GFAstats error about redundans HOT 3 CLOSED

Hi @Dfupa , I think I found the problem with gfa file generation.
I'm working with Oncopeltus fasciatus and the folder that I'm using is "/home/data/ofas/...", which caused an incorrect replacement to the path from "/home/data/ofas/.." to "/home/data/.gfas/.." crashing the next steps and aborting the proccess.
Now it's running flawlessly!

from redundans.

Hi @aabaricalla,

Glad to see you found and solved the problem!

from redundans.

Saludos @aabaricalla,

Si no te parece mal, continuamos la conversación en inglés para el resto de la comunidad, dado que puede ser de interés general.

I've tried to reproduce the issue by relaunching redundans both in my local environment as well as my docker and singularity images and I was not able to do so. As this issue was specifically found on singularity, Ill provide a bit more information regarding my tests on it.

After setting up my redundans singularity image, I ran the example commands to test it resuming the same steps you mentioned, i.e.:

singularity exec redundans.sif bash -c "/root/src/redundans/redundans.py -v -i /root/src/redundans/test/*_?.fq.gz -f /root/src/redundans/test/contigs.fa -o /tmp/run1 --resume"

There were no errors reported and the .gfa files were generated correctly:

Singularity> tail -n 2  /tmp/run1/contigs.reduced.gfa

P	NODE_84_length_296_cov_37.2407_ID_167	NODE_84_length_296_cov_37.2407_ID_167.1+	*
P	NODE_91_length_243_cov_37.1489_ID_181	NODE_91_length_243_cov_37.1489_ID_181.1+	*

I need more information in order to find where the issue lies ( a more complete log, the command used...). In the meantime I've decided to upload the redundans.sif singularity image I used to https://cloud.sylabs.io/

singularity pull library://cgenomics/redundans/redundans

Please let me know if your issue persists after using the .sif image I provided and feel free to share the logs or commands used so I can try to fix the issue.

Cheers,

from redundans.