# Failed to import pandas in python process

**URL:** <https://community.seqera.io/t/failed-to-import-pandas-in-python-process/1033>\
**Category:** Ask for help\
**Tags:** nextflow, config\
**Created:** [July 31, 2024, 3:41am UTC](https://community.seqera.io/t/failed-to-import-pandas-in-python-process/1033 "2024-07-31T03:41:47Z")\
**Posts on this page:** 5\
**Page:** 1

<div class="post-metadata">

**Author:** ![saif\_s](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/saif_s/32/895_2.png) [@saif\_s](https://community.seqera.io/u/saif_s)\
**Post date:** [July 31, 2024, 3:41am UTC](https://community.seqera.io/t/failed-to-import-pandas-in-python-process/1033/1 "2024-07-31T03:41:47Z")

</div>

Hello,

I have this nf script below that has a simple python process that starts by importing pandas then reading a csv file. The conda environment that I utilize is created is in the config file. However, everytime I run the nf script it produces an error no module names pandas.

```auto
#!/usr/bin/env nextflow
process PYMANIFESTCREATOR {
	debug true
	label 'pandasenv'
	input:
	path manifesto_file
	output:
	stdout
	script:
	"""
	#!/usr/bin/env python3
	try:
    	import pandas as pd
    	from pathlib import Path
    	import shutil
    	import glob
    	import os
    	print("All necessary modules imported successfully.")
	except ImportError as e:
    	print(f"An error occurred while importing modules: {e}")
	manifest_csv = "$manifesto_file"
	print(manifest_csv)
	"""
}
workflow {
	input_ch = channel.fromPath("$projectDir/*_Manifest.csv")
	PYMANIFESTCREATOR(input_ch)
}

```

nextflow.config

```auto
profiles{
	singularity{
    	singularity.enabled = true
    	process{
    	process.executor = 'slurm'
    	withLabel: qiime {
        	cpus = 10
        	memory = 100.GB
        	container = '/uufs/chpc.utah.edu/common/home/kapheim-group2/Sief/nextflow_script/singularity/amplicon_latest.sif'
    	}
    	}
	}
	conda{
    	conda.enabled = true
    	process{
        	process.executor = 'slurm'
        	withLabel: pandasenv{
            	cpus = 10
            	memory = 50.GB
            	conda = '/uufs/chpc.utah.edu/common/home/u6060645/software/pkg/miniconda3/envs/pandaenv'
        	}
    	}
	}
}

```

---

<div class="post-metadata">

**Author:** ![saif\_s](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/saif_s/32/895_2.png) [@saif\_s](https://community.seqera.io/u/saif_s)\
**Post date:** [July 31, 2024, 3:46am UTC](https://community.seqera.io/t/failed-to-import-pandas-in-python-process/1033/2 "2024-07-31T03:46:20Z")

</div>

If I activate the environment first manually using conda activate envname and then run nextflow script it works … I thought nextflow config file activates the environment automatically?!

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<div class="post-metadata">

**Author:** ![mribeirodantas](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/mribeirodantas/32/235_2.png) [@mribeirodantas](https://community.seqera.io/u/mribeirodantas)\
**Post date:** [July 31, 2024, 1:09pm UTC](https://community.seqera.io/t/failed-to-import-pandas-in-python-process/1033/3 "2024-07-31T13:09:59Z")

</div>

Hello @saif_s,

What command line you are typing to run this pipeline? Don’t forget to pick your profile with `-profile conda`. Would you, by any chance, be picking both the `singularity` and the `conda` profiles? Because there’s a conflict here. Either you use containers or conda for a process. You can’t tell Nextflow to use both strategies at the same time.

Could you please share your `.nextflow.log` file? Running with `NXF_TRACE=nextflow` before your command line (`NXF_TRACE=nextflow nextflow...`) enables trace-level logging, which is useful for debugging too. Consider doing that too.

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<div class="post-metadata">

**Author:** ![saif\_s](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/saif_s/32/895_2.png) [@saif\_s](https://community.seqera.io/u/saif_s)\
**Post date:** [August 1, 2024, 11:33pm UTC](https://community.seqera.io/t/failed-to-import-pandas-in-python-process/1033/4 "2024-08-01T23:33:47Z")

</div>

Hello,

Thank you so much, I did figure it out and you are totally correct. I didn’t add a profile in my nextflow run command, that solved the main issue.

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<div class="post-metadata">

**Author:** ![system](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/system/32/2402_2.png) [@system](https://community.seqera.io/u/system)\
**Post date:** [August 8, 2024, 11:34pm UTC](https://community.seqera.io/t/failed-to-import-pandas-in-python-process/1033/5 "2024-08-08T23:34:15Z")

</div>

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