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MergeBamAlignment output no file

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Phuoc-Dung Nguyen

Hi, I'm quite new to using gatk and terminal-based software. I was following this guide:

https://gatk.broadinstitute.org/hc/en-us/articles/360039568932--How-to-Map-and-clean-up-short-read-sequence-data-efficiently#step1

At the step of 'Restore altered data and apply & adjust meta information using MergeBamAlignment', I encountered a problem with MergeBamAlignment:

Unable to load libgkl_compression.dylib from native/libgkl_compression.dylib (/private/var/folders/3g/tdldfbp90x14fgb8x9vyz4z00000gn/T/phuoc-dungnguyen/libgkl_compression12594550774796112558.dylib: dlopen(/private/var/folders/3g/tdldfbp90x14fgb8x9vyz4z00000gn/T/phuoc-dungnguyen/libgkl_compression12594550774796112558.dylib, 0x0001): tried: '/private/var/folders/3g/tdldfbp90x14fgb8x9vyz4z00000gn/T/phuoc-dungnguyen/libgkl_compression12594550774796112558.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64e' or 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/private/var/folders/3g/tdldfbp90x14fgb8x9vyz4z00000gn/T/phuoc-dungnguyen/libgkl_compression12594550774796112558.dylib' (no such file), '/private/var/folders/3g/tdldfbp90x14fgb8x9vyz4z00000gn/T/phuoc-dungnguyen/libgkl_compression12594550774796112558.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64e' or 'arm64')))
 
I am using Mac M1 arm64 so I don't know what caused this error. I could not find any post related to MergeBamAlignment and libgkl error.
I am quite new, so any help would be very appreciated! Thank you very much!

REQUIRED for all errors and issues:
a) GATK version used: 

(GATK) v4.6.2.0-1-g657b4ee-SNAPSHOT

HTSJDK Version: 4.2.0

Picard Version: 3.4.0

b) Exact command used:

./gatk MergeBamAlignment -O /Users/phuoc-dungnguyen/gatk/gatk/data/R5/R5_mergebamalign.bam -R /Users/phuoc-dungnguyen/gatk/gatk/data/AP019723_107605.fasta -UNMAPPED /Users/phuoc-dungnguyen/gatk/gatk/data/R5/R5_uBAM.bam -ALIGNED /Users/phuoc-dungnguyen/gatk/gatk/data/R5/R5_bwa-mem2.sam --CREATE_INDEX true --ADD_MATE_CIGAR true --CLIP_ADAPTERS false --CLIP_OVERLAPPING_READS true --INCLUDE_SECONDARY_ALIGNMENTS true --MAX_INSERTIONS_OR_DELETIONS -1 --PRIMARY_ALIGNMENT_STRATEGY MostDistant --ATTRIBUTES_TO_RETAIN XS


c) Entire program log: 

(gatk) phuoc-dungnguyen@Phuoc-Dungs-MacBook-Pro gatk % ./gatk MergeBamAlignment -O /Users/phuoc-dungnguyen/gatk/gatk/data/R5/R5_mergebamalign.bam -R /Users/phuoc-dungnguyen/gatk/gatk/data/AP019723_107605.fasta -UNMAPPED /Users/phuoc-dungnguyen/gatk/gatk/data/R5/R5_uBAM.bam -ALIGNED /Users/phuoc-dungnguyen/gatk/gatk/data/R5/R5_bwa-mem2.sam --CREATE_INDEX true --ADD_MATE_CIGAR true --CLIP_ADAPTERS false --CLIP_OVERLAPPING_READS true --INCLUDE_SECONDARY_ALIGNMENTS true --MAX_INSERTIONS_OR_DELETIONS -1 --PRIMARY_ALIGNMENT_STRATEGY MostDistant --ATTRIBUTES_TO_RETAIN XS

Using GATK jar /Users/phuoc-dungnguyen/gatk/gatk/build/libs/gatk-package-4.6.2.0-1-g657b4ee-SNAPSHOT-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 -jar /Users/phuoc-dungnguyen/gatk/gatk/build/libs/gatk-package-4.6.2.0-1-g657b4ee-SNAPSHOT-local.jar MergeBamAlignment -O /Users/phuoc-dungnguyen/gatk/gatk/data/R5/R5_mergebamalign.bam -R /Users/phuoc-dungnguyen/gatk/gatk/data/AP019723_107605.fasta -UNMAPPED /Users/phuoc-dungnguyen/gatk/gatk/data/R5/R5_uBAM.bam -ALIGNED /Users/phuoc-dungnguyen/gatk/gatk/data/R5/R5_bwa-mem2.sam --CREATE_INDEX true --ADD_MATE_CIGAR true --CLIP_ADAPTERS false --CLIP_OVERLAPPING_READS true --INCLUDE_SECONDARY_ALIGNMENTS true --MAX_INSERTIONS_OR_DELETIONS -1 --PRIMARY_ALIGNMENT_STRATEGY MostDistant --ATTRIBUTES_TO_RETAIN XS

00:32:36.298 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/phuoc-dungnguyen/gatk/gatk/build/libs/gatk-package-4.6.2.0-1-g657b4ee-SNAPSHOT-local.jar!/com/intel/gkl/native/libgkl_compression.dylib

00:32:36.321 WARN NativeLibraryLoader - Unable to load libgkl_compression.dylib from native/libgkl_compression.dylib (/private/var/folders/3g/tdldfbp90x14fgb8x9vyz4z00000gn/T/phuoc-dungnguyen/libgkl_compression12594550774796112558.dylib: dlopen(/private/var/folders/3g/tdldfbp90x14fgb8x9vyz4z00000gn/T/phuoc-dungnguyen/libgkl_compression12594550774796112558.dylib, 0x0001): tried: '/private/var/folders/3g/tdldfbp90x14fgb8x9vyz4z00000gn/T/phuoc-dungnguyen/libgkl_compression12594550774796112558.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64e' or 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/private/var/folders/3g/tdldfbp90x14fgb8x9vyz4z00000gn/T/phuoc-dungnguyen/libgkl_compression12594550774796112558.dylib' (no such file), '/private/var/folders/3g/tdldfbp90x14fgb8x9vyz4z00000gn/T/phuoc-dungnguyen/libgkl_compression12594550774796112558.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64e' or 'arm64')))

00:32:36.322 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/phuoc-dungnguyen/gatk/gatk/build/libs/gatk-package-4.6.2.0-1-g657b4ee-SNAPSHOT-local.jar!/com/intel/gkl/native/libgkl_compression.dylib

00:32:36.325 WARN NativeLibraryLoader - Unable to load libgkl_compression.dylib from native/libgkl_compression.dylib (/private/var/folders/3g/tdldfbp90x14fgb8x9vyz4z00000gn/T/phuoc-dungnguyen/libgkl_compression15284358877015822145.dylib: dlopen(/private/var/folders/3g/tdldfbp90x14fgb8x9vyz4z00000gn/T/phuoc-dungnguyen/libgkl_compression15284358877015822145.dylib, 0x0001): tried: '/private/var/folders/3g/tdldfbp90x14fgb8x9vyz4z00000gn/T/phuoc-dungnguyen/libgkl_compression15284358877015822145.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64e' or 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/private/var/folders/3g/tdldfbp90x14fgb8x9vyz4z00000gn/T/phuoc-dungnguyen/libgkl_compression15284358877015822145.dylib' (no such file), '/private/var/folders/3g/tdldfbp90x14fgb8x9vyz4z00000gn/T/phuoc-dungnguyen/libgkl_compression15284358877015822145.dylib' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64e' or 'arm64')))

[Thu Apr 24 00:32:36 JST 2025] MergeBamAlignment --UNMAPPED_BAM /Users/phuoc-dungnguyen/gatk/gatk/data/R5/R5_uBAM.bam --ALIGNED_BAM /Users/phuoc-dungnguyen/gatk/gatk/data/R5/R5_bwa-mem2.sam --OUTPUT /Users/phuoc-dungnguyen/gatk/gatk/data/R5/R5_mergebamalign.bam --CLIP_ADAPTERS false --MAX_INSERTIONS_OR_DELETIONS -1 --ATTRIBUTES_TO_RETAIN XS --PRIMARY_ALIGNMENT_STRATEGY MostDistant --CLIP_OVERLAPPING_READS true --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --CREATE_INDEX true --REFERENCE_SEQUENCE /Users/phuoc-dungnguyen/gatk/gatk/data/AP019723_107605.fasta --ADD_PG_TAG_TO_READS true --PAIRED_RUN true --IS_BISULFITE_SEQUENCE false --ALIGNED_READS_ONLY false --ATTRIBUTES_TO_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --HARD_CLIP_OVERLAPPING_READS false --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false

[Thu Apr 24 00:32:36 JST 2025] Executing as phuoc-dungnguyen@Phuoc-Dungs-MacBook-Pro.local on Mac OS X 15.3.2 aarch64; Java HotSpot(TM) 64-Bit Server VM 17.0.12+8-LTS-286; Deflater: Jdk; Inflater: Jdk; Provider GCS is available; Picard version: Version:4.6.2.0-1-g657b4ee-SNAPSHOT

INFO 2025-04-24 00:32:36 SamAlignmentMerger Processing SAM file(s): [/Users/phuoc-dungnguyen/gatk/gatk/data/R5/R5_bwa-mem2.sam]

00:32:36.398 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater

00:32:36.400 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater

[Thu Apr 24 00:32:36 JST 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.

Runtime.totalMemory()=113246208

To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp

htsjdk.samtools.SAMException: Could not find dictionary next to reference file file:///Users/phuoc-dungnguyen/gatk/gatk/data/AP019723_107605.fasta

at htsjdk.variant.utils.SAMSequenceDictionaryExtractor$TYPE$1.extractDictionary(SAMSequenceDictionaryExtractor.java:58)

at htsjdk.variant.utils.SAMSequenceDictionaryExtractor.extractDictionary(SAMSequenceDictionaryExtractor.java:170)

at picard.sam.SamAlignmentMerger.getDictionaryForMergedBam(SamAlignmentMerger.java:192)

at picard.sam.AbstractAlignmentMerger.mergeAlignment(AbstractAlignmentMerger.java:384)

at picard.sam.SamAlignmentMerger.mergeAlignment(SamAlignmentMerger.java:181)

at picard.sam.MergeBamAlignment.doWork(MergeBamAlignment.java:375)

at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:281)

at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.instanceMain(PicardCommandLineProgramExecutor.java:37)

at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166)

at org.broadinstitute.hellbender.Main.mainEntry(Main.java:209)

at org.broadinstitute.hellbender.Main.main(Main.java:306)
0

2 comments

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  • Avatar
    Can Kockan

    The warning message you've mentioned regarding compression libraries is most likely not the problem here. The program should just use a different compression/decompression library.

    You must have a sequence dictionary in the same directory as your reference genome (so right next to file:///Users/phuoc-dungnguyen/gatk/gatk/data/AP019723_107605.fasta)

    Check out https://gatk.broadinstitute.org/hc/en-us/articles/30332041832731-CreateSequenceDictionary-Picard and build a sequence dictionary first with that tool, then retry your original command.

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  • Avatar
    Phuoc-Dung Nguyen

    Thank you very much! I have retrieved the dictionary file.

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