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langmead-lab / monorail-external

examples to run monorail externally
MIT License
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"404: Not Found" error on `get_human_ref_indexes.sh` #24

Closed lthiberiol closed 1 year ago

lthiberiol commented 1 year ago

The 404: Not Found error is repeated for all files get_human_ref_indexes.sh try to download ( salmon_index.tar.gz, unmapped_hisat2_idx.tar.gz, gtf.tar.gz, and fasta.tar.gz). This also occurs when trying the get_mouse_ref_indexes.sh and get_ce_ref_indexes.sh.

--2023-05-23 11:57:29--  https://recount-ref.s3.amazonaws.com/hg38/star_idx.tar.gz
Resolving recount-ref.s3.amazonaws.com (recount-ref.s3.amazonaws.com)... 52.217.110.156, 52.217.236.201, 54.231.134.225, ...
Connecting to recount-ref.s3.amazonaws.com (recount-ref.s3.amazonaws.com)|52.217.110.156|:443... connected.
HTTP request sent, awaiting response... 404 Not Found
2023-05-23 11:57:29 ERROR 404: Not Found.

tar (child): star_idx.tar.gz: Cannot open: No such file or directory
tar (child): Error is not recoverable: exiting now
tar: Child returned status 2
tar: Error is not recoverable: exiting now
BenLangmead commented 1 year ago

Aha, yes, this is due to a recent move of those files into a public AWS bucket. I will submit a fix for this in a moment and reply here when it's ready...

But I can tell you that the fix is to replace the prefix https://recount-ref.s3.amazonaws.com/... with the prefix https://genome-idx.s3.amazonaws.com/recount/recount-ref/....

BenLangmead commented 1 year ago

I believe I have now fixed this with my latest commit: https://github.com/langmead-lab/monorail-external/commit/72c3b878e63772bc202096ce8837292a64ff1215

rahulsimham commented 1 year ago

Your new commit fixed the problem. Thanks!

ChristopherWilks commented 1 year ago

thanks Ben!