Error upon running flair collapse

[paulatin4mente]

I am running flair collapse after running bam2Bed12 and flair correct
I have had no issue with the two previous commands, but upon running the collapse function I am getting an error message:

count_sam_transcripts.py --sam - -o BC-astro-24e-rep1.firstpass.q.counts -t 4 --quality 0 -w 100 --stringent --check_splice -i BC-astro-24e-rep1.firstpass.bed --trust_ends --generate_map BC-astro-24e-rep1.isoform.read.map.txt Traceback (most recent call last): File "/home/pj392/miniconda3/envs/flair/bin/flair", line 10, in <module> sys.exit(main()) ^^^^^^ File "/home/user/miniconda3/envs/flair/lib/python3.12/site-packages/flair/flair_cli.py", line 57, in main collapse() File "/home/user/miniconda3/envs/flair/lib/python3.12/site-packages/flair/flair_collapse.py", line 413, in collapse pipettor.run([mm2_cmd, count_cmd]) File "/home/user/miniconda3/envs/flair/lib/python3.12/site-packages/pipettor/__init__.py", line 35, in run Pipeline(cmds, stdin=stdin, stdout=stdout, stderr=stderr, logger=logger, logLevel=logLevel).wait() File "/home/user/miniconda3/envs/flair/lib/python3.12/site-packages/pipettor/processes.py", line 470, in wait self._wait_guts() File "/home/user/miniconda3/envs/flair/lib/python3.12/site-packages/pipettor/processes.py", line 463, in _wait_guts self._raise_if_failed() File "/home/user/miniconda3/envs/flair/lib/python3.12/site-packages/pipettor/processes.py", line 426, in _raise_if_failed raise ex File "/home/user/miniconda3/envs/flair/lib/python3.12/site-packages/pipettor/processes.py", line 423, in _raise_if_failed raise p.procExcept pipettor.exceptions.ProcessException: process exited 1: count_sam_transcripts.py --sam - -o BC-astro-24e-rep1.firstpass.q.counts -t 4 --quality 0 -w 100 --stringent --check_splice -i BC-astro-24e-rep1.firstpass.bed --trust_ends --generate_map BC-astro-24e-rep1.isoform.read.map.txt: Traceback (most recent call last): File "/home/user/miniconda3/envs/flair/lib/python3.12/site-packages/flair/count_sam_transcripts.py", line 11, in <module> from flair import remove_internal_priming ModuleNotFoundError: No module named 'flair'

I have no idea what could be wrong and would appreciate some help.
I am running all three under the same conda environment, created exclusively for running flair.

[cafelton]

This seems like a FLAIR install issue. How did you install FLAIR?

[paulatin4mente]

I installed it with all its dependencies with bioconda: conda create -n flair -c conda-forge -c bioconda flair

[cafelton]

Not sure why you're specifically having this issue and I'm not on my end, but I suspect you can fix this by editing the line in /home/user/miniconda3/envs/flair/lib/python3.12/site-packages/flair/count_sam_transcripts.py
from:
from flair import remove_internal_priming
to:
import flair.remove_internal_priming

[diekhans]

I think that would need to be import flair.remove_internal_priming as remove_internal_priming However, this should not be happening. I would suggest removing your conda env and then recreating . Something is off here. cafelton ***@***.***> writes:

…

Not sure why you're specifically having this issue and I'm not on my end, but I suspect you can fix this by editing the line in /home/user/miniconda3/envs/flair/lib/python3.12/site-packages/flair/count_sam_transcripts.py from: from flair import remove_internal_priming to: import flair.remove_internal_priming -- Reply to this email directly or view it on GitHub: #533 (comment) You are receiving this because you are subscribed to this thread. Message ID: ***@***.***>

[paulatin4mente]

I did just that. Error is persisting...

[cafelton]

Sorry to hear that. We're truly unable to replicate this error. At this point, all I can suggest is that you reinstall using the github release:
conda env create -n flair --file https://github.com/BrooksLabUCSC/flair/releases/download/v2.2.0/flair_conda_env.yaml
conda activate flair

[claudiamedrano97]

Hi Just wondering if there was a solution found for this? I'm having the exact same error when running flair transcriptome. I also installed using conda create -n flair -c conda-forge -c bioconda flair

[claudiamedrano97]

forgot to mention I can't install with the .yaml, as I get sudo apt permission error

[diekhans]

claudiamedrano97 ***@***.***> writes:

forgot to mention I can't install with the .yaml, as I get sudo apt permission error

That is a starting point. Conda is all about installing software as a user, not as root. There show be no sudo or apt involved. How have you installed conda? It is hard to debug someone else's install problems without being on the system, so we will have to walk through this.

[claudiamedrano97]

Hi, thanks for your response! I'm still not sure what the issue is but I figured out that it runs fine when not running in a screen

[diekhans]

claudiamedrano97 ***@***.***> writes:

Hi, thanks for your response! I'm still not sure what the issue is but I figured out that it runs fine when not running in a screen

That is very odd. I am always running in screen. Something is lurking in your environment. Happy to bounce ideas of things to look at, but not much to can be done to directly figure it out One thing is his to compare the output of the env command in an shell where it fails and one where it doesn't.