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IGS / portal_client

Python-based client for downloading data made available through portals powered by the GDC-based portal system..
MIT License
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Not all biological observation matrix are downloaded #19

Open ManarRashad opened 4 years ago

ManarRashad commented 4 years ago

Hi all, First, I tried alot to download the biological observation matrix and this error always appear: Not all files (total of 2308) were downloaded successfully. Number of failures: 0 -- no valid URL in the manifest file 5 -- URL is present in manifest, but not accessible at the location specified 10 -- MD5 checksum failed for file (file is corrupted or the wrong MD5 is associated)

I tried alot and each time not all files are downloaded just 2209 out of 2308 are downloaded and others not. By the way, my manifest file like this form: 9dc112963819ad139611820d22966777 2821344a48240f0fb288e6f0f016d7c5 86000 fasp://aspera.ihmpdcc.org/t2d/genome/microbiome/16s/analysis/hmqcp/HMP2_J79630_1_NS_T0_B0_0120_ZRLZ98T-6031_B9GWL.biom 5a950f27980b5d93e4c16da124908ee3

Second, I found that the URLs that are unique in manifest is 2209, this indicates what was happened and why this error appear or not? Beside the unique sample ids in manifest is nearly 1900, so 1 sample may have more than 1 URL or not ? Anyone can help???

ManarRashad commented 4 years ago

@victor73 could you help, please?

AhmedElsherbini commented 2 years ago

Hi Manar, Long time I know , if you are still interested in this topic. I made a simple script to overcome it. https://github.com/AhmedElsherbini/download_hmp_data try it if you still has the problem