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error at "extracting meta data from VRanges" #35

Closed gianfilippo closed 4 years ago

gianfilippo commented 5 years ago

Hi,

I am testing SMuRF on a set of files I generated running the individual callers. I am getting an "Error in normalizeDoubleBracketSubscript". It seems that the expected data type is not there. Are there specific requirements for the input vcfs ?

Thanks Gianfilippo

Below is my command line and the output myresults = smurf(directory = "Variants_hg38_BWA_ensemble/Sample_G1700T_012",mode="combined",nthreads=20,output.dir="Variants_hg38_BWA_ensemble/Sample_G1700T_012",build="hg38",check.packages=T) [1] "SMuRFv1.6 (3rd Oct 2019)" [1] "Saving output files to: Variants_hg38_BWA_ensemble/Sample_G1700T_012" Connection successful!

R is connected to the H2O cluster: H2O cluster version: 3.26.0.2 H2O cluster version age: 2 months and 25 days
H2O cluster total nodes: 1 H2O cluster total memory: 26.63 GB H2O cluster total cores: 20 H2O cluster allowed cores: 1 H2O cluster healthy: TRUE H2O API Extensions: Amazon S3, XGBoost, Algos, AutoML, Core V3, Core V4 R Version: R version 3.5.0 (2018-04-23)

Accessing files: Variants_hg38_BWA_ensemble/Sample_G1700T_012/mutect2.vcf.gz Variants_hg38_BWA_ensemble/Sample_G1700T_012/freebayes.vcf.gz Variants_hg38_BWA_ensemble/Sample_G1700T_012/varscan.vcf.gz Variants_hg38_BWA_ensemble/Sample_G1700T_012/vardict.vcf.gz [1] "Parsing step" [1] "reading vcfs" [1] "reading mutect2" [1] "reading freebayes" [1] "reading varscan" [1] "reading vardict" Time difference of 16.48991 secs [1] "extracting calls passed by at least 1 caller" Time difference of 0.82076 secs [1] "extracting meta data from VRanges" Error in normalizeDoubleBracketSubscript(i, x, exact = exact, allow.NA = TRUE, : invalid [[ subscript type: NULL

tyler5huang commented 5 years ago

Hi Gianfilippo,

I have recently encountered this error because the tumour sample name and normal sample name could be identified correctly.

I have resolved this identifying the T and N sample names from the vcf files. Do you happen to know your sample names? They should be your bam file names

Regards, Weitai

On 22 Oct 2019, at 1:05 PM, Gianfilippo Coppola notifications@github.com wrote:



Hi,

I am testing SMuRF on a set of files I generated running the individual callers. I am getting an "Error in normalizeDoubleBracketSubscript". It seems that the expected data type is not there. Are there specific requirements for the input vcfs ?

Thanks Gianfilippo

Below is my command line and the output myresults = smurf(directory = "Variants_hg38_BWA_ensemble/Sample_G1700T_012",mode="combined",nthreads=20,output.dir="Variants_hg38_BWA_ensemble/Sample_G1700T_012",build="hg38",check.packages=T) [1] "SMuRFv1.6 (3rd Oct 2019)" [1] "Saving output files to: Variants_hg38_BWA_ensemble/Sample_G1700T_012" Connection successful!

R is connected to the H2O cluster: H2O cluster version: 3.26.0.2 H2O cluster version age: 2 months and 25 days H2O cluster total nodes: 1 H2O cluster total memory: 26.63 GB H2O cluster total cores: 20 H2O cluster allowed cores: 1 H2O cluster healthy: TRUE H2O API Extensions: Amazon S3, XGBoost, Algos, AutoML, Core V3, Core V4 R Version: R version 3.5.0 (2018-04-23)

Accessing files: Variants_hg38_BWA_ensemble/Sample_G1700T_012/mutect2.vcf.gz Variants_hg38_BWA_ensemble/Sample_G1700T_012/freebayes.vcf.gz Variants_hg38_BWA_ensemble/Sample_G1700T_012/varscan.vcf.gz Variants_hg38_BWA_ensemble/Sample_G1700T_012/vardict.vcf.gz [1] "Parsing step" [1] "reading vcfs" [1] "reading mutect2" [1] "reading freebayes" [1] "reading varscan" [1] "reading vardict" Time difference of 16.48991 secs [1] "extracting calls passed by at least 1 caller" Time difference of 0.82076 secs [1] "extracting meta data from VRanges" Error in normalizeDoubleBracketSubscript(i, x, exact = exact, allow.NA = TRUE, : invalid [[ subscript type: NULL

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gianfilippo commented 5 years ago

Hi,

thanks.

I can see the sample names (tumor and normal) in each of the 4 files (I have Mutect2, VarSvan2, VarDict, freebayes). They all are from the same sample, but I can see each has a different name. I guess I have to fix that. Also, VarScan used the whole file path as sample names. And in my freebayes vcf I can see an extra column that you do not have in your sample freebayes vcf. How do I get rid of it ?

Thanks

gianfilippo commented 5 years ago

Hi,

I just edited the freebayes vcf and made sure all samples names in the various vcfs are consistent (see below). I am still getting the exact same error.

Do you have any other thought ?

Thanks

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample_G1700T_012 Sample_G1700N_006

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample_G1700N_006 Sample_G1700T_012

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample_G1700T_012 Sample_G1700N_006

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample_G1700N_006 Sample_G1700T_012

tyler5huang commented 5 years ago

Resolving error: Error in normalizeDoubleBracketSubscript(i, x, exact = exact, allow.NA = TRUE, : invalid [[ subscript type: NULL

Cause: vcf sample names for tumour and normal files not detected automatically.

Solution: Manually state your tumor file tag. Example: t.label='-T t.label='_tumor' t.label='T001' t.label='T' #also works for you

Error message: 't.label for tumor sample is not unique, duplicated or missing'

myresults = smurf(directory = "Variants_hg38_BWA_ensemble/Sample_G1700T_012",
mode="combined",
t.label='T_012',
nthreads=20,
output.dir="Variants_hg38_BWA_ensemble/Sample_G1700T_012",
build="hg38",
check.packages=T)

Please download the latest patch SMuRF-v1.6.2. Thanks!

gianfilippo commented 5 years ago

thanks!! I will try this