GATK error while performing WES for the HG100 downloaded from 1000genomes

Question

[shuksi1984]

I ran following command for the exome data:

sudo java -jar path/to/GenomeAnalysisTK.jar -T HaplotypeCaller -R path/to/hg38gatkbundle/Homo_sapiens_assembly38.fasta -I HG100.printReads.bam -o HG100.rawVariants.vcf

I got following error.

[WARN 12:03:26,931 RestStorageService - Error Response: PUT '/ZlUNWMSjp2SlZO6LJC9TVbVlRDXGRbg8.report.xml.gz' -- ResponseCode: 403, ResponseStatus: Forbidden, Request Headers: [Content-Length: 414, x-amz-meta-md5-hash: 852ba495699bf928c7d4e24d9aace283, Content-Type: application/octet-stream, Content-MD5: hSuklWmb+SjH1OJNmqzigw==, Date: Fri, 13 Apr 2018 06:33:25 GMT, Authorization: AWS AKIAI22FBBJ37D5X62OQ:38RYxtX/vpFIHRd/jCORybPptdE=, User-Agent: JetS3t/0.8.1 (Linux/3.19.0-84-generic; amd64; en; JVM 1.8.0_45-internal), Host: broad.gsa.gatk.run.reports.s3.amazonaws.com, Expect: 100-continue], Response Headers: [x-amz-request-id: 1CDEC0E3C6A71B78, x-amz-id-2: FWhDmnAAoAjKTZgeIU8uerduJlXPv8WwKVoM5qaSQrPAOwCqRmBGSZGAM2btfKfSmzf99v5Wqzo=, Content-Type: application/xml, Transfer-Encoding: chunked, Date: Fri, 13 Apr 2018 06:12:51 GMT, Connection: close, Server: AmazonS3] WARN 12:03:28,446 RestStorageService - Adjusted time offset in response to RequestTimeTooSkewed error. Local machine and S3 server disagree on the time by approximately -1235 seconds. Retrying connection.]

Also, I am getting same kind of warning when I used various GATK tools, such as: RealignerTargetCreator, VariantFiltration, AnalyzeCovariates, and PrintReads in various steps of the pipeline. Output files are generated by almost all the tools, but dont know whether the files are malformed.

BaseRecalibrator and SelectVariants did not throw any such error, I am using (GATK) v3.5-0-g36282e4.

[WouterDeCoster]

There is no good reason to use sudo for running commands like this, and you should only use sudo when you absolutely have to for e.g. sysadmin stuff!

Answer 1

[Pierre Lindenbaum]

your version of GATK is old. It is still trying to connect to amazon to register your GATK-usage a.k.a "PHONE HOME".

see https://gatkforums.broadinstitute.org/gatk/discussion/1250/what-is-phone-home-and-how-does-it-affect-me

In GATK versions produced between September 2010 and May 2016, the GATK had a "Phone Home" usage reporting feature that sent us information about each GATK run via the Broad filesystem (within the Broad) and Amazon's S3 cloud storage service (outside the Broad). This feature was enabled by default and required a key to be disabled (for running offline or for regulatory reasons).

The Phone Home feature was removed in version 3.6. Keys are no longer necessary, so if you had one, you can stop using it. We do not expect that including Phone Home arguments in GATK command lines would cause any errors (so this should not break any scripts), but let us know if you run into any trouble.

Note that keys remain necessary for disabling Phone Home in older versions of GATK. See further below for details on how to obtain a key.

[shuksi1984]

I updated my GATK3 to GATK4. I ran the following command in GATK4:

gatk -T VariantFiltration -R /path/to/reference -V /path/to/input.vcf --filterExpression 'QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0 || SOR > 4.0' --filterName "basic_snp_filter" -o /path/to/out.vcf.

I got following error: A USER ERROR has occurred: '-T' is not a valid command.

While going through the GATK forum, I came to know -T was removed from GATK4. Some of the switches are supported by GATK3 and some by GATK4. My question is which version of GATK should be used to run end to end NGS pipeline?

[Pierre Lindenbaum]

did you try

gatk   VariantFiltration -R /path/to/reference ...

?

[shuksi1984]

Yes I did. My command was: gatk VariantFiltration -R /path/to/reference -V /path/to/input.vcf --filterExpression 'QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0 || SOR > 4.0' --filterName "basic_snp_filter" -o /path/to/out.vcf

The error I got was:

A USER ERROR has occurred: filterExpression is not a recognized option

[xiaoyi]

Hi,How do you finally fix this problem “A USER ERROR has occurred: filterExpression is not a recognized option”?