Issue in reading param file through docker

[kaanokay]

Hi,

Thank you for developing such a tool.

I have an issue in reading param files. Before this issue, I had another issue in reading input files but I figured it out.

I followed steps below:

1. BASE="${HOME}/margin_phasing"
2. INPUT_DIR="${BASE}/input/data"
3. REF="Mus_musculus..fa"
4. BAM="Remora.bam"
5. paramfile="allParams.haplotag.ont-r94g507.json"
6. THREADS="10"
7. OUTPUT_DIR="${BASE}/output"
8. OUTPUT_PREFIX="Ep300"
9. OUTPUT_VCF="Ep300.vcf.gz"
10. TRUTH_VCF="FVB_NJ.vcf"
11. mkdir -p "${OUTPUT_DIR}"
12. mkdir -p "${INPUT_DIR}"
13. paramdirectory="${BASE}/paramfiles"
14. mkdir -p "${paramdirectory}"
15. sudo docker pull jmcdani20/hap.py:v0.3.12
16. sudo docker pull kishwars/pepper_deepvariant:r0.8
17. sudo docker run -v "${INPUT_DIR}":"${INPUT_DIR}"
    -v "${OUTPUT_DIR}":"${OUTPUT_DIR}"
    kishwars/pepper_deepvariant:r0.8 margin phase
    "${INPUT_DIR}/${BAM}"
    "${INPUT_DIR}/${REF}"
    "${INPUT_DIR}/${TRUTH_VCF}"
    "${paramdirectory}/${paramfile}"
    -o "${OUTPUT_DIR}"
    -p "${OUTPUT_PREFIX}"
    -t ${THREADS}

and then

I got this error: "Could not read from params file: /home/ko/margin_phasing/paramfiles/allParams.haplotag.ont-r94g507.json".

I also created a directory where paramfile is existed. But, when my run read inputs, it did not read paramfile with the same way. In addition to that, I put a path where I have all param files default (I downloaded them from GitHub). Despite that, I got the same error again. How can I do my run can read param files? Could you help me with this?

I addition to that, another question in my mind is that is margin consistent with R.10.4.1 flowcell output of ONT?

Kind regards.

[Jerry-bioinformatics]

Hi, I ran into the same issue with you. How do you deal with it finally?

[Jerry-bioinformatics]

@kaanokay Do you have any suggestions? I had tried both docker and singularity, but they failed on it.