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bioinform / somaticseq

An ensemble approach to accurately detect somatic mutations using SomaticSeq
http://bioinform.github.io/somaticseq/
BSD 2-Clause "Simplified" License
189 stars 53 forks source link

In training mode, error: invalid choice. #95

Closed wjianga closed 3 years ago

wjianga commented 3 years ago

Hi,

I have the following error message when I tried to run the training mode. While I imitated the syntax in the manual and specified the "single" mode, I cannot understand the error message, especially the fact that it is pointing to my "ground truth" vcf files.

Error message: somaticseq_parallel.py: error: invalid choice: 'ALMC1.SNPs_only.recode.vcf' (choose from 'paired', 'single')

Commands: somaticseq_parallel.py \ --output-directory ALMC1_DJ_p27_CL_Whole_T1_A2S4U_K03485_D1KLRACXX_AACCGAGA \ --genome-reference GRCh38.p7.genome.fa \ --truth−snv ALMC1.SNPs_only.recode.vcf \ --truth−indel ALMC1.Indels_only.recode.vcf \ --somaticseq−algorithm xgboost \ --somaticseq−train \ single \ --bam-file ALMC1_DJ_p27_CL_Whole_T1_A2S4U_K03485_D1KLRACXX_AACCGAGA.recalibrated.bam \ --varscan-vcf ALMC1_DJ_p27_CL_Whole_T1_A2S4U_K03485_D1KLRACXX_AACCGAGA.vcf \ --mutect2-vcf ALMC1_DJ_p27_CL_Whole_T1_A2S4U_K03485_D1KLRACXX_AACCGAGA.filterdvar.vcf

Thanks!

litaifang commented 3 years ago

Try replacing --somaticseq-algorithm xgboost with --algorithm xgboost.

wjianga commented 3 years ago

It is still reporting the same error.

litaifang commented 3 years ago

Try typing out the command again. Make sure the hyphens are real hyphens -, instead of some characters that look like hyphens. I copy-and-pasted the commands and it didn't work, and noticed there is some difference in the hyphens between what I typed vs. the ones I copied, i.e, --truth−snv vs. --truth-snv. Notice the hyphen just before snv. They are different lengths, i.e., they are actually different characters.

wjianga commented 3 years ago

It works now. The error was due to a wrong hyphen. Thank you!