和线程关系不大，需要检查一下前面的g.vcf.gz都正不正常，以及他们的索引文件是否正常，如果涉及到染色体长度超过512M可能会引起一些索引的问题。或者你选择继续往下跑一下看看有在db变成vcf这一步有没有更明确的报错。
以下是关于“htsjdk.samtools.SAMFormatException: Did not inflate expected amount” GATK作者做出的答复，以及最后的解决方案：
GATK 将VCF文件导入db出现问题
再用GATK 将VCF文件导入db的时候，用如下命令：gatk --java-options "-Xmx50g" GenomicsDBImport \
-L intervals.list --tmp-dir $tmpdir -R $REF --batch-size 5 \
--reader-threads 1 --max-num-intervals-to-import-in-parallel 5 \
--genomicsdb-workspace-path db --sample-name-map cohort.sample_map。生成的db文件夹中有这几个文件：
drwx------ 4 root root 4096 Aug 4 16:55 Chr1$1$48169259
-rwx------ 1 root root 0 Aug 4 16:55 __tiledb_workspace.tdb
-rwx------ 1 root root 17408 Aug 4 16:55 vcfheader.vcf
-rwx------ 1 root root 3417 Aug 4 16:55 vidmap.json
感觉是不完成整的。
生成的日志文件是这样的：
Using GATK jar /share/work/biosoft/GATK/gatk-4.4.0.0/gatk-package-4.4.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx50g -jar /share/work/biosoft/GATK/gatk-4.4.0.0/gatk-package-4.4.0.0-local.jar GenomicsDBImport -L intervals.list --tmp-dir /work/my_reseq/tmp -R /work/my_reseq/ref/Dongzao.fa --batch-size 5 --reader-threads 1 --max-num-intervals-to-import-in-parallel 5 --genomicsdb-workspace-path db --sample-name-map cohort.sample_map
14:56:31.470 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/share/work/biosoft/GATK/gatk-4.4.0.0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
14:56:31.552 INFO GenomicsDBImport - ------------------------------------------------------------
14:56:31.556 INFO GenomicsDBImport - The Genome Analysis Toolkit (GATK) v4.4.0.0
14:56:31.556 INFO GenomicsDBImport - For support and documentation go to https://software.broadinstitute.org/gatk/
14:56:31.556 INFO GenomicsDBImport - Executing as root@ed01a5f7cf62 on Linux v4.15.0-112-generic amd64
14:56:31.556 INFO GenomicsDBImport - Java runtime: Java HotSpot(TM) 64-Bit Server VM v19.0.1+10-21
14:56:31.556 INFO GenomicsDBImport - Start Date/Time: August 4, 2025 at 2:56:31 PM CST
14:56:31.557 INFO GenomicsDBImport - ------------------------------------------------------------
14:56:31.557 INFO GenomicsDBImport - ------------------------------------------------------------
14:56:31.557 INFO GenomicsDBImport - HTSJDK Version: 3.0.5
14:56:31.558 INFO GenomicsDBImport - Picard Version: 3.0.0
14:56:31.558 INFO GenomicsDBImport - Built for Spark Version: 3.3.1
14:56:31.558 INFO GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 2
14:56:31.558 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:56:31.558 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:56:31.558 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:56:31.558 INFO GenomicsDBImport - Deflater: IntelDeflater
14:56:31.558 INFO GenomicsDBImport - Inflater: IntelInflater
14:56:31.559 INFO GenomicsDBImport - GCS max retries/reopens: 20
14:56:31.559 INFO GenomicsDBImport - Requester pays: disabled
14:56:31.559 INFO GenomicsDBImport - Initializing engine
14:56:31.799 INFO IntervalArgumentCollection - Processing 393332932 bp from intervals
14:56:31.817 INFO GenomicsDBImport - Done initializing engine
14:56:32.064 INFO GenomicsDBLibLoader - GenomicsDB native library version : 1.4.4-ce4e1b9
14:56:32.065 INFO GenomicsDBImport - Vid Map JSON file will be written to /work/my_reseq/4.snp_indel/GATK/db/vidmap.json
14:56:32.065 INFO GenomicsDBImport - Callset Map JSON file will be written to /work/my_reseq/4.snp_indel/GATK/db/callset.json
14:56:32.065 INFO GenomicsDBImport - Complete VCF Header will be written to /work/my_reseq/4.snp_indel/GATK/db/vcfheader.vcf
14:56:32.065 INFO GenomicsDBImport - Importing to workspace - /work/my_reseq/4.snp_indel/GATK/db
14:56:32.565 INFO GenomicsDBImport - Importing batch 1 with 5 samples
14:56:32.565 INFO GenomicsDBImport - Importing batch 1 with 5 samples
14:56:32.565 INFO GenomicsDBImport - Importing batch 1 with 5 samples
14:56:32.565 INFO GenomicsDBImport - Importing batch 1 with 5 samples
14:56:32.565 INFO GenomicsDBImport - Importing batch 1 with 5 samples
14:56:33.775 INFO GenomicsDBImport - Importing batch 1 with 5 samples
14:56:33.781 INFO GenomicsDBImport - Importing batch 1 with 5 samples
14:56:33.801 INFO GenomicsDBImport - Importing batch 1 with 5 samples
14:56:33.801 INFO GenomicsDBImport - Importing batch 1 with 5 samples
14:56:33.967 INFO GenomicsDBImport - Importing batch 1 with 5 samples
14:56:33.976 INFO GenomicsDBImport - Importing batch 1 with 5 samples
14:56:33.983 INFO GenomicsDBImport - Importing batch 1 with 5 samples
14:57:24.783 INFO GenomicsDBImport - Shutting down engine
[August 4, 2025 at 2:57:24 PM CST] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.89 minutes.
Runtime.totalMemory()=5838471168
htsjdk.samtools.SAMFormatException: Did not inflate expected amount
at htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:147)
at htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:96)
at htsjdk.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:550)
at htsjdk.samtools.util.BlockCompressedInputStream.processNextBlock(BlockCompressedInputStream.java:532)
at htsjdk.samtools.util.BlockCompressedInputStream.nextBlock(BlockCompressedInputStream.java:468)
at htsjdk.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:458)
at htsjdk.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:196)
at htsjdk.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:241)
at htsjdk.tribble.readers.TabixReader.readLine(TabixReader.java:215)
at htsjdk.tribble.readers.TabixReader.access$300(TabixReader.java:48)
at htsjdk.tribble.readers.TabixReader$IteratorImpl.next(TabixReader.java:434)
at htsjdk.tribble.readers.TabixIteratorLineReader.readLine(TabixIteratorLineReader.java:46)
at htsjdk.tribble.TabixFeatureReader$FeatureIterator.readNextRecord(TabixFeatureReader.java:170)
at htsjdk.tribble.TabixFeatureReader$FeatureIterator.next(TabixFeatureReader.java:205)
at htsjdk.tribble.TabixFeatureReader$FeatureIterator.next(TabixFeatureReader.java:149)
at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport$1$NoMnpIterator.next(GenomicsDBImport.java:950)
at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport$1$NoMnpIterator.next(GenomicsDBImport.java:941)
at org.genomicsdb.importer.GenomicsDBImporterStreamWrapper.next(GenomicsDBImporterStreamWrapper.java:110)
at org.genomicsdb.importer.GenomicsDBImporter.doSingleImport(GenomicsDBImporter.java:583)
at org.genomicsdb.importer.GenomicsDBImporter.lambda$null$4(GenomicsDBImporter.java:733)
at java.base/java.util.concurrent.CompletableFuture$AsyncSupply.run(CompletableFuture.java:1768)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
at java.base/java.lang.Thread.run(Thread.java:1589)
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- 郭老师 提出于 5天前