Entering edit mode
14 months ago
fra.r.silvestro
▴
10
The code I run:
1.
BIN_VERSION="1.5.0"
sudo apt -y update
sudo apt-get -y install docker.io
sudo docker pull google/deepvariant:"${BIN_VERSION}"
2.
# Pull the image
singularity pull docker://google/deepvariant:"${BIN_VERSION}"
3.
mkdir 04.deepvariant
# Run singularity
singularity run -B /mountpoint/fastQ/:/input \
deepvariant_1.5.0.sif \
/opt/deepvariant/bin/run_deepvariant \
--model_type WES \
--ref $REF \
--reads 03.align/$FQ.align.sort.marked.bam \
--output_vcf /input/04.deepvariant/$FQ.output.vcf.gz
It doesn't work. The message:
INFO: converting sif file to temporary sandbox. INFO: cleaning up image.
It prints all the flags related to /opt/deepvariant/bin/run_deepvariant.py
Maybe some flags are wrong.
I don't know if the output directory could be the root directory where my reads and reference are located.
I moved my data (reference .fasta, .fai and .bam, .bai) inside the INPUT_DIR. Then edit the code following this instruction https://github.com/google/deepvariant/blob/r1.5/docs/deepvariant-quick-start.md:
This the error message:
Have you tried to build the container first and got the .sif file?
Now I'm trying. By running:
I got this ERROR:
I don't think is the solution. The image pull (the .sif file) from the Docker hub should be right.
What do you fin for build the container? As the command have I posted? Otherwise, do you suggest a tutorial?
Hi, sorry for late reply - what are you building this on is it a HPC?
When I built my sif container I did it in the login node of my HPC and loaded singularity and then ran singularity pull docker://google/deepvariant:1.3.0
No HPC, just my personal computer to test it. https://github.com/google/deepvariant/blob/r1.5/docs/deepvariant-quick-start.md This is the tutorial I've followed. I'm using conda package manager to install singularity I get a .sif file.
I get this output:
All flags are right, I hope.
Your output should be in
/mountpoint/fastQ/04.deepvariant/
outside of the Singularity image, is it not there?are
$REF
and$FQ
set to something? what doesecho $REF
andecho $FQ
say?$FQ is just the ID sample. $REF is the path of my reference .fasta file. I already edited --output_vcf with output directory as you suggested, but it doesn't work as well.
Have you tried using the full file name to see if that works? Feel free to email me HousemanA@cardiff.ac.uk
I am having a similar issue was this ever resolved? Getting this error: I0922 22:22:08.794076 140356687390528 make_examples_core.py:257] Overhead for preparing inputs: 0 seconds I0922 22:22:08.795082 140356687390528 make_examples_core.py:257] 0 candidates (0 examples) [0.00s elapsed]
I'm pretty sure all the inputs are correct as I've bound each one individually, but the error still persists.