Exception caught Cannot open file XXX/.bin_reads/paired_0.off': iostream error

[gorfol]

Description of bug

Hi,
Our server has 512 GB of RAM and 256 cores. I have an issue shown in the spades.log. If I run spades with root privileges, the results are the same. There is a paired_0.off file in the .bin_reads directory. We had an SSD change before this error happened, but the Linux and SPAdes version (however compiled again on the new system), the fastq files and parameters are the same.
Thank you!

spades.log

spades.log

params.txt

params.txt

SPAdes version

3.15.5

Operating System

Ubuntu 22.04.1

Python Version

Python 3.11.5

Method of SPAdes installation

manual

No errors reported in spades.log

• Yes

[asl]

Hello

There is an I/O problem. SPAdes was unable to read one of its intermediate files. So, maybe more information is available in the system log? Does moving output / scratch dir to other volume helps?

[gorfol]

Thank you! Unfortunately I cannot find anything in the syslog and moving the whole spades directory to a mounted NAS drive does not solve the problem. I see the intermediate file and can access by my user, so I do not know why spades cannot handle it.

[asl]

Does it reproduce with another dataset? How about running spades.py --test?

[gorfol]

Yes, I tried different datasets.

The test ran with this result:
== Running: /home/gorfol/miniconda3/bin/python /home/gorfol/spades-3.15.5/assembler/src/spades_pipeline/scripts/check_test_script.py --mode common --result_contigs_filename /home/gorfol/spades-3.15.5/assembler/spades_test/contigs.fasta --result_scaffolds_filename /home/gorfol/spades-3.15.5/assembler/spades_test/scaffolds.fasta

========= TEST PASSED CORRECTLY.
.
.
.
======= SPAdes pipeline finished WITH WARNINGS!

=== Error correction and assembling warnings:

• 0:00:00.957 1M / 280M WARN General (launcher.cpp : 178) Your data seems to have high uniform coverage depth. It is strongly recommended to use --isolate option.
  ======= Warnings saved to /home/gorfol/spades-3.15.5/assembler/spades_test/warnings.log