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

galaxy gatk deprecated cloudmap • 245 views
ADD COMMENTlink written 7 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.

Cheers!

PS: Using "BOTH" was a prior issue, not corrected (https://biostar.usegalaxy.org/p/10504/). These tools have been deprecated.
ADD REPLYlink written 7 months ago by Jennifer Hillman Jackson25k
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