DaniPaulo

Hi @wgallin . I'm still trying to figure out how to run NextDenovo in a HPC environment using SLURM. Would you be able to share your `script.slurm.sh` with me?

Hi @wgallin, Thanks for your response. Let's see if I understand. So basically, you set up your `script.slurm.sh` to: ``` #SBATCH --nodes 1 #SBATCH --ntasks 1 #SBATCH --cpus-per-task 32 #SBATCH...

Was this solved? I'm having a similar issue: [INFO] 2024-04-30 18:24:00 Initialize graph and reading... /90daydata/tephritid_gss/dani/nextDenovo/SMB_Q12L5K_nextDenovo/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph1/nextDenovo.sh: line 5: 267342 Segmentation fault (core dumped) /project/tephritid_gss/daniel.paulo/envs/nextDenovo/lib/python3.10/site-packages/nextdenovo/bin/nextgraph -a 1 -f /90daydata/tephritid_gss/d ani/nextDenovo/SMB_Q12L5K_nextDenovo/.//03.ctg_graph/01.ctg_graph.input.seqs /90daydata/tephritid_gss/dani/nextDenovo/SMB_Q12L5K_nextDenovo/.//03.ctg_graph/01...

Oh, forgot to say. This is what I get when trying to retrain azimuth: python model_comparison.py /opt/homebrew/Caskroom/miniconda/base/envs/crispor/lib/python3.9/site-packages/openpyxl/worksheet/_read_only.py:81: UserWarning: Unknown extension is not supported and will be removed for idx, row...

Thank you so much for replying Max. I'm using Python 3.9.17, because that's what is in the manual ("Crispor pretty much requires Python 3.9 now since V5.2"). But I guess...

Thank you for your consideration Max. Indeed installing software is the worst part of bioinformatics, specially for a newbie like me. Compatibility is definitely an issue here. Anyway, I try...

Thank you for the suggestions. Following what I got ### CRISPOR py27 in macOS conda env: I ran the following: `/opt/homebrew/Caskroom/miniconda/base/envs/crispor/bin/python2.7` ```python >>> import matplotlib >>> import pandas >>> import...

Hi, sorry I was super busy this week and just now had the time to go through your messages. I have ZERO experience with docker (I think Conda spoiled me),...

Hi @cj2jy, I'm still trying to understand how to run NextDenovo using SLURM. Could you share your `script.slurm.sh`? In the `run.cfg` you set `submit = sbatch --cpus-per-task=20 --mem-per-cpu=4g`, so that...

Hi, thank you for the response. It turned out that I had some corrupted fastq.gz files. All it's good now. Thank you again, - Dani.