I am trying to run Platanus_allee genome assembler to assemble a genome. However, when I run phase command, it gives the following error:
My command:
bio#bio-XPS-8700:~/Fareeha/Platanus/Platanus_allee_v2.0.2_Linux_x86_64$ ./platanus_allee phase -c out_contig.fa out_junctionKmer.fa \platanus_allee phase \ -c out_contig.fa out_junctionKmer.fa \ -IP1 /home/bio/Fareeha/test/SMIX_test_data/Unzip/SDNA-270_1_head-3000000.fq /home/bio/Fareeha/test/SMIX_test_data/Unzip/SDNA-270_2_head-3000000.fq \ 2>phase.log
Output :
platanus_allee version: 2.0.2
./platanus_allee phase -c out_contig.fa out_junctionKmer.fa platanus_allee phase -c out_contig.fa out_junctionKmer.fa -IP1 /home/bio/Fareeha/test/SMIX_test_data/Unzip/SDNA-270_1_head-3000000.fq /home/bio/Fareeha/test/SMIX_test_data/Unzip/SDNA-270_2_head-3000000.fq 2
Error(13): Error, SolveDBG exception!!
platanus_allee solve_DBG command failed.
Can anyone please help me solve it ?
In the phase stage of platanus2 I have solved it by installing minimap2 with conda and everything should work.
conda install -c bioconda minimap2
Related
I`m using MacBook with M1 chip and seems like multiple things arent optimised for it.
pyodbc didnt work for me, so I wanted to use pymssql.
Though, I encountered this issue when I tried to run pip install pymssql.
The error is as below.
Using cached pymssql-2.2.2.tar.gz (170 kB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Building wheels for collected packages: pymssql
Building wheel for pymssql (pyproject.toml) ... error
ERROR: Command errored out with exit status 1:
Your project path and someinfo about it.
Complete output (25 lines):
setup.py: platform.system() => Darwin
setup.py: platform.architecture() => ('64bit', '')
setup.py: platform.libc_ver() => ('', '')
setup.py: include_dirs => []
setup.py: library_dirs => []
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-10.9-universal2-3.9
creating build/lib.macosx-10.9-universal2-3.9/pymssql
copying src/pymssql/__init__.py -> build/lib.macosx-10.9-universal2-3.9/pymssql
running build_ext
cythoning src/pymssql/_mssql.pyx to src/pymssql/_mssql.c
cythoning src/pymssql/_pymssql.pyx to src/pymssql/_pymssql.c
building 'pymssql._mssql' extension
creating build/temp.macosx-10.9-universal2-3.9
creating build/temp.macosx-10.9-universal2-3.9/src
creating build/temp.macosx-10.9-universal2-3.9/src/pymssql
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -I/Users/lakshayrohilla/SMS Project Files /cracs-backend/.venv/include -I/Library/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c src/pymssql/_mssql.c -o build/temp.macosx-10.9-universal2-3.9/src/pymssql/_mssql.o -DMSDBLIB
src/pymssql/_mssql.c:682:10: fatal error: 'sqlfront.h' file not found
#include "sqlfront.h"
^~~~~~~~~~~~
1 error generated.
error: command '/usr/bin/gcc' failed with exit code 1
----------------------------------------
**ERROR: Failed building wheel for pymssql**
Failed to build pymssql
**ERROR: Could not build wheels for pymssql, which is required to install pyproject.toml-based projects**
On trying loads of solutions for fixing this issue, Seems like something worked out for me.
I`m providing the code below for solving this issue.
Important Note:
Change the path as per your system.
1. brew install freetds
2. brew install openssl
3. export LDFLAGS="-L/opt/homebrew/Cellar/freetds/1.3.3/lib -L/opt/homebrew/Cellar/openssl#1.1/1.1.1l_1/lib"
4. export CFLAGS="-I/opt/homebrew/Cellar/freetds/1.3.3/include"
5. pip install pymssql
Just run the above commands & it should solve your issue, as it worked out for me.
Running the following commands fixed my issue
$ brew install freetds openssl
$ echo 'export LDFLAGS="-L/opt/homebrew/opt/freetds/lib -L/opt/homebrew/opt/openssl#3/lib"' >> ~/.zshrc
$ echo 'export CFLAGS="-I/opt/homebrew/opt/freetds/include"' >> ~/.zshrc
$ echo 'export CPPFLAGS="-I/opt/homebrew/opt/openssl#3/include"' >> ~/.zshrc
$ source ~/.zshrc
$ pip3 install pymssql
I am trying to build a singularity container for use in a cluster running centOS 6. Some of the packages i need are in python. The problem is that installing by pip requires glibc-2.14 and glibc-2.17. I installed those according to here and here.
Here is my definition file:
Bootstrap: docker
From: conda/miniconda3-centos6
%files
conda_env.yml
glibc-2.14
CentOS-Base.repo
glibc-2.17-55.el6.x86_64.rpm
glibc-common-2.17-55.el6.x86_64.rpm
glibc-devel-2.17-55.el6.x86_64.rpm
glibc-headers-2.17-55.el6.x86_64.rpm
glibc-static-2.17-55.el6.x86_64.rpm
glibc-utils-2.17-55.el6.x86_64.rpm
nscd-2.17-55.el6.x86_64.rpm
%post
rm /etc/yum.repos.d/CentOS-Base.repo
mv CentOS-Base.repo /etc/yum.repos.d/
yum install -y wget bzip2 gcc perl bzip2-devel gd
HOME="$PWD"
cd glibc-2.14
mkdir build
cd build
../configure --prefix=/opt/glibc-2.14
make -j8
make install
export LD_LIBRARY_PATH=/opt/glibc-2.14/lib
cd "$HOME"
rpm -Uvh glibc-2.17-55.el6.x86_64.rpm \
glibc-common-2.17-55.el6.x86_64.rpm \
glibc-devel-2.17-55.el6.x86_64.rpm \
glibc-headers-2.17-55.el6.x86_64.rpm \
glibc-static-2.17-55.el6.x86_64.rpm \
glibc-utils-2.17-55.el6.x86_64.rpm \
/usr/local/bin/conda env create -f conda_env.yml
glibc-2.14 installs fine, but installing glibc-2.17 proves to be difficult. The installion fails with the following errors:
warning: glibc-2.17-55.el6.x86_64.rpm: Header V3 RSA/SHA1 Signature, key ID 73ec361c: NOKEY
Preparing... ########################################### [100%]
1:glibc-common ########################################### [ 17%]
2:glibc ########################################### [ 33%]
/usr/sbin/glibc_post_upgrade: While trying to execute /usr/sbin/iconvconfig.x86_64 child terminated abnormally
warning: %post(glibc-2.17-55.el6.x86_64) scriptlet failed, exit status 115
error: %pre(glibc-headers-2.17-55.el6.x86_64) scriptlet failed, signal 11
error: install: %pre scriptlet failed (2), skipping glibc-headers-2.17-55.el6
3:glibc-devel ########################################### [ 50%]
error: %post(glibc-devel-2.17-55.el6.x86_64) scriptlet failed, signal 11
4:glibc-static ########################################### [ 67%]
5:glibc-utils ########################################### [ 83%]
FATAL: While performing build: while running engine: exit status 6
Installing glibc-2.17 the same way as 2.14 will result in a segfault when python is called. Can anybody with more experienced provide some insights into possible solutions? Or if there are containers for centOS 6 with newer glibc out there?
Thanks in advance!
The problem is that installing by pip requires glibc-2.14 and glibc-2.17.
There is no way that something requires both GLIBC-2.14 and GLIBC-2.17 -- these versions do not normally coexist on a single system.
Installing GLIBC-2.17 should satisfy all the requirements (it provides both GLIBC-2.17 and all previous version symbols).
I am trying to build a python (2.7) module using cygwin:
D:\Python27\python.exe setup.py build -c cygwin
However I get the following error:
running build
running build_ext
building 'mod' extension
D:\cygwin64\bin\gcc.exe -mcygwin -mdll -O -Wall -ID:\Python27\include -ID:\Python27\PC -c my_mod.c -o build\temp.win32-2.7\Release\my_mod.o
gcc: error: unrecognized command line option '-mcygwin'
error: command 'D:\\cygwin64\\bin\\gcc.exe' failed with exit status 1
What does this mean? How do I fix it?
My question is two fold:
Firefox browser
I compiled firefox source-code in releases :
https://archive.mozilla.org/pub/firefox/releases/52.0/source/
but after I finish compiling, I met Nightly, not Firefox browser.
I would execute Firefox.
Might be there is any option to build Firefox?
( I searched the build configuration, but cannot find the option about browser)
If anyone have an experience about compiling Firefox from its source code, please help :)
Rust dependency
When I compiled Firefox, I encountered error below:
0:06.97 Compiling mp4parse_capi v0.6.0 (file:///home/signal/Desktop/firefox_source/firefox-53.0/media/libstagefright/binding/mp4parse_capi)
0:06.97 Running /home/signal/.cargo/bin/rustc --crate-name build_script_build /home/signal/Desktop/firefox_source/firefox-53.0/media/libstagefright/binding/mp4parse_capi/build.rs --color always --crate-type bin --emit=dep-info,link -C opt-level=2 -C codegen-units=1 -C debuginfo=2 -C metadata=2476a8a7a86fe109 -C extra-filename=-2476a8a7a86fe109 --out-dir /home/signal/Desktop/firefox_source/firefox-53.0/obj-x86_64-pc-linux-gnu/toolkit/library/gtest/rust/./release/build/mp4parse_capi-2476a8a7a86fe109 -L dependency=/home/signal/Desktop/firefox_source/firefox-53.0/obj-x86_64-pc-linux-gnu/toolkit/library/gtest/rust/./release/deps
0:07.05 error[E0463]: can't find crate for cheddar
0:07.05 --> /home/signal/Desktop/firefox_source/firefox-53.0/media/libstagefright/binding/mp4parse_capi/build.rs:1:1
0:07.05 |
0:07.05 1 | extern crate cheddar;
0:07.05 | ^^^^^^^^^^^^^^^^^^^^^ can't find crate
0:07.05
0:07.05 error: aborting due to previous error
0:07.05
0:07.06 error: Could not compile mp4parse_capi.
0:07.06
0:07.06 Caused by:
0:07.06 process didn't exit successfully: /home/signal/.cargo/bin/rustc --crate-name build_script_build /home/signal/Desktop/firefox_source/firefox-53.0/media/libstagefright/binding/mp4parse_capi/build.rs --color always --crate-type bin --emit=dep-info,link -C opt-level=2 -C codegen-units=1 -C debuginfo=2 -C metadata=2476a8a7a86fe109 -C extra-filename=-2476a8a7a86fe109 --out-dir /home/signal/Desktop/firefox_source/firefox-53.0/obj-x86_64-pc-linux-gnu/toolkit/library/gtest/rust/./release/build/mp4parse_capi-2476a8a7a86fe109 -L dependency=/home/signal/Desktop/firefox_source/firefox-53.0/obj-x86_64-pc-linux-gnu/toolkit/library/gtest/rust/./release/deps (exit code: 101)
0:07.06 Build failed, waiting for other jobs to finish...
0:08.68 error: build failed
0:08.68 /home/signal/Desktop/firefox_source/firefox-53.0/config/rules.mk:966: recipe for target 'force-cargo-library-build' failed
0:08.68 make[5]: *** [force-cargo-library-build] Error 101
0:08.68 /home/signal/Desktop/firefox_source/firefox-53.0/config/recurse.mk:71: recipe for target 'toolkit/library/gtest/rust/target' failed
That seems I need a rust package to resolve dependecny.
But in the latest version, I could complie firefox without any error.
Could anyone give any advice?
Adding
build = false
to media/libstagefright/binding/mp4parse_capi/Cargo.toml fixed the issue.
More info here: don't try to build mp4parse
Bazel build crashes while building a python package on Ubuntu.
Full report:
sudo bazel-bin/tensorflow/tools/pip_package/build_pip_package /tmp/tensorflow_pkg
Tue Mar 14 02:41:24 IST 2017 : === Using tmpdir: /tmp/tmp.ZAETGIkAd2
~/git/tensorflow/bazel-bin/tensorflow/tools/pip_package/build_pip_package.runfiles
~/git/tensorflow
~/git/tensorflow
/tmp/tmp.ZAETGIkAd2 ~/git/tensorflow
Tue Mar 14 02:41:26 IST 2017 : === Building wheel
error: can't copy 'tensorflow/python/pywrap_tensorflow_internal.py': doesn't exist or not a regular file
I have seen the earlier bug reports filed on this and have installed swig that is required for TensorFlow on Ubuntu. Still same error log.
System details
uname -a :
Linux - 3.13.0-107-generic
This is most likely not a problem with the build_pip_package command. I had a failed bazel build command that I have erroneously overlooked.
Here is the error log:
ERROR: /home/annanay/.cache/bazel/_bazel_root/9b62c7240de3d9136528cdded945b550/external/llvm/BUILD:418:5: Generating code from table: lib/Target/AArch64/AArch64.td #llvm//:aarch64_target_gen__gen_fast_isel_genrule failed: bash failed: error executing command
(cd /home/annanay/.cache/bazel/_bazel_root/9b62c7240de3d9136528cdded945b550/execroot/tensorflow && \
exec env - \
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin \
/bin/bash -c 'source external/bazel_tools/tools/genrule/genrule-setup.sh; bazel-out/host/bin/external/llvm/llvm-tblgen -I external/llvm/include -I external/llvm/tools/clang/include -I $(dirname external/llvm/lib/Target/AArch64/AArch64.td) -gen-fast-isel external/llvm/lib/Target/AArch64/AArch64.td -o bazel-out/local-opt/genfiles/external/llvm/lib/Target/AArch64/AArch64GenFastISel.inc'): com.google.devtools.build.lib.shell.BadExitStatusException: Process exited with status 127.
bazel-out/host/bin/external/llvm/llvm-tblgen: relocation error: bazel-out/host/bin/external/llvm/llvm-tblgen: symbol _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE9_M_createERmm, version GLIBCXX_3.4.21 not defined in file libstdc++.so.6 with link time reference
Target //tensorflow/tools/pip_package:build_pip_package failed to build
Try to change from build directory to some other directory.
This works for me.