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mquinodo / AutoMap

Tool to find regions of homozygosity (ROHs) from sequencing data.
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getting bcftools error when running AutoMap_v1.2.sh script on singularity container #23

Closed Arth032 closed 1 month ago

Arth032 commented 4 months ago

getting below bcftools error when running AutoMap_v1.2.sh script on singularity container

Homozygosity regions will be extended to nearest variant with maximum of 1 Mb. /opt/Container/AutoMap/AutoMap_v1.2.sh: line 309: /opt/Container/AutoMap/.log: Read-only file system

ERROR: The input VCF format is incorrect ('bcftools query -l' was unsuccessful). Exit.

When running bash AutoMap_v1.2.sh on local system its running correctly

Container localSystem

mquinodo commented 3 months ago

Hello, I would change line 219 in the main script from "2> $here/.log" to "2> /dev/null". Could you tell me if that works?

Arth032 commented 3 months ago

Sure @mquinodo though we have removed it already ($here/.log" to "2> /dev/null), and it is running as expected now. thanks