Error while running the pipeline

[Ahmad Lutfi]

Hi,

thanks for providing this tool, I was testing some examples on the pipeline but I am getting the error:

---

Estimating background: 2/5, 00:03, refining background...]
Traceback (most recent call last):
File "/usr/local/bin/ortho2align", line 33, in
sys.exit(load_entry_point('ortho2align==1.0.5', 'console_scripts', 'ortho2align')())
File "/usr/local/lib/python3.10/dist-packages/ortho2align-1.0.5-py3.10.egg/ortho2align/cli_scripts.py", line 561, in ortho2align
func(**dict_args)
File "/usr/local/lib/python3.10/dist-packages/ortho2align-1.0.5-py3.10.egg/ortho2align/pipeline.py", line 356, in estimate_background
lifted_query_ranges = _lift_granges(query_genes,
File "/usr/local/lib/python3.10/dist-packages/ortho2align-1.0.5-py3.10.egg/ortho2align/pipeline.py", line 289, in _lift_granges
with open(temp_result_filename, 'r') as infile:
FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmplrwltd28/result.bed'

Used Command:
ortho2align run_pipeline -query_genes /data/gencode.v43.long_noncoding_RNAs.gtf -query_genome /data/hg38.fa\ -subject_annotation /data/calJac4.gtf -subject_genome /data/calJac4.fa -liftover_chains /data/hg38ToCalJac4.over.chain -outdir /output -cores 7 --annotate

So the main problem is not finding the file: /tmp/tmplrwltd28/result.bed. I am working as root, so the tool can write,read and delete files.

PS: I am also getting same error while running your test.sh.
Thanks!

Best
Ahmad

[Elizaveta Kulaeva]

I'm also facing this problem now :( @lutfia95 were you able to solve this problem?

[Dmitry Mylarshchikov]

Hi!
@lutfia95 Sorry for delayed response — I didn't recieve any notification.

Since ortho2align failed with both your data and my test example, I suspect the problem is either with code or the environment.

To reproduce the problem, I installed ortho2align 1.0.5 in a new clean conda environment with python 3.7.15 on WSL and my test example worked correctly. So it seems there is either a problem with making temporary directories (either OS related or python related) or with liftOver.

I have several hypotheses what might be wrong and what you can try doing to check:

1. The tool has been tested on Linux (WSL) with python 3.7, while you use python 3.10. I suggest using python 3.7 and Linux.
2. liftOver might simply not be available. Please check that it is in the path.
3. It doesn't seem like the package is installed with conda. Please use conda for managing the environment and dependencies.

Hope any of this helps! Please let me know your results.

[Dmitry Mylarshchikov]

Please also double check versions of the dependencies. For instance, it is important for liftOver to be exactly version 377.

[Ahmad Lutfi]

Can you please share your test conda environment? when I am trying to install liftOver 377 with python 3.7.15, many conflicts are shown. Maybe if I build your environment, it will solve the problem.

Best,

[Dmitry Mylarshchikov]

I also checked that everything works with python 3.9, so here's an output from conda env export --from-history:

name: test_ortho
channels:
  - bioconda
  - conda-forge
  - defaults
dependencies:
  - python=3.9
  - ortho2align

[Ahmad Lutfi]

Is ortho2align also in bioconda channel? I am trying to install it always from dmitrymyl channel

[Dmitry Mylarshchikov]

Nope, only in dmitrymyl channel

[Ahmad Lutfi]

Hi,

I updated conda and created it a clean environment without any other dependencies:

name: orthtest_1
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- python=3.9

Next, I tried to install ortho2align from dmitrymyl channel :
conda install -c dmitrymyl ortho2align

So this process could build the tool and run the code correctly without any problem. @lizakulaeva I could solve the problem like that.

@dmitrymyl Thank you very much, from my side this issue can be closed.

Best,
Ahmad

[Dmitry Mylarshchikov]

Perfect, thanks for the feedback and your conda env config! I believe we have also solved the problem with @lizakulaeva, so I close this issue.