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skandlab / SMuRF

MIT License
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error at or after formatting step #40

Closed gianfilippo closed 4 years ago

gianfilippo commented 4 years ago

Hi,

I am afraid I am having another issue. An error at or after the formatting step. What do you think ?

My command line is myresults = smurf(directory="Sampletest", mode="combined", check.packages=T, t.label="T") the dir sample test contains the 4 required files

The output is below (reporting only the relevant part) Accessing files: Sample_test/mutect2.vcf.gz Sample_test/freebayes.vcf.gz Sample_test/varscan.vcf.gz Sample_test/vardict.vcf.gz [1] "Parsing step" [1] "reading vcfs" [1] "reading mutect2" [1] "reading freebayes" [1] "reading varscan" [1] "reading vardict" Time difference of 12.42901 secs [1] "extracting calls passed by at least 1 caller" Time difference of 0.7296524 secs [1] "extracting meta data from VRanges" Time difference of 3.151198 secs [1] "merge 4 vcfs and meta data" Time difference of 0.5899651 secs [1] "formating" Time difference of 0.7452195 secs Error in [.data.frame(meta_data, , c("MQ_Mutect2", "MQRankSum_Mutect2", : undefined columns selected

tyler5huang commented 4 years ago

Hi

May I know if the Sample_test files are the ones provided in the SMuRF package? If not, I would request you to send me a link to your vcf files via my email: huangwt@gis.a-star.edu.sg

gianfilippo commented 4 years ago

Hi,

it works with your files, I just tested it. I will send you a link.

Thanks Gianfilippo

tyler5huang commented 4 years ago

Issue resolved - SMuRFv1.6.4