no space on disk

[jahn...@gmail.com]

hi,

I am running this command in an attempt to reduce the number of contigs in my canu-generated assembly:

redundans.py -v -i /data/kvijed/Anitra/Illumina/AnitraIllumina_R1.fastq /data/kvijed/Anitra/Illumina/AnitraIllumina_R2.fastq -l /data/kvijed/Anitra/PacBio/PacBioAll.fastq -f /data/kvijed/Anitra/canuAss/AnitraPilon2020ED.fasta -t 24 -o /data/kvijed/Anitra/redundans/AnitraRedund

However, the tmp directory runs out of space even though 15Gb is allocated to that folder. 

Help is highly appreciated.

Thank you

jahn

[Leszek]

Hi Jahn, at which step does it crash? Could you send me the log please?

Cheers,

L.

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[jahn...@gmail.com]

Hi,

Please find the log attached.

[Leszek]

Ok, so it happens during long-read scaffolding. How big is your genome and data?

Frankly speaking, I've never managed to finish long-read support (pyScaf) and it's still rather experimental.

I just had a rather simple idea that may work ok. I'll try to dedicate some time to it in the coming days if you wish to test it later with your data.

Cheers,

L.

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