System call for spades-core finished abnormally, OS return value: -11

[domenico-simone]

Hello,

I am using spades v3.14 in --meta mode. I got an error, these are the last lines in the log file:

  2:34:39.146    46G / 105G  INFO   StageManager             (stage.cpp                 : 166)   STAGE == Mismatch Correction
  2:34:39.146    46G / 105G  INFO    General                 (graph_pack.hpp            : 113)   Normalizing k-mer map. Total 185971569 kmers to process
  2:35:41.277    46G / 105G  INFO    General                 (graph_pack.hpp            : 115)   Normalizing done
  2:53:20.943    60G / 105G  INFO    General                 (mismatch_shall_not_pass.hp: 195)   Finished collecting potential mismatches positions


== Error ==  system call for: "['/domus/h1/domeni/bin/SPAdes-3.14.1/bin/spades-core', '/scratch/14643818/assembly/normalized/40_2/metaspades_compiled_2_1TB/P1_peat/K55/configs/config.info', '/scratch/14643818/assembly/normalized/40_2/metaspades_compiled_2_1TB/P1_peat/K55/configs/mda_mode.info', '/scratch/14643818/assembly/normalized/40_2/metaspades_compiled_2_1TB/P1_peat/K55/configs/meta_mode.info']" finished abnormally, OS return value: -11

The complete log is here.

Thank you,

Domenico

[asl]

Hello

Something is strange here. Does the problem reproduce if you'd restart (you could use spades.py --continue)?

[Sidduppal]

Having the same problem with v3.14.1 and specifically with --meta mode. Problem persist after using --continue as well.

[vasudhajain29]

Hi, did you find any solution to this issue?

Regards, Vasudha :)

[Sidduppal]

@vasudhajain29 I remember this error popping up when there was something funny with my reads. In my case, I had concatenated two different pairs of sequencing runs and was trying to run metaSPades on that.

[Aiswarya-prasad]

@Sidduppal Is it expected to throw up issues if reads from different runs are concatenated? Are they supposed to be assembled independently and then combined? What did you end up doing?

[Sidduppal]

@Aiswarya-prasad I think I just ended up using Megahit to analyze the reads. However, you can also just use normal SPades instead of metaSPades. The results are usually comparable.