Hi, I am using one of the CloudMap workflow to run my pair-end data. I use this one, 'CloudMap Hawaiian and Variant Discovery Mapping on Hawaiian Mapped Samples (and Variant Calling) workflow _2-7-2014'. However, it keep stuck in this step, Unified Genotyper SNP and indel caller (Galaxy Version 0.0.6). And the error message is this, "Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/jobdir/018/635/18635134/_job_tmp -Xmx15g -Xms256m [Wed Mar 07 00:37:17 CST 2018] net.sf.picard.sam.CreateSequenceDictionary REFERENCE=/galaxy-repl/main/jobdir/018/635/18635134/_job_tmp/tmp-gatk". If I change the "Genotype likelihoods calculation model to employ", and only choose SNP, it can run through this step and give me the result. However, If I choose INDEL or BOTH, it will crash in this step. How can I fix this problem?
Heads up! This is a static archive of our support site. Please go to help.galaxyproject.org if you want to reach the Galaxy community. If you want to search this archive visit the Galaxy Hub search
Question: (Closed) CloudMap stuck on "Unified Genotyper SNP and indel caller (Galaxy Version 0.0.6)" -- Deprecated tools
8 months ago by
ironjoba • 0
ironjoba • 0 wrote:
ADD COMMENT • link •
Please log in to add an answer.
The thread is closed. No new answers may be added.
Powered by Biostar version 16.09
Traffic: 169 users visited in the last hour