Error == system call for: ....." finished abnormally, OS return value: -6 None when running rnaspades

[komorn]

Description of bug

I get this:

Verification of expression 'stream_.good()' failed in function 'void io::BinaryFileStream<SeqT>::Init() [with SeqT = io::SingleReadSeq]'. In file '/opt/conda/conda-bld/spades_1664217775513/work/src/common/io/reads/binary_streams.hpp' on line 37. Message 'Stream is not good(), offset_ 24 count_ 0'.
Verification of expression 'stream_.good()' failed in function 'void io::BinaryFileStream<SeqT>::Init() [with SeqT = io::SingleReadSeq]'. In file '/opt/conda/conda-bld/spades_1664217775513/work/src/common/io/reads/binary_streams.hpp' on line 37. Message 'Stream is not good(), offset_ 24 count_ 0'.
spades-core: /opt/conda/conda-bld/spades_1664217775513/work/src/common/io/reads/binary_streams.hpp:37: void io::BinaryFileStream<SeqT>::Init() [with SeqT = io::SingleReadSeq]: Assertion `stream_.good()' failed.

Error ==  system call for: "['/home2/komornikova/Lana/transXpress/.snakemake/conda/b931f9b9648ab1026edec7f1284d36bf_/bin/spades-core', '/home2/komornikova/Lana/transXpress/rnaspades_out/K49/configs/config.info', '/home2/komornikova/Lana/transXpress/rnaspades_out/K49/configs/mda_mode.info', '/home2/komornikova/Lana/transXpress/rnaspades_out/K49/configs/rna_mode.info']" finished abnormally, OS return value: -6
None

I don't understand what it means.

spades.log

spades.log

params.txt

params.txt

SPAdes version

SPAdes version: 3.15.5

Operating System

OS: Linux-5.14.0-362.18.1.el9_3.0.1.x86_64-x86_64-with-glibc2.34

Python Version

Python version: 3.12.1

Method of SPAdes installation

conda

No errors reported in spades.log

• [X] Yes

[asl]

Hello

It looks like an I/O issue on your end. SPAdes was unable to get access to one of intermediate files that were created seconds before