search

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 #20

Closed mattdmem closed 6 years ago

mattdmem commented 6 years ago

I get the following error when trying to run parliament2

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

docker run -v :/home/dnanexus/in -v :/home/dnanexus/out dnanexus/parliament2:0.1.8 --bam .sorted.markdup.bam --bai .sorted.markdup.bam.bai -r --breakdancer --cnvnator --manta --genotype

slzarate commented 6 years ago

Hi,

You haven't included a reference genome. Use -r <INPUT_FASTA>.

Samantha

ManavalanG commented 4 years ago

I receive this error v0.1.11 even when -r is specified. Command used:

$ LANG= singularity run \
    >             -B `pwd`/input:/home/dnanexus/in \
    >             -B `pwd`/output:/home/dnanexus/out \
    >             parliament2.simg   \
    >                 --bam aaa.bam \
    >                 --bai aaa.bam.bai \
    >                 -r hs37d5.fa