QSamToFastq.java exception #281
Description
Describe the bug
There is an in-house tool converting BAM to Fastq, but it throws exceptions now.
To Reproduce
Steps to reproduce the behavior:
- run 'java -cp $ADAMA_HOME/build/lib/qpicard.jar org.qcmg.picard.fastq.QSamToFastq I=$bam FASTQ=$fr1 SECOND_END_FASTQ=$fr2 RC=Boolean'
- get exception
Expected behavior
no Exception expected
Screenshots
`$bash run.sh
Picked up JAVA_TOOL_OPTIONS: -XX:+UseSerialGC
[Tue Sep 21 09:19:48 AEST 2021] org.qcmg.picard.fastq.QSamToFastq INPUT=/mnt/lustre/working/genomeinfo/share/testdataXu/qprofiler2/bam2fastq/test.bam FASTQ=/mnt/lustre/working/genomeinfo/share/testdataXu/qprofiler2/bam2fastq/qsam2fastq/r1.fastq SECOND_END_FASTQ=/mnt/lustre/working/genomeinfo/share/testdataXu/qprofiler2/bam2fastq/qsam2fastq/r2.fastq RE_REVERSE=false OUTPUT_PER_RG=false INCLUDE_NON_PF_READS=false READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
Exception in thread "main" java.lang.NoSuchMethodError: htsjdk.samtools.util.zip.DeflaterFactory.usingIntelDeflater()Z
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:174)
at org.qcmg.picard.fastq.QSamToFastq.main(QSamToFastq.java:111)`
Desktop (please complete the following information):
- OS: linux on cluster
- Version: adama java 78-43982c9
Additional context
I guess the imported libraries version conflicts