COSMIC download system failed #71
Description
Hey there!
I am trying to use this pipeline 3 years before the last update, so my expectations about getting an answer here are not very high. This is my last try.
The pipeline is not working because of a problem with the COSMIC download system, something must have changed and it is impossible to download any files from this database. It is not a problem with the credentials. The debug file for the COSMIC database download gave me these messages:
2024-11-12 11:17:02,001 [ DEBUG][ pypgatk.toolbox.general][ general, 83] Logging system initialized
2024-11-12 11:17:02,001 [ DEBUG][ pypgatk.toolbox.general][ cosmic_downloader, 47] Preparing local cbioportal repository, root folder - './database_cosmic/'
2024-11-12 11:17:02,002 [ DEBUG][ pypgatk.toolbox.general][ cosmic_downloader, 50] Local path for cbioportal Release - './database_cosmic/'
2024-11-12 11:17:03,779 [ DEBUG][ pypgatk.toolbox.general][ cosmic_downloader, 122] Downloading file from url 'https://cog.sanger.ac.uk/cosmic/GRCh38/cosmic/v88/CosmicMutantExport.tsv.gz?AWSAccessKeyId=KRV7P7QR9DL41J9EWGA2&Expires=1731407223&Signature=%2BpzBRgqFZOLYpaewtVwegSVWXvI%3D'
2024-11-12 11:17:05,284 [ DEBUG][ pypgatk.toolbox.general][ cosmic_downloader, 122] Downloading file from url 'https://cog.sanger.ac.uk/cosmic/GRCh38/cosmic/v88/All_COSMIC_Genes.fasta.gz?AWSAccessKeyId=KRV7P7QR9DL41J9EWGA2&Expires=1731407225&Signature=iH57uXUfc07Sf3jUhxO7p4XRijs%3D'
2024-11-12 11:17:06,843 [ DEBUG][ pypgatk.toolbox.general][ cosmic_downloader, 122] Downloading file from url 'https://cog.sanger.ac.uk/cosmic/GRCh38/cell_lines/v92/All_CellLines_Genes.fasta.gz?AWSAccessKeyId=KRV7P7QR9DL41J9EWGA2&Expires=1731407226&Signature=cySuBiaV3mds%2Fst1L%2F5Q0Z1et2Q%3D'
2024-11-12 11:17:08,254 [ DEBUG][ pypgatk.toolbox.general][ cosmic_downloader, 122] Downloading file from url 'https://cog.sanger.ac.uk/cosmic/GRCh38/cell_lines/v92/CosmicCLP_MutantExport.tsv.gz?AWSAccessKeyId=KRV7P7QR9DL41J9EWGA2&Expires=1731407228&Signature=HDrIv8K203Eeg%2BPma6WcHgskghY%3D'
And if I tried to do it by myself, as it is explained in this webpage, I also got the following error message:
<?xml version="1.0" encoding="UTF-8"?><Error><Code>NoSuchKey</Code><Message></Message><BucketName>cosmic</BucketName><RequestId>tx00000b6e702fe1551a038-0067349d79-3ba5c45f-default</RequestId><HostId>3ba5c45f-default-default</HostId></Error>
Even though you, reader, do not know how to fix the error, could anybody tell me other ways of bulding a proteogenomic database with variant information from public databases??? As far as I am concern, there are other proteogenomic tools, but these usually require a bam file from the alignment of transcriptomic data, and this is not my goal.
Thank you in advanced for any kind of help!!
Julia