sanger-pathogens/saffrontree

SaffronTree: Reference free rapid phylogenetic tree construction from raw read data

saffrontree's Issues

wrong tree from example data

Hello
I use ubuntu 18.04 and i install with : Debian Testing/Ubuntu 16.04 (Xenial)

apt-get update -qq
apt-get install -y git python3 python3-setuptools python3-biopython python3-pip kmc
pip3 install git+git://github.com/sanger-pathogens/saffrontree.git

I find the file in my path ~/.local/lib/python3.6/site-packages/saffrontree
but there is no run_test.py
when i run example saffrontree output_directory saffrontree/example_data/fastas/*.fa my tree is wrong :
[&R] (('saffrontree/example_data/fastas/start_Salmonella_enterica_subsp_enterica_serovar_Typhi_Ty2_v1.fa':0.5,('saffrontree/example_data/fastas/start_Salmonella_enterica_subsp_enterica_serovar_Typhi_str_CT18_v1.fa':0.5,'saffrontree/example_data/fastas/start_Salmonella_enterica_subsp_enterica_serovar_Typhimurium_str_LT2_v1.fa':0.5):0.0):0.0,(('saffrontree/example_data/fastas/start_Salmonella_enterica_subsp_enterica_serovar_Weltevreden_str_10259_v0.2.fa':0.5,'saffrontree/example_data/fastas/start_Salmonella_enterica_subsp_enterica_serovar_Typhimurium_SL1344_v4.fa':0.5):0.0,('saffrontree/example_data/fastas/start_Salmonella_enterica_subsp_enterica_serovar_Paratyphi_A_str_AKU_12601_v2.fa':0.5,'saffrontree/example_data/fastas/start_Salmonella_enterica_subsp_enterica_serovar_Typhimurium_DT104_v1.fa':0.5):0.0):0.0);

Do you know what appends?
Best,

What is [&R] at start of .newick file?

[&R] ('file1':888 ....

pip install

Hello,
I couldn't install saffrontree by pip install git+git://github.com/sanger-pathogens/saffrontree.git
because of this error:
ERROR: Command errored out with exit status 128: git clone -q git://github.com/sanger-pathogens/saffrontree.git /tmp/pip-req-build-7mm6vj45 Check the logs for full command output.

Instead, I have install it like this:
pip install git+https://github.com/sanger-pathogens/saffrontree.git

Maybe will be useful to someone!
L

Temp files not cleaned up?

saffrontree -v -t 72 out1 *.gz

ls out1/
kmer_tree.newick 
 tmp4037372r  tmpafetgs9d  tmpeohwu5zr  tmpiktm7wbp  tmppa9dp89c  tmpt_y411ch  tmpyyyfzoaw
tmp02movqb_       tmp5oxycwr7  tmpag5o2eia  tmpfw22dg7c  tmpjzo7wosr  tmpptyagnj5  tmptcj9ezgv
tmp088xwgb3       tmp5quf9a99  tmpayt9w_t1  tmpgq4mqgol  tmpjzyyqup2  tmpqr8mgj48  tmptcjbxdw6
tmp0rtnxzvw       tmp6whv4zzf  tmpbxqrdi4x  tmpgt2dgdng  tmpk4fixrsj  tmpr6dt0s4r  tmpuddotnoe
tmp12rxjbjk       tmp8rq5trlz  tmpca6rh5yf  tmph1lvw4j5  tmpkgx_e7fv  tmprmvtd4af  tmpvflj5_qc
tmp14mwdjfs       tmp92g6__au  tmpccjyh3x3  tmphh7bwucq  tmpkwwksw2n  tmprtm8t0y5  tmpxuv7o3u3
tmp2viwsdve       tmp_jw5pw4h  tmpd8moshp7  tmphn_u97y8  tmpm27z1z7z  tmpslfuddqb  tmpy4qtrq01
tmp3pgnnosn       tmpa7u01vwt  tmpebdaapp6  tmphvdzidfa  tmpmphe0s6e  tmpsyhi1uqk  tmpyjxhs1ov

No such file or directory: 'kmc'

saffrontree saffrontree_out Results/tree_estimation.fasta 
Traceback (most recent call last):
  File "/home/lenore/.local/bin/saffrontree", line 4, in <module>
    __import__('pkg_resources').run_script('saffrontree==0.1.2', 'saffrontree')
  File "/home/lenore/.local/lib/python3.10/site-packages/pkg_resources/__init__.py", line 662, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/home/lenore/.local/lib/python3.10/site-packages/pkg_resources/__init__.py", line 1466, in run_script
    exec(script_code, namespace, namespace)
  File "/home/lenore/.local/lib/python3.10/site-packages/saffrontree-0.1.2-py3.10.egg/EGG-INFO/scripts/saffrontree", line 35, in <module>
  File "/home/lenore/.local/lib/python3.10/site-packages/saffrontree-0.1.2-py3.10.egg/saffrontree/SaffronTree.py", line 37, in __init__
  File "/home/lenore/.local/lib/python3.10/site-packages/saffrontree-0.1.2-py3.10.egg/saffrontree/KmcVersionDetect.py", line 11, in __init__
  File "/home/lenore/.local/lib/python3.10/site-packages/saffrontree-0.1.2-py3.10.egg/saffrontree/KmcVersionDetect.py", line 21, in find_version
  File "/home/lenore/Python-3.10.3/Lib/subprocess.py", line 420, in check_output
    return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
  File "/home/lenore/Python-3.10.3/Lib/subprocess.py", line 501, in run
    with Popen(*popenargs, **kwargs) as process:
  File "/home/lenore/Python-3.10.3/Lib/subprocess.py", line 966, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/home/lenore/Python-3.10.3/Lib/subprocess.py", line 1842, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'kmc'

Running on fastqs produces matrix full of "1"

Running on bunch of fastq files, either .gz or ungzipped produces a matrix of identical distances full of 1s.
Running on fasta seems to work. Looks like it fails reading kmers from fastqs.