CODEWITHSUNDEEP
javarubuntuvariantgatk
user22752471
user22752471

Reputation: 3

I dont get the output file to "gatk CollectAlignmentSummaryMetrics" that use to get alignment and insert size metrics in variant calling process

The 2 command I used: gatk CollectAlignmentSummaryMetrics -I /home/osh/Documents/aligned_reads/M2/S2_sorted_dedup_bqsr.bam -R /home/osh/Documents/data/ref/resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta -O /home/osh/Documents/aligned_reads/M2/Alignment_metrics_S2.txt

gatk CollectInsertSizeMetrics -I /home/osh/Documents/aligned_reads/M2/S2_sorted_dedup_bqsr.bam -O /home/osh/Documents/aligned_reads/M2/S2_insert_size_metrics.txt -H /home/osh/Documents/bam_reads/insert_size_histogram.pdf

It gives an error as follows and doesn't generate outputfiles:

Using GATK jar /home/osh/Documents/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 -jar /home/osh/Documents/gatk-4.4.0.0/gatk-package-4.4.0.0-local.jar CollectAlignmentSummaryMetrics -I /home/osh/Documents/aligned_reads/M2/S2_sorted_dedup_bqsr.bam -R /home/osh/Documents/data/ref/resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta -O /home/osh/Documents/aligned_reads/M2/Alignment_metrics_S2.txt 22:58:27.695 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/osh/Documents/gatk-4.4.0.0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so [Tue Jan 16 22:58:27 IST 2024] CollectAlignmentSummaryMetrics --INPUT /home/osh/Documents/aligned_reads/M2/S2_sorted_dedup_bqsr.bam --OUTPUT /home/osh/Documents/aligned_reads/M2/Alignment_metrics_S2.txt --REFERENCE_SEQUENCE /home/oshi/Documents/data/ref/resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta --MAX_INSERT_SIZE 100000 --EXPECTED_PAIR_ORIENTATIONS FR --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG --ADAPTER_SEQUENCE AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT --ADAPTER_SEQUENCE AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG --METRIC_ACCUMULATION_LEVEL ALL_READS --IS_BISULFITE_SEQUENCED false --COLLECT_ALIGNMENT_INFORMATION true --ASSUME_SORTED true --STOP_AFTER 0 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Tue Jan 16 22:58:27 IST 2024] Executing as oshi@oshi-VirtualBox on Linux 5.15.0-91-generic amd64; OpenJDK 64-Bit Server VM 17.0.9+9-Ubuntu-120.04; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.4.0.0 [Tue Jan 16 22:58:29 IST 2024] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.03 minutes. Runtime.totalMemory()=70488064 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp htsjdk.samtools.util.SequenceUtil$SequenceListsDifferException: Sequence dictionaries are not the same size (26, 3366) at htsjdk.samtools.util.SequenceUtil.assertSequenceListsEqual(SequenceUtil.java:259) at htsjdk.samtools.util.SequenceUtil.assertSequenceDictionariesEqual(SequenceUtil.java:342) at htsjdk.samtools.util.SequenceUtil.assertSequenceDictionariesEqual(SequenceUtil.java:328) at picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:117) at picard.analysis.SinglePassSamProgram.doWork(SinglePassSamProgram.java:94) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:289) at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.instanceMain(PicardCommandLineProgramExecutor.java:37) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203) at org.broadinstitute.hellbender.Main.main(Main.java:289)

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