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wdecoster / nanocomp

Comparison of multiple long read datasets
MIT License
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TypeError: write_stats() got an unexpected keyword argument 'as_tsv' #40

Closed Annie-msi closed 3 years ago

Annie-msi commented 3 years ago

Hello, I used this command to compare 5 nanopore runs and getting this following error:

NanoComp --summary CFrun1_sequencing_summary.txt CFrun2_sequencing_summary_FAO02660_9be575fb.txt WCrun1_sequencing_summary.txt WCrun3_sequencing_summary_FAO69991_ee9098dc.txt Winona_sequencing_summary_FAP07387_60b4a7a5.txt --names A B C D E Traceback (most recent call last): File "/home/plarsen/jahan036/miniconda3/envs/Nanocomp/bin/NanoComp", line 10, in sys.exit(main()) File "/home/plarsen/jahan036/miniconda3/envs/Nanocomp/lib/python3.6/site-packages/nanocomp/NanoComp.py", line 72, in main as_tsv=args.tsv_stats) TypeError: write_stats() got an unexpected keyword argument 'as_tsv'

wdecoster commented 3 years ago

Hi,

Thanks for reporting this. Could you let me know how you installed NanoComp? It seems the nanomath submodule is outdated, which you could update using either pip install nanomath ---upgrade or conda upgrade nanomath.

Cheers, Wouter

Annie-msi commented 3 years ago

I used conda install with the following command conda install -c bioconda NanoComp And i did 'conda upgrade nanomath' '(Nanocomp) jahan036@ln0003 [~] % conda upgrade nanomath Solving environment: done

==> WARNING: A newer version of conda exists. <== current version: 4.5.4 latest version: 4.9.2

Please update conda by running

$ conda update -n base conda

All requested packages already installed."

Then i ran the same command "NanoComp --summary CFrun1_sequencing_summary.txt CFrun2_sequencing_summary_FAO02660_9be575fb.txt WCrun1_sequencing_summary.txt WCrun3_sequencing_summary_FAO69991_ee9098dc.txt Winona_sequencing_summary_FAP07387_60b4a7a5.txt --names A B C D E" Got following error Traceback (most recent call last): File "/panfs/roc/groups/0/plarsen/jahan036/miniconda3/envs/Nanocomp/bin/NanoComp", line 10, in sys.exit(main()) File "/home/plarsen/jahan036/miniconda3/envs/Nanocomp/lib/python3.6/site-packages/nanocomp/NanoComp.py", line 72, in main as_tsv=args.tsv_stats) TypeError: write_stats() got an unexpected keyword argument 'as_tsv'

I tried to update conda and following error occured "(Nanocomp) jahan036@ln0003 [~/Nanocomp_results] % conda update -n base conda Solving environment: failed

InvalidVersionSpecError: Invalid version spec: =2.7"

Annie-msi commented 3 years ago

I reinstalled using mamba, its working now. Thanks