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how to figure out the error when running PathSeq?

Hello GATKer,
I run PathSeq using snakemake. When I run for a single sample, it works. But when I run for multiple samples parallelly, it threw an error as below. Could you please help me figure it out? Thanks a lot!

My command:
gatk PathSeqPipelineSpark \
--input /liulab/jinwang/rnaseq/analysis/star/SRR3184301/SRR3184301.sorted.bam \
--kmer-file /liulab/jinwang/reference/pathseq_gdc_index/hg38/hg38_k31.hss \
--filter-bwa-image /liulab/jinwang/reference/pathseq_gdc_index/hg38/GRCh38.d1.vd1.fa.img \
--microbe-fasta /liulab/jinwang/reference/pathseq_gdc_index/hg38/pathseq_microbe.fa \
--microbe-bwa-image /liulab/jinwang/reference/pathseq_gdc_index/hg38/pathseq_microbe.fa.img \
--taxonomy-file /liulab/jinwang/reference/pathseq_gdc_index/hg38/pathseq_microbe.db \
--output /liulab/jinwang/rnaseq/analysis/test.pathseq_bam \
--scores-output /liulab/jinwang/rnaseq/analysis/test_score_output.txt \
--min-score-identity 0.85 \
--min-clipped-read-length 70 \
--filter-metrics /liulab/jinwang/rnaseq/analysis/test_filter_metrics.txt \
--score-metrics /liulab/jinwang/rnaseq/analysis/test_score_metrics.txt \
--create-output-bam-index false

Error:
htsjdk.samtools.util.RuntimeIOException: java.io.IOException: Stream closed
at htsjdk.samtools.IndexStreamBuffer.readFully(IndexStreamBuffer.java:23)
at htsjdk.samtools.IndexStreamBuffer.readLong(IndexStreamBuffer.java:62)
at htsjdk.samtools.AbstractBAMFileIndex.readLong(AbstractBAMFileIndex.java:436)
at htsjdk.samtools.AbstractBAMFileIndex.query(AbstractBAMFileIndex.java:311)
at htsjdk.samtools.CachingBAMFileIndex.getQueryResults(CachingBAMFileIndex.java:159)
at htsjdk.samtools.BAMIndexMerger.processIndex(BAMIndexMerger.java:43)
at htsjdk.samtools.BAMIndexMerger.processIndex(BAMIndexMerger.java:16)
at org.disq_bio.disq.impl.file.IndexFileMerger.mergeParts(IndexFileMerger.java:90)
at org.disq_bio.disq.impl.formats.bam.BamSink.save(BamSink.java:132)
at org.disq_bio.disq.HtsjdkReadsRddStorage.write(HtsjdkReadsRddStorage.java:225)
at org.broadinstitute.hellbender.engine.spark.datasources.ReadsSparkSink.writeReads(ReadsSparkSink.java:155)
at org.broadinstitute.hellbender.engine.spark.datasources.ReadsSparkSink.writeReads(ReadsSparkSink.java:120)
at org.broadinstitute.hellbender.engine.spark.datasources.ReadsSparkSink.writeReads(ReadsSparkSink.java:74)
at org.broadinstitute.hellbender.tools.spark.pathseq.PathSeqPipelineSpark.runTool(PathSeqPipelineSpark.java:291)
at org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:528)
at org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205)
at org.broadinstitute.hellbender.Main.main(Main.java:291)
Caused by: java.io.IOException: Stream closed
at java.io.BufferedInputStream.getBufIfOpen(BufferedInputStream.java:170)
at java.io.BufferedInputStream.read(BufferedInputStream.java:336)
at java.io.DataInputStream.read(DataInputStream.java:149)
at java.io.DataInputStream.read(DataInputStream.java:149)
at org.disq_bio.disq.impl.file.HadoopFileSystemWrapper$SeekableHadoopStream.read(HadoopFileSystemWrapper.java:232)
at java.io.BufferedInputStream.fill(BufferedInputStream.java:246)
at java.io.BufferedInputStream.read1(BufferedInputStream.java:286)
at java.io.BufferedInputStream.read(BufferedInputStream.java:345)
at htsjdk.samtools.seekablestream.SeekableBufferedStream.read(SeekableBufferedStream.java:133)
at htsjdk.samtools.IndexStreamBuffer.readFully(IndexStreamBuffer.java:21)
... 21 more
19/07/04 05:39:47 INFO ShutdownHookManager: Shutdown hook called
19/07/04 05:39:47 INFO ShutdownHookManager: Deleting directory /tmp/spark-af167378-3b0c-40b1-8d64-97b4b89a10aa

Answers

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