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Using SortSamSpark, Spark cluster output file cannot be used

jackyhuangjackyhuang Taiwan,R.O.CMember
Hello team,

When I use the spark cluster output file, the output will be show this sentence.
htsjdk.samtools.util.RuntimeIOException: java.io.IOException: Invalid BAM file header

First command is normal.
gatk SortSamSpark \
--input "hdfs://172.16.72.8:9000/mnt/jacky/hdfs_tmp/ERR194147.bam" \
--output /mnt/jacky/before_hdfs_tmp/ERR194147.sorted.bam \
--tmp-dir .\
-- --spark-runner SPARK \
--spark-master spark://172.16.72.8:7077 --executor-memory 120G

The second command will have the above mentioned error.
gatk MarkDuplicatesSpark \
--input hdfs://172.16.72.8:9000/mnt/jacky/before_hdfs_tmp/ERR194147.sorted.bam \
--output /mnt/jacky/before_hdfs_tmp/ERR194147.sorted.dedup.bam \
--metrics-file /mnt/jacky/before_hdfs_tmp/ERR194147.markDuplicates.metrics \
--read-index hdfs:///72.16.72.8:9000/mnt/jacky/before_hdfs_tmp/ERR194147.sorted.bam.sbi \
-- --spark-runner SPARK \
--spark-master spark://172.16.72.8:7077 --executor-memory 120G

When I use picard ValidateSamFile, the output will be show this sentence.
Exception in thread "main" htsjdk.samtools.SAMException: SAMFormatException on record 01

Below is my tool version:
GATK: 4.1.4.0
Hadoop: 2.7
Spark: 2.4.4
Java: 1.8.0_222
picard-tools 1.138
ubuntu: 18.04

Thanks,
Jacky

Answers

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