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AWS Service is down, what's an alternative to run GATk VariantsToTable?

nroaknroak HoustonMember

Hi I'm running the following command:
java -Xmx56g -Djava.io.tmpdir=$workDir/tmp -jar /share/apps/gatk/3.4-46/GenomeAnalysisTK.jar -T VariantsToTable -R $refGenome --allowMissingData --splitMultiAllelic \
-F CHROM -F POS -F ID -F REF -F ALT -F QUAL -F FILTER \
-V $workDir/VCF/gnomad.genomes.r2.0.1.sites.$sample.vcf.gz -o $workDir/tsv/gnomad.genomes.sites.$sample.annotated.table

And getting an error:
INFO 14:42:17,718 HttpMethodBase - 100 (continue) read timeout. Resume sending the request
WARN 14:42:20,010 StorageService - Encountered 1 Internal Server error(s), will retry in 50ms
WARN 14:42:20,061 RestStorageService - Error Response: PUT '/RLQcYZ6ZyTxwOErFCE4NmfppmMi0nsxP.report.xml.gz' -- ResponseCode: 500, ResponseStatus: Internal Server Error, Request Headers: [Content-Length: 403, Content-MD5: 7SwaVCjuUn/N4G+dqRR51Q==, Content-Type: application/octet-stream, x-amz-meta-md5-hash: ed2c1a5428ee527fcde06f9da91479d5, Date: Tue, 28 Feb 2017 20:42:14 GMT, Authorization: AWS AKIAI22FBBJ37D5X62OQ:UtX3g5HrpEMkfskaKD00nIyIq54=, User-Agent: JetS3t/0.8.1 (Linux/2.6.32-358.el6.x86_64; amd64; en; JVM 1.7.0_13), Host: broad.gsa.gatk.run.reports.s3.amazonaws.com], Response Headers: [x-amz-request-id: 32CB3F8373E21855, x-amz-id-2: wwPr+j244QRqhdKZUpkCwBABhBEVX9YaS8aNXrc/rAuK1yniGZbh4Tg+7urXw28gk5aJZDIvXtM=, Content-Type: application/xml, Transfer-Encoding: chunked, Date: Tue, 28 Feb 2017 20:42:19 GMT, Connection: close, Server: AmazonS3]
..
..
..
WARN 14:42:41,974 StorageService - Encountered 5 Internal Server error(s), will retry in 1250ms
WARN 14:42:43,225 RestStorageService - Error Response: PUT '/RLQcYZ6ZyTxwOErFCE4NmfppmMi0nsxP.report.xml.gz' -- ResponseCode: 500, ResponseStatus: Internal Server Error, Request Headers: [Content-Length: 403, Content-MD5: 7SwaVCjuUn/N4G+dqRR51Q==, Content-Type: application/octet-stream, x-amz-meta-md5-hash: ed2c1a5428ee527fcde06f9da91479d5, User-Agent: JetS3t/0.8.1 (Linux/2.6.32-358.el6.x86_64; amd64; en; JVM 1.7.0_13), Date: Tue, 28 Feb 2017 20:42:37 GMT, Authorization: AWS AKIAI22FBBJ37D5X62OQ:9c843/9MTcnsERL0Iak/Tq2JPAs=, Host: broad.gsa.gatk.run.reports.s3.amazonaws.com], Response Headers: [x-amz-request-id: C66FAF50C96C05FA, x-amz-id-2: FGPYZnPnJSY07EiaH7uf3bi9G4Sw7trw3X+846c2iTNgKB+jFC51ncENKKPloUeIhNNJM3k/MUY=, Content-Type: application/xml, Transfer-Encoding: chunked, Date: Tue, 28 Feb 2017 20:42:41 GMT, Connection: close, Server: AmazonS3]

Please let me know if there's a better option than waiting for AWS to sort itself out.

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