anilkumar@ak-omen-laptop:~/NGStools/gatk-4.4.0.0$ gatk --java-options "-DGATK_STACKTRACE_ON_USER_EXCEPTION=true" BaseRecalibrator -I "/media/anilkumar/My Passport/CRC/fastq/C_4_mkdp.bam" -R "/media/anilkumar/My Passport/CRC/fastq/hg19.fa" --known-sites "/media/anilkumar/My Passport/CRC/fastq/dbsnp_138.b37.vcf" --known-sites "/media/anilkumar/My Passport/CRC/fastq/Mills_and_1000G_gold_standard.indels.b37.vcf" --known-sites "/media/anilkumar/My Passport/CRC/fastq/1000G_phase1.indels.b37.vcf" -O "/media/anilkumar/My Passport/CRC/fastq/C_4_bqsr.table" Using GATK jar /home/anilkumar/NGStools/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 -DGATK_STACKTRACE_ON_USER_EXCEPTION=true -jar /home/anilkumar/NGStools/gatk-4.4.0.0/gatk-package-4.4.0.0-local.jar BaseRecalibrator -I /media/anilkumar/My Passport/CRC/fastq/C_4_mkdp.bam -R /media/anilkumar/My Passport/CRC/fastq/hg19.fa --known-sites /media/anilkumar/My Passport/CRC/fastq/dbsnp_138.b37.vcf --known-sites /media/anilkumar/My Passport/CRC/fastq/Mills_and_1000G_gold_standard.indels.b37.vcf --known-sites /media/anilkumar/My Passport/CRC/fastq/1000G_phase1.indels.b37.vcf -O /media/anilkumar/My Passport/CRC/fastq/C_4_bqsr.table 11:52:33.495 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/anilkumar/NGStools/gatk-4.4.0.0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 11:52:33.536 INFO BaseRecalibrator - ------------------------------------------------------------ 11:52:33.540 INFO BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.4.0.0 11:52:33.540 INFO BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/ 11:52:33.540 INFO BaseRecalibrator - Executing as anilkumar@ak-omen-laptop on Linux v5.15.0-87-generic amd64 11:52:33.540 INFO BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.8.1+1-Ubuntu-0ubuntu120.04 11:52:33.540 INFO BaseRecalibrator - Start Date/Time: 28 October 2023 at 11:52:33 am IST 11:52:33.541 INFO BaseRecalibrator - ------------------------------------------------------------ 11:52:33.541 INFO BaseRecalibrator - ------------------------------------------------------------ 11:52:33.541 INFO BaseRecalibrator - HTSJDK Version: 3.0.5 11:52:33.542 INFO BaseRecalibrator - Picard Version: 3.0.0 11:52:33.542 INFO BaseRecalibrator - Built for Spark Version: 3.3.1 11:52:33.542 INFO BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2 11:52:33.542 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 11:52:33.543 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 11:52:33.543 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 11:52:33.543 INFO BaseRecalibrator - Deflater: IntelDeflater 11:52:33.543 INFO BaseRecalibrator - Inflater: IntelInflater 11:52:33.543 INFO BaseRecalibrator - GCS max retries/reopens: 20 11:52:33.543 INFO BaseRecalibrator - Requester pays: disabled 11:52:33.544 INFO BaseRecalibrator - Initializing engine 11:52:34.111 INFO FeatureManager - Using codec VCFCodec to read file file:///media/anilkumar/My%20Passport/CRC/fastq/dbsnp_138.b37.vcf 11:52:34.140 INFO FeatureManager - Using codec VCFCodec to read file file:///media/anilkumar/My%20Passport/CRC/fastq/Mills_and_1000G_gold_standard.indels.b37.vcf 11:52:34.153 INFO FeatureManager - Using codec VCFCodec to read file file:///media/anilkumar/My%20Passport/CRC/fastq/1000G_phase1.indels.b37.vcf 11:52:34.163 INFO BaseRecalibrator - Shutting down engine [28 October 2023 at 11:52:34 am IST] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=104857600
A USER ERROR has occurred: Input files reference and features have incompatible contigs: No overlapping contigs found. reference contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chrX, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr20, chrY, chr19, chr22, chr21, chr6_ssto_hap7, chr6_mcf_hap5, chr6_cox_hap2, chr6_mann_hap4, chr6_apd_hap1, chr6_qbl_hap6, chr6_dbb_hap3, chr17_ctg5_hap1, chr4_ctg9_hap1, chr1_gl000192_random, chrUn_gl000225, chr4_gl000194_random, chr4_gl000193_random, chr9_gl000200_random, chrUn_gl000222, chrUn_gl000212, chr7_gl000195_random, chrUn_gl000223, chrUn_gl000224, chrUn_gl000219, chr17_gl000205_random, chrUn_gl000215, chrUn_gl000216, chrUn_gl000217, chr9_gl000199_random, chrUn_gl000211, chrUn_gl000213, chrUn_gl000220, chrUn_gl000218, chr19_gl000209_random, chrUn_gl000221, chrUn_gl000214, chrUn_gl000228, chrUn_gl000227, chr1_gl000191_random, chr19_gl000208_random, chr9_gl000198_random, chr17_gl000204_random, chrUn_gl000233, chrUn_gl000237, chrUn_gl000230, chrUn_gl000242, chrUn_gl000243, chrUn_gl000241, chrUn_gl000236, chrUn_gl000240, chr17_gl000206_random, chrUn_gl000232, chrUn_gl000234, chr11_gl000202_random, chrUn_gl000238, chrUn_gl000244, chrUn_gl000248, chr8_gl000196_random, chrUn_gl000249, chrUn_gl000246, chr17_gl000203_random, chr8_gl000197_random, chrUn_gl000245, chrUn_gl000247, chr9_gl000201_random, chrUn_gl000235, chrUn_gl000239, chr21_gl000210_random, chrUn_gl000231, chrUn_gl000229, chrM, chrUn_gl000226, chr18_gl000207_random] features contigs = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y, MT, GL000207.1, GL000226.1, GL000229.1, GL000231.1, GL000210.1, GL000239.1, GL000235.1, GL000201.1, GL000247.1, GL000245.1, GL000197.1, GL000203.1, GL000246.1, GL000249.1, GL000196.1, GL000248.1, GL000244.1, GL000238.1, GL000202.1, GL000234.1, GL000232.1, GL000206.1, GL000240.1, GL000236.1, GL000241.1, GL000243.1, GL000242.1, GL000230.1, GL000237.1, GL000233.1, GL000204.1, GL000198.1, GL000208.1, GL000191.1, GL000227.1, GL000228.1, GL000214.1, GL000221.1, GL000209.1, GL000218.1, GL000220.1, GL000213.1, GL000211.1, GL000199.1, GL000217.1, GL000216.1, GL000215.1, GL000205.1, GL000219.1, GL000224.1, GL000223.1, GL000195.1, GL000212.1, GL000222.1, GL000200.1, GL000193.1, GL000194.1, GL000225.1, GL000192.1] please give me suggestions
GATK Input files reference and features have incompatible contigs: No overlapping contigs found. ; GATK BaseRecalibrator error: input files reference and features have incompatible contigs ; GATK: Input files reads and reference have incompatible contigs: No overlapping contigs found ; GATK BaseRecalibrator No overlapping contigs found ERROR ; GATK BaseRecalibrator - Input files knownSites and reference have incompatible contigs ; and more ....