Anton Korobeynikov

@vivaxp5 How do you know if the resources are sufficient? It seems you provided 400 Gb of RAM to SPAdes and sadly your assembly requires more, everything stopped when these...

The log reads: ``` spades-hammer: /spades/assembler/src/projects/hammer/kmer_cluster.cpp:621: void KMerClustering::process(const string&): Assertion `is.good()' failed. ``` Here, it means that one of SPAdes intermediate files got corrupted or SPAdes was unable to read...

This looks like a known issue with CQF implementation. The only workaround is to skip read correction via `--only-assembler`

> Thank you for your quick reply. I was wondering if skipping read correction would lead to any mistakes in the final results? The genome assembly process is always heuristic...

> 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...

> 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...

> To troubleshoot, I tried increasing the available RAM How have you did it?

The problem likely stems from an I/O problem at your end as SPAdes intermediate files got corrupted. You might want to talk to your system administrator.

You're using terrible old version of SPAdes. Does the problem reproduce with the recent 4.1?

You're right, this seems to be some kind of issue. Is it possible for you to share a reproducer with us?