chmccarthy / pangloss Goto Github PK

Hello,
Is there a way to configure pipeline to use only nucleotide info?

Hi there and thanks for making this tool!

I have already generated gff annotations through braker for my genomes and am wondering if I can pipe these into Pangloss and skip the annotations steps Pangloss does?

Hello,
Could you help me check the config file is correct? I try to run Pangloss.py with test dataset. However, I always get the error as following. I set the config file as following what you introduced. But I am not sure it is correct.
The attachment
config.txt

is my config file.

./Pangloss.py: line 81:
Pangloss: A pipeline for pan-genome analysis of microbial eukaryotes.

Written by Charley McCarthy, Genome Evolution Lab, Department of Biology,
Maynooth University between 2017-2019 ([email protected]).

See Pangloss/README.md for more information.

To-do:
- Improve logging.

Recent changes:
v0.9.1 (August 2019)
- Fixes to how Pangloss reads in config file.
- Made Pangloss.py executable.
- Fixes to yn00 parsing.
- Disabled tarballing prediction temp files because of how slow it seemed to be.
- Other minor changes.

v0.9.0 (June 2019)
- Tested out InterProScan and GOATools pipelines.
- Changed how UpSet plots are generated, now done through Cairo (on Mac at least).

v0.8.0 (May 2019)
- Rejigged when exactly amino acid, nucleotide and attribute datasets are concatenated.
- Loads of changes to R scripts.
- Fully implemented pangenome refinement using gap: No such file or directory

import: unable to open X server ' @ error/import.c/ImportImageCommand/369. import: unable to open X server ' @ error/import.c/ImportImageCommand/369.
import: unable to open X server ' @ error/import.c/ImportImageCommand/369. import: unable to open X server ' @ error/import.c/ImportImageCommand/369.
./Pangloss.py: line 87: from: command not found
./Pangloss.py: line 88: from: command not found
./Pangloss.py: line 89: from: command not found
./Pangloss.py: line 90: from: command not found
./Pangloss.py: line 91: from: command not found
./Pangloss.py: line 93: from: command not found
./Pangloss.py: line 94: from: command not found
./Pangloss.py: line 97: syntax error near unexpected token (' ./Pangloss.py: line 97: def PanGuessHandler(ex_path, gm_path, tp_path, tl_path,'

python Pangloss.py -h
File "Pangloss.py", line 334
print "{0}, {1} has unusual frameshift mutation and can't be run through yn00.".format(e, cluster)
^
SyntaxError: invalid syntax

Opening this issue to remind myself to update Pangloss to Python3 before the end of the year.

Hi,
I want to know what's the python version. It really bothers me.
Thank you

Hello,
I have pangloss pipeline setup and ran successfully on the test data provided.

We have used alternative gene pred pipeline so have nucleotide and amino seq for our isolates.
We will use --no_pred argument, however it is not clear what directory structure, files, and file locations are needed for this to function properly. We would still like to run all other arguments (e.g. blastall, panoct etc). Can you clarify how to arrange files for this?
Thanks!

I have some issues executing Pangloss. I have all the paths declared in the config file, but the following error shows up:
$ python Pangloss.py --pred --busco --refine --ips --go --yn00 --plots config_asp.ini
/usr/lib/python2.7/dist-packages/Bio/SearchIO/init.py:211: BiopythonExperimentalWarning: Bio.SearchIO is an experimental submodule which may undergo significant changes prior to its future official release.
BiopythonExperimentalWarning)
Traceback (most recent call last):
File "Pangloss.py", line 631, in
main()
File "Pangloss.py", line 531, in main
PanGuessHandler(*panguess_args)
File "Pangloss.py", line 151, in PanGuessHandler
exonerate_genes = PanGuess.RunExonerate(cmds, cores)
File ".../Pangloss/Pangloss/PanGuess.py", line 132, in RunExonerate
genes = farm.map(ExonerateCmdLine, cmds)
File "/usr/lib/python2.7/multiprocessing/pool.py", line 251, in map
return self.map_async(func, iterable, chunksize).get()
File "/usr/lib/python2.7/multiprocessing/pool.py", line 567, in get
raise self._value
AssertionError

As I thought this could be an exonerate bug, I tried the --no_exonerate flag, but another bug appears:
$ python Pangloss.py --pred --busco --refine --ips --go --yn00 --plots --no_exonerate config_asp.ini
/usr/lib/python2.7/dist-packages/Bio/SearchIO/init.py:211: BiopythonExperimentalWarning: Bio.SearchIO is an experimental submodule which may undergo significant changes prior to its future official release.
BiopythonExperimentalWarning)
Traceback (most recent call last):
File "Pangloss.py", line 631, in
main()
File "Pangloss.py", line 531, in main
PanGuessHandler(*panguess_args)
File "Pangloss.py", line 167, in PanGuessHandler
genemark_gtf = PanGuess.RunGeneMark(genome, gm_path, gm_branch, cores)
File ".../Pangloss/Pangloss/PanGuess.py", line 171, in RunGeneMark
sp.call([gm_path, "--ES", "--fungus", "--cores", cores, "--sequence", genome])
File "/usr/lib/python2.7/subprocess.py", line 523, in call
return Popen(*popenargs, **kwargs).wait()
File "/usr/lib/python2.7/subprocess.py", line 711, in init
errread, errwrite)
File "/usr/lib/python2.7/subprocess.py", line 1343, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory

Could you please help me solve this? I really need this analysis for an upcoming article.
Thank you very much for your attention

Hi,
recently, when I run pangloss on some fungi data, I alawys met this error,

Can't load '~/miniconda3/lib/site_perl/5.26.2/x86_64-linux-thread-multi/auto/Cwd/Cwd.so'
Traceback (most recent call last):
IOError: [Errno 2] No such file or directory: 'genemark.gtf'

How can I fix it?
Thank you~

I keep getting this error when i run. It stops at INFO: PanGuess: Running Exonerate searches on 3 threads according to the log. I am just running the testconfig.ini

File "/anaconda2/envs/python2/lib/python2.7/multiprocessing/pool.py", line 572, in get
raise self._value
OSError: [Errno 13] Permission denied

Hello,

I am also having an issue with exonerate. Although this may be a problem with my set up.

I have run Pangloss successfully on the test data. However, if I run it on my data I get an error message when performing gene prediction on the second fasta listed in genomes. txt.

With this error:

image

Pangloss successfully performs gene prediction for the first fasta in genome.txt, but stops at 'INFO:PanGuess: Running Exonerate searches on 9 threads' on the second fasta.

I have so far been unable to work out why it will not run on the second fasta. I have tried swapping the second fasta for others, but it still fails on the second. Are you able to help?