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dnanexus-archive / parliament2

Runs a combination of tools to generate structural variant calls on whole-genome sequencing data
Apache License 2.0
102 stars 39 forks source link

cp: cannot stat '/home/dnanexus/in/None': No such file or directory #85

Closed YTLogos closed 4 years ago

YTLogos commented 4 years ago

Hi @Maciek416 These days I have tried the parliament2 to call SVs. I get the following error:

cp: cannot stat '/home/dnanexus/in/None': No such file or directory

current working directory is named /home/dnanexus/ and looks like this:

.
├── input.bam
├── input.bai
├── ref_genome.fa.gz
└── outputs

Command used as follow:

docker run -v /home/dnanexus/:/home/dnanexus/in -v /home/dnanexus/outputs/:/home/dnanexus/out dnanexus/parliament2:latest --bam input.bam --bai input.bai -r ref_genome.fa.gz --breakdancer --cnvnator --manta --genotype
ManavalanG commented 4 years ago

This was reported before but no solution yet.

husamia commented 4 years ago

I am having this same problem with docker

cp: cannot stat '/home/dnanexus/in/None': No such file or directory mv: cannot stat '/home/dnanexus/in/None': No such file or directory