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xjtu-omics / msisensor-pro

Microsatellite Instability (MSI) detection using high-throughput sequencing data.
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fatal error: failed to open ref file #24

Closed lancermiss closed 3 years ago

lancermiss commented 3 years ago

When i use the docker to run msisensor-pro, at the scan the default reference.fa. The terminal alarm: fatal error: failed to open ref file How to solve this problem? many thanks!

PengJia6 commented 3 years ago

@lancermiss I think maybe you do not tranfer you local path to the docker path with -v /local/path:/docker/path. We have update the demo script for docker. plese find the script here.

BastienNguyen commented 2 years ago

I have the same error with the conda install. How to solve this?

asalimih commented 1 year ago

I also have encountered this error using the conda install. the only output is failed to open file
it worked on the hg19 reference but on the hg38 one didn't

asalimih commented 1 year ago

I think the problem was with the sequence names. I only kept the chromosome names using the following command and it worked:

sed -E 's/>([^ ]+).*/>\1/' Homo_sapiens_assembly38.fasta > Homo_sapiens_assembly38_simplified_chr_names.fasta