Sender: LSF System Subject: Job 216077: in cluster Done Job was submitted from host by user in cluster . Job was executed on host(s) <2*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 EUR_NA20534_chip #BSUB -n 2 #BSUB -e bsub_log/EUR_NA20534_chip.run.err #BSUB -o bsub_log/EUR_NA20534_chip.run.out #BSUB -q vvl sed -i '1 i##fileformat=VCFv4.2' /public-supool/home/igdb/human/test_sample/EUR_NA20534_chip.vcf sed 's/^chr//i' -i /public-supool/home/igdb/human/test_sample/EUR_NA20534_chip.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/EUR_NA20534_chip.vcf --prefix EUR_NA20534_chip.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/EUR_NA20534_chip.vcf --prefix EUR_NA20534_chip.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/EUR_NA20534_chip.vcf --prefix EUR_NA20534_chip.PanelO_chr22.imputed --meta --cpus 2 echo "End O TimeTamp:"`date +%s` /public-supool/home/igdb/bin/MetaMinimac2 -i EUR_NA20534_chip.PanelA_chr22.imputed:EUR_NA20534_chip.PanelB_chr22.imputed -o EUR_NA20534_chip.meta_chr22.imputed echo "End meta TimeTamp:"`date +%s` ------------------------------------------------------------ Successfully completed. Resource usage summary: CPU time : 103.50 sec. Max Memory : 1 GB Average Memory : 0.55 GB Total Requested Memory : - Delta Memory : - Max Swap : - Max Processes : 4 Max Threads : 6 Run time : 344 sec. Turnaround time : 346 sec. The output (if any) follows: Start TimeTamp:1655028197 -------------------------------------------------------------------------------- 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/EUR_NA20534_chip.vcf] Output Parameters : --prefix [EUR_NA20534_chip.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/EUR_NA20534_chip.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 8516 variants ... 8516 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 4269/ 615350/ 0.69% 2 29249667 32517792 50808014 50808014 5594/ 615338/ 0.91% ------------------------------------------------------------------------------ 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 (1 seconds) !!! Starting Imputation ... Imputing Samples 1-1 [100%] out of 1 samples ... Saving Samples in temporary VCF file ... Imputation successful (0 seconds) !!! Appending chunk to final output VCF File : EUR_NA20534_chip.PanelA_chr22.imputed.dose.vcf.gz Appending successful (3 seconds) !!! Time taken for this chunk = 9 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 (1 seconds) !!! Starting Imputation ... Imputing Samples 1-1 [100%] out of 1 samples ... Saving Samples in temporary VCF file ... Imputation successful (0 seconds) !!! Appending chunk to final output VCF File : EUR_NA20534_chip.PanelA_chr22.imputed.dose.vcf.gz Appending successful (3 seconds) !!! Time taken for this chunk = 8 seconds. ------------------------------------------------------------------------------ SUMMARY OF ANALYSIS ------------------------------------------------------------------------------ Info file written to : EUR_NA20534_chip.PanelA_chr22.imputed.info Imputed VCF information written to : EUR_NA20534_chip.PanelA_chr22.imputed.dose.vcf.gz Empirical Dosage VCF written to : EUR_NA20534_chip.PanelA_chr22.imputed.empiricalDose.vcf.gz Time Taken for Reading File = 16 seconds Time Taken for Re-compression = 2 seconds Time Taken for Imputation = 0 seconds Time Taken for Writing File = 6 seconds ------------------------------------------------------------------------------ END OF PROGRAM ------------------------------------------------------------------------------ Program Successfully Implemented... Total Run completed in 0 hours, 0 mins, 26 seconds. Thank You for using Minimac4 !!! End A TimeTamp:1655028303 -------------------------------------------------------------------------------- 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/EUR_NA20534_chip.vcf] Output Parameters : --prefix [EUR_NA20534_chip.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/EUR_NA20534_chip.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 8516 variants ... 8516 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 4269/ 615340/ 0.69% 2 29249787 32517792 50808014 50808014 5594/ 615335/ 0.91% ------------------------------------------------------------------------------ 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 (1 seconds) !!! Starting Imputation ... Imputing Samples 1-1 [100%] out of 1 samples ... Saving Samples in temporary VCF file ... Imputation successful (1 seconds) !!! Appending chunk to final output VCF File : EUR_NA20534_chip.PanelB_chr22.imputed.dose.vcf.gz Appending successful (2 seconds) !!! Time taken for this chunk = 11 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 (1 seconds) !!! Starting Imputation ... Imputing Samples 1-1 [100%] out of 1 samples ... Saving Samples in temporary VCF file ... Imputation successful (1 seconds) !!! Appending chunk to final output VCF File : EUR_NA20534_chip.PanelB_chr22.imputed.dose.vcf.gz Appending successful (2 seconds) !!! Time taken for this chunk = 11 seconds. ------------------------------------------------------------------------------ SUMMARY OF ANALYSIS ------------------------------------------------------------------------------ Info file written to : EUR_NA20534_chip.PanelB_chr22.imputed.info Imputed VCF information written to : EUR_NA20534_chip.PanelB_chr22.imputed.dose.vcf.gz Empirical Dosage VCF written to : EUR_NA20534_chip.PanelB_chr22.imputed.empiricalDose.vcf.gz Time Taken for Reading File = 23 seconds Time Taken for Re-compression = 2 seconds Time Taken for Imputation = 0 seconds Time Taken for Writing File = 6 seconds ------------------------------------------------------------------------------ END OF PROGRAM ------------------------------------------------------------------------------ Program Successfully Implemented... Total Run completed in 0 hours, 0 mins, 33 seconds. Thank You for using Minimac4 !!! End B TimeTamp:1655028417 -------------------------------------------------------------------------------- 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/EUR_NA20534_chip.vcf] Output Parameters : --prefix [EUR_NA20534_chip.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/EUR_NA20534_chip.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 8516 variants ... 8516 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 4269/ 615360/ 0.69% 2 29249787 32517792 50808014 50808014 5594/ 615335/ 0.91% ------------------------------------------------------------------------------ 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 (2 seconds) !!! Starting Imputation ... Imputing Samples 1-1 [100%] out of 1 samples ... Saving Samples in temporary VCF file ... Imputation successful (1 seconds) !!! Appending chunk to final output VCF File : EUR_NA20534_chip.PanelO_chr22.imputed.dose.vcf.gz Appending successful (2 seconds) !!! Time taken for this chunk = 15 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 (2 seconds) !!! Starting Imputation ... Imputing Samples 1-1 [100%] out of 1 samples ... Saving Samples in temporary VCF file ... Imputation successful (0 seconds) !!! Appending chunk to final output VCF File : EUR_NA20534_chip.PanelO_chr22.imputed.dose.vcf.gz Appending successful (3 seconds) !!! Time taken for this chunk = 15 seconds. ------------------------------------------------------------------------------ SUMMARY OF ANALYSIS ------------------------------------------------------------------------------ Info file written to : EUR_NA20534_chip.PanelO_chr22.imputed.info Imputed VCF information written to : EUR_NA20534_chip.PanelO_chr22.imputed.dose.vcf.gz Empirical Dosage VCF written to : EUR_NA20534_chip.PanelO_chr22.imputed.empiricalDose.vcf.gz Time Taken for Reading File = 28 seconds Time Taken for Re-compression = 4 seconds Time Taken for Imputation = 0 seconds Time Taken for Writing File = 6 seconds ------------------------------------------------------------------------------ END OF PROGRAM ------------------------------------------------------------------------------ Program Successfully Implemented... Total Run completed in 0 hours, 0 mins, 41 seconds. Thank You for using Minimac4 !!! End O TimeTamp:1655028538 ------------------------------------------------------------------------------ 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 [EUR_NA20534_chip.PanelA_chr22.imputed:EUR_NA20534_chip.PanelB_chr22.imputed], --output [EUR_NA20534_chip.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 : EUR_NA20534_chip.PanelA_chr22.imputed -- Study 2 Prefix : EUR_NA20534_chip.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 = 8516 -- Study 2 #Genotyped Sites = 8516 -- Found 8516 commonly genotyped! -- Successful (0 seconds) !!! Checking phasing consistency across input files ... -- Consistent among commonly genotyped sites. -- Completed in 0 seconds. ------------------------------------------------------------------------------ WEIGHT ESTIMATION ------------------------------------------------------------------------------ Estimate Meta-Weights for Sample 1-1 [100.0%] ... -- Loading Empirical Dosage Data ... -- Calculating Weights ... -- Successful (0 seconds) !!! Weight Estimation Completed in 0 hours, 0 mins, 0 seconds. ------------------------------------------------------------------------------ FINAL ANALYSIS ------------------------------------------------------------------------------ End meta TimeTamp:1655028539 PS: Read file for stderr output of this job. Sender: LSF System Subject: Job 216208: in cluster Done Job was submitted from host by user in cluster . Job was executed on host(s) <8*c603>, 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 EUR_NA20534_chip #BSUB -n 8 #BSUB -e bsub_log/EUR_NA20534_chip.run.err #BSUB -o bsub_log/EUR_NA20534_chip.run.out #BSUB -q vvl sed -i '1 i##fileformat=VCFv4.2' /public-supool/home/igdb/human/test_sample/EUR_NA20534_chip.vcf sed 's/^chr//i' -i /public-supool/home/igdb/human/test_sample/EUR_NA20534_chip.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/EUR_NA20534_chip.vcf --prefix EUR_NA20534_chip.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/EUR_NA20534_chip.vcf --prefix EUR_NA20534_chip.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/EUR_NA20534_chip.vcf --prefix EUR_NA20534_chip.PanelO_chr22.imputed --meta --cpus 8 #echo "End O TimeTamp:"`date +%s` /public-supool/home/igdb/bin/MetaMinimac2 -i EUR_NA20534_chip.PanelA_chr22.imputed:EUR_NA20534_chip.PanelB_chr22.imputed -o EUR_NA20534_chip.meta_chr22.imputed echo "End meta TimeTamp:"`date +%s` ------------------------------------------------------------ Successfully completed. Resource usage summary: CPU time : 0.45 sec. Max Memory : - Average Memory : - Total Requested Memory : - Delta Memory : - Max Swap : - Max Processes : 4 Max Threads : 5 Run time : 1 sec. Turnaround time : 3 sec. The output (if any) follows: Start TimeTamp:1655032550 ------------------------------------------------------------------------------ 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 [EUR_NA20534_chip.PanelA_chr22.imputed:EUR_NA20534_chip.PanelB_chr22.imputed], --output [EUR_NA20534_chip.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 : EUR_NA20534_chip.PanelA_chr22.imputed -- Study 2 Prefix : EUR_NA20534_chip.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 = 8516 -- Study 2 #Genotyped Sites = 8516 -- Found 8516 commonly genotyped! -- Successful (0 seconds) !!! Checking phasing consistency across input files ... -- Consistent among commonly genotyped sites. -- Completed in 0 seconds. ------------------------------------------------------------------------------ WEIGHT ESTIMATION ------------------------------------------------------------------------------ Estimate Meta-Weights for Sample 1-1 [100.0%] ... -- Loading Empirical Dosage Data ... -- Calculating Weights ... -- Successful (0 seconds) !!! Weight Estimation Completed in 0 hours, 0 mins, 0 seconds. ------------------------------------------------------------------------------ FINAL ANALYSIS ------------------------------------------------------------------------------ End meta TimeTamp:1655032550 PS: Read file for stderr output of this job. Sender: LSF System Subject: Job 216320: in cluster Done Job was submitted from host by user in cluster . Job was executed on host(s) <8*c604>, 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 EUR_NA20534_chip #BSUB -n 8 #BSUB -e bsub_log/EUR_NA20534_chip.run.err #BSUB -o bsub_log/EUR_NA20534_chip.run.out #BSUB -q vvl #sed -i '1 i##fileformat=VCFv4.2' /public-supool/home/igdb/human/test_sample/EUR_NA20534_chip.vcf #sed 's/^chr//i' -i /public-supool/home/igdb/human/test_sample/EUR_NA20534_chip.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/EUR_NA20534_chip.vcf --prefix EUR_NA20534_chip.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/EUR_NA20534_chip.vcf --prefix EUR_NA20534_chip.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/EUR_NA20534_chip.vcf --prefix EUR_NA20534_chip.PanelO_chr22.imputed --meta --cpus 8 #echo "End O TimeTamp:"`date +%s` /public-supool/home/igdb/bin/MetaMinimac2 --skipPhasingCheck -s -i EUR_NA20534_chip.PanelA_chr22.imputed:EUR_NA20534_chip.PanelB_chr22.imputed -o EUR_NA20534_chip.meta_chr22.imputed echo "End meta TimeTamp:"`date +%s` ------------------------------------------------------------ Successfully completed. Resource usage summary: CPU time : 8.76 sec. Max Memory : - Average Memory : - Total Requested Memory : - Delta Memory : - Max Swap : - Max Processes : 4 Max Threads : 5 Run time : 9 sec. Turnaround time : 11 sec. The output (if any) follows: Start TimeTamp:1655044010 ------------------------------------------------------------------------------ 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 [EUR_NA20534_chip.PanelA_chr22.imputed:EUR_NA20534_chip.PanelB_chr22.imputed], --output [EUR_NA20534_chip.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 : EUR_NA20534_chip.PanelA_chr22.imputed -- Study 2 Prefix : EUR_NA20534_chip.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 = 8516 -- Study 2 #Genotyped Sites = 8516 -- Found 8516 commonly genotyped! -- Successful (0 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 (0 seconds) !!! Weight Estimation Completed in 0 hours, 0 mins, 0 seconds. ------------------------------------------------------------------------------ FINAL ANALYSIS ------------------------------------------------------------------------------ Gathering dosege information and saving results for all samples ... Final Analysis Completed in 0 hours, 0 mins, 8 seconds. ------------------------------------------------------------------------------ END OF PROGRAM ------------------------------------------------------------------------------ Meta-Imputation Completed in 0 hours, 0 mins, 8 seconds. Study 1 #Markers = 1066555 Study 2 #Markers = 1066555 Total #Markers = 1066555 Thank You for using MetaMinimac2 !!! End meta TimeTamp:1655044018 PS: Read file for stderr output of this job.