Closed suegrimes closed 1 year ago
nrhorner
commented
1 year ago Hi @suegrimes
You are running this with a local profile, which we do not support as it's not possible for us to know which versions of dependencies you are using. But I think this is caused by using a new version of Polars. We use 18.1.5 in our docker containers, which you would get using -profile standard or -profile singularity
suegrimes
commented
1 year ago Hi Neil,
Thank you for responding even though I’m doing this in a non-supported way. You’re correct that I have a newer version of polars. I’m trying to set up a condas environment with packages needed, and have polars 0.19.6 installed, so will downgrade that. Is there a way to see what versions of packages are installed in your docker containers? I will try again with singularity later, but wasn’t able to figure out what was going on that was making running under singularity problematic, and we are not able to run with docker. Thanks again,
Sue.
From: Neil Horner @.> Sent: Wednesday, October 4, 2023 1:18 AM To: epi2me-labs/wf-single-cell @.> Cc: Sue M Grimes @.>; Mention @.> Subject: Re: [epi2me-labs/wf-single-cell] ERROR: calc_saturation.py unexpected keyword 'frac' (Issue #50)
Hi @suegrimeshttps://github.com/suegrimes
You are running this with a local profile, which we do not support as it's not possible for us to know which versions of dependencies you are using. But I think this is caused by using a new version of Polars. We use 18.1.5 in our docker containers, which you would get using -profile standard or -profile singularity
— Reply to this email directly, view it on GitHubhttps://github.com/epi2me-labs/wf-single-cell/issues/50#issuecomment-1746370440, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AADNHNN53PBZMX7L25UI4CLX5ULUBAVCNFSM6AAAAAA5RYJD7KVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONBWGM3TANBUGA. You are receiving this because you were mentioned.Message ID: @.**@.>>
Operating System
Windows 10
Other Linux
Ubuntu 20.04
Workflow Version
v0.2.7-g9272e2c
Workflow Execution
EPI2ME Desktop application
EPI2ME Version
No response
CLI command run
nextflow run epi2me-labs/wf-single-cell \ -w output/workspace \ -profile local \ --fastq wf-single-cell-demo/chr17.fq.gz \ --kit_name 3prime \ --kit_version v3 \ --expected_cells 100 \ --ref_genome_dir wf-single-cell-demo/ \ --out_dir output \ --plot_umaps
Workflow Execution - CLI Execution Profile
None
What happened?
File "/home/sgrimes/.nextflow/assets/epi2me-labs/wf-single-cell/bin/workflow_glue/calc_saturation.py", line 96, in downsample_dataframe df_scaled = df.sample(frac=fraction) TypeError: sample() got an unexpected keyword argument 'frac'
Relevant log output
Application activity log entry
No response