space/_projects/clinsv_b38/refdata-b38_v1.0.tar Resolving nci.space (nci.space)... 130.56.242.205 Connecting to nci.space (nci.space)|130.56.242.205|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 38952581120 (36G) [application/x-tar] Saving to: ‘refdata-b38_v1.0.tar’

refdata-b38_v1.0.tar 74%[==================================================================================> ] 26.95G 5.50MB/s in 80m 19s

Cannot write to ‘refdata-b38_v1.0.tar’ (Success).

I tried a second time and the same thing happened, the download stopped at 64%.

Please can you let me know what might be causing this problem.

Thanks, Melissa

J-Bradlee commented 2 years ago

Hi Melissa,

Just confirming you have at least 37gb worth of space on your machine? The tar file is 37gb.

melnel000 commented 2 years ago

Yes, I have just checked and I still have 178GB available.

J-Bradlee commented 2 years ago

Strange, it should work. I will upload that file to a public bucket and share with you the link when its ready. Is there any other files you are having issues getting?

melnel000 commented 2 years ago

No, it's just this file that is a problem. Thanks for trying the public bucket option.

J-Bradlee commented 2 years ago

@melnel000 try downloading it now from https://storage.googleapis.com/refb38/refdata-b38_v1.0.tar

melnel000 commented 2 years ago

Thanks, I was able to download the reference data. How long does it take to run the pipeline on a single sample?

J-Bradlee commented 2 years ago

depends on the size of the bam/bai files. A 60gb bam file takes around 24 hours, a 5-6gb bam file takes roughly 6 hours.

KCCG / ClinSV

Unable to download reference data #29