Issue : 'Step1' object has no attribute 'print_headers'

[stephamor]

Hello,

I am very new in using ipyrad and gbioinformatic tools in general. My dataset consists in Demultiplexed ddrad sequences, fastqc format. When I try to run ipyrad on my sample dataset, I get stuck on the first step with the following error message :

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ipyrad [v.0.9.90] Interactive assembly and analysis of RAD-seq data

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Parallel connection | ThinkPad-E15-Gen-4: 4 cores

Encountered an Error. Message: 'Step1' object has no attribute 'print_headers' Parallel connection closed.

Before running the code : ipyrad -p params-modelsp.txt -s 1 -c 4, I fulfilled the param.file according to the tutorials found here : https://radcamp.github.io/NYC2018/02_ipyrad_partI_CLI.html https://ipyrad.readthedocs.io/en/master/tutorial_intro_cli.html

I entered the path of my working directory, the path of my fasqc.files (that I had unzipped) and indicated my two restriction sites accordingly.

i am using conda 23.5, on Ubuntu jammy computer system.

I do neither understand where does this issue comes from, nor how to fix this issue. Could I have get some clues ?

I Thank you very much in advance for your help.

[isaacovercast]

Hello there, hmm, this is a weird problem. It looks like the ipyrad install is messed up and you have checked out a branch other than 'main'. I am not sure how this would have happened, but the easiest thing to do is to create a new conda environment, install ipyrad in the new clean conda environment and then try again.

If you still have problems after that can you create a new Issue? I'm going to close this pull request because we're not ready to merge ipyrad2 into main yet :)

[stephamor]

Dear Isaac,

Thank you very much for your quick answer.

I am still struggling with very basics of Python environments.

I followed your advice. Suppressed my conda and reinstalled a clean version with ipyRAD in my project directory.

Now, it works perferctly, so I can go further into my datas ! =)

Thank you agian for your help,

I wish you a very nice day,

All The Best,

Stéphanie

[Université de Neuchâtel]https://www.unine.ch/[Facebook]https://www.facebook.com/UniNeuchatel[Instagram]https://www.instagram.com/unineuchatel/[Twitter]https://twitter.com/unineuchatel[Youtube]https://www.youtube.com/user/uninepromotion[LinkedIn]https://www.linkedin.com/edu/school?id=10933&trk=edu-hp-follow-name Stéphanie Morelon @.**@.> PHD student Laboratory of Evolutionary Genetics, D322, Université de Neuchâtel Emile-Argand 11, CH-2000 Neuchâtel Tél. +41 32 123 45 67 www.unine.chhttps://www.unine.ch/

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De : Isaac Overcast @.***> Envoyé : samedi, 3 juin 2023 17:31:38 À : dereneaton/ipyrad Cc : MORELON Stéphanie; Author Objet : [FROM EXTERNAL] Re: [dereneaton/ipyrad] Issue : 'Step1' object has no attribute 'print_headers' (PR #512)

Hello there, hmm, this is a weird problem. It looks like the ipyrad install is messed up and you have checked out a branch other than 'main'. I am not sure how this would have happened, but the easiest thing to do is to create a new conda environment, install ipyrad in the new clean conda environment and then try again.

If you still have problems after that can you create a new Issue? I'm going to close this pull request because we're not ready to merge ipyrad2 into main yet :)

— Reply to this email directly, view it on GitHubhttps://github.com/dereneaton/ipyrad/pull/512#issuecomment-1575022524, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BAJLQAU3VAL4UIUQBLYOB7DXJNKFVANCNFSM6AAAAAAYZLFFFA. You are receiving this because you authored the thread.Message ID: @.***>

[isaacovercast]

wonderful! Thanks for letting me know. Good luck with the rest of the assembly