i am beginner bioinformatician!
i run CTAT for fusion analysis
here is my code
docker run -v `pwd`:/data --rm trinityctat/starfusion \
STAR-Fusion \
--left_fq /data/reads_1.fq.gz \
--right_fq /data/reads_2.fq.gz \
--genome_lib_dir /data/ctat_genome_lib_build_dir \
-O /data/StarFusionOut \
--FusionInspector validate \
--examine_coding_effect \
--denovo_reconstruct
i thought fusioninspector's role is just validation for fusions which STAR-Fuision predicted
. But final results are different from my expactation
i wonder why fusioninspector's results have more fusions and how fusioninspector's results have fusions which are not included in STAR-Fusion result!!
please help me..!
Related
I am trying to create a podman image that allows me to run rootless podman inside rootless podman.
I have read https://www.redhat.com/sysadmin/podman-inside-container
and tried to build an image analogous to quay.io/podman/stable:latest based on top of docker.io/python:3.10-slim-bullseye or docker.io/ubuntu:22.04,
but somehow my images require --privileged which the quay.io/podman fedora-based image does not.
For reference, here what does work for quay.io/podman/stable:latest:
$ podman run --rm \
--security-opt label=disable \
--device /dev/fuse \
--user podman \
quay.io/podman/stable:latest podman info
prints the podman info and no warning/errors, also podman run hellow-world works inside the container as expected.
I have created a dockerfile for a debian/ubuntu-based image that allows running rootless podman inside. The dockerfile closely follows https://www.redhat.com/sysadmin/podman-inside-container and https://github.com/containers/podman/blob/main/contrib/podmanimage/stable/Containerfile
and is shown at the bottom.
However, the resulting image (call it podinpodtest) does not work as expected:
$ podman run --rm \
--security-opt label=disable \
--device /dev/fuse \
--user podman \
podinpodtest podman info
results in Error: cannot setup namespace using newuidmap: exit status 1.
Adding --privileged makes the image work:
$ podman run --rm \
--security-opt label=disable \
--device /dev/fuse \
--user podman \
--privileged \
podinpodtest podman info
correctly prints the podman info.
Why does the debian/ubuntu based image require --privileged for running rootless podman inside of it?
I do not want to run the image with --privileged – can the debian/ubuntu based image be fixed to work similarly to the quay.io/podman image?
#FROM docker.io/python:3.10-slim-bullseye
FROM docker.io/ubuntu:22.04
RUN apt-get update && apt-get install -y \
containers-storage \
fuse-overlayfs \
libvshadow-utils \
podman \
&& rm -rf /var/lib/apt/lists/*
RUN useradd podman; \
echo "podman:1:999\npodman:1001:64535" > /etc/subuid; \
echo "podman:1:999\npodman:1001:64535" > /etc/subgid;
ARG _REPO_URL="https://raw.githubusercontent.com/containers/podman/main/contrib/podmanimage/stable"
ADD $_REPO_URL/containers.conf /etc/containers/containers.conf
ADD $_REPO_URL/podman-containers.conf /home/podman/.config/containers/containers.conf
RUN mkdir -p /home/podman/.local/share/containers && \
chown podman:podman -R /home/podman && \
chmod 644 /etc/containers/containers.conf
# Copy & modify the defaults to provide reference if runtime changes needed.
# Changes here are required for running with fuse-overlay storage inside container.
RUN sed -e 's|^#mount_program|mount_program|g' \
-e '/additionalimage.*/a "/var/lib/shared",' \
-e 's|^mountopt[[:space:]]*=.*$|mountopt = "nodev,fsync=0"|g' \
/usr/share/containers/storage.conf \
> /etc/containers/storage.conf
# Note VOLUME options must always happen after the chown call above
# RUN commands can not modify existing volumes
VOLUME /var/lib/containers
VOLUME /home/podman/.local/share/containers
RUN mkdir -p /var/lib/shared/overlay-images \
/var/lib/shared/overlay-layers \
/var/lib/shared/vfs-images \
/var/lib/shared/vfs-layers && \
touch /var/lib/shared/overlay-images/images.lock && \
touch /var/lib/shared/overlay-layers/layers.lock && \
touch /var/lib/shared/vfs-images/images.lock && \
touch /var/lib/shared/vfs-layers/layers.lock
ENV _CONTAINERS_USERNS_CONFIGURED=""
I've got HaplotypeCaller working nicely in standard mode, like so:
# Run haplotypcaller
gatk --java-options "-Xmx4g" HaplotypeCaller \
--intervals "$INTERVALS" \
-R "$REF" \
-I "$OUT"/results/alignment/${SN}_sorted_marked_recalibrated.bam \
-O "$OUT"/results/variants/${SN}_g.vcf.gz \
-ERC GVCF
But when I try in allele-specific mode, I get the following error. All I've done is add the -G annotations at the end, as suggested here.
# Haplytype caller with allele-specific annotations
gatk --java-options "-Xmx4g" HaplotypeCaller \
--intervals "$INTERVALS" \
-R "$REF" \
-I "$OUT"/results/alignment/${SN}_sorted_marked_recalibrated.bam \
-O "$OUT"/results/variants/${SN}_g.vcf.gz \
-ERC GVCF \
-G Standard \
-G AS_Standard
Here's the error:
***********************************************************************
A USER ERROR has occurred: Unrecognized annotation group name: Standard
***********************************************************************
I think that those options should be:
-G StandardAnnotation
-G AS_StandardAnnotation
At least, when I changed them to that, it didn't throw an error message.
However, I haven't used GATK much, so I'm not sure that's correct. I posted on the relevant Broad page, so more info may show up there.
My command in python is
feature_file_folder -f allure_behave.formatter:AllureFormatter -o target/allure-results --no-capture --no-capture-stderr
This runs all the feature files but if i want to run only 2 feature files out of 10 i am having problems i can run 1 or all feature file.
You can mention feature file names while executing.
behave -f allure_behave.formatter:AllureFormatter \
-o target/allure-results \
--no-capture \
--no-capture-stderr \
example1.feature example2.feature
This is what tags are used for. Lets say, hypothetically, the two you want to run are related to logging into a system:
login-from-main-page.feature:
#login-tests
Feature: Test logging in from the main page
Scenario: ...
login-from-mobile.feature
#login-tests
Feature: Test logging in from iOS App
Scenario: ...
Then you would run behave, specifying those tags:
feature_file_folder -f allure_behave.formatter:AllureFormatter \
-o target/allure-results \
--no-capture \
--no-capture-stderr \
--tags login-tests
I've been trying to get a virtual machine working with a cfg file on centos but unfortunately, I'm getting the error that ks.cfg file does not exist.
Below is the command I ran to enable the VM.
virt-install --name FedoraTest --ram 1024 --disk pool=default,size=10 --location ~/Desktop/CentosOS --initrd-inject ks.cfg --extra-args "ks=file:~/Desktop/ks.cfg"
I am new to the VM setup and am unsure if I'm doing it right.
Any advice on how to fix this will be greatly appreciated.
Also, what does initrd-inject do? And is it possible to save the above command into a file and run the file instead?
I suppose you have switched the meaning of 'initrd-inject' and 'extra-args' parameters. The initrd-inject should contain path to the ks file in your file system, while in 'extra-args' you should specify kernel to use the injected ks file. See the snippet:
virt-install --connect=qemu:///system \
--network=bridge:br0 \
--initrd-inject=/export/rhel.ks \
--extra-args="ks=file:/rhel.ks console=tty0 console=ttyS0,115200" \
--name=$domname \
--disk /export/vmimgs/$domname.img,size=20 \
--ram 2048 \
--vcpus=2 \
--check-cpu \
--accelerate \
--hvm \
--location=$location1 \
--nographics
The snippet comes from here
And all I get with the below call of rrdtool is an empty graph, but why? No data in database?
rrdtool create connecteclients.rrd --step 300
DS:ConnectedClients:GAUGE:600:0:U
RRA:AVERAGE:0.5:1:432
RRA:AVERAGE:0.5:1:2016
RRA:AVERAGE:0.5:3:2880
RRA:AVERAGE:0.5:12:8640
rrdtool update connectedclients.rrd N:39
-- .. After 5 min again and again.. --
rrdtool graph picture.png \
--imgformat=PNG \
--start=-86400 \
--end=now \
--title="Clients" \
--rigid \
--base=1000 \
--height=96 \
--width=400 \
--upper-limit=2000000 \
--lower-limit=0 \
--slope-mode \
--color "BACK#4095FF" \
DEF:a=connectedclients.rrd:ConnectedClients:AVERAGE \
AREA:a#00CF00:"Clients" \
I notice as well that you setup two RRA files for a one step interval, this should not be a problem, but it is a waste of space and a source of confusion at best.
By setting the upper limit to 2 million and specifying --rigid, your data will be hugging the 0 line so tightly that you might not see it.
Try some examples from the tutorial RRDtutorial to see RRDtool at work.