Hi,

I'm using the picard SamtoFastq method in Terra and am getting the error pasted below on some bam files. Please see below for the command that I'm using. Additionally, I'm using gatk version as found on the docker: broadinstitute/genomes-in-the-cloud:2.3.1-1500064817. The version of picard.jar samtofastq is Version: 2.8.3-SNAPSHOT.

Please let me know if you may have an idea as to what is causing this error. 

Thanks!

Error:

Exception in thread "main" java.lang.ClassCastException: java.lang.Character cannot be cast to java.lang.Integer at picard.sam.SamToFastq.writeRecord(SamToFastq.java:305) at picard.sam.SamToFastq.doWork(SamToFastq.java:195) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:205) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:94) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:104)

Command

java -jar /usr/gitc/picard.jar SamToFastq \
TMP_DIR=. \
INPUT=${inputBam} \
FASTQ=${sampleName}.1.fastq.gz \
INTERLEAVE=false \
SECOND_END_FASTQ=${sampleName}.2.fastq.gz \
INCLUDE_NON_PF_READS=true \
CLIPPING_ATTRIBUTE=XT \
CLIPPING_ACTION=2 \
UNPAIRED_FASTQ=${sampleName}.unpaired.fastq.gz

Can you please provide
a) GATK version used
b) Exact GATK commands used
c) The entire error log if applicable.