filter_outliers fails with a strange message of a missing file

[ralsallaq]

Hi, I am having trouble executing filter_outliers.filter_sequences. It throws the following error:

Traceback (most recent call last): File "/hpcf/apps/python/install/2.7.13/lib/python2.7/site-packages/deenurp-0.0.0-py2.7.egg/deenurp/subcommands/filter_outliers.py", line 373, in filter_sequences sequence_file, prefix, cpu=threads or wrap.CMALIGN_THREADS) File "/hpcf/apps/python/install/2.7.13/lib/python2.7/site-packages/deenurp-0.0.0-py2.7.egg/deenurp/subcommands/filter_outliers.py", line 258, in distmat_cmalign taxa, distmat = outliers.fasttree_dists(a_fasta.name) File "/hpcf/apps/python/install/2.7.13/lib/python2.7/site-packages/deenurp-0.0.0-py2.7.egg/deenurp/outliers.py", line 52, in fasttree_dists proc = subprocess.Popen(cmd, stdout=stdout, stderr=devnull) File "/hpcf/apps/python/install/2.7.13/lib/python2.7/subprocess.py", line 390, in init errread, errwrite) File "/hpcf/apps/python/install/2.7.13/lib/python2.7/subprocess.py", line 1024, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory

Thus, it seems it is complaining about a missing file which puzzles me. I have supplied both a sequence fasta file to save filtered sequences and a taxa fasta file for the unfiltered sequences with taxa info. Both the filtered and the unfiltered fasta files are initially identical (before filtering) and I verified that both o the files do exist before entering the filter_outliers.filter_sequences step. Not sure what file is missing that the OS via subprocess is complaining about. Your help is appreciated especially if you have a detailed example on how to use filter_outliers and fill_lonely. Thanks much in advance.

[ralsallaq]

I found the cause. I just forgot to load fasttree on the cluster! but the message does not indicate anything about fasttree. Thanks

[crosenth]

Agreed, adding this Issue as part of next release. Thank you

[ralsallaq]

Hi Chris, Just a follow up on my earlier question regarding fill_lonely. I am trying to find examples of using fill_lonely on branches of a tree built using RAxML. Could you please be so kind to point me to where I can find such examples? An example snippet posted here could also help. Thanks in advance for your time.

[crosenth]

I apologize for the slim documentation. We are working on it.

An example you can look at is in tests/fill-lonely. The sh script in that folder will run the fill_lonely example.