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mquinodo / AutoMap

Tool to find regions of homozygosity (ROHs) from sequencing data.
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Error #21

Closed ramikheireddine closed 1 year ago

ramikheireddine commented 1 year ago

bash /home/databench/AutoMap_v1.2_nonhuman.sh --vcf Routput_raw_variants.vcf --out Routput_directory --DP 8 --binomial 0.000001 --percaltlow 0.25 --percalthigh 0.75 --window 7 --windowthres 5 --minsize 2 --minvar 2 --minperc 88 --maxgap 10 --chrX No --extend 1

bcftools higher or equal to v1.9

bedtools higher or equal to v2.24.0

perl higher or equal to v5.22.0

R higher or equal to v3.2.0

ERROR: Usage: /home/databench/AutoMap_v1.2_nonhuman.sh [--vcf ] [--out ] [--common] [--id ] [--panel ] [--panelname ] [--DP <0-99>] [--binomial <0-1.0>] [--percaltlow <0-1.0>] [--percalthigh <0-1.0>] [--window <3-999>] [--windowthres <1-999>] [--minsize <0-99>] [--minvar <1-999>] [--minperc <0-100>] [--maxgap <0-1000Mb>] [--chrX] [--extend <0-100Mb>]. Exit

Any suggestions on how to fix this error?

mquinodo commented 1 year ago

Dear user,

The option chrX show be used without argument. So either you put --chrX or nothing if you don't want it.

Best, Mathieu