Metaspades Hybrid Assembly Error Code: -11 (Spades 3.13.1)

[k0n5]

Hi!

Thank you for your great tool. I am trying to do hybrid metagenomic assembly of Illumina and Nanopore data. If I only use the Illumina data it works just fine. For hybrid assembly, however, I keep running into one particular error:

  2:36:48.508    19G / 44G   INFO   StageManager             (stage.cpp                 : 132)   STAGE == Hybrid Aligning
  2:36:48.508    19G / 44G   INFO   HybridAligning           (hybrid_aligning.cpp       : 322)   Hybrid library detected: #1
  2:36:48.508    19G / 44G   INFO    General                 (hybrid_aligning.cpp       : 288)   Aligning long reads with bwa-mem based aligner
  2:37:43.796    20G / 44G   INFO    General                 (hybrid_aligning.cpp       : 268)   Prepared batch 0 of 50000 reads.

== Error ==  system call for: "['/fast/work/users/myusername/flye-exp/.snakemake/conda/36a7fd42/share/spades-3.13.1-0/bin/spades-core', '/fast/users/myusername/scratch/NGP_metaspades_genomesize3m/K77/configs/config.info']" finished abnormally, err code: -11

It does not seem to be a memory issue as it arises even when I assign >450GB RAM to the job which already seems to be by far too much for the dataset.

The problem looks almost identical with an issue (#246) posted in March 2019. Did you find a solution back then?

I would be very grateful for your help! Thank you!

warnings.log spades.log params.txt

[k0n5]

Hi!

I have not heard back from you. Can I provide you with further information that would be useful for you?

If not: Just an update on issue #246 would be enormously helpful for now as well. Then, I could try that on my setup.

Thanks a lot!