Hi,
I am upgrading my analysis pipeline from GATK 3.3-0 to 3.6-0 on a CentOS 6.x machine and came across a problem with GATK stalling at the following point in the output below (I know that it is not a complete GATK command, but the command below does not even generate an error message:
[jelber2@localhost sandbox]$ ~/bin/jdk1.8.0_111/bin/java -jar ~/bin/GATK-3.6/GenomeAnalysisTK.jar -T FindCoveredIntervals -R GCF_000241765.3_Chrysemys_picta_bellii-3.0.3_genomic.fna
INFO 20:26:32,905 HelpFormatter - ----------------------------------------------------------------------------------
INFO 20:26:32,908 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.6-0-g89b7209, Compiled 2016/06/01 22:27:29
INFO 20:26:32,909 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO 20:26:32,909 HelpFormatter - For support and documentation go to https://www.broadinstitute.org/gatk
INFO 20:26:32,909 HelpFormatter - [Mon Nov 21 20:26:32 CST 2016] Executing on Linux 2.6.32-642.11.1.el6.x86_64 amd64
INFO 20:26:32,910 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_111-b14 JdkDeflater
INFO 20:26:32,914 HelpFormatter - Program Args: -T FindCoveredIntervals -R GCF_000241765.3_Chrysemys_picta_bellii-3.0.3_genomic.fna
INFO 20:26:32,919 HelpFormatter - Executing as jelber2@localhost.localdomain on Linux 2.6.32-642.11.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_111-b14.
INFO 20:26:32,919 HelpFormatter - Date/Time: 2016/11/21 20:26:32
INFO 20:26:32,919 HelpFormatter - ----------------------------------------------------------------------------------
INFO 20:26:32,920 HelpFormatter - ----------------------------------------------------------------------------------
INFO 20:26:32,928 GenomeAnalysisEngine - Strictness is SILENT
---it will sit at Strictness is Silent for hours
I thought maybe my reference genome, it's index, or dictionary might have been corrupted, so I reacquired the reference:
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF_000241765.3_Chrysemys_picta_bellii-3.0.3/GCF_000241765.3_Chrysemys_picta_bellii-3.0.3_genomic.fna.gz
gunzip GCF_000241765.3_Chrysemys_picta_bellii-3.0.3_genomic.fna.gz
made it's index with samtools-1.3.1
~/bin/samtools-1.3.1/samtools faidx GCF_000241765.3_Chrysemys_picta_bellii-3.0.3_genomic.fna
made it's sequence dictionary with picard-tools-2.7.1
~/bin/jdk1.8.0_111/bin/java -jar ~/bin/picard-tools-2.7.1/picard.jar CreateSequenceDictionary R=GCF_000241765.3_Chrysemys_picta_bellii-3.0.3_genomic.fna O=GCF_000241765.3_Chrysemys_picta_bellii-3.0.3_genomic.fna.dict
The problem is if I repeat the above steps with a different NCBI created reference genome, GATK at least doesn't stall and tells me to provide
ERROR MESSAGE: Walker requires reads but none were provided.
Best,
Gopo