search

ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
Other
763 stars 138 forks source link

spades-hammer error : OS return value: -6 #1402

Open AmaliT opened 4 weeks ago

AmaliT commented 4 weeks ago

Description of bug

The assembly run keeps dying at the spades-hammer step, although it worked fine on the other samples. I have tried re-installing spades; fresh set of fastqs etc.

spades.log

spades.log

params.txt

params.txt

SPAdes version

SPAdes version: 3.15.3

Operating System

OS: Linux-5.14.0-427.37.1.el9_4.x86_64-x86_64-with-glibc2.34

Python Version

Python version: 3.9.18

Method of SPAdes installation

github

No errors reported in spades.log

asl commented 4 weeks ago

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 the data from one of its intermediate files indicating a possible I/O problem on your end.

You could probably talk to your system administrator, ensure there is enough disk quota, etc.