Invalid argument on log file

[vikshiv]

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/pggb However, 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 argument The 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 argument

I figured this might be an issue linking directories through singularity, and installed PGGB through Conda instead: mamba create -n pggb -c bioconda pggb mamba activate pggb

I 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 argument

I'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:

chm13#1#chr19   61707364        15      61707364        61707365
HG00438#1#chr19 60772275        61707397        60772275        60772276
HG00438#2#chr19 61080741        122479690       61080741        61080742
HG00621#1#chr19 61442093        183560449       61442093        61442094
HG00621#2#chr19 61506976        245002560       61506976        61506977
HG00673#1#chr19 63033057        306509554       63033057        63033058
HG00673#2#chr19 62744279        369542629       62744279        62744280
HG00733#1#chr19 61934365        432286926       61934365        61934366
HG00733#2#chr19 61328042        494221309       61328042        61328043
HG00735#1#chr19 60499191        555549369       60499191        60499192
HG00735#2#chr19 61874577        616048578       61874577        61874578
HG00741#1#chr19 61637809        677923173       61637809        61637810

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!

[nicmoya]

I am facing the same issue. Running pggb using conda install.

$ pggb -i CE_chr1_5hifi.rff.fa -o 5hifi -t 16 -p 80 -s 5k -V 'N2:1000' -n 1
/home/nmoya1/mambaforge/envs/pggb/bin/pggb: line 437: 5hifi/CE_chr1_5hifi.rff.fa.304cbb4.11fba48.69afeb3.smooth.10-15-2024_14:17:00.log: Invalid argument

I am using newly assembled C. elegans genomes, single chromosome, single haplotype.

ECA738#1#I      15574207        13      15574207        15574208
N2#1#I  15072434        15574229        15072434        15072435
QG4021#1#I      15321380        30646676        15321380        15321381
QX1794#1#I      15402706        45968069        15402706        15402707
XZ1516#1#I      15720420        61370788        15720420        15720421

[AndreaGuarracino]

@vikshiv , @nicmoya , could you please try again with pggb v0.7.0? I would appreciate feedback about the Docker/Singularity/Bioconda installation. The latter just worked on my laptop.

[vikshiv]

Hi, I get the same issue on v0.7.0. I updated on Bioconda and get this error (same as above, I believe):

(pggb) $ pggb --version
pggb 0.7.0
(pggb) $ pggb -i chr19_renamed.fa -o chr19_pggb -t 16
/conda/envs/pggb/bin/pggb: line 488: chr19_pggb/chr19_renamed.fa.bf3285f.11fba48.07bc622.smooth.10-17-2024_22:43:28.log: Invalid argument

Also occurs with Singularity (after re-pulling the image and the repo to the latest commit, tagged 0.7.0)

(pggb) $ singularity run -e -B ./:/data ../pggb_latest.sif pggb -i /data/chr19_renamed.fa -t 16 -o /data/chr19_pggb
/usr/local/bin/pggb: line 487: /data/chr19_pggb/chr19_renamed.fa.bf3285f.11fba48.07bc622.smooth.10-17-2024_23:16:56.log: Invalid argument