kdm9 / axe Goto Github PK

Hi I am trying to install axe and am facing this error:

[  3%] Building C object src/libqes/src/CMakeFiles/qes_static.dir/qes_compat.c.o
clang: error: no such file or directory: 'NOTFOUND'
make[2]: *** [src/libqes/src/CMakeFiles/qes_static.dir/qes_compat.c.o] Error 1
make[1]: *** [src/libqes/src/CMakeFiles/qes_static.dir/all] Error 2
make: *** [all] Error 2

Find out why erroneous barcodes are mis-assigned, e.g in http://nbviewer.ipython.org/github/kdmurray91/lab-notebook/blob/master/topics/axe/AxeBenchmarking.ipynb cell 41, we have many erroneous assignments.

This is a pretty critical bug.

Hello Kevin,
I got this error when I use axe-demux: Barcode file must be provided.
The script is as below, and I am trying to demultiplex a fastq file with 96 samples.
axe-demux -m -barcodes barcode_box5_axe.csv -f Lane_2_S2_L002_R1_001.fastq -F axe_demux

The barcode file (csv file, separated by Tab) looks like this:
Barcode ID
ACGAGTGCGT Lane2Sample1
ACGCTCGACA Lane2Sample2
AGACGCACTC Lane2Sample3
AGCACTGTAG Lane2Sample4
ATCAGACACG Lane2Sample5

Hi Kevin,

Many thanks for providing Axe to the community!

I've just come across your tool and would be interested to give it a try – however for my downstream applications it'd be rather essential not to trim off the barcodes (neither R1 nor R2) upon demultiplexing. Could you possibly add this option "--no-trim"?

Best wishes,
Max

Possibly change "[FILE]" to "[DIRECTORY]" ?

I should include the relevant GSL source with AXE, to remove the build/install dependency on the GSL.

Make the summary use less exact numbers for ease of reading, i.e. make the number of reads counted in thousands/millions. "125.4M read pairs" is easier to read than "125443344 read pairs".

I have been trying to install axe on my computer. Here is my code:
brew install cmake
git clone --recursive https://github.com/kdmurray91/axe.git axe
cd axe
cmake .
make install axe

I have installed bioconda, so there is (base) in front of my username. Firstly, I doubt that there is something wrong with my enviornment, so I have tried to leave the base environment, but I got same error message.

Here is the error message:

WARNING: unknown config value 'latex_paper_size' in override, ignoring
WARNING: html_static_path entry '.static' does not exist

Exception occurred:
File "/opt/anaconda3/lib/python3.9/site-packages/sphinx/application.py", line 376, in build
os.unlink(envfile)
PermissionError: [Errno 13] Permission denied: '/Users/kenhsu/axe/doc/man/.doctrees/environment.pickle'
The full traceback has been saved in /var/folders/tt/22nmrjys36s6lql2bl2czw9w0000gq/T/sphinx-err-si44dp0u.log, if you want to report the issue to the developers.
Please also report this if it was a user error, so that a better error message can be provided next time.
A bug report can be filed in the tracker at https://github.com/sphinx-doc/sphinx/issues. Thanks!
make[2]: *** [docs/CMakeFiles/doc_man] Error 2
make[1]: *** [docs/CMakeFiles/doc_man.dir/all] Error 2
make: *** [all] Error 2

While working with a corrupt gzipped sequence file, axe-demux 'finished' but did not throw an error or otherwise alert me to a problem. Having fraction of the expected sequences in the summary table did alert me to the problem.

I'm not sure how one would catch this error....

In any case. This works very well. Thank Kevin for making it. This is the first program I've used that takes advantage of the hamming distances that I designed into the molecular part of GBS!

Hey Kevin,

Just stumbled across this, and it's exactly what I was looking for, and works great!

Would you consider putting it on bioconda if only to make my life slightly easier when deploying it in our pipeline? If it's a hassle, I could give it a go.

Cheers,
Jesse

• A run through of an example implementation.

Hello and thank you for the tool.
When I run it without "-m, --mismatch", the run is successful. When I want to specify it as -m 1 or --mismatch 1, in fisrt case it gives me an error:

[F] load_tries -- Barcode ATCACGTC already in fwd trie (2mm) GTCACGTC
[main] ERROR: axe_load_tries returned 1

and no output (in output folder and in terminal) in second case.

Without this option I still can get an output, but I would like to try this option as well to see if it will improve some of the samples.

Forgot to add that I am using combinatorial mode.

I get this installation error on macOS 10.13.5 (using Apple's native compilers)

Scanning dependencies of target doc_onehtml
WARNING: latex_paper_size is deprecated. Define a latex_elements dict with a 'papersize' key.
WARNING: LaTeX command 'latex' cannot be run (needed for math display), check the imgmath_latex setting
WARNING: html_static_path entry '/Users/Negorashi2011/src/axe/docs/.static' does not exist
[ 0%] Built target doc_onehtml
Scanning dependencies of target doc_man
WARNING: latex_paper_size is deprecated. Define a latex_elements dict with a 'papersize' key.

[ 0%] Built target doc_man
Scanning dependencies of target doc_html
WARNING: latex_paper_size is deprecated. Define a latex_elements dict with a 'papersize' key.
WARNING: LaTeX command 'latex' cannot be run (needed for math display), check the imgmath_latex setting
WARNING: html_static_path entry '/Users/Negorashi2011/src/axe/docs/.static' does not exist
[ 0%] Built target doc_html
Scanning dependencies of target doc
[ 0%] Built target doc
Scanning dependencies of target setup_tests
[ 0%] Built target setup_tests
Scanning dependencies of target qes_static
[ 4%] Building C object src/libqes/src/CMakeFiles/qes_static.dir/qes_compat.c.o
clang: error: no such file or directory: 'NOTFOUND'
make[2]: *** [src/libqes/src/CMakeFiles/qes_static.dir/qes_compat.c.o] Error 1
make[1]: *** [src/libqes/src/CMakeFiles/qes_static.dir/all] Error 2
make: *** [all] Error 2

As suggested by a reviewer of the paper.

• Add command line option, -e, which takes the RE site remnant
• Add RE sequence to end of each barcode read from keyfile
• Trim len(RE_seq) bases left of the end of the match, i.e. at the start of the RE site.

I need to remove the copy-pasted code from process_file_single, as I did for process_file_combo