Anton Korobeynikov

@katebowie This is pretty strange, the process is pretty deterministic there. Is there by any chance a possibility for to share data with us so we can reproduce?

We just need the one that stalled :) Working one is, well, working. We are pretty flexible with data sharing. And you know the size and limitations on your side.

Hello Does the issue reproduce with the latest SPAdes release?

> [Errno 39] Directory not empty: '/data2/User_Remote/All_data/HiAS/For_Gh/spades_short_read_assembly_merged/tmp/hammer_ajj3_epz/kmer_splitter_JV9jJU' This is an I/O error on your end. Essentially after SPAdes tried to remove the temporary folder it still appeared as non-empty. Usually...

> Since we are working with the metagenome, estimating the genome size is not straightforward; however, I estimate it to be around 3 Mb to 6 Mb. You wanted to...

> 3 to 6 Mb refers to the ideal situation (if we are really able to recover a complete bacterial genome from our metagenome assembly) But this is just a...

> Background: In HPC systems we set a hard limit on the allowed memory and apparently metaSPAdes uses more that specified via the command line (we use the hard limit...

@yhezema How much free RAM is available for your SPAdes job? Overall the error message is quite clear: ``` 0:27:03.628 1M / 16G ERROR General (mmapped_reader.hpp : 52) mmap(2) failed....

This likely indicates some memory corruption as one of internal SPAdes data structure invariants was violated. Does restart yields the same error?