No scaffold/contig files after run - corrected_contigs.fasta not found!

[AlWa1]

Description of bug

For genome assembly of paired end Illumina reads, I am using this code:

spades.py -1 /home/aw932/rds/rds-ss2123-team_seb_storage/projects/20250328_spades_densochile/fastp/SRR17035067_trimmed_1.fastq -2 /home/aw932/rds/rds-ss2123-team_seb_storage/projects/20250328_spades_densochile/fastp/SRR17035067_trimmed_2.fastq -o spades_output_cclake2 --careful -t 54

After the run finishes, I can't find any config/scaffold files in the folder. Following error message turns up in my log:

mismatch correction finished abnormally: /rds/project/ss2123/rds-ss2123-team_seb_storage/projects/20250328_spades_densochile/spades/spades_output_cclake2/mismatch_corrector/scaffolds/corrected_contigs.fasta not found!

I am running the code on an HPC (SLURM) with following settings:

#SBATCH --ntasks=1 #SBATCH --cpus-per-task=54 #SBATCH -A SCHORNACK-SL2-CPU #SBATCH -p cclake #SBATCH -t 36:00:00

Any idea what could go wrong at this stage?

Many thanks!

spades.log

spades.log

params.txt

params.txt

SPAdes version

SPAdes genome assembler v4.1.0

Operating System

Rocky Linux 8

Python Version

Python 3.13.2

Method of SPAdes installation

conda

No errors reported in spades.log

• [x] Yes

[asl]

Any idea what could go wrong at this stage?

Something is strange. So, the file (/rds/project/ss2123/rds-ss2123-team_seb_storage/projects/20250328_spades_densochile/spades/spades_output_cclake2/mismatch_corrector/scaffolds/corrected_contigs.fasta) presented first time, but was not found second time. Looks like some I/O issue? Could it be some scratch storage doing crazy things?

[AlWa1]

Thanks for the answer - trying to follow, how do you know that it presented correctly the first time?

[asl]

Thanks for the answer - trying to follow, how do you know that it presented correctly the first time?

Because the program aligned reads to these contigs. So these files definitely were read. They disappeared when the changes are to be written back.