Sender: LSF System Subject: Job 216117: in cluster Done Job was submitted from host by user in cluster . Job was executed on host(s) <2*c504>, in queue , as user in cluster . was used as the home directory. was used as the working directory. Started at Results reported on Your job looked like: ------------------------------------------------------------ # LSBATCH: User input #BSUB -J AMR_HG01077 #BSUB -n 2 #BSUB -e bsub_log/AMR_HG01077.run.err #BSUB -o bsub_log/AMR_HG01077.run.out #BSUB -q vvl sed -i '1 i##fileformat=VCFv4.2' /public-supool/home/igdb/human/test_sample/AMR_HG01077.vcf sed 's/^chr//i' -i /public-supool/home/igdb/human/test_sample/AMR_HG01077.vcf echo "Start TimeTamp:"`date +%s` /public-supool/home/igdb/bin/minimac4 --refHaps /public-supool/home/igdb/human/PanelA_chr22.m3vcf.gz --haps /public-supool/home/igdb/human/test_sample/AMR_HG01077.vcf --prefix AMR_HG01077.PanelA_chr22.imputed --meta --cpus 2 echo "End A TimeTamp:"`date +%s` /public-supool/home/igdb/bin/minimac4 --refHaps /public-supool/home/igdb/human/PanelB_chr22.m3vcf.gz --haps /public-supool/home/igdb/human/test_sample/AMR_HG01077.vcf --prefix AMR_HG01077.PanelB_chr22.imputed --meta --cpus 2 echo "End B TimeTamp:"`date +%s` /public-supool/home/igdb/bin/minimac4 --refHaps /public-supool/home/igdb/human/PanelO_chr22.m3vcf.gz --haps /public-supool/home/igdb/human/test_sample/AMR_HG01077.vcf --prefix AMR_HG01077.PanelO_chr22.imputed --meta --cpus 2 echo "End O TimeTamp:"`date +%s` /public-supool/home/igdb/bin/MetaMinimac2 -i AMR_HG01077.PanelA_chr22.imputed:AMR_HG01077.PanelB_chr22.imputed -o AMR_HG01077.meta_chr22.imputed echo "End meta TimeTamp:"`date +%s` ------------------------------------------------------------ Successfully completed. Resource usage summary: CPU time : 25.30 sec. Max Memory : - Average Memory : - Total Requested Memory : - Delta Memory : - Max Swap : - Max Processes : 4 Max Threads : 5 Run time : 258 sec. Turnaround time : 259 sec. The output (if any) follows: Start TimeTamp:1655028210 -------------------------------------------------------------------------------- Minimac4 - Fast Imputation Based on State Space Reduction HMM -------------------------------------------------------------------------------- (c) 2014 - Sayantan Das, Christian Fuchsberger, David Hinds Mary Kate Wing, Goncalo Abecasis Version: 1.0.3; Built: Wed Jun 8 16:57:40 CST 2022 by root Command Line Options: Reference Haplotypes : --refHaps [/public-supool/home/igdb/human/PanelA_chr22.m3vcf.gz], --passOnly, --rsid, --referenceEstimates [ON], --mapFile [docs/geneticMapFile.b38.map.txt.gz] Target Haplotypes : --haps [/public-supool/home/igdb/human/test_sample/AMR_HG01077.vcf] Output Parameters : --prefix [AMR_HG01077.PanelA_chr22.imputed], --estimate, --nobgzip, --vcfBuffer [200], --format [GT,DS], --allTypedSites, --meta [ON], --memUsage Chunking Parameters : --ChunkLengthMb [20.00], --ChunkOverlapMb [3.00] Subset Parameters : --chr [], --start, --end, --window Approximation Parameters : --minimac3, --probThreshold [0.01], --diffThreshold [0.01], --topThreshold [0.01] Other Parameters : --log, --help, --cpus [2], --params PhoneHome : --noPhoneHome, --phoneHomeThinning [50] URL = http://genome.sph.umich.edu/wiki/Minimac4 Starting Main Imputation/Estimation Analysis ... Performing preliminary check on input parameters... ------------------------------------------------------------------------------ PRELIMINARY FILE CHECK ------------------------------------------------------------------------------ Checking GWAS haplotype file : /public-supool/home/igdb/human/test_sample/AMR_HG01077.vcf Gathering variant information ... ERROR !!! Duplicate Variant found chr:22:22857056 with identical REF = T and ALT = Use handle "--ignoreDuplicates" to ignore duplicate instances ... Program Exiting ... End A TimeTamp:1655028291 -------------------------------------------------------------------------------- Minimac4 - Fast Imputation Based on State Space Reduction HMM -------------------------------------------------------------------------------- (c) 2014 - Sayantan Das, Christian Fuchsberger, David Hinds Mary Kate Wing, Goncalo Abecasis Version: 1.0.3; Built: Wed Jun 8 16:57:40 CST 2022 by root Command Line Options: Reference Haplotypes : --refHaps [/public-supool/home/igdb/human/PanelB_chr22.m3vcf.gz], --passOnly, --rsid, --referenceEstimates [ON], --mapFile [docs/geneticMapFile.b38.map.txt.gz] Target Haplotypes : --haps [/public-supool/home/igdb/human/test_sample/AMR_HG01077.vcf] Output Parameters : --prefix [AMR_HG01077.PanelB_chr22.imputed], --estimate, --nobgzip, --vcfBuffer [200], --format [GT,DS], --allTypedSites, --meta [ON], --memUsage Chunking Parameters : --ChunkLengthMb [20.00], --ChunkOverlapMb [3.00] Subset Parameters : --chr [], --start, --end, --window Approximation Parameters : --minimac3, --probThreshold [0.01], --diffThreshold [0.01], --topThreshold [0.01] Other Parameters : --log, --help, --cpus [2], --params PhoneHome : --noPhoneHome, --phoneHomeThinning [50] URL = http://genome.sph.umich.edu/wiki/Minimac4 Starting Main Imputation/Estimation Analysis ... Performing preliminary check on input parameters... ------------------------------------------------------------------------------ PRELIMINARY FILE CHECK ------------------------------------------------------------------------------ Checking GWAS haplotype file : /public-supool/home/igdb/human/test_sample/AMR_HG01077.vcf Gathering variant information ... ERROR !!! Duplicate Variant found chr:22:22857056 with identical REF = T and ALT = Use handle "--ignoreDuplicates" to ignore duplicate instances ... Program Exiting ... End B TimeTamp:1655028373 -------------------------------------------------------------------------------- Minimac4 - Fast Imputation Based on State Space Reduction HMM -------------------------------------------------------------------------------- (c) 2014 - Sayantan Das, Christian Fuchsberger, David Hinds Mary Kate Wing, Goncalo Abecasis Version: 1.0.3; Built: Wed Jun 8 16:57:40 CST 2022 by root Command Line Options: Reference Haplotypes : --refHaps [/public-supool/home/igdb/human/PanelO_chr22.m3vcf.gz], --passOnly, --rsid, --referenceEstimates [ON], --mapFile [docs/geneticMapFile.b38.map.txt.gz] Target Haplotypes : --haps [/public-supool/home/igdb/human/test_sample/AMR_HG01077.vcf] Output Parameters : --prefix [AMR_HG01077.PanelO_chr22.imputed], --estimate, --nobgzip, --vcfBuffer [200], --format [GT,DS], --allTypedSites, --meta [ON], --memUsage Chunking Parameters : --ChunkLengthMb [20.00], --ChunkOverlapMb [3.00] Subset Parameters : --chr [], --start, --end, --window Approximation Parameters : --minimac3, --probThreshold [0.01], --diffThreshold [0.01], --topThreshold [0.01] Other Parameters : --log, --help, --cpus [2], --params PhoneHome : --noPhoneHome, --phoneHomeThinning [50] URL = http://genome.sph.umich.edu/wiki/Minimac4 Starting Main Imputation/Estimation Analysis ... Performing preliminary check on input parameters... ------------------------------------------------------------------------------ PRELIMINARY FILE CHECK ------------------------------------------------------------------------------ Checking GWAS haplotype file : /public-supool/home/igdb/human/test_sample/AMR_HG01077.vcf Gathering variant information ... ERROR !!! Duplicate Variant found chr:22:22857056 with identical REF = T and ALT = Use handle "--ignoreDuplicates" to ignore duplicate instances ... Program Exiting ... End O TimeTamp:1655028454 ------------------------------------------------------------------------------ MetaMinimac2 -- An Efficient Tool for Meta-Imputation ------------------------------------------------------------------------------ (c) 2019 - Ketian Yu, Sayantan Das, Goncalo Abecasis Version : 1.0.0; Built : Sun May 29 22:39:04 CST 2022 by root URL = http://genome.sph.umich.edu/wiki/MetaMinimac2 GIT = https://github.com/yukt/MetaMinimac2.git Command Line Options: --input [AMR_HG01077.PanelA_chr22.imputed:AMR_HG01077.PanelB_chr22.imputed], --output [AMR_HG01077.meta_chr22.imputed], --format [GT,DS,HDS], --skipPhasingCheck [OFF], --skipInfo [OFF], --nobgzip [OFF], --weight [OFF], --log [OFF]. ------------------------------------------------------------------------------ INPUT VCF DOSAGE FILE ------------------------------------------------------------------------------ Number of Studies : 2 -- Study 1 Prefix : AMR_HG01077.PanelA_chr22.imputed -- Study 2 Prefix : AMR_HG01077.PanelB_chr22.imputed Checking sample compatibility across files ... No VCF file found (AMR_HG01077.PanelA_chr22.imputed.dose.vcf or AMR_HG01077.PanelA_chr22.imputed.dose.vcf.gz) Please check input file prefix [AMR_HG01077.PanelA_chr22.imputed] properly ... Program Exiting ... End meta TimeTamp:1655028454 PS: Read file for stderr output of this job. Sender: LSF System Subject: Job 216248: in cluster Done Job was submitted from host by user in cluster . Job was executed on host(s) <1*c504>, in queue , as user in cluster . <7*c501> was used as the home directory. was used as the working directory. Started at Results reported on Your job looked like: ------------------------------------------------------------ # LSBATCH: User input #BSUB -J AMR_HG01077 #BSUB -n 8 #BSUB -e bsub_log/AMR_HG01077.run.err #BSUB -o bsub_log/AMR_HG01077.run.out #BSUB -q vvl sed -i '1 i##fileformat=VCFv4.2' /public-supool/home/igdb/human/test_sample/AMR_HG01077.vcf sed 's/^chr//i' -i /public-supool/home/igdb/human/test_sample/AMR_HG01077.vcf echo "Start TimeTamp:"`date +%s` #/public-supool/home/igdb/bin/minimac4 --refHaps /public-supool/home/igdb/human/PanelA_chr22.m3vcf.gz --haps /public-supool/home/igdb/human/test_sample/AMR_HG01077.vcf --prefix AMR_HG01077.PanelA_chr22.imputed --meta --cpus 8 #echo "End A TimeTamp:"`date +%s` #/public-supool/home/igdb/bin/minimac4 --refHaps /public-supool/home/igdb/human/PanelB_chr22.m3vcf.gz --haps /public-supool/home/igdb/human/test_sample/AMR_HG01077.vcf --prefix AMR_HG01077.PanelB_chr22.imputed --meta --cpus 8 #echo "End B TimeTamp:"`date +%s` #/public-supool/home/igdb/bin/minimac4 --refHaps /public-supool/home/igdb/human/PanelO_chr22.m3vcf.gz --haps /public-supool/home/igdb/human/test_sample/AMR_HG01077.vcf --prefix AMR_HG01077.PanelO_chr22.imputed --meta --cpus 8 #echo "End O TimeTamp:"`date +%s` /public-supool/home/igdb/bin/MetaMinimac2 -i AMR_HG01077.PanelA_chr22.imputed:AMR_HG01077.PanelB_chr22.imputed -o AMR_HG01077.meta_chr22.imputed echo "End meta TimeTamp:"`date +%s` ------------------------------------------------------------ Successfully completed. Resource usage summary: CPU time : 20.23 sec. Max Memory : - Average Memory : - Total Requested Memory : - Delta Memory : - Max Swap : - Max Processes : 4 Max Threads : 5 Run time : 13 sec. Turnaround time : 20 sec. The output (if any) follows: Start TimeTamp:1655032568 ------------------------------------------------------------------------------ MetaMinimac2 -- An Efficient Tool for Meta-Imputation ------------------------------------------------------------------------------ (c) 2019 - Ketian Yu, Sayantan Das, Goncalo Abecasis Version : 1.0.0; Built : Sun May 29 22:39:04 CST 2022 by root URL = http://genome.sph.umich.edu/wiki/MetaMinimac2 GIT = https://github.com/yukt/MetaMinimac2.git Command Line Options: --input [AMR_HG01077.PanelA_chr22.imputed:AMR_HG01077.PanelB_chr22.imputed], --output [AMR_HG01077.meta_chr22.imputed], --format [GT,DS,HDS], --skipPhasingCheck [OFF], --skipInfo [OFF], --nobgzip [OFF], --weight [OFF], --log [OFF]. ------------------------------------------------------------------------------ INPUT VCF DOSAGE FILE ------------------------------------------------------------------------------ Number of Studies : 2 -- Study 1 Prefix : AMR_HG01077.PanelA_chr22.imputed -- Study 2 Prefix : AMR_HG01077.PanelB_chr22.imputed Checking sample compatibility across files ... No VCF file found (AMR_HG01077.PanelA_chr22.imputed.dose.vcf or AMR_HG01077.PanelA_chr22.imputed.dose.vcf.gz) Please check input file prefix [AMR_HG01077.PanelA_chr22.imputed] properly ... Program Exiting ... End meta TimeTamp:1655032568 PS: Read file for stderr output of this job. Sender: LSF System Subject: Job 216360: in cluster Done Job was submitted from host by user in cluster . Job was executed on host(s) <8*c102>, in queue , as user in cluster . was used as the home directory. was used as the working directory. Started at Results reported on Your job looked like: ------------------------------------------------------------ # LSBATCH: User input #BSUB -J AMR_HG01077 #BSUB -n 8 #BSUB -e bsub_log/AMR_HG01077.run.err #BSUB -o bsub_log/AMR_HG01077.run.out #BSUB -q vvl #sed -i '1 i##fileformat=VCFv4.2' /public-supool/home/igdb/human/test_sample/AMR_HG01077.vcf #sed 's/^chr//i' -i /public-supool/home/igdb/human/test_sample/AMR_HG01077.vcf echo "Start TimeTamp:"`date +%s` #/public-supool/home/igdb/bin/minimac4 --refHaps /public-supool/home/igdb/human/PanelA_chr22.m3vcf.gz --haps /public-supool/home/igdb/human/test_sample/AMR_HG01077.vcf --prefix AMR_HG01077.PanelA_chr22.imputed --meta --cpus 8 #echo "End A TimeTamp:"`date +%s` #/public-supool/home/igdb/bin/minimac4 --refHaps /public-supool/home/igdb/human/PanelB_chr22.m3vcf.gz --haps /public-supool/home/igdb/human/test_sample/AMR_HG01077.vcf --prefix AMR_HG01077.PanelB_chr22.imputed --meta --cpus 8 #echo "End B TimeTamp:"`date +%s` #/public-supool/home/igdb/bin/minimac4 --refHaps /public-supool/home/igdb/human/PanelO_chr22.m3vcf.gz --haps /public-supool/home/igdb/human/test_sample/AMR_HG01077.vcf --prefix AMR_HG01077.PanelO_chr22.imputed --meta --cpus 8 #echo "End O TimeTamp:"`date +%s` /public-supool/home/igdb/bin/MetaMinimac2 --skipPhasingCheck -s -i AMR_HG01077.PanelA_chr22.imputed:AMR_HG01077.PanelB_chr22.imputed -o AMR_HG01077.meta_chr22.imputed echo "End meta TimeTamp:"`date +%s` ------------------------------------------------------------ Successfully completed. Resource usage summary: CPU time : 0.06 sec. Max Memory : - Average Memory : - Total Requested Memory : - Delta Memory : - Max Swap : - Max Processes : 1 Max Threads : 1 Run time : 1 sec. Turnaround time : 5 sec. The output (if any) follows: Start TimeTamp:1655044014 ------------------------------------------------------------------------------ MetaMinimac2 -- An Efficient Tool for Meta-Imputation ------------------------------------------------------------------------------ (c) 2019 - Ketian Yu, Sayantan Das, Goncalo Abecasis Version : 1.0.0; Built : Sun May 29 22:39:04 CST 2022 by root URL = http://genome.sph.umich.edu/wiki/MetaMinimac2 GIT = https://github.com/yukt/MetaMinimac2.git Command Line Options: --input [AMR_HG01077.PanelA_chr22.imputed:AMR_HG01077.PanelB_chr22.imputed], --output [AMR_HG01077.meta_chr22.imputed], --format [GT,DS,HDS], --skipPhasingCheck [ON], --skipInfo [ON], --nobgzip [OFF], --weight [OFF], --log [OFF]. ------------------------------------------------------------------------------ INPUT VCF DOSAGE FILE ------------------------------------------------------------------------------ Number of Studies : 2 -- Study 1 Prefix : AMR_HG01077.PanelA_chr22.imputed -- Study 2 Prefix : AMR_HG01077.PanelB_chr22.imputed Checking sample compatibility across files ... No VCF file found (AMR_HG01077.PanelA_chr22.imputed.dose.vcf or AMR_HG01077.PanelA_chr22.imputed.dose.vcf.gz) Please check input file prefix [AMR_HG01077.PanelA_chr22.imputed] properly ... Program Exiting ... End meta TimeTamp:1655044014 PS: Read file for stderr output of this job. Sender: LSF System Subject: Job 216445: in cluster Done Job was submitted from host by user in cluster . Job was executed on host(s) <8*c302>, in queue , as user in cluster . was used as the home directory. was used as the working directory. Started at Results reported on Your job looked like: ------------------------------------------------------------ # LSBATCH: User input #BSUB -J AMR_HG01077 #BSUB -n 8 #BSUB -e bsub_log/AMR_HG01077.run.err #BSUB -o bsub_log/AMR_HG01077.run.out #BSUB -q vvl #sed -i '1 i##fileformat=VCFv4.2' /public-supool/home/igdb/human/test_sample/AMR_HG01077.vcf #sed 's/^chr//i' -i /public-supool/home/igdb/human/test_sample/AMR_HG01077.vcf echo "Start TimeTamp:"`date +%s` /public-supool/home/igdb/bin/minimac4 --ignoreDuplicates --refHaps /public-supool/home/igdb/human/PanelA_chr22.m3vcf.gz --haps /public-supool/home/igdb/human/test_sample/AMR_HG01077.vcf --prefix AMR_HG01077.PanelA_chr22.imputed --meta --cpus 8 echo "End A TimeTamp:"`date +%s` /public-supool/home/igdb/bin/minimac4 --ignoreDuplicates --refHaps /public-supool/home/igdb/human/PanelB_chr22.m3vcf.gz --haps /public-supool/home/igdb/human/test_sample/AMR_HG01077.vcf --prefix AMR_HG01077.PanelB_chr22.imputed --meta --cpus 8 echo "End B TimeTamp:"`date +%s` /public-supool/home/igdb/bin/minimac4 --ignoreDuplicates --refHaps /public-supool/home/igdb/human/PanelO_chr22.m3vcf.gz --haps /public-supool/home/igdb/human/test_sample/AMR_HG01077.vcf --prefix AMR_HG01077.PanelO_chr22.imputed --meta --cpus 8 echo "End O TimeTamp:"`date +%s` /public-supool/home/igdb/bin/MetaMinimac2 --skipPhasingCheck -s -i AMR_HG01077.PanelA_chr22.imputed:AMR_HG01077.PanelB_chr22.imputed -o AMR_HG01077.meta_chr22.imputed echo "End meta TimeTamp:"`date +%s` ------------------------------------------------------------ Successfully completed. Resource usage summary: CPU time : 2067.15 sec. Max Memory : 22 GB Average Memory : 6.62 GB Total Requested Memory : - Delta Memory : - Max Swap : - Max Processes : 4 Max Threads : 12 Run time : 2139 sec. Turnaround time : 2141 sec. The output (if any) follows: Start TimeTamp:1655045389 -------------------------------------------------------------------------------- Minimac4 - Fast Imputation Based on State Space Reduction HMM -------------------------------------------------------------------------------- (c) 2014 - Sayantan Das, Christian Fuchsberger, David Hinds Mary Kate Wing, Goncalo Abecasis Version: 1.0.3; Built: Wed Jun 8 16:57:40 CST 2022 by root Command Line Options: Reference Haplotypes : --refHaps [/public-supool/home/igdb/human/PanelA_chr22.m3vcf.gz], --passOnly, --rsid, --referenceEstimates [ON], --mapFile [docs/geneticMapFile.b38.map.txt.gz] Target Haplotypes : --haps [/public-supool/home/igdb/human/test_sample/AMR_HG01077.vcf] Output Parameters : --prefix [AMR_HG01077.PanelA_chr22.imputed], --estimate, --nobgzip, --vcfBuffer [200], --format [GT,DS], --allTypedSites, --meta [ON], --memUsage Chunking Parameters : --ChunkLengthMb [20.00], --ChunkOverlapMb [3.00] Subset Parameters : --chr [], --start, --end, --window Approximation Parameters : --minimac3, --probThreshold [0.01], --diffThreshold [0.01], --topThreshold [0.01] Other Parameters : --log, --help, --cpus [8], --params PhoneHome : --noPhoneHome, --phoneHomeThinning [50] Additional Options: --ignoreDuplicates [1] URL = http://genome.sph.umich.edu/wiki/Minimac4 Starting Main Imputation/Estimation Analysis ... Performing preliminary check on input parameters... ------------------------------------------------------------------------------ PRELIMINARY FILE CHECK ------------------------------------------------------------------------------ Checking GWAS haplotype file : /public-supool/home/igdb/human/test_sample/AMR_HG01077.vcf Gathering variant information ... Successful !!! Checking Reference haplotype file : /public-supool/home/igdb/human/PanelA_chr22.m3vcf.gz Gathering variant information ... Successful !!! Reference Panel : Found 1166 samples (2332 haplotypes) and 1066555 variants ... Target/GWAS Panel : Found 1 samples (2 haplotypes) and 1066555 variants ... 1066555 variants overlap with Reference panel 0 variants imported that exist only in Target/GWAS panel ------------------------------------------------------------------------------ CHUNKING INFORMATION ------------------------------------------------------------------------------ Chunking region into 2 chunk(s) with atleast 533277 variants in each chunk ... Details of chunks is given below ... No LeftBuffer LeftEnd RightPoint RightBuffer #Sites(GWAS/Ref/%) ------------------------------------------------------------------------------- 1 10519265 10519265 32517791 35512616 615350/ 615350/ 100.00% 2 29249667 32517792 50808014 50808014 615338/ 615338/ 100.00% ------------------------------------------------------------------------------ MAIN IMPUTATION ANALYSIS ------------------------------------------------------------------------------ Starting imputation analysis of 2 chunk(s) ... ------------------------------------------- Analyzing Chunk 1/2 [22:10519265-35512616] ------------------------------------------- Reading chunk from reference panel ... Reading chunk from target/GWAS panel ... Compressing reference panel at GWAS sites ... Re-compression successful (155 seconds) !!! Starting Imputation ... Imputing Samples 1-1 [100%] out of 1 samples ... Saving Samples in temporary VCF file ... Imputation successful (3 seconds) !!! Appending chunk to final output VCF File : AMR_HG01077.PanelA_chr22.imputed.dose.vcf.gz Appending successful (2 seconds) !!! Time taken for this chunk = 170 seconds. ------------------------------------------- Analyzing Chunk 2/2 [22:29249667-50808014] ------------------------------------------- Reading chunk from reference panel ... Reading chunk from target/GWAS panel ... Compressing reference panel at GWAS sites ... Re-compression successful (160 seconds) !!! Starting Imputation ... Imputing Samples 1-1 [100%] out of 1 samples ... Saving Samples in temporary VCF file ... Imputation successful (2 seconds) !!! Appending chunk to final output VCF File : AMR_HG01077.PanelA_chr22.imputed.dose.vcf.gz Appending successful (2 seconds) !!! Time taken for this chunk = 172 seconds. ------------------------------------------------------------------------------ SUMMARY OF ANALYSIS ------------------------------------------------------------------------------ Info file written to : AMR_HG01077.PanelA_chr22.imputed.info Imputed VCF information written to : AMR_HG01077.PanelA_chr22.imputed.dose.vcf.gz Empirical Dosage VCF written to : AMR_HG01077.PanelA_chr22.imputed.empiricalDose.vcf.gz Time Taken for Reading File = 22 seconds Time Taken for Re-compression = 315 seconds Time Taken for Imputation = 4 seconds Time Taken for Writing File = 8 seconds ------------------------------------------------------------------------------ END OF PROGRAM ------------------------------------------------------------------------------ Program Successfully Implemented... Total Run completed in 0 hours, 5 mins, 58 seconds. Thank You for using Minimac4 !!! End A TimeTamp:1655045828 -------------------------------------------------------------------------------- Minimac4 - Fast Imputation Based on State Space Reduction HMM -------------------------------------------------------------------------------- (c) 2014 - Sayantan Das, Christian Fuchsberger, David Hinds Mary Kate Wing, Goncalo Abecasis Version: 1.0.3; Built: Wed Jun 8 16:57:40 CST 2022 by root Command Line Options: Reference Haplotypes : --refHaps [/public-supool/home/igdb/human/PanelB_chr22.m3vcf.gz], --passOnly, --rsid, --referenceEstimates [ON], --mapFile [docs/geneticMapFile.b38.map.txt.gz] Target Haplotypes : --haps [/public-supool/home/igdb/human/test_sample/AMR_HG01077.vcf] Output Parameters : --prefix [AMR_HG01077.PanelB_chr22.imputed], --estimate, --nobgzip, --vcfBuffer [200], --format [GT,DS], --allTypedSites, --meta [ON], --memUsage Chunking Parameters : --ChunkLengthMb [20.00], --ChunkOverlapMb [3.00] Subset Parameters : --chr [], --start, --end, --window Approximation Parameters : --minimac3, --probThreshold [0.01], --diffThreshold [0.01], --topThreshold [0.01] Other Parameters : --log, --help, --cpus [8], --params PhoneHome : --noPhoneHome, --phoneHomeThinning [50] Additional Options: --ignoreDuplicates [1] URL = http://genome.sph.umich.edu/wiki/Minimac4 Starting Main Imputation/Estimation Analysis ... Performing preliminary check on input parameters... ------------------------------------------------------------------------------ PRELIMINARY FILE CHECK ------------------------------------------------------------------------------ Checking GWAS haplotype file : /public-supool/home/igdb/human/test_sample/AMR_HG01077.vcf Gathering variant information ... Successful !!! Checking Reference haplotype file : /public-supool/home/igdb/human/PanelB_chr22.m3vcf.gz Gathering variant information ... Successful !!! Reference Panel : Found 1986 samples (3972 haplotypes) and 1066555 variants ... Target/GWAS Panel : Found 1 samples (2 haplotypes) and 1066555 variants ... 1066555 variants overlap with Reference panel 0 variants imported that exist only in Target/GWAS panel ------------------------------------------------------------------------------ CHUNKING INFORMATION ------------------------------------------------------------------------------ Chunking region into 2 chunk(s) with atleast 533277 variants in each chunk ... Details of chunks is given below ... No LeftBuffer LeftEnd RightPoint RightBuffer #Sites(GWAS/Ref/%) ------------------------------------------------------------------------------- 1 10519265 10519265 32517791 35512136 615340/ 615340/ 100.00% 2 29249787 32517792 50808014 50808014 615335/ 615335/ 100.00% ------------------------------------------------------------------------------ MAIN IMPUTATION ANALYSIS ------------------------------------------------------------------------------ Starting imputation analysis of 2 chunk(s) ... ------------------------------------------- Analyzing Chunk 1/2 [22:10519265-35512136] ------------------------------------------- Reading chunk from reference panel ... Reading chunk from target/GWAS panel ... Compressing reference panel at GWAS sites ... Re-compression successful (254 seconds) !!! Starting Imputation ... Imputing Samples 1-1 [100%] out of 1 samples ... Saving Samples in temporary VCF file ... Imputation successful (3 seconds) !!! Appending chunk to final output VCF File : AMR_HG01077.PanelB_chr22.imputed.dose.vcf.gz Appending successful (2 seconds) !!! Time taken for this chunk = 274 seconds. ------------------------------------------- Analyzing Chunk 2/2 [22:29249787-50808014] ------------------------------------------- Reading chunk from reference panel ... Reading chunk from target/GWAS panel ... Compressing reference panel at GWAS sites ... Re-compression successful (261 seconds) !!! Starting Imputation ... Imputing Samples 1-1 [100%] out of 1 samples ... Saving Samples in temporary VCF file ... Imputation successful (3 seconds) !!! Appending chunk to final output VCF File : AMR_HG01077.PanelB_chr22.imputed.dose.vcf.gz Appending successful (3 seconds) !!! Time taken for this chunk = 277 seconds. ------------------------------------------------------------------------------ SUMMARY OF ANALYSIS ------------------------------------------------------------------------------ Info file written to : AMR_HG01077.PanelB_chr22.imputed.info Imputed VCF information written to : AMR_HG01077.PanelB_chr22.imputed.dose.vcf.gz Empirical Dosage VCF written to : AMR_HG01077.PanelB_chr22.imputed.empiricalDose.vcf.gz Time Taken for Reading File = 28 seconds Time Taken for Re-compression = 515 seconds Time Taken for Imputation = 5 seconds Time Taken for Writing File = 9 seconds ------------------------------------------------------------------------------ END OF PROGRAM ------------------------------------------------------------------------------ Program Successfully Implemented... Total Run completed in 0 hours, 9 mins, 27 seconds. Thank You for using Minimac4 !!! End B TimeTamp:1655046477 -------------------------------------------------------------------------------- Minimac4 - Fast Imputation Based on State Space Reduction HMM -------------------------------------------------------------------------------- (c) 2014 - Sayantan Das, Christian Fuchsberger, David Hinds Mary Kate Wing, Goncalo Abecasis Version: 1.0.3; Built: Wed Jun 8 16:57:40 CST 2022 by root Command Line Options: Reference Haplotypes : --refHaps [/public-supool/home/igdb/human/PanelO_chr22.m3vcf.gz], --passOnly, --rsid, --referenceEstimates [ON], --mapFile [docs/geneticMapFile.b38.map.txt.gz] Target Haplotypes : --haps [/public-supool/home/igdb/human/test_sample/AMR_HG01077.vcf] Output Parameters : --prefix [AMR_HG01077.PanelO_chr22.imputed], --estimate, --nobgzip, --vcfBuffer [200], --format [GT,DS], --allTypedSites, --meta [ON], --memUsage Chunking Parameters : --ChunkLengthMb [20.00], --ChunkOverlapMb [3.00] Subset Parameters : --chr [], --start, --end, --window Approximation Parameters : --minimac3, --probThreshold [0.01], --diffThreshold [0.01], --topThreshold [0.01] Other Parameters : --log, --help, --cpus [8], --params PhoneHome : --noPhoneHome, --phoneHomeThinning [50] Additional Options: --ignoreDuplicates [1] URL = http://genome.sph.umich.edu/wiki/Minimac4 Starting Main Imputation/Estimation Analysis ... Performing preliminary check on input parameters... ------------------------------------------------------------------------------ PRELIMINARY FILE CHECK ------------------------------------------------------------------------------ Checking GWAS haplotype file : /public-supool/home/igdb/human/test_sample/AMR_HG01077.vcf Gathering variant information ... Successful !!! Checking Reference haplotype file : /public-supool/home/igdb/human/PanelO_chr22.m3vcf.gz Gathering variant information ... Successful !!! Reference Panel : Found 3152 samples (6304 haplotypes) and 1066555 variants ... Target/GWAS Panel : Found 1 samples (2 haplotypes) and 1066555 variants ... 1066555 variants overlap with Reference panel 0 variants imported that exist only in Target/GWAS panel ------------------------------------------------------------------------------ CHUNKING INFORMATION ------------------------------------------------------------------------------ Chunking region into 2 chunk(s) with atleast 533277 variants in each chunk ... Details of chunks is given below ... No LeftBuffer LeftEnd RightPoint RightBuffer #Sites(GWAS/Ref/%) ------------------------------------------------------------------------------- 1 10519265 10519265 32517791 35513154 615360/ 615360/ 100.00% 2 29249787 32517792 50808014 50808014 615335/ 615335/ 100.00% ------------------------------------------------------------------------------ MAIN IMPUTATION ANALYSIS ------------------------------------------------------------------------------ Starting imputation analysis of 2 chunk(s) ... ------------------------------------------- Analyzing Chunk 1/2 [22:10519265-35513154] ------------------------------------------- Reading chunk from reference panel ... Reading chunk from target/GWAS panel ... Compressing reference panel at GWAS sites ... Re-compression successful (427 seconds) !!! Starting Imputation ... Imputing Samples 1-1 [100%] out of 1 samples ... Saving Samples in temporary VCF file ... Imputation successful (5 seconds) !!! Appending chunk to final output VCF File : AMR_HG01077.PanelO_chr22.imputed.dose.vcf.gz Appending successful (2 seconds) !!! Time taken for this chunk = 453 seconds. ------------------------------------------- Analyzing Chunk 2/2 [22:29249787-50808014] ------------------------------------------- Reading chunk from reference panel ... Reading chunk from target/GWAS panel ... Compressing reference panel at GWAS sites ... Re-compression successful (444 seconds) !!! Starting Imputation ... Imputing Samples 1-1 [100%] out of 1 samples ... Saving Samples in temporary VCF file ... Imputation successful (5 seconds) !!! Appending chunk to final output VCF File : AMR_HG01077.PanelO_chr22.imputed.dose.vcf.gz Appending successful (2 seconds) !!! Time taken for this chunk = 469 seconds. ------------------------------------------------------------------------------ SUMMARY OF ANALYSIS ------------------------------------------------------------------------------ Info file written to : AMR_HG01077.PanelO_chr22.imputed.info Imputed VCF information written to : AMR_HG01077.PanelO_chr22.imputed.dose.vcf.gz Empirical Dosage VCF written to : AMR_HG01077.PanelO_chr22.imputed.empiricalDose.vcf.gz Time Taken for Reading File = 34 seconds Time Taken for Re-compression = 871 seconds Time Taken for Imputation = 9 seconds Time Taken for Writing File = 8 seconds ------------------------------------------------------------------------------ END OF PROGRAM ------------------------------------------------------------------------------ Program Successfully Implemented... Total Run completed in 0 hours, 15 mins, 40 seconds. Thank You for using Minimac4 !!! End O TimeTamp:1655047498 ------------------------------------------------------------------------------ MetaMinimac2 -- An Efficient Tool for Meta-Imputation ------------------------------------------------------------------------------ (c) 2019 - Ketian Yu, Sayantan Das, Goncalo Abecasis Version : 1.0.0; Built : Sun May 29 22:39:04 CST 2022 by root URL = http://genome.sph.umich.edu/wiki/MetaMinimac2 GIT = https://github.com/yukt/MetaMinimac2.git Command Line Options: --input [AMR_HG01077.PanelA_chr22.imputed:AMR_HG01077.PanelB_chr22.imputed], --output [AMR_HG01077.meta_chr22.imputed], --format [GT,DS,HDS], --skipPhasingCheck [ON], --skipInfo [ON], --nobgzip [OFF], --weight [OFF], --log [OFF]. ------------------------------------------------------------------------------ INPUT VCF DOSAGE FILE ------------------------------------------------------------------------------ Number of Studies : 2 -- Study 1 Prefix : AMR_HG01077.PanelA_chr22.imputed -- Study 2 Prefix : AMR_HG01077.PanelB_chr22.imputed Checking sample compatibility across files ... -- Found 1 samples (2 haplotypes). Scanning input empirical VCFs for commonly typed SNPs ... -- Study 1 #Genotyped Sites = 1066555 -- Study 2 #Genotyped Sites = 1066555 -- Found 1066555 commonly genotyped! -- Successful (5 seconds) !!! Warning !!! Phasing Consistency Check is Skipped. User is responsible for making sure the phasing are consistent across input files. If phasing is inconsistent, meta-imputed results will not make sense. ------------------------------------------------------------------------------ WEIGHT ESTIMATION ------------------------------------------------------------------------------ Estimate Meta-Weights for Sample 1-1 [100.0%] ... -- Loading Empirical Dosage Data ... -- Calculating Weights ... -- Successful (10 seconds) !!! Weight Estimation Completed in 0 hours, 0 mins, 10 seconds. ------------------------------------------------------------------------------ FINAL ANALYSIS ------------------------------------------------------------------------------ Gathering dosege information and saving results for all samples ... Final Analysis Completed in 0 hours, 0 mins, 13 seconds. ------------------------------------------------------------------------------ END OF PROGRAM ------------------------------------------------------------------------------ Meta-Imputation Completed in 0 hours, 0 mins, 29 seconds. Study 1 #Markers = 1066555 Study 2 #Markers = 1066555 Total #Markers = 1066555 Thank You for using MetaMinimac2 !!! End meta TimeTamp:1655047527 PS: Read file for stderr output of this job.