Santy-8128
commented
5 years ago Hmm this is very strange. Jonathon would u have any suggestions?
Will it be possible to share the input files? That would make it very easy to debug. Sorry for the inconvenience.
On Fri, Nov 1, 2019, 8:19 PM scau-drr notifications@github.com wrote:
Hello, thank you for the software minimac3. I have a problem now. When I am imputing the pig's chromosome 18 (the reference group is 30 pigs, the imputed group is 8), I will report such an error.
Terminate called after throwing an instance of 'std::bad_alloc' What(): std::bad_alloc Aborted
I tried the 50G, 100G, 200G, 300G and 500G memory in the Linux system, all of which are the same mistakes.
Thanks for your help.
My code is: ~/software/Minimac3/bin/Minimac3 --refHaps cv2/chr18.m3vcf.gz --haps cv2/Yorkshire_8_chip.chr18_haps.vcf.gz --prefix cv2/Yorkshire_8_chip.chr18_haps_imputation At runtime, the screen output is:
Minimac3 - Fast Imputation Based on State Space Reduction HMM
(c) 2014 - Sayantan Das, Christian Fuchsberger, David Hinds Mary Kate Wing, Goncalo AbecasisVersion: 2.0.1; Built: Wed Oct 16 21:28:06 EDT 2019 by dingrong
URL = http://genome.sph.umich.edu/wiki/Minimac3
Command Line Options: Reference Haplotypes : --refHaps [cv2/chr18.m3vcf.gz], --passOnly, --rsid Target Haplotypes : --haps [cv2/Yorkshire_8_chip.chr18_haps.vcf.gz] Output Parameters : --prefix [cv2/Yorkshire_8_chip.chr18_haps_imputation], --processReference, --updateModel, --nobgzip, --vcfOutput [ON], --doseOutput, --hapOutput, --format [GT,DS], --allTypedSites Subset Parameters : --chr [], --start, --end, --window Starting Parameters : --rec [], --err [] Estimation Parameters : --rounds [5], --states [200] Other Parameters : --log, --lowMemory, --help, --cpus [1], --params PhoneHome : --noPhoneHome, --phoneHomeThinning [50]
PRELIMINARY GWAS/TARGET FILE CHECK
Performing basic file check on target/GWAS haplotype file : cv2/Yorkshire_8_chip.chr18_haps.vcf.gz
Checking File ... File Exists ...
Checking File Type ... VCF File Type Detected ...
NOTE: Samples will be assumed to be phased irrespective of GT delimiter (| or /) in VCF file !!!
Checking variant information ... 1490 variants in file with 0 variants passing filters ...
Checking sample information ... 8 samples found in file ...
Initial basic file check on target/GWAS haplotype file successful !!!
PRELIMINARY REFERENCE FILE CHECK
Performing basic file check on Reference haplotype file ...
Checking File ... File Exists ...
Checking File Format ...
Reference File Format = M3VCF (Minimac3 VCF File)
NOTE: For M3VCF files, if parameter estimates are available in the file, they will be used by default (RECOMMENDED !). If the user has reasons to believe that updating the parameters would increase accuracy, they should use handle "--updateModel" (not required in typical GWAS studies). If estimates are NOT available in file, it will estimate by default.
NOTE: For M3VCF files, if estimates are available in file value of "--rounds" will be ignored unless user has "--updateModel" ON (since, otherwise estimates are not going to be updated and value of "--rounds" would not make sense) !!!
REFERENCE HAPLOTYPE PANEL
Format = M3VCF (Minimac3 VCF File)
Reading Reference Haplotype information from M3VCF files : cv2/chr18.m3vcf.gz
Reading 60 haplotypes from data ...
Loading Block 1 out of 11481 blocks to be loaded... [0.0%] Loading Block 1001 out of 11481 blocks to be loaded... [8.7%] Loading Block 2001 out of 11481 blocks to be loaded... [17.4%] Loading Block 3001 out of 11481 blocks to be loaded... [26.1%] Loading Block 4001 out of 11481 blocks to be loaded... [34.8%] Loading Block 5001 out of 11481 blocks to be loaded... [43.6%] Loading Block 6001 out of 11481 blocks to be loaded... [52.3%] Loading Block 7001 out of 11481 blocks to be loaded... [61.0%] Loading Block 8001 out of 11481 blocks to be loaded... [69.7%] Loading Block 9001 out of 11481 blocks to be loaded... [78.4%] Loading Block 10001 out of 11481 blocks to be loaded... [87.1%] Loading Block 11001 out of 11481 blocks to be loaded... [95.8%]
Reference Haplotype information succesfully recorded.
Number of Markers in File : 428844
Number of Markers Recorded : 428844 Number of Haplotypes Recorded : 60
Haplotype Set successfully loaded from M3VCF File : cv2/chr18.m3vcf.gz
Time taken to load reference haplotype set = 2 seconds.
TARGET/GWAS HAPLOTYPE PANEL
Format = VCF (Variant Call Format)
Loading Target Haplotype SNP List from VCF File : cv2/Yorkshire_8_chip.chr18_haps.vcf.gz
Number of Markers read from VCF File : 1490 Number of Markers with more than One Allele : 0 Number of Markers failing FILTER = PASS : 1490 Number of Markers with inconsistent Ref/Alt Allele : 0 Number of Markers on other chromosomes (Non-Ref) : 0
Number of Markers overlapping with Reference List : 1266 Number of Markers Only in Target Panel : 224 Number of Markers to be Recorded : 1266
Loading Target Haplotype Set from VCF File : cv2/Yorkshire_8_chip.chr18_haps.vcf.gz
Loading markers 1 out of 1266 markers to be loaded... [0.1%]
Number of Haplotypes Recorded : 16 Number of Markers Recorded for Imputation : 1266
Haplotype Set successfully loaded from VCF File : cv2/Yorkshire_8_chip.chr18_haps.vcf.gz
Time taken to load target haplotype set = 0 seconds.
PARAMETER ESTIMATION
Reading pre-calculated estimates located in M3VCF file ...
Using pre-calculated estimates in Markov Model ...
Saving estimated parameters for future use/reference to ...
Recombination Rates : cv2/Yorkshire_8_chip.chr18_haps_imputation.rec Error Rates : cv2/Yorkshire_8_chip.chr18_haps_imputation.erate Time taken for parameter estimation = 2 seconds.
MAIN IMPUTATION
Starting Imputation ...
Setting up Markov Model for Imputation ...
Processing Haplotype 1 of 16 ... terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc Aborted
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Hello, thank you for the software minimac3. I have a problem now. When I am imputing the pig's chromosome 18 (the reference group is 30 pigs, the imputed group is 8), I will report such an error.
Terminate called after throwing an instance of 'std::bad_alloc' What(): std::bad_alloc Aborted
I tried the 50G, 100G, 200G, 300G and 500G memory in the Linux system, all of which are the same mistakes.
Thanks for your help.
My code is: ~/software/Minimac3/bin/Minimac3 --refHaps cv2/chr18.m3vcf.gz --haps cv2/Yorkshire_8_chip.chr18_haps.vcf.gz --prefix cv2/Yorkshire_8_chip.chr18_haps_imputation
At runtime, the screen output is:
Version: 2.0.1; Built: Wed Oct 16 21:28:06 EDT 2019 by dingrong
URL = http://genome.sph.umich.edu/wiki/Minimac3
Command Line Options: Reference Haplotypes : --refHaps [cv2/chr18.m3vcf.gz], --passOnly, --rsid Target Haplotypes : --haps [cv2/Yorkshire_8_chip.chr18_haps.vcf.gz] Output Parameters : --prefix [cv2/Yorkshire_8_chip.chr18_haps_imputation], --processReference, --updateModel, --nobgzip, --vcfOutput [ON], --doseOutput, --hapOutput, --format [GT,DS], --allTypedSites Subset Parameters : --chr [], --start, --end, --window Starting Parameters : --rec [], --err [] Estimation Parameters : --rounds [5], --states [200] Other Parameters : --log, --lowMemory, --help, --cpus [1], --params PhoneHome : --noPhoneHome, --phoneHomeThinning [50]
Performing basic file check on target/GWAS haplotype file : cv2/Yorkshire_8_chip.chr18_haps.vcf.gz
Checking File ... File Exists ...
Checking File Type ... VCF File Type Detected ...
NOTE: Samples will be assumed to be phased irrespective of GT delimiter (| or /) in VCF file !!!
Checking variant information ... 1490 variants in file with 0 variants passing filters ...
Checking sample information ... 8 samples found in file ...
Initial basic file check on target/GWAS haplotype file successful !!!
Performing basic file check on Reference haplotype file ...
Checking File ... File Exists ...
Checking File Format ...
Reference File Format = M3VCF (Minimac3 VCF File)
NOTE: For M3VCF files, if parameter estimates are available in the file, they will be used by default (RECOMMENDED !). If the user has reasons to believe that updating the parameters would increase accuracy, they should use handle "--updateModel" (not required in typical GWAS studies). If estimates are NOT available in file, it will estimate by default.
NOTE: For M3VCF files, if estimates are available in file value of "--rounds" will be ignored unless user has "--updateModel" ON (since, otherwise estimates are not going to be updated and value of "--rounds" would not make sense) !!!
Format = M3VCF (Minimac3 VCF File)
Reading Reference Haplotype information from M3VCF files : cv2/chr18.m3vcf.gz
Reading 60 haplotypes from data ...
Loading Block 1 out of 11481 blocks to be loaded... [0.0%] Loading Block 1001 out of 11481 blocks to be loaded... [8.7%] Loading Block 2001 out of 11481 blocks to be loaded... [17.4%] Loading Block 3001 out of 11481 blocks to be loaded... [26.1%] Loading Block 4001 out of 11481 blocks to be loaded... [34.8%] Loading Block 5001 out of 11481 blocks to be loaded... [43.6%] Loading Block 6001 out of 11481 blocks to be loaded... [52.3%] Loading Block 7001 out of 11481 blocks to be loaded... [61.0%] Loading Block 8001 out of 11481 blocks to be loaded... [69.7%] Loading Block 9001 out of 11481 blocks to be loaded... [78.4%] Loading Block 10001 out of 11481 blocks to be loaded... [87.1%] Loading Block 11001 out of 11481 blocks to be loaded... [95.8%]
Reference Haplotype information succesfully recorded.
Number of Markers in File : 428844
Number of Markers Recorded : 428844 Number of Haplotypes Recorded : 60
Haplotype Set successfully loaded from M3VCF File : cv2/chr18.m3vcf.gz
Time taken to load reference haplotype set = 2 seconds.
Format = VCF (Variant Call Format)
Loading Target Haplotype SNP List from VCF File : cv2/Yorkshire_8_chip.chr18_haps.vcf.gz
Number of Markers read from VCF File : 1490 Number of Markers with more than One Allele : 0 Number of Markers failing FILTER = PASS : 1490 Number of Markers with inconsistent Ref/Alt Allele : 0 Number of Markers on other chromosomes (Non-Ref) : 0
Number of Markers overlapping with Reference List : 1266 Number of Markers Only in Target Panel : 224 Number of Markers to be Recorded : 1266
Loading Target Haplotype Set from VCF File : cv2/Yorkshire_8_chip.chr18_haps.vcf.gz
Loading markers 1 out of 1266 markers to be loaded... [0.1%]
Number of Haplotypes Recorded : 16 Number of Markers Recorded for Imputation : 1266
Haplotype Set successfully loaded from VCF File : cv2/Yorkshire_8_chip.chr18_haps.vcf.gz
Time taken to load target haplotype set = 0 seconds.
Reading pre-calculated estimates located in M3VCF file ...
Using pre-calculated estimates in Markov Model ...
Saving estimated parameters for future use/reference to ...
Recombination Rates : cv2/Yorkshire_8_chip.chr18_haps_imputation.rec Error Rates : cv2/Yorkshire_8_chip.chr18_haps_imputation.erate
Time taken for parameter estimation = 2 seconds.
Starting Imputation ...
Setting up Markov Model for Imputation ...
Processing Haplotype 1 of 16 ... terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc Aborted