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Problem running Dockerized protect / where to find SSE-C key for downloading reference data? #294

@anttikos

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@anttikos

I'm having a trouble running protect, and figuring out what exactly is failing, as the output is 4655 lines long.. I'm most probably just missing some parameters, but I'm not sure which ones exactly.

Starting from line 1143 I start getting errors related to Amazon S3 authentication:
0091ac8c0f62 2021-06-16 13:00:23,448 MainThread WARNING toil.leader: H/2/jobmrdMHX RuntimeError: s3am failed with (boto.exception.NoAuthHandlerFound: No handler was ready to authenticate. 1 handlers were checked. ['HmacAuthV1Handler'] Check your credentials) while downloading (S3://protect-data/hg38_references/gencode.v25.pc_transcripts.fa.tar.gz) 0091ac8c0f62 2021-06-16 13:00:23,448 MainThread WARNING toil.leader: H/2/jobmrdMHX ERROR:toil.worker:Exiting the worker because of a failed job on host 0091ac8c0f62

I'm assuming I should use the --sse-key and --sse-key-is-master parameters to set up the SSE-C key in order to download the reference genome files, but I have trouble finding where could I find the actual key files. Also, I'm not sure if this is the main issue, or are the other issues as well.

Any help is highly appreciated!

Here is the command I'm using to run protect
docker run -v /var/run/docker.sock:/var/run/docker.sock -v /data:/data/ quay.io/ucsc_cgl/protect:2.5.6-1.13.0 --sample-name sample_name --tumor-dna /data/dna/tumor_dna_sample.merged_1.fq.gz --tumor-dna2 /data/dna/tumor_dna_sample.merged_2.fq.gz --normal-dna /data/dna/normal_dna_sample.merged_1.fq.gz --normal-dna2 /data/dna/normal_dna_sample.merged_2.fq.gz --tumor-rna /data/rna/tumor_rna_sample_1.fq.gz --tumor-rna2 /data/rna/tumor_rna_sample_2.fq.gz --reference-build hg38 --tumor-type PRAD --work-mount /data/protect 2> error_log_2021-06-16.txt

Attached is the full output log

error_log_2021-06-16.txt

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