COSMIC download system failed

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

Start at the cosmic_downloader entry point shown in the debug log and inspect how it handles the COSMIC download URLs; compare the behavior with the linked COSMIC download-service guidance. Done means the pipeline can retrieve the required COSMIC files again, but the issue names no repository test or precise replacement endpoint.