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.
Related
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..!
I am trying to run a script inside a docker that was published by google.
The command I use mounts some datafiles onto the docker in a file called '/input' (inside the docker).
When I run the script, it says that it does not find the input file.
However, I do use the -v flag, and I ran a script that makes sure the input file is there (inside the docker).
So in summary - when I run
find /input -name "*.fasta"
It outputs:
/input/ucsc.hg19.chr20.unittest.fasta
As needed, but when I run the script, it says
./dv-quick-start: 19: ./dv-quick-start: --ref=/input/ucsc.hg19.chr20.unittest.fasta: not found
Full Script:
#!/bin/sh
BIN_VERSION="1.0.0"
INPUT_DIR="${PWD}/quickstart-testdata"
DATA_HTTP_DIR="https://storage.googleapis.com/deepvariant/quickstart-testdata"
OUTPUT_DIR="${PWD}/quickstart-output"
sudo docker run \
-v "${INPUT_DIR}":"/input" \
-v "${OUTPUT_DIR}":"/output" \
google/deepvariant:"${BIN_VERSION}" \
find /input -name "*.fasta"
sudo docker run \
-v "${INPUT_DIR}":"/input" \
-v "${OUTPUT_DIR}":"/output" \
google/deepvariant:"${BIN_VERSION}" \
/opt/deepvariant/bin/run_deepvariant \
--model_type=WGS \ **Replace this string with exactly one of the following [WGS,WES,PACBIO,HYBRID_PACBIO_ILLUMINA]**
--ref=/input/ucsc.hg19.chr20.unittest.fasta \
--reads=/input/NA12878_S1.chr20.10_10p1mb.bam \
--regions "chr20:10,000,000-10,010,000" \
--output_vcf=/output/output.vcf.gz \
--output_gvcf=/output/output.g.vcf.gz \
--intermediate_results_dir /output/intermediate_results_dir \ **This flag is optional. Set to keep the intermediate results.
Full output:
/input/ucsc.hg19.chr20.unittest.fasta
--ref is required.
Pass --helpshort or --helpfull to see help on flags.
./dv-quick-start: 19: ./dv-quick-start: --ref=/input/ucsc.hg19.chr20.unittest.fasta: not found
I feel there is some misunderstanding on my behalf, and I would appreciate any help.
Should more information be needed to answer the question, let me know.
You have some extraneous text in your shell script that's causing a problem. Delete the "replace this string" and "this flag is optional" text and all of the whitespace before them, making the \ the very last character on those lines.
In a shell script you can break commands across multiple lines using a \. But, the \ must be the absolute very last character in the line; if it's not, it escapes the character that comes after it.
# one line: ls -al $HOME
ls -al \
$HOME
# two lines: ls -al " " more text here; $HOME
ls -al \ more text here
$HOME
In your example you've left some explanatory text in
sudo docker run \
...\
--model_type=WGS \ **Replace this string with exactly one of the following [WGS,WES,PACBIO,HYBRID_PACBIO_ILLUMINA]**
# This is seen as a separate command
--ref=/input/ucsc.hg19.chr20.unittest.fasta \
...
Since the "Replace this string..." text makes the \ not be the absolute last character in the line, it causes the shell to break the command. You then get two commands, a docker run command without the --ref option and what looks like trying to run --ref=... as a separate command; that corresponds to the two errors you get.
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
When I build x264 with android-ndk it not done.
Unknown option file/x264/android/armeabi, ignored
Unknown option --target-os=android, ignored
Unknown option --enable-cross-compile, ignored
Unknown option --arch=arm, ignored
Unknown option --cpu=armv5te, ignored
Unknown option --enable-armv5te, ignored
Unknown option --disable-stripping, ignored
No working C compiler found.
Makefile:3: config.mak: No such file or directory
./configure
platform: X86_64
byte order: little-endian
system: LINUX
cli: yes
libx264: internal
shared: no
static: no
asm: yes
interlaced: yes
avs: avxsynth
lavf: no
ffms: no
mp4: no
gpl: yes
thread: posix
opencl: yes
filters: crop select_every
lto: no
debug: no
gprof: no
strip: no
PIC: no
bit depth: all
chroma format: all
My build file
#!/bin/bash
TOOLCHAIN=/home/s/my_toolchains/arm
CROSS_PREFIX=$TOOLCHAIN/bin/arm-linux-androideabi-
rm -f $(pwd)/compat/strtod.o
function build_one
{
./configure --prefix=$PREFIX --enable-static --enable-pic --target-os=android --enable-cross- compile --cross-prefix=$CROSS_PREFIX --extra-cflags="-Os -fpic $ADDI_CFLAGS" --extra-ldflags="$ADDI_LDFLAGS" --sysroot=$TOOLCHAIN/sysroot $ADDITIONAL_CONFIG_FLAG
make clean
make
make install
}
CPU=armeabi
mkdir -p $(pwd)/android/$CPU
PREFIX=$(pwd)/android/$CPU
ADDI_CFLAGS="-marm -march=armv5te -mtune=arm9tdmi -msoft-float"
ADDI_LDFLAGS=""
ADDITIONAL_CONFIG_FLAG="--arch=arm --cpu=armv5te --enable-armv5te --disable-asm --disable-stripping"
build_one
How can I solve this?
why this is not done? I made the build file properly but this is not done?
I use ubuntu os to build this file.
It comes Unknown option --target-os=android, ignored.
I assume you use a deprecated version of x264, because i succeed compiled the latest version form here https://www.videolan.org/developers/x264.html using the following scripts:
armeabi-v7a
#!/bin/bash
export NDK=F:/Android/Sdk/ndk-bundle # your android ndk folder
export HOST_TAG=windows-x86_64 # adjust to your building host
export TOOLCHAIN=$NDK/toolchains/llvm/prebuilt/$HOST_TAG
export CC=$TOOLCHAIN/bin/armv7a-linux-androideabi18-clang # c compiler path
export CXX=$TOOLCHAIN/bin/armv7a-linux-androideabi18-clang++ # c++ compiler path
function build_armeabi-v7a
{
./configure \
--prefix=./android/armeabi-v7a \
--enable-static \
--enable-pic \
--disable-asm \
--disable-opencl \
--disable-cli \
--host=arm-linux \
--cross-prefix=$TOOLCHAIN/bin/arm-linux-androideabi- \
--sysroot=$TOOLCHAIN/sysroot \
make clean
make
make install
}
build_armeabi-v7a
echo build_armeabi-v7a finished
arm64-v8a
#!/bin/bash
export NDK=F:/Android/Sdk/ndk-bundle
export HOST_TAG=windows-x86_64 # adjust to your building host
export TOOLCHAIN=$NDK/toolchains/llvm/prebuilt/$HOST_TAG
export CC=$TOOLCHAIN/bin/aarch64-linux-android21-clang
export CXX=$TOOLCHAIN/bin/aarch64-linux-android21-clang++
function build_arm64-v8a
{
./configure \
--prefix=./android/arm64-v8a \
--enable-static \
--enable-pic \
--disable-asm \
--disable-opencl \
--disable-cli \
--host=aarch64-linux \
--cross-prefix=$TOOLCHAIN/bin/aarch64-linux-android- \
--sysroot=$TOOLCHAIN/sysroot \
make clean
make
make install
}
build_arm64-v8a
echo build_arm64-v8a finished
x86
#!/bin/bash
export NDK=F:/Android/Sdk/ndk-bundle
export HOST_TAG=windows-x86_64 # adjust to your building host
export TOOLCHAIN=$NDK/toolchains/llvm/prebuilt/$HOST_TAG
export CC=$TOOLCHAIN/bin/i686-linux-android18-clang
export CXX=$TOOLCHAIN/bin/i686-linux-android18-clang++
function build_x86
{
./configure \
--prefix=./android/x86 \
--enable-static \
--enable-pic \
--disable-asm \
--disable-opencl \
--disable-cli \
--host=i686-linux \
--cross-prefix=$TOOLCHAIN/bin/i686-linux-android- \
--sysroot=$TOOLCHAIN/sysroot \
make clean
make
make install
}
build_x86
echo build_x86 finished
x86_64
#!/bin/bash
export NDK=F:/Android/Sdk/ndk-bundle
export HOST_TAG=windows-x86_64 # adjust to your building host
export TOOLCHAIN=$NDK/toolchains/llvm/prebuilt/$HOST_TAG
export CC=$TOOLCHAIN/bin/x86_64-linux-android21-clang
export CXX=$TOOLCHAIN/bin/x86_64-linux-android21-clang++
function build_x86_64
{
./configure \
--prefix=./android/x86_64 \
--enable-static \
--enable-pic \
--disable-asm \
--disable-opencl \
--disable-cli \
--host=x86_64-linux \
--cross-prefix=$TOOLCHAIN/bin/x86_64-linux-android- \
--sysroot=$TOOLCHAIN/sysroot \
make clean
make
make install
}
build_x86_64
echo build_x86_64 finished
And don't forget to change export variables that i described in armeabi-v7a script.
I'm trying to boot up a guest os to continue with my work but I have a problem with my virsh installation.
Here is the part of installation script:
qemu-img create -f qcow2 -o preallocation=metadata ~/images/${vm_name}.qcow2 ${pool_size}G
# create dir for images
mkdir ~/images/
virt-install \
--connect qemu:///system \
--name $vm_name \
--ram 10240 \
--vcpus 4 \
--disk ~/images/${vm_name}.qcow2,size=$pool_size,bus=virtio,sparse=false,format=qcow2 \
--network network=default,model=virtio \
--location http://ua.archive.ubuntu.com/dists/trusty-updates/main/installer-amd64/ \
--initrd-inject=$current_dir/preseed.cfg \
--extra-args="file=file:/preseed.cfg vga=788 quiet console=tty0 utf8 console=ttyS0,115200" \
--os-type=linux \
--virt-type kvm \
--video=vga \
--noreboot \
--cpu host \
--hvm
virsh start $vm_name
echo "----------Login to console----------"
virsh console $vm_name
WHen Im trying to run this script as a file like ./script.sh it produces an error:
Formatting '/home/{username}/images/test.qcow2', fmt=qcow2 size=53687091200 encryption=off cluster_size=65536 preallocation='metadata' lazy_refcounts=off refcount_bits=16
mkdir: cannot create directory '/home/flash/images/': File exists
ERROR 'DebianDistro' object has no attribute '_prefix'
error: failed to get domain 'test'
error: Domain not found: no domain with matching name 'test'
----------Login to console----------
error: failed to get domain 'test'
error: Domain not found: no domain with matching name 'test'
I have tried already reinstalling kvm qemu packages using this guide - https://help.ubuntu.com/community/KVM/Installation
and everything completed successfully.
I am sure that script will work file as I was using it before on the other machine without any problems.
Another try:
Using that script below
virt-install --connect qemu:///system -n test -r 10240 \
--vcpus=4 \
--disk path=/data0/images/test.img,size=50,format=qcow2,bus=virtio,cache=none \
--cdrom /home/{username}/Downloads/kvm/ubuntu-14.iso \
--vnc \
--os-type=linux \
--accelerate \
--network network=default \
--hvm
Produces an error:
ERROR internal error: process exited while connecting to monitor: Could not access KVM kernel module: Permission denied
failed to initialize KVM: Permission denied
Also when I'm trying to list all os variants by virt-install --os-variant list it cannot recognize this command and trying to boot up a guest os instead of listing variants.
Can you please help me to find out what is the problem here?
To fix this error:
ERROR 'DebianDistro' object has no attribute '_prefix'
Edit the file /usr/share/virt-manager/virtinst/urlfetcher.py and change this in line 1034:
if self._prefix:
to this:
if self._url_prefix:
Ubuntu 14.04.