Runing citup: pypeliner.scheduler - ERROR - exception

[EsterAH89]

Hello, i'm running citup and getting an error for some of the input files, while it works for some others, so I do not think it is a problem of citup installation, or python version or etc.
On the other side, could be a problem of the input files, however, all the input files look the same: txt file with 2 or more columns with numbers regarding mutation frequencies (see an example of input files on comments). The problem is that it worked for some of the input files and not for others without apparent reason. I have tried running it in cluster and locally. The code I'm running looks like this:

run_citup_iter.py PATH_TO_INPUT_FILE/citup_input_1.txt PATH_TO_OUTPUT_FILE/citup_output_1.h5 --submit local

The error I got is this:

2023-07-25 16:49:13,628 - pypeliner.scheduler - ERROR - exception
Traceback (most recent call last):
File "/miniconda/miniconda3/envs/citup_env/lib/python2.7/site-packages/pypeliner/scheduler.py", line 95, in run
self._wait_next_job(exec_queue, workflow)
File "/miniconda/miniconda3/envs/citup_env/lib/python2.7/site-packages/pypeliner/scheduler.py", line 195, in _wait_next_job
self._handle_error(job, received.log_text(), "failed to complete\n", exec_queue)
File "/miniconda/miniconda3/envs/citup_env/lib/python2.7/site-packages/pypeliner/scheduler.py", line 174, in _handle_error
raise pypeliner.graph.IncompleteJobException()
IncompleteJobException
2023-07-25 16:49:13,629 - pypeliner.scheduler - ERROR - pipeline failed
log file: ./tmp/log/20230725-164836/pipeline.log
Traceback (most recent call last):
File "/miniconda/miniconda3/envs/citup_env/bin/run_citup_iter.py", line 4, in
import('pkg_resources').run_script('citup==0.1.0', 'run_citup_iter.py')
File "/miniconda/miniconda3/envs/citup_env/lib/python2.7/site-packages/pkg_resources/init.py", line 666, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/miniconda/miniconda3/envs/citup_env/lib/python2.7/site-packages/pkg_resources/init.py", line 1469, in run_script
exec(script_code, namespace, namespace)
File "/miniconda/miniconda3/envs/citup_env/lib/python2.7/site-packages/citup-0.1.0-py2.7.egg/EGG-INFO/scripts/run_citup_iter.py", line 82, in

File "/miniconda/miniconda3/envs/citup_env/lib/python2.7/site-packages/pypeliner/app.py", line 260, in run
self.sch.run(workflow, self.exec_queue, self.file_storage, self.runskip)
File "/miniconda/miniconda3/envs/citup_env/lib/python2.7/site-packages/pypeliner/scheduler.py", line 113, in run
raise PipelineException('pipeline failed')
pypeliner.scheduler.PipelineException: pipeline failed

Does anyone has a clue on what is happening??
I would really appreciate your help!!!

Rergards,

Ester

[EsterAH89]

Here an example of one input file that rise an error:

0.9272 0.0141
0.9272 0.0141
0.0019 0.8817
0.9272 0.0141
0.0019 0.8817
0.9842 0.9488
0.0019 0.8817
0.0019 0.8817
0.0019 0.8817
0.0019 0.8817
0.0019 0.8817
0.0019 0.8817
0.9272 0.0141
0.9272 0.0141

[hanlu20221104]

Hi,@EsterAH89 Have you resolved this bug now? I also encountered the same problem.

[EsterAH89]

Hello @hanlu20221104 just realized that if you run the Citup QIP instead (check run_citup_qip.py -h) it works. In this case, you need to provide a table of mutation frequencies.

More info here: https://github.com/amcpherson/citup

Hope it helps :)

[hanlu20221104]

Thanks for your reply @EsterAH89. I have used the command run_citup_qip.py, and the input files are freq.txt and clusters.txt, I still
get pypeliner.scheduler.PipelineException: pipeline failed.