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ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
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Spades finished abnormally #1332

Closed stopguessingwho1am closed 3 months ago

stopguessingwho1am commented 3 months ago

Description of bug

Spades finished abnormally after 16 hours. Not sure what is wrong.

== Error == system call for: "['/gpfs1/home/xinylim/SPAdes-4.0.0-Linux/bin/spades-hammer', '/scratch/ResearchGroups/ace_amytan/rita_spades/Dig1_7_19_21B/corrected/configs/config.info']" finished abnormally, OS return value: 12

spades.log

diespades.log

params.txt

params.txt

SPAdes version

Spades 4.0

Operating System

linux hpc

Python Version

No response

Method of SPAdes installation

conda

No errors reported in spades.log

asl commented 3 months ago

The log reads:

  0:15:49.423     1M / 16G   INFO    General                 (kmer_index_builder.hpp    : 264)   Starting k-mer counting.
  0:15:49.521     1M / 16G   ERROR   General                 (mmapped_reader.hpp        :  52)   mmap(2) failed. Reason: Cannot allocate memory. Error code: 12
  0:15:49.521     1M / 16G   ERROR   General                 (mmapped_reader.hpp        :  52)   mmap(2) failed. Reason: Cannot allocate memory. Error code: 12=== Stack Trace ===
  0:15:49.521     1M / 16G   ERROR   General                 (mmapped_reader.hpp        :  52)   mmap(2) failed. Reason: Cannot allocate memory. Error code: 12

So, you are running out of RAM. Please ensure that enough RAM is available to your SPAdes job (especially if you're running within some resource-constrained job submission system).