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License: GNU General Public License v3.0

Python 61.19% Shell 0.14% HyPhy 37.78% Dockerfile 0.89%

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fustr's Issues

Error running FUSTr

Hi,
I am running FUSTr on my transcriptome datasets. I am running it on my local machine as docker is failing to run. I am getting the following error message, but all the dependencies seems to be fine.

Traceback (most recent call last):
File "/home/uom/FUSTr/bin/FUSTr", line 135, in
output = subprocess.check_output(['bash','-c', bashCommand])
File "/home/uom/anaconda3/lib/python3.6/subprocess.py", line 336, in check_output
**kwargs).stdout
File "/home/uom/anaconda3/lib/python3.6/subprocess.py", line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['bash', '-c', 'snakemake --snakefile $(which FUSTrSnakefile) -d /home/uom/FUSTr/Nas --cores 16 --use-conda --configfile configure.json']' returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/uom/FUSTr/bin/FUSTr", line 144, in
output = subprocess.check_output(['bash','-c', bashCommand])
File "/home/uom/anaconda3/lib/python3.6/subprocess.py", line 336, in check_output
**kwargs).stdout
File "/home/uom/anaconda3/lib/python3.6/subprocess.py", line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['bash', '-c', 'snakemake --snakefile $(which FUSTrSnakefile) -d /home/uom/FUSTr/Nas --cores 16 --use-conda --configfile configure.json']' returned non-zero exit status 1.

I also have one more clarification to be made regarding the usage. I have 2 parental transcriptomes and 3 hybrid transcriptomes. Is it fine if I run FUSTr on individual samples? Or does FUSTr needs more than one dataset for comparisons?

Any chance FURSTr can be installed via conda? Thanks

Docker and Singularity

Hi there,
I would like to use FUSTr, the challenge is Docker is not allowed on our linux server. I was wondering if there a way to use FUSTr with Singularity instead?

thanks
Kay

Problems installing FUSTr with Docker

Hi,
I am having trouble installing FUSTr with Docker. It returns messages as follows. Does anyone know how to solve?

Writing /tmp/easy_install-10ka1v8r/pip-19.3.1/setup.cfg
Running pip-19.3.1/setup.py -q bdist_egg --dist-dir /tmp/easy_install-10ka1v8r/pip-19.3.1/egg-dist-tmp-xdpmz9w4
/usr/lib/python3.4/distutils/dist.py:260: UserWarning: Unknown distribution option: 'python_requires'
warnings.warn(msg)
warning: no files found m

In the end:

The command '/bin/sh -c pip install numpy biopython scipy' returned a non-zero code: 1

Error in running FUSTr: "NameError: name 'dynamic' is not defined"

Hi,
We are trying to run FUSTr in a Linux Cluster. We installed all the required dependencies as you have mentioned in - "Installation without Docker". However, we are unable to run the analysis and this is the error that is showing up:

Traceback (most recent call last):
  File "/home/pragya/bin/miniconda3/envs/FUSTr_env/lib/python3.12/site-packages/snakemake/cli.py", line 1887, in args_to_api
    dag_api = workflow_api.dag(
              ^^^^^^^^^^^^^^^^^
  File "/home/pragya/bin/miniconda3/envs/FUSTr_env/lib/python3.12/site-packages/snakemake/api.py", line 326, in dag
    return DAGApi(
           ^^^^^^^
  File "<string>", line 6, in __init__
  File "/home/pragya/bin/miniconda3/envs/FUSTr_env/lib/python3.12/site-packages/snakemake/api.py", line 421, in __post_init__
    self.workflow_api._workflow.dag_settings = self.dag_settings
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/pragya/bin/miniconda3/envs/FUSTr_env/lib/python3.12/site-packages/snakemake/api.py", line 372, in _workflow
    workflow.include(
  File "/home/pragya/bin/miniconda3/envs/FUSTr_env/lib/python3.12/site-packages/snakemake/workflow.py", line 1369, in include
    exec(compile(code, snakefile.get_path_or_uri(), "exec"), self.globals)
  File "/home/pragya/bin/FUSTr/bin/FUSTrSnakefile", line 419, in <module>
    longIsoform_CDS_combined[GeneID] = seq
    ^^^^^^^
NameError: name 'dynamic' is not defined
Traceback (most recent call last):
  File "/home/pragya/bin/miniconda3/envs/FUSTr_env/lib/python3.12/site-packages/snakemake/cli.py", line 1887, in args_to_api
    dag_api = workflow_api.dag(
              ^^^^^^^^^^^^^^^^^
  File "/home/pragya/bin/miniconda3/envs/FUSTr_env/lib/python3.12/site-packages/snakemake/api.py", line 326, in dag
    return DAGApi(
           ^^^^^^^
  File "<string>", line 6, in __init__
  File "/home/pragya/bin/miniconda3/envs/FUSTr_env/lib/python3.12/site-packages/snakemake/api.py", line 421, in __post_init__
    self.workflow_api._workflow.dag_settings = self.dag_settings
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/pragya/bin/miniconda3/envs/FUSTr_env/lib/python3.12/site-packages/snakemake/api.py", line 372, in _workflow
    workflow.include(
  File "/home/pragya/bin/miniconda3/envs/FUSTr_env/lib/python3.12/site-packages/snakemake/workflow.py", line 1369, in include
    exec(compile(code, snakefile.get_path_or_uri(), "exec"), self.globals)
  File "/home/pragya/bin/FUSTr/bin/FUSTrSnakefile", line 419, in <module>
    longIsoform_CDS_combined[GeneID] = seq
    ^^^^^^^
NameError: name 'dynamic' is not defined
Picking up from where we left off!
1 snakemake --snakefile $(which FUSTrSnakefile) -d ./main_folder_annotated_trctms_CCMB --cores 32 --use-conda --configfile configure.json  --unlock
Traceback (most recent call last):
  File "/home/pragya/bin/FUSTr/bin/FUSTr", line 135, in <module>
    output = subprocess.check_output(['bash','-c', bashCommand])
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/pragya/bin/miniconda3/envs/FUSTr_env/lib/python3.12/subprocess.py", line 466, in check_output
    return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/pragya/bin/miniconda3/envs/FUSTr_env/lib/python3.12/subprocess.py", line 571, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['bash', '-c', 'snakemake --snakefile $(which FUSTrSnakefile) -d ./main_folder_annotated_trctms_CCMB --cores 32 --use-conda --configfile configure.json']' returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/pragya/bin/FUSTr/bin/FUSTr", line 141, in <module>
    output = subprocess.check_output(['bash','-c', bashCommand])
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/pragya/bin/miniconda3/envs/FUSTr_env/lib/python3.12/subprocess.py", line 466, in check_output
    return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/pragya/bin/miniconda3/envs/FUSTr_env/lib/python3.12/subprocess.py", line 571, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['bash', '-c', 'snakemake --snakefile $(which FUSTrSnakefile) -d ./main_folder_annotated_trctms_CCMB --cores 32 --use-conda --configfile configure.json  --unlock']' returned non-zero exit status 1.

Could you please us figure out the remedy?
Thanks,
pragyadeep

CodeML not working

Hi,

I am trying to run FUSTr with CodeML on transcriptome datasets.
I made sure that Biopython and CodeML are installed and loaded, and used the designated script. FUSTr ran successfully, however it did not run CodeML. There were no errors.
Not quite sure what I could try differently.

Thanks for your help!

If you already have a protein reference set prepared

Hi,
Thanks for your awesome pipeline, which is a very useful and user-friendly especially for those just starting out in bioinformatics. Could you please tell if you plan to add the ability to use not only fasta with nucleotide sequences, but also fasta with amino acid sequences as input? And what strategy do you think is preferable for those who already have prepared protein reference sets but want to conduct the analysis for which your pipeline is designed? Run separately the programs included in the pipeline with the parameters specified in the code?
Thank you!

How to cite your article?

Does FUSTr select only complete ORFs from TransDecoder?

I.e. ORFs that contain both a start and stop codon?
I couldn't find any information about this in the documentation.

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