Picard liftover Issue bostau8 to bostau6
Answered
Hi,
I want to liftover vcf file from bostau8 to bostau6 version. But I am getting this error and resulted file is empty. Kindly help me with this issue.
java -jar /home/Software/picard/build/libs/picard.jar LiftoverVcf I=bostau8_rmpcr_r0.80_vcf_ordered_export_populations.snps.vcf O=bostau8_rmpcr_r0.80_vcf_ordered_export_populations.snps_liftover.vcf CHAIN=bosTau8ToBosTau6.over.chain REJECT=rejected_variants.vcf R=/media/s/GBS_DATA/BISON_GBS_DATA/Bison_Project_1/Bostau8_Wisent_Genome/Bos_taurus_Ensembl_UMD3.1/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/version0.6.0/genome.fa
INFO 2021-05-31 11:57:22 LiftoverVcf
********** NOTE: Picard's command line syntax is changing.
**********
********** For more information, please see:
********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)
**********
********** The command line looks like this in the new syntax:
**********
********** LiftoverVcf -I bostau8_rmpcr_r0.80_vcf_ordered_export_populations.snps.vcf -O bostau8_rmpcr_r0.80_vcf_ordered_export_populations.snps_liftover.vcf -CHAIN bosTau8ToBosTau6.over.chain -REJECT rejected_variants.vcf -R /media/shazia/GBS_DATA/BISON_GBS_DATA/Bison_Project_1/Bostau8_Wisent_Genome/Bos_taurus_Ensembl_UMD3.1/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/version0.6.0/genome.fa
**********
11:57:23.068 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/Software/picard/build/libs/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Mon May 31 11:57:23 CEST 2021] LiftoverVcf INPUT=bostau8_rmpcr_r0.80_vcf_ordered_export_populations.snps.vcf OUTPUT=bostau8_rmpcr_r0.80_vcf_ordered_export_populations.snps_liftover.vcf CHAIN=bosTau8ToBosTau6.over.chain REJECT=rejected_variants.vcf REFERENCE_SEQUENCE=/media/shazia/GBS_DATA/BISON_GBS_DATA/Bison_Project_1/Bostau8_Wisent_Genome/Bos_taurus_Ensembl_UMD3.1/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/version0.6.0/genome.fa WARN_ON_MISSING_CONTIG=false LOG_FAILED_INTERVALS=true WRITE_ORIGINAL_POSITION=false WRITE_ORIGINAL_ALLELES=false LIFTOVER_MIN_MATCH=1.0 ALLOW_MISSING_FIELDS_IN_HEADER=false RECOVER_SWAPPED_REF_ALT=false TAGS_TO_REVERSE=[AF] TAGS_TO_DROP=[MAX_AF] DISABLE_SORT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
[Mon May 31 11:57:23 CEST 2021] Executing as shazia@shazia-Lin on Linux 4.15.0-142-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_152-release-1056-b12; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.23.7-SNAPSHOT
INFO 2021-05-31 11:57:23 LiftoverVcf Loading up the target reference genome.
ERROR 2021-05-31 11:57:23 LiftoverVcf Reference /media/shazia/GBS_DATA/BISON_GBS_DATA/Bison_Project_1/Bostau8_Wisent_Genome/Bos_taurus_Ensembl_UMD3.1/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/version0.6.0/genome.fa must have an associated Dictionary .dict file in the same directory.
[Mon May 31 11:57:23 CEST 2021] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1011351552
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
-
Even I had used dict file, but Results are same means resulted file is empty.
java -jar /home/shazia/Software/picard/build/libs/picard.jar LiftoverVcf I=bostau8_rmpcr_r0.80_vcf_ordered_export_populations.snps.vcf O=bostau8_rmpcr_r0.80_vcf_ordered_export_populations.snps_liftover.vcf CHAIN=bosTau8ToBosTau6.over.chain REJECT=rejected_variants.vcf R=/media/shazia/GBS_DATA/BISON_GBS_DATA/Bison_Project_1/Bostau8_Wisent_Genome/Bos_taurus_Ensembl_UMD3.1/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa
INFO 2021-05-31 11:54:02 LiftoverVcf********** NOTE: Picard's command line syntax is changing.
**********
********** For more information, please see:
********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)
**********
********** The command line looks like this in the new syntax:
**********
********** LiftoverVcf -I bostau8_rmpcr_r0.80_vcf_ordered_export_populations.snps.vcf -O bostau8_rmpcr_r0.80_vcf_ordered_export_populations.snps_liftover.vcf -CHAIN bosTau8ToBosTau6.over.chain -REJECT rejected_variants.vcf -R /media/shazia/GBS_DATA/BISON_GBS_DATA/Bison_Project_1/Bostau8_Wisent_Genome/Bos_taurus_Ensembl_UMD3.1/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa
**********
11:54:03.062 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/shazia/Software/picard/build/libs/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Mon May 31 11:54:03 CEST 2021] LiftoverVcf INPUT=bostau8_rmpcr_r0.80_vcf_ordered_export_populations.snps.vcf OUTPUT=bostau8_rmpcr_r0.80_vcf_ordered_export_populations.snps_liftover.vcf CHAIN=bosTau8ToBosTau6.over.chain REJECT=rejected_variants.vcf REFERENCE_SEQUENCE=/media/shazia/GBS_DATA/BISON_GBS_DATA/Bison_Project_1/Bostau8_Wisent_Genome/Bos_taurus_Ensembl_UMD3.1/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa WARN_ON_MISSING_CONTIG=false LOG_FAILED_INTERVALS=true WRITE_ORIGINAL_POSITION=false WRITE_ORIGINAL_ALLELES=false LIFTOVER_MIN_MATCH=1.0 ALLOW_MISSING_FIELDS_IN_HEADER=false RECOVER_SWAPPED_REF_ALT=false TAGS_TO_REVERSE=[AF] TAGS_TO_DROP=[MAX_AF] DISABLE_SORT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
[Mon May 31 11:54:03 CEST 2021] Executing as shazia@shazia-Lin on Linux 4.15.0-142-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_152-release-1056-b12; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.23.7-SNAPSHOT
INFO 2021-05-31 11:54:03 LiftoverVcf Loading up the target reference genome.
INFO 2021-05-31 11:54:19 LiftoverVcf Lifting variants over and sorting (not yet writing the output file.)
ERROR 2021-05-31 11:54:19 LiftoverVcf Encountered a contig, chr10 that is not part of the target reference.
[Mon May 31 11:54:19 CEST 2021] picard.vcf.LiftoverVcf done. Elapsed time: 0.27 minutes.
Runtime.totalMemory()=4576509952
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp -
Hi Abrish,
It looks like you are encountering an error message involving your liftover files.
ERROR 2021-05-31 11:54:19 LiftoverVcf Encountered a contig, chr10 that is not part of the target reference.
You'll need to resolve this issue with your chain file and target reference for LiftOver to run correctly. Here is another forum posts from a user with a similar issue:
Best,
Genevieve
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