The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
RNAseq varaint calling error
I'm following the Calling variants in RNAseq algorithm and I'm having an error message during the Split'N'Trim and reassign mapping qualities step.
The command I'm using is:
java -jar /usr/lib/jvm/java-7-oracle/jre/lib/ext/GenomeAnalysisTK-3.1-1/GenomeAnalysisTK.jar -T SplitNCigarReads -R ../hg38_V22.fa -I ./110222_SN627_0062_A81FPKABXX.1_CA_dedupped.bam -o ./gatk3/110222_SN627_0062_A81FPKABXX.1_CA_split.bam -rf ReassignOneMappingQuality -RMQF 255 -RMQT 60 -U ALLOW_N_CIGAR_READS
And the error message is:
WARN 12:39:54,935 RestStorageService - Error Response: PUT '/9BHFgamBejq4vpq1609HSe5uaERoVKJg.report.xml.gz' -- ResponseCode: 403, ResponseStatus: Forbidden, Request Headers: [Content-Length: 1082, Content-MD5: eL7RUPoOe7Z5TAcnnuJyJA==, Content-Type: application/octet-stream, x-amz-meta-md5-hash: 78bed150fa0e7bb6794c07279ee27224, Date: Mon, 12 Dec 2016 14:39:53 GMT, Authorization: AWS AKIAI22FBBJ37D5X62OQ:lQXmnB3764v81X8SEvKZHnuuvD4=, User-Agent: JetS3t/0.8.1 (Linux/4.4.0-38-generic; amd64; en; JVM 1.7.0_80), Host: broad.gsa.gatk.run.reports.s3.amazonaws.com, Expect: 100-continue], Response Headers: [x-amz-request-id: 925E9C0064AB10AB, x-amz-id-2: habdpwVI552GHzAepL8UX//6EEwYcEsR4Xa1SiXSM/nGWQ0ldREV/zLjcv2zmCZ4Rp6wQDohikU=, Content-Type: application/xml, Transfer-Encoding: chunked, Date: Mon, 12 Dec 2016 15:35:01 GMT, Connection: close, Server: AmazonS3]
WARN 12:39:56,173 RestStorageService - Adjusted time offset in response to RequestTimeTooSkewed error. Local machine and S3 server disagree on the time by approximately 3306 seconds. Retrying connection.
INFO 12:39:56,932 GATKRunReport - Uploaded run statistics report to AWS S3
ERROR A USER ERROR has occurred (version 3.1-1-g07a4bf8):
ERROR This means that one or more arguments or inputs in your command are incorrect.
ERROR The error message below tells you what is the problem.
ERROR If the problem is an invalid argument, please check the online documentation guide
ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
ERROR MESSAGE: Couldn't write file /home/HDD3/sorted_bam_files/gatk/./gatk3/110222_SN627_0062_A81FPKABXX.1_CA_split.bam because file could not be created with exception Error opening file: /home/HDD3/sorted_bam_files/gatk/./gatk3/110222_SN627_0062_A81FPKABXX.1_CA_split.bam
Looks like there is a problem with Amazon server connection.
Am I able to fix this changing the -et argument?
Thanks in advance