Question: (Closed) CloudMap stuck on "Unified Genotyper SNP and indel caller (Galaxy Version 0.0.6)" -- Deprecated tools
gravatar for ironjoba
8 months ago by
ironjoba0 wrote:

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: -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? snapshot

galaxy gatk deprecated cloudmap • 319 views
ADD COMMENTlink written 8 months ago by ironjoba0

Hello ironjoba!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.


PS: Using "BOTH" was a prior issue, not corrected ( These tools have been deprecated.
ADD REPLYlink written 8 months ago by Jennifer Hillman Jackson25k
Please log in to add an answer.
The thread is closed. No new answers may be added.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 169 users visited in the last hour