Invalid argument on log file #412
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I am facing the same issue. Running pggb using conda install. I am using newly assembled C. elegans genomes, single chromosome, single haplotype. |
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Hi, I get the same issue on Also occurs with Singularity (after re-pulling the image and the repo to the latest commit, tagged 0.7.0) |
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@vikshiv, thank you for trying again! Could you please start from scratch and report all commands you execute? For me, it was a simple conda install -c bioconda -c conda-forge pggband then I was able to run Please also report your operating system information and the output of |
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@AndreaGuarracino I tried a fresh install using the conda command you shared. I am running into the same issue (line 488 this time instead of 437 in my first issue): I am on Rocky Linux 8.8 (Green Obsidian). I'm deploying the environment with Mamba 1.5.5. Here is my list output: |
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Sure. Here is the exact process from scratch: Same exact issue as above. I am also on Rocky Linux (8.8) GreenObsidian. x86_64 cpu. Mamba version 1.4.2, conda version 23.3.1. I have an identical conda list as above. I just checked with @nicmoya and we both happen to be using the same cluster at the same institution by coincidence. So that might be the root issue here. Let me know if we can be of some help tracking this down! |
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What sometimes happened to me is that although I created an environment from scratch, the a Bioconda package was not updated, because it was cached. What does The line in question is Maybe on your cluster |
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Version returns: And |
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Just to clarify, using alternative syntax |
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After testing some minor tweaks, it seems that removing |
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Can confirm, removing the |
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No problem, I can do the PR sometime tomorrow. Thank you. |
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PR at #419 |
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Long live to @nicmoya! |
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Hi, I'm running PGGB on HPRC haplotypes of a single chromosome. I tried Singularity to run PGGB:
singularity run -e -B ../chr19_test/:/data ../pggb_latest.sif pggb -i /data/chr19_renamed.fa -t 16 -V 'chm13#1#chr19' -o /data/pggbHowever, I get an error without much output info:
/usr/local/bin/pggb: line 487: /data/pggb/chr19_renamed.fa.bf3285f.11fba48.07bc622.smooth.09-25-2024_19:19:29.log: Invalid argumentThe output directory is empty (no log files etc.).
I get the same error when I try to run the test data from the Singularity section of the README:
singularity run -e -B ${PWD}/data:/data ../pggb_latest.sif pggb -i /data/HLA/DRB1-3123.fa.gz -p 70 -s 3000 -n 10 -t 16 -o /data/out/usr/local/bin/pggb: line 487: /data/out/DRB1-3123.fa.gz.7bf7864.11fba48.5180c7d.smooth.09-25-2024_19:20:13.log: Invalid argumentI figured this might be an issue linking directories through singularity, and installed PGGB through Conda instead:
mamba create -n pggb -c bioconda pggbmamba activate pggbI get a similar (but slightly different) error for this command:
pggb -i chr19_renamed.fa -t 16 -V 'chm13#1#chr19' -o pggb/conda/envs/pggb/bin/pggb: line 437: pggb/chr19_renamed.fa.bf3285f.11fba48.07bc622.smooth.09-25-2024_19:22:34.log: Invalid argumentI'm running it on haplotypes of chr19 from HPRC, one sequence per line in the fasta. Here is a snippet of the fasta index for reference:
I'm not sure what the issue is here, I've checked the read/write permissions in the directory (which I've had no issue with setting up and manipulating the input FASTAs). Any help would be appreciated!
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