Numerous errors during Spades running

[DenisGoryunov]

Description of bug

Hello,
There are two errors and one warning in the attached Spades log file.

1. ```mimalloc: error: thread 0x7f294b7af640: unable to allocate OS memory (67108864 bytes, error code: 12 [Cannot allocate memory], address: (nil), large only: 0, allow large: 1)
mimalloc: process [info:](url)
   elapsed:  160563.809 s
   process: user: 1224599.957 s, system: 14503.077 s, faults: 26306211
       rss: current: 579801792512, peak: 480573063168
    commit: current: 579801792512, peak: 579801792512

The above error is clearly related to the lack of required RAM. Is there a way from the log file i already have to figure out an approximate RAM amount i need for the successful Spades run? Besides, i'm wondering what is the actual peak of memory 480573063168 or 579801792512? Can you recommend a tool to check RAM consumption during Spades run or the information which is already present in the log file is sufficient for that?

2. Why i can not to save the check point and got the warning:
   * 0:00:00.028     1M / 18M   WARN   StageManager             (stage.cpp                 : 162)   No saved checkpoint

3.  * 1:35:39.164  9053M / 9053M ERROR   General                 (kmer_splitter.hpp         : 151)   I/O error! Incomplete write! Reason: No space left on device. Error code: 28

There is approximately 1.5 Tb of free space on the mounted file storage i use on my virtual machine. What is the possible reason for that error message and how to fix it?

Many thanks,
Denis

spades.log

spades_out-5.txt

params.txt

params-3.txt

SPAdes version

4.0.0

Operating System

Ubuntu 22.04.3 LTS

Python Version

3.13.1

Method of SPAdes installation

conda

No errors reported in spades.log

• Yes

[asl]

Hello

Is there a way from the log file i already have to figure out an approximate RAM amount i need for the successful Spades run?

The amount of RAM required depends on many factors including (but not limited to) genome size, repeat content & complexity, ploidy & strain contents, error rate, etc. It is not possible to estimate this in advance. And it is not possible to estimate the amount of RAM required in advance as well.

Besides, i'm wondering what is the actual peak of memory

The peak resident set size was approx 440 before memory allocation failed. And your OS failed to fulfil SPAdes request to allocate 64M more.

Can you recommend a tool to check RAM consumption during Spades run

There are multiple tools available around for measuring memory consumption including e.g. top, htop, atop, etc. You may always consult with your system administrator what is available on a particular system. SPAdes-internal monitoring provides SPAdes-internal way, but certainly does not account for e.g. OS-imposed overheads, etc.

Why i can not to save the check point and got the warning:

Checkpoints are disabled by default. Refer to manual for description of checkpoint-related options.

I/O error! Incomplete write! Reason: No space left on device. Error code: 28
There is approximately 1.5 Tb of free space on the mounted file storage i use on my virtual machine. What is the possible reason for that error message and how to fix it?

Well, the error is clear: write failed and this was the error message provided by your system. If you're suspecting some system misconfiguration, you might want to ask your system administrator.