2.9.3 docker crashes

[JWDebler]

Hi, I have tried running the latest flye as a docker image from quai.io (https://quay.io/repository/biocontainers/flye?tab=tags&tag=2.9.3--py310h2b6aa90_0). It keeps crashing with below error. I have retried the older version 2.9.2 from quai.io and that works fine. I have also tried installing the latest version via conda, and that one works fine. It's only the latest version through docker that crashes.

Any ideas?

Thank you.

[2023-12-06 13:01:57] INFO: Starting Flye 2.9.3-b1797                                                                                                                                                                                        
 [2023-12-06 13:01:57] INFO: >>>STAGE: configure                                                                                                                                                                                              
 [2023-12-06 13:01:57] INFO: Configuring run                                                                                                                                                                                                  
 [2023-12-06 13:03:32] INFO: Total read length: 6047618719                                                                                                                                                                                    
 [2023-12-06 13:03:32] INFO: Input genome size: 42000000                                                                                                                                                                                      
 [2023-12-06 13:03:32] INFO: Estimated coverage: 143                                                                                                                                                                                          
 [2023-12-06 13:03:32] INFO: Reads N50/N90: 7717 / 2548                                                                                                                                                                                       
 [2023-12-06 13:03:32] INFO: Minimum overlap set to 3000
  [2023-12-06 13:03:32] INFO: Using longest 50x reads for contig assembly
  [2023-12-06 13:03:32] INFO: >>>STAGE: assembly
  [2023-12-06 13:03:32] INFO: Assembling disjointigs
  [2023-12-06 13:03:32] INFO: Reading sequences
  [2023-12-06 13:04:52] INFO: Building minimizer index
  [2023-12-06 13:04:52] ERROR: Caught unhandled exception: Operation not permitted
  [2023-12-06 13:04:52] ERROR:  flye-modules(+0x3eb10) [0x555eaacafb10]
  [2023-12-06 13:04:52] ERROR:  /usr/local/bin/../lib/libstdc++.so.6(+0xb643c) [0x7ff7024b043c]
  [2023-12-06 13:04:52] ERROR:  /usr/local/bin/../lib/libstdc++.so.6(+0xb648e) [0x7ff7024b048e]
  [2023-12-06 13:04:52] ERROR:  /usr/local/bin/../lib/libstdc++.so.6(__cxa_rethrow+0) [0x7ff7024b0680]
  [2023-12-06 13:04:52] ERROR:  /usr/local/bin/../lib/libstdc++.so.6(_ZSt20__throw_system_errori+0x78) [0x7ff7024aa92b]
  [2023-12-06 13:04:52] ERROR:  /usr/local/bin/../lib/libstdc++.so.6(_ZNSt6thread15_M_start_threadESt10unique_ptrINS_6_StateESt14default_deleteIS1_EEPFvvE+0x6f) [0x7ff7024cddff]
  [2023-12-06 13:04:52] ERROR:  flye-modules(+0x736a8) [0x555eaace46a8]
  [2023-12-06 13:04:52] ERROR:  flye-modules(+0x78f61) [0x555eaace9f61]
  [2023-12-06 13:04:52] ERROR:  flye-modules(+0x3a400) [0x555eaacab400]
  [2023-12-06 13:04:52] ERROR:  flye-modules(+0x16b62) [0x555eaac87b62]
  [2023-12-06 13:04:52] ERROR: Command '['flye-modules', 'assemble', '--reads', 'SHPK01.duplex.chopper.fastq.gz,SHPK01.simplex.chopper.fastq.gz', '--out-asm', 'SHPK01.flye/00-assembly/draft_assembly.fasta', '--config', '/usr/local/lib/python3.10/site-packages/flye/config/bin_cfg/asm_nano_hq.cfg', '--log', 'SHPK01.flye/flye.log', '--threads', '15', '--genome-size', '42000000', '--min-ovlp', '3000', '--min-read', '11168', '--extra-params', 'assemble_ovlp_divergence=0.03,repeat_graph_ovlp_divergence=0.03']' died with <Signals.SIGABRT: 6>.
  [2023-12-06 13:04:52] ERROR: Pipeline aborted

[mikolmogorov]

Interesting, does the bioconda package (2.9.3) works for you? These docker images are built automatically from the bioconda packages, and I have little control over how they are built unfortunately. If bioconda builds work for you, we may need to forward this to the bioconda team.

[JWDebler]

Yes, the same version installed via mamba/conda works fine:

Conda version:

Docker version:

Any chance you can try to replicate this via docker to rule out any problems on my side?